Methods, kits and systems for cancer diagnosis and treatment

Abstract

The present disclosure includes, among other things, methods, kits, and systems that can be used to select subjects for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), to identify subpopulations of subjects that respond to treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), to monitor subjects during treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), etc. In various embodiments, the present disclosure relates to the use of one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors that that are characteristic of promoter and / or enhancer activity that is associated with select genes for ADC target antigens or genes that modulate ADC response / resistance.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Application No. 63 / 575,697, filed on 6 April 2024 which is incorporated herein in its entirety by this reference. BACKGROUND

[0002] Cancer ranks as the primary or secondary cause of premature death in many countries. Antibody-drug conjugates (ADCs) were ushered into oncology clinical practice in 2000 with the FDA’s approval of Mylotarg™ for the treatment of acute myeloid leukemia (AML). ADC molecules marry the precision of antibody-mediated tumor antigen targeting with potent cytotoxic agents, thereby creating a targeted delivery vehicle for malignant tumors. In this manner, ADCs provide a means to reduce off-tumor toxicities by limiting payload exposure in normal tissues. While most / ADC clinical candidates utilize cytotoxic chemotherapeutic payloads, recent ADC candidates have also incorporated targeted small molecules and immunomodulatory agents. Since Mylotarg™’ s first registration, hundreds of ADCs have been evaluated in the investigational setting and several have made it to regulatory approval including Trodelvy®. Adcetris™, Kadcyla™, Besponsa™, Enhertu™, Padcev'“, Polivy™, Blenrep™, Todelvy'” Tivdak™, Zylonta‘“ and Elahere™.

[0003] T 'arget antigen expression is currently used as the primary biomarker for patient selection and ADC efficacy has been shown to correlate with the level of target antigen expression in some studies. However, IHC methods for quantifying target antigen expression are invasive, requiring tissue biopsies. In addition, for many targets, there is limited information about their expression across a variety of tumor types, as well as intratumoral heterogeneity and evolution of expression with tumor progression and metastasis. The effects of different intervening therapies on expression are also largely unknown. Data also suggests that there can be clinical efficacy in patients who also have low target antigen expression, shifting toward a threshold expression that is still unknown for many target antigens over which ADCs have therapeutic efficacy.

[0004] Target assessment has also been challenging as a result of known challenges with IHC assessment / interpretation. There therefore remains a need for new biomarkers and improved methods of selecting patients for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand). Improved diagnostic methods would also better support future clinical trials that seek to identify subpopulations of patients that respond to ADCs. They would also expand our understanding of the underlying biology of cancer and help identify new treatments. SUMMARY

[0005] The present disclosure is based, at least in part, on the demonstration that certain genomic loci associated with select genes for ADC target antigens or genes that modulate ADC response / resistance have different histone modification levels (e.g., histone methylation marks such as H3K4me3 and histone acetylation marks such as H3K27ac) in plasma samples from cancer patients as compared to plasma samples from healthy volunteers.

[0006] The present disclosure encompasses methods, kits and systems that use these epigenomic differences (alone or in combination with each other and / or with other biomarkers) io select subjects for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), to identify subpopulations of subjects that respond to treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), to monitor subjects during treatment -with an agent that is directed to an ADC target, antigen (e.g., an ADC therapy or radioligand), etc. by detecting and quantifying the presence of histone modifications at these one or more genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample, e.g., a plasma sample obtained or derived from a subject. The present disclosure also encompasses methods where chromatin accessibility and / or binding of one or more transcription factors are detected at the one or more genomic loci instead of (or in addition to) histone modifications. The present disclosure also encompasses methods, kits and systems where the genomic loci that are differentially modified based on different types of histone modifications (e.g., histone methylation marks such as H3K4me3 and histone acetylation marks such as H3K27ac) are combined into multimodal classifiers to select subjects for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), etc. These monomodal and multimodal classifiers can provide minimally invasive ways of selecting subjects for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), etc. that are more accurate, objective, and comprehensive than the current tissue-based approaches. 100071 The present disclosure includes, among other things, technologies for the determination of the activation status of genes for ADC target antigens (“ADC target status”) or genes that modulate ADC response / resistance and for the detection, monitoring, and / or treatment of cancer (including, e.g., breast, small cell lung cancer (SCLC), non-small cell lung cancer NSCLC, neuroendocrine prostate cancer (NEPC), prostate adenocarcinoma (PRAD), etc.) based on the activation status of these genes. In various embodiments, the present disclosure relates to the measurement of histone modifications in a sample obtained or derived from a subject to detect and / or treat cancer (including, e.g., breast, SCLC, NSCLC, NEPC, PRAD, etc.) based on the activation status of these genes. The present disclosure includes, among other things, histone modification measurements in cell-free DNA (cfDNA) that are characteristic of the activation status of genes for ADC target antigens (“ADC target status”) or genes that modulate ADC response / resistance, and which in various embodiments are useful, e.g, for detecting, monitoring, selecting treatment for, and / or treating cancer (including, e.g., breast, SCLC, NSCLC, NEPC, PRAD, etc.) based on the activation status of these genes. In some embodiments, histone modification measurements in cfDNA can be used to detect or determine resistance of a cancer (e.g., breast, SCLC, NSCLC, NEPC, PRAD, etc.) to treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) or transformation of a cancer from one subtype to another. In various embodiments, the present disclosure includes exemplary genomic loci that are differentially modified in different cancer patients (including, e.g, breast cancer, SCLC, NSCLC, NEPC, PRAD, etc. patients) and / or between cancer patients and healthy volunteers. In various embodiments, genomic loci differentially modified in cfDNA are or include one or more enhancers. In various embodiments, genomic loci differentially modified in cfDNA are or include one or more promoters.

[0008] In various embodiments, a genomic locus is differentially modified if it is characterized by increased or decreased histone modification as compared to a reference (e.g., a sample from an ADC target-negative or healthy subject). Increased or decreased histone modification can be or include, e.g., increased or decreased histone methylation (hypermethylation or hypomethylation, respectively) of one or more particular methylation marks, or a combination thereof; increased or decreased pan-methylation; increased or decreased histone acetylation (hyperacetylation or hypoacetylation, respectively) of one or more particular acetylation marks, or a combination thereof, and / or increased or decreased pan-acetylation (e.g., pan-H3 acetylation). In various embodiments, histone methylation can be or include histone methylation marks selected from H3K4mel, H3K4me2, H3K4me3, or a combination thereof. In various embodiments, histone methylation can be or include H3K4me3. In various embodiments, histone acetylation can be or include histone acetylation marks selected from H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, or a combination thereof. In various embodiments, histone acetylation can be or include H3K27ac.

[0009] The present disclosure further relates, in various embodiments, to the measurement of chromatin accessibility in cell-free DNA (cfDNA) to determine the activation status of genes for ADC target antigens (“ADC target status”) or genes that modulate ADC response / resistance. The present disclosure includes, among other things, chromatin accessibility measurements in cfDNA that are characteristic of ADC target-positive cancers, which in various embodiments are useful, e.g., in detecting, monitoring, selecting treatment for, and / or treating an ADC target-positive cancer. In some embodiments, chromatin accessibility measurements in cfDNA can be used to detect or determine resistance of a cancer (e.g, breast, SCLC, NSCLC, NEPC, PRAD, etc.) to treatment with an agent that is directed to an ADC target antigen (e.g., an .ADC therapy or radioligand) or transformation of a cancer from one subtype to another. In various embodiments, the present disclosure includes genomic loci that are differentially accessible in ADC target-positive vs. ADC target-negative cancers. In various embodiments, genomic loci differentially accessible in cfDNA are or include one or more enhancers. In various embodiments, genomic loci differentially accessible in cfDNA are or include one or more promoters.

[0010] In various embodiments, without wishing to be bound by any particular scientific theory, histone acetylation (e.g., H3K27ac) corresponds and / or is correlated with chromatin accessibility. In various embodiments, without wishing to be bound by any particular scientific theory, histone methylation (e.g., H3K4me3) corresponds and / or is correlated with chromatin accessibility.

[0011] In various embodiments, a genomic locus is differentially accessible if it is characterized by increased or decreased chromatin accessibility as compared to a reference (e.g., a sample from an ADC target-negative or healthy subject). Increased or decreased histone modification can be or include, e.g., increased or decreased accessibility as determined by various chromatin accessibility assays known in the art.

[0012] The present disclosure further relates, in various embodiments, to the measurement of transcription factor binding in cell-free DNA (cfDNA) to determine the activation status of genes for ADC target antigens (“ADC target status”) or genes that modulate ADC response / resistance. The present disclosure includes, among other things, transcription factor binding measurements in cfDNA that are characteristic of ADC target-positive cancers, which in various embodiments are useful, e.g., in detecting, monitoring, selecting treatment for, and / or treating an ADC target-positive cancer. In some embodiments, transcription factor binding measurements in cfDNA can be used to detect or determine resistance of a cancer (e.g., breast, SCLC, NSCLC, NEPC, PRAD, etc. ) to a therapy or transformation of a cancer from one subtype to another. In various embodiments, the present disclosure includes genomic loci that are differentially bound by transcription factors in ADC target-positive vs. ADC target-negative cancers. In various embodiments, genomic loci that are differentially bound by transcription factors in cfDNA are or include one or more enhancers. In various embodiments, genomic loci that are differentially bound by transcription factors in cfDNA are or include one or more promoters.

[0013] In various embodiments, without wishing to be bound by any particular scientific theory, histone acetylation (e.g., H3K27ac) corresponds and / or is correlated with transcription factor binding. In various embodiments, without wishing to be bound by any particular scientific theory, histone methylation (e.g., H3K4me3) corresponds and / or is correlated with transcription factor binding.

[0014] In various embodiments, a genomic locus is differentially bound by transcription factors if it is characterized, by increased or decreased transcription factor binding as compared, to a reference (e.g., a sample from an ADC target-negative or healthy subject). Increased or decreased transcription factor binding can be or include, e.g., increased or decreased transcription factor binding as determined by various transcription factor binding assays known in the art.

[0015] In one aspect the present disclosure provides a method comprising quantifying, at one or more genomic loci in a biological sample, optionally in cell-free DNA (cfDNA) from a liquid biopsy sample, obtained or derived from a subject: (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) binding of one or more trail script! on factors, wherein the one or more genomic loci are (a) within a gene encoding an ADC target antigen or within a gene that modulates ADC response / resistance; and / or (b) associated with a promoter or an enhancer of: (I) a gene that modulates ADC response / resistance; and / or (II) a gene encoding an ADC target antigen.

[0016] In some embodiments, a method comprises quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1, Table 2, Table 3, Table 4, Table 5, or Table 6.

[0017] In some embodiments, the one or more genomic loci are associated with a promoter and are located within + / - 200 kB (e.g., + / - 10 kB or + / - Ikb) of the transcription site (TSS) of a gene encoding an ADC target antigen or a gene that modulates ADC response / resistance, e.g., a genomic locus that is located within a region defined by a pair of genomic coordinates in Table 1, Table 2, Table 4, Table 5, or Table 6.

[0018] In some embodiments, the one or more genomic loci are associated with an enhancer and are located within + / - 200 kB (e.g., + / - lOkb) of the transcription site (TSS) of a gene encoding an ADC target antigen or a gene that modulates ADC response / resistance, e.g., a genomic locus that is located within a region defined by a pair of genomic coordinates in Table 3, Table 4, Table 5, or Table 6.

[0019] In some embodiments, the one or more genomic loci are located within + / - 200 kB of the TSS of a gene encoding an ADC target antigen or a gene that modulates ADC response / resistance, e.g., a genomic locus that is located within a region defined by a pair of genomic coordinates in Table 4, Table 5, or Table 6.

[0020] In some embodiments, the subject is a breast cancer patient and the gene encoding an ADC target antigen is selected from the group consisting of AXL, CCR2, CEACAM5, CD44, CLDN6, DLLS, EGFR, FAP, POLHL IHFRSFIOB. FN-I, ESRL FGFR2. B4GALNTL GPC1, GRPR, ITGB6, IGF J R, MUGI, CDH3, CD274, PTK7, SSTR2, STEAPi, STEAP2, IM4SF1, RO RI, SEZ6, SLC34A2, TACSTD2, VTCN1, RECTIN4, ERBB3, ERBB2, EPHA 5, ROR2, F3, FOLRJ, CD276, MSLN, SLC39A6, LY75, LY75-CD302, CDH6, KAAGJ, TPBG wdMET. In some embodiments, the subject is a breast cancer patient and the gene encoding an ADC target antigen is selected from the group consisting of VTCN1, NEC TINT , ERBB2, EPHA5, ROR2, CDH6 and MET. In some embodiments, the subject is a breast cancer patient and the gene encoding an ADC target antigen is selected from the group consisting of TACSTD2, ERBB3, F3, CD2 76, LY7S and KAAGL [0921J In some embodiments, the subject is small cell lung cancer (SCLC) patient and the gene encoding an ADC target antigen is selected from the group consisting of TACSTD2, FOLHi, NCAM1, ERBB3, CD276, MSEC, SEZ6, DLL3, wdFAP.

[0022] In some embodiments, the subject is a non-small cell lung cancer (NSCLC) patient and the gene encoding an .ADC target antigen is selected from the group consisting of TACSTD2, F3, FECTIN4, FOLRI, ERBB3, CD276, ERBB2, AXL, CEACAM5, TFRC, SLC34A2, PTK7, GPNMB, EGFR, MET and RGR2

[0023] In some embodiments, a subject is an NEPC or PRAD patient and the gene encoding an ADC target antigen is selected from the group consisting of A / ?, STEAP1, CHGA, SEZ6, SSTR2, DLL3, KLK2, and KLK3.

[0024] In some embodiments, the gene encoding an ADC target gene is DLLS.

[0025] In some embodiments, a method comprises quantifying, in a biological sample, at (a) one or more genomic loci (i) within DLLS', and / or (ii) associated with a promoter or an enhancer of DLL3, and (b) one or more genomic loci (i) within RAB3 / P, PAK5, or TTPRJPL2, or any combination thereof; and / or (ii) associated with a promoter or an enhancer of RAB3IP, PAK5, or ITPR1PL2, or any combination thereof: (A) one or more histone modifications, (B) DNA methylation, (C) chromatin accessibility, and / or (D) binding of one or more transcription factors.

[0026] In some embodiments, one or more genomic loci within RAB3IP, PAKS, or ITPRIPL2, or any combination thereof, and / or associated with a promoter or an enhancer of RAB3 / P, PAKS, or 11PRIPL2, or any combination thereof, are located within + / - 200 kB of the TSS of RAB3IP, PAK5, or ITPRIPL2, or any combination thereof, e.g., a genomic locus that is defined by a pair of genomic coordinates in Table 6.

[0027] In some embodiments, the subject is a breast cancer patient. In some embodiments, the subject is a metastatic breast cancer patient.

[0028] In some embodiments, the gene that, modulates ADC response / resistance is selected from the group consisting of SH3GL1, HSP90AAL SLC46A3, ABCBL ABCG2, SLPNLk CCNB1, and TUBB3. In some embodiments, the subject is a breast, cancer patient, a small cell lung cancer (SCLC) patient, a non-small cell lung cancer (NSCLC) patient, a neuroendocrine prostate cancer (NEPC) patient, or prostate adenocarcinoma patient (PRAD).

[0029] In some embodiments, the one or more histone modifications are quantified using a histone modification assay that measures one or more of H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, H3K4mel, H3K4me2, H3K4me3, and pan-acetylation. In some embodiments, histone modification assay detects H3K4me3 modifications. In some embodiments, the histone modification assay detects H3K27ac modifications. In some embodiments, the histone modification assay is selected from ChlP-seq (Chromatin ImmunoPrecipitation sequencing), CUT&RUN (Cleavage Under Targets and Release Using Nuclease) sequencing, and CUT&Tag (Cleavage Under Targets and Tagmentation) sequencing.

[0030] In some embodiments, chromatin accessibility is quantified using a chromatin accessibility assay selected from ATAC-seq (Assay of Transpose Accessible Chromatin sequencing), NOMe-seq (Nucleosome Occupancy and Methylome sequencing), FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing), MNase-seq (Micrococcal Nuclease digestion with sequencing), a DNase hypersensitivity assay, and a fragmentomics assay.

[0031] In some embodiments, the binding of one or more transcription factors is quantified using a transcription factor binding assay that detects binding of one or more of p300, mediator complex, cohesin complex, RNA pol II, FOXA1, ESRI, PR, MYC, ENI, FOXM1, KLF4, AP-2, RARa, or RUNX1. In some embodiments, the transcription factor binding assay is selected from ChlP-seq (Chromatin ImmunoPrecipitation sequencing), CUT&RUN (Cleavage Under Targets and Release Using Nuclease) sequencing, and CUT&Tag (Cleavage Under Targets and Tagmentation) sequencing.

[0032] In some embodiments, the method comprises quantifying two or more of the following, each at. one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject: (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and (iv) transcription factor binding. In some embodiments, the method comprises quantifying two or more histone modifications for the same gene. In some embodiments, the method comprises quantifying H3K4me3 and H3K27ac modifications for the same gene. In some embodiments, the quantified H3K4me3 and H3K27ac modifications are combined to generate an activation score for the gene. In some embodiments, the quantified H3K4me3 and H3K27ac modifications are summed, optionally with weighting, to generate an activation score for the gene. In some embodiments, the gene encodes an ADC target antigen. In some embodiments, the target antigen is TROP2. In some embodiments, the gene modulates ADC response / resistance.

[0033] In some embodiments, the liquid biopsy sample is a plasma sample, serum sample, or urine sample. In some embodiments, the liquid biopsy sample is a plasma sample, optionally a 1 mL plasma sample.

[0034] In some embodiments, quantification of one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors, at the one or more genomic loci as compared to a reference indicates whether an ADC target is being expressed and / or provides a prediction or measurement of the expression level of the ADC target.

[0035] In some embodiments, the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have undetectable or low expression of the ADC target based on IHC testing, or to be cancer free. In some embodiments, the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have high expression of the ADC target based on IHC testing.

[0036] In some embodiments, quantification of one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors, at the one or more genomic loci as compared to a reference indicates whether a gene that modulates ADC response / resistance is active. In some embodiments, the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a. measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have low or undetectable activity of the gene that modulates ADC response / resistance. In some embodiments, the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have high activity of a gene that modulates ADC response / resistance.

[0037] In some embodiments, quantification of one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors, at the one or more genomic loci as compared to a reference indicates whether the subject is likely to respond to treatment with an ADC for the ADC target. In some embodiments, the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to not respond to treatment with the ADC for the / ADC target. In some embodiments, the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to respond to treatment with the ADC for the ADC target.

[0038] In some embodiments, the method comprises quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1, Table 2, Table 3, Table 4, Table 5, or Table 6. In some embodiments, the method comprises quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1. In some embodiments, the method comprises quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2. In some embodiments, the method comprises quantifying H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3, In some embodiments, the method comprises quantifying H3K27ac or H3K4me3 modifications and / or DNA methylation for at least 1,2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4. In some embodiments, the method comprises quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 5. In some embodiments, the method comprises quantifying H3K27ac or H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6.

[0039] In some embodiments, the subject has previously been determined to have cancer. In some embodiments, the subject has previously been determined to have breast cancer, prostate cancer, or lung cancer. In some embodiments, the lung cancer is SCLC, the prostate cancer is PRAD or NEPC, or the breast cancer is metastatic breast cancer (e.g., HR+ / HER2- metastatic breast cancer).

[0040] In some embodiments, the method further comprises administering an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) to the subject. In some embodiments, the agent that is directed to an ADC target antigen (e.g., ADC therapy or radioligand) is selected at least in part based on a quantified level of (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) transcription factor binding at the one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject. In some embodiments, the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene encoding a first ADC target antigen and the selected agent that is directed to an ADC target antigen (e.g., ADC therapy or radioligand) targets the first ADC target antigen. In some embodiments, the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene that modulates response / resistance to a first ADC and the selected agent that is directed to an ADC target antigen (e.g., ADC therapy or radioligand) does not include the first ADC. In some embodiments, the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene that modulates response / resistance to a first ADC and the selected ADC therapy: (i) includes the first ADC if increased activity of a gene associated with resistance to the first ADC is not detected; and (ii) does not include the first ADC if increased activity of a gene associated with resi stance to the first ADC is detected.

[0041] In some embodiments, the agent that is directed to an .ADC target antigen is an anti-TROP2 .ADC and / or comprises a Topoisomerase I (TOPI) inhibitor moiety, optionally wherein the ADC is sacituzuniab govitecan (SG). In some embodiments, the TOPI inhibitor moiety comprises SN-38.

[0042] In one aspect the present disclosure provides a method of treating a subject having cancer with an agent that is directed to an ADC target antigen (e.g., an .ADC therapy or radioligand), the method comprising administering an agent that is directed to an ADC targetantigen (e.g., an ADC therapy or radioligand) to the subject that has been selected at least in part based on a quantified level, at one or more genomic loci, of: (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) transcription factor binding at one or more genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject, wherein the one or more genomic loci are (a) within a. gene encoding an ADC target antigen or a gene that modulates / ADC response / resistance and / or (b) are associated with a promoter or an enhancer of a gene encoding an ADC target antigen or a gene that modulates ADC response / resistance. In some embodiments, the one or more genomic loci are: (a) within a gene encoding an ADC target antigen or within a gene that modulates ADC response / resistance; and / or (b) are associated with a promoter or an enhancer of:(I) a gene that modulates ADC response / resistance; and / or (II) a gene encoding an ADC target antigen.

[0043] In one aspect the present disclosure provides, a method of determining whether a subject is likely to respond to treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), comprising quantifying, at one or more genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject:(i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) binding of one or more transcription factors, wherein the one or more genomic loci are: (a) within a gene encoding an ADC target antigen or within a gene that modulates ADC response / resistance; and / or (b) are associated with a promoter or an enhancer of: (1) a gene that modulates ADC response / resistance; and / or (II) a gene encoding an ADC target antigen.

[0044] In some embodiments, the gene that modulates ADC response / resistance is selected from the group consisting of SH3GL1, HSP90AA1, SLC46A3, ABCB1, ABCG2, SLFNH, CCNB1, and TUBB3.

[0045] In some embodiments, the quantification of (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) transcription factor binding at one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject was performed in accordance with a method described herein. In some embodiments, the method further comprises quantifying (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) transcription factor binding at one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject in accordance with a method described herein. In some embodiments, the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene encoding a first ADC target antigen and the selected agent, that is directed to an ADC target antigen (e.g., ADC therapy or radioligand) targets the first ADC target antigen. In some embodiments, the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene that modulates response / resi stance to a first ADC and the selected ADC therapy does not include the first ADC,

[0046] In one aspect the present disclosure provides a method of monitoring a subject receiving an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) during a treatment period, the method comprising quantifying (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) transcription factor binding at one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject in accordance with a method described herein at first and second time points during the treatment period. In some embodiments, the agent that is directed to an ADC target antigen (e.g., .ADC therapy or radioligand) is modified (e.g., the ADC therapy or radioligand is discontinued, the ADC used in the ADC therapy or radioligand is changed to a different ADC or radioligand, the dose of the ADC used in the ADC therapy or the radioligand is increased or decreased, the frequency of administration of the ADC used in the ADC therapy or the radioligand is increased or decreased) after the second time point at least in part based on a quantified level of (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) transcription factor binding at the one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject at the second time point. (0047] In one aspect the present, disclosure provides a kit comprising reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci, wherein the one or more genomic loci are located within one or more regions defined by pairs of genomic coordinates in Table 1, Table 2, Table 3, Table 4, Table 5, or Table 6. In some embodiments, the kit comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1. In some embodiments, the kit comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2. In some embodiments, the kit comprises reagents for quantifying H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3. In some embodiments, the kit comprises reagents for quantifying H3K4me3 or H3K27ac modifications or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4. In some embodiments, the kit comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 5. In some embodiments, the kit. comprises reagents for quantifying H3K4me3 or H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6. In some embodiments, the kit comprises one or more antibodies for use in ChlP-seq, optionally wherein the one or more antibodies specifically bind H3K4me3- or H3K27ac-modified histones. In some embodiments, the kit comprises reagents for isolation of cell-free DNA (cfDNA) from a liquid biopsy sample. In some embodiments, the kit comprises reagents for libraiy preparation for sequencing. In some embodiments, kit comprises reagents for sequencing.

[0048] In one aspect the present disclosure provides a non-transitory computer readable storage medium encoded with a computer program, wherein the program comprises instructions that when executed by one or more processors cause the one or more processors to perform operations io perform a method described herein.

[0049] In one aspect the present, disclosure provides a computer system comprising a memory and one or more processors coupled to the memory, wherein the one or more processors are configured to perform operations to perform a method described herein.

[0050] In one aspect the present disclosure provides a system comprising a sequencer configured to generate a sequencing dataset from a sample, and the non-transitory computer readable storage medium and / or the computer system, in some embodiments, the sequencer is configured to generate a Whole Genome Sequencing (WGS) dataset from the sample. In some embodiments, the system further comprises a sample preparation device configured to prepare the sample for sequencing from a biological sample, optionally a liquid biopsy sample. In some embodiments, the sample preparation device comprises reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci in cell-free DNA (cfDNA) from the biological sample, optionally the liquid biopsy sample. In some embodiments, the device comprises reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Tables 1-6 . In some embodiments, the device comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in 'Fable I. In some embodiments, the device comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2. In some embodiments, the device comprises reagents for quantifying H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3. In some embodiments, the device comprises reagents for quantifying H3K27ac or H3K4me3 modifications or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4. In some embodiments, the device comprises reagents for quantifying H3K4me3 modifications for at least. 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 5. In some embodiments, the device comprises reagents for quantifying H3K27ac or H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6. In some embodiments, the reagents comprise one or more antibodies for use in ChlP-seq, optionally wherein the one or more antibodies specifically bind H3K4me3- or H3K27ac-modified histones. In some embodiments, the device comprises reagents for isolation of cell-free DNA (cfDNA) from the biological sample, optionally the liquid biopsy sample. In some embodiments, the device comprises reagents for library preparation for sequencing. In some embodiments, the sequencer comprises reagents for sequencing. BRIEF DESCRIPTION OF THE DRAWING [0051J       Fig. 1 (A) shows a qualitative track view displaying promoter (H3K4me3) signals across breast cancer-relevant ADC target antigens (plus housekeeping genes GAPDH and ACTB). Rows represent select breast cancer patient plasma, samples sorted by ichorCNA ctDNA fraction estimate or healthy volunteer plasma samples. Fig. 1 (B) shows a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for each ADC target antigen. Patient-specific epigenomic activation scores for each gene are represented on a white (low) to dark (high) gradient.

[0052] Figs. 2-8 show graphs showing trend lines and confidence intervals for promoter signals (H3K4me3; (A) in each of Figs. 2-8) and enhancer signals (H3K27ac; (B) in each of Figs. 2-8) relative to ctDNA% for individual breast cancer-relevant ADC target antigens.

[0053] Fig. 9 (A) shows a qualitative track view displaying promoter (H3K4me3) signals across SCLC-relevant ADC target antigens (plus housekeeping genes GAPDH and ACTB). Rows represent select SCLC patient plasma samples sorted by ichorCNA ctDNA fraction estimate or healthy volunteer plasma samples. Fig. 9 (B) shows a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for each ADC target antigen. Patient-specific epigenomic activation scores for each gene are represented on a white (low) to dark (high) gradient.

[0054] Figs. 10-18 show graphs showing trend lines and confidence intervals for promoter signals (H3K4me3; (A) in each of Figs. 10-18) and enhancer signals (H3K27ac; (B) in each of Figs. 10-18) relative to ctDNA% for individual SCLC-relevant ADC target antigens.

[0055] Fig. 19 (A) shows a qualitative track view displaying promoter (H3K4me3) signals across NSCLC-relevant ADC target antigens (plus housekeeping genes GAPDH and ACTB). Rows represent select NSCLC patient plasma samples sorted by ichorCNA ctDNA fraction estimate or healthy volunteer plasma samples. Fig. 19 (B) shows a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for each ADC target antigen. Patient-specific epigenomic activation scores for each gene are represented on a white (low) to dark (high) gradient.

[0056] Figs. 20-35 show graphs showing trend lines and confidence intervals for promoter signals (H3K4me3; (A) in each of Figs. 20-35) and enhancer signals (H3K27ac; (B) in each of Figs. 20-3 5(B)) based on ctDNA% for individual NSCLC-relevant ADC target antigens.

[0057] Figs. 36-51 show data obtained for breast cancer-relevant ADC target antigens using breast cancer patient plasma samples and healthy volunteer plasma samples. Each figure is for a different ADC target antigen identified in the top left-hand comer of the figure (e.g., TR.OP2 in Figure 35, ROR2 in Figure 36, etc.). In each figure, (A) shows a qualitative track view displaying promoter (H3K4me3) signals for the gene encoding the indicated ADC target antigen and other transcripts of interest in breast cancer for context (HER2, anti MYC) plus housekeeping genes (GAPDH and ACTB) as controls. Rows represent select breast cancer patient plasma samples sorted by ichorCNA ctDNA. fraction estimate or healthy volunteer plasma samples. The ER and HER2 status (based on IHC) is also shown for each sample. Blue boxes identify samples for which ER status was unknown. In each figure, (B) show's a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for the indicated ADC target antigen compared to the other transcripts of interest in breast cancer CHER2, FOXA1 and MYC). Patient-specific epigenomic activation scores for each gene are represented on a gradient (regressed out and scaled to the min and the max of the ADC target antigen in these samples). (C) and (D) in each figure show graphs showing trend lines and confidence intervals for the promoter signal (H3K4me3) and enhancer signal (H3K27ac), respectively, relative to ctDNA% for the indicated ADC target antigen.

[0058] Fig. 52 show graphs with trend lines and confidence intervals for the promoter signal (H3K4me3; (A)) and enhancer signal (H3K27ac; (B)) relative to ctDNA% for certain transcripts of interest in breast cancer (HER2, FOXA1 and MYC).

[0059] Fig. 53 show's qualitative track view promoter epigenomic activation signals at select genes known to modulate ADC response / resistance in SCLC patient plasma samples. Altered expression of these genes could impart payload resistance (SLFNH: topoisomerase inhibitor resistance, TUBB3: microtubule inhibitor resistance, CCNB1) or induce payload efflux (increase in drug efflux pumps ABCG2, ABCBJ). Boxed activation signals illustrate exemplary patterns associated with predicted sensitivity to an ADC.

[0060] Fig. 54 show qualitative track views showing promoter epigenomic activation signals at select genes known to modulate ADC response / resi stance in breast cancer, NSCLC and SCLC patient plasma samples. Altered expression of these genes could impair ADC internalization (chaperone proteins Endophilin A2, HSP90}, disrupt lysosomal processing (SLC46A3), induce payload efflux (increase in drug efflux pumps ABCG2, ABCBB) or impart payload resistance (SLFN11: topoisomerase inhibitor resistance, CCNB1).

[0061] Fig. 55 (A) shows a qualitative track view displaying histone modification signal across certain NEPC and PRAD-relev ant A DC target antigens (plus housekeeping gene GAPDH) in plasma samples obtained from patients with NEPC or PRAD or healthy subjects. Rows represent select NEPC or PRAD patient plasma samples sorted by ichorCNA ctDNA. fraction estimate or healthy volunteer plasma samples. (B) shows H3K27ac signal at an enhancer region associated with AR in plasma samples obtained from AR+ / NE- PRAD subjects. Also shown is a measure of H3K27ac signal at the locus, which demonstrates an ability to detect increased H3K27ac signal at the AR locus in prostate cancer patients as compared to healthy subjects. (C) shows H3K27ac signal at an enhancer region associated with DLL3 in NE+ tumors. Also shown is a measure of H3K27ac signal at the locus, which demonstrates an ability to detect increased H3K27ac signal at the DLLS locus in NEPC subjects as compared to PRAD subjects.

[0062] Fig. 56 shows graphs predicting expression of clinically relevant drug targets in breast cancer. (A) Shows the performance of methods described herein for predicting the expression of certain drug targets at 10% ctDNA fraction, including targets of antibody-drug conjugates (ADC’s), hormone therapy, and other oncology drugs. Each point represents a gene, with the Spearman correlation coefficient between actual expression (as measured by RNA-seq) and predicted expression (as calculated using cfDNA epigenomic features) plotted on the x-axis and model AUG plotted on the y-axis. (B) Shows validation of B7-H4 (VTCN1) expression predictions across 35 breast cancer cell lines at 10% ctDNA. Each point represents a different cell line. Plotted on the x-axis is actual RNA expression (as measured by RNA-seq) and plotted on the y-axis is predicted RNA expression (predicted using cfDNA epigenomic features). (C) Shows graphs showing the stability of predictions across varying ctDNA fractions for certain genes. Plotted on the x-axis of each graph is tumor (ctDN A) fraction. Plotted on the y-axis of each graph is the Spearman correlation coefficient between RNA expression (as measured by RNA-seq) and predicted expression (as measured using epigenomic features). The horizontal line in each graph indicates the Spearman correlation coefficient at a tumor fraction of 0.10. Regression lines indicate model fit, and shaded regions represent confidence intervals.

[0063] Fig. 57 provides scatter plots that show expression predicted using epigenetic modifications in plasma samples (y-axis) vs. RNA-seq expression values measured in matched tumor biopsies (x-axis) for the 3 indicated genes. N™12, ctDNA >3%. Regression lines indicate model fit and shaded regions represent confidence intervals.

[0064] Fig. 58 provides a graph depicting correlation between certain loci and DLLS expression at varying ctDNA%. “Pearson’s r” refers to the Pearson correlation coefficient determined by comparing predicted expression (as determined using epigenetic modifications) in (a) plasma samples having a high ctDNA fraction (30% ctDNA), and (b) the same samples serially diluted in silico with healthy plasma sequencing data. “’Single Gene Model” (purple data points, connected by the bottom purple line) refers to prediction values generated using a model that incorporates only loci that are proximal to the DLL3 locus. “Multigene Model” (black points connected by the top black line) refers to prediction values determined using a model that incorporates loci that are proximal to DLL3 and several additional genes whose expression is correlated with that oiDLL3. DLL3 expression prediction was found to be improved (including improved model precision, i.e., a stronger correlation between expression predictions at a high ctDNA fracti on and lower ctDNA%) by incorporating additional loci of genes whose expression is correlated with that of DLLS.

[0065] Fig. 59 shows data related to measuring epigenetic markers associated with ADC targets and NEPC / PRAD markers in patient plasma samples. (A) Provides measures of promoter signal (H3K4me3), corrected for ctDNA%, measured at a promoter region of each eLDLLS, SEZ6, CHGA, KLK3, and KLK2 in plasma samples obtained from patients diagnosed with neuroendocrine prostate cancer (NEPC) or prostate adenocarcinoma (PRAD). (B) Shows a combined DLLS. SEZ6, CHGA score, calculated by taking the .mean of the promoter (H3K4me3) signal measured in a promoter region associated with each gene. Circled is a group of patients having a high DLJ3ISEZ6ICHGA score despite having been diagnosed with PRAD, indicating that these patients may have been misdiagnosed. In each graph, left box-and-whiskers bar indicates signal measured in NEPC subjects, and right box-and-whiskers bar indicates signal measured in PRAD subjects, and each point represents a measurement from an individual patient. DETAILED DESCRIPTION

[0066] The present disclosure is based, at least in part, on the demonstration that certain genomic loci associated with select genes for ADC target antigens or genes that modulate ADC response / resistance have different histone modification levels (e.g., histone methylation marks such as H3K4nie3 and histone acetylation marks such as H3K27ac) in plasma samples from cancer patients as compared to plasma samples from healthy volunteers.

[0067] The present disclosure encompasses methods, kits and systems that use these epigenomic differences (alone or in combination with each other and / or with other biomarkers) to select subjects for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), to identify subpopulations of subjects that respond to ADCs, to monitor subjects during treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), etc. by detecting and quantifying the presence of histone modifications at these one or more genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample, e.g., a plasma sample obtained or derived from a subject. The present disclosure also encompasses methods where chromatin accessibility and / or binding of one or more transcription factors are detected at the one or more genomic loci instead of (or in addition to) histone modifications. The present disclosure also encompasses methods, kits and systems where the genomic loci that are differentially modified based on different types of histone modifications (e.g, histone methylation marks such as H3K4me3 and histone acetylation marks such as H3K27ac) are combined into multimodal classifiers to select subjects for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), etc. These monomodal and multimodal classifiers can provide minimally invasive ways of selecting subjects for treatment with an agent that is directed to an / ADC target antigen (e.g., an ADC therapy or radioligand), etc. that are more accurate, objective, and comprehensive than the current tissue-based approaches. Antibody-drug conjugates (ADCs) and ADC target antigens |'0068'| An antibody-drug conjugate (ADC) includes an antibody or antibody fragment linked to a chemotherapeutic agent or “payload”. The antibody or antibody fragment acts like a homing signal by attaching to an ADC target antigen on cancer cells, bringing the chemotherapeutic agent directly to the cancer cells. While most ADC clinical candidates utilize cytotoxic chemotherapeutic payloads, recent ADC candidates have also incorporated targeted small molecules and immunomodulatory agents.

[0069] Genes for ADC target antigens (and the encoded ADC target antigen) include, without limitation, TACSTD2 (TROP2), VTCNI (B7H4 or B7-H4), NECTIN4, ERBB3 (HER3), ERBB2 (HER2), EPHA5, R0R1, R0R2, F3 (Tissue factor or TF), FOLRI (FRa), CD276 (B7H3 or B7-H3), MSLN (Mesothelin), SLC39A6 (LIV1 or LIV-1), LY75 (CD205), LY75-CD302, CDH6 (Cadherin-6), KAAG1 (Kidney associated antigen 1), TPBG(5T4 or 5T-4), MET (HGF receptor), FOLH1 (PSMA), NCAM1 (CD56), SEZ6, DLL3, FAP (FAP-alpha), AXL (UFO), CEACAM5, TFRC (CD71), SLC34A2 (NaPi2b), PTK7 (PTK-7 or CCK4), GPNMB (NMB), CCR2, CD44, CLDN6, TNFRSF10B (DR-5), FN-1 (EDB), ESRI (ER), FGFR2, B4GALNT1 (GD2), GPC1 (GPC-1), GRPR, ITGB6 (IB-6 or integrin £6), IGF1R (IGF-1R), MUC1, CDH3 (P-CAD), CD274 (PD-L1), SSTR2, STEAP1, STEAP2, TM4SF1, CHGA (CgA), and EGFR. A number of ADCs are either approved or in development, for these ADC target antigens. See Maecker et al., mAbs (2023) 15(1):2229101 and Fang et al., Cancer Gene Therapy (2024) 31(2):273-284 which are both incorporated herein by reference in their entirety.

[0070] ADCs that have been approved include sacituzumab govitecan (TROP2), enfortumab vedotin (NECTIN4), trastuzumab emtansine and trastuzumab deruxtecan (HER2), tisotumab vedotin (Tissue factor) and Mirvetuximab soravtansine-gynx (FOLRI). Sacituzumab govitecan is an ADC that includes the TROP2-targeted antibody sacituzumab conjugated to the chemotherapeutic agent SN-38, an active metabolite of irinotecan, a TOPI inhibitor (DNA targeting). Enfortumab vedotin is an ADC that includes the NECTIN4-targeted antibody enfortumab conjugated to the chemotherapeutic agent Monomethyl auristatin E (MMAE) (microtubule targeting). Trastuzumab emtansine is an ADC that includes the HER2-targeted antibody trastuzumab conjugated to the chemotherapeutic agent DM1, a maytansinoid derivative (microtubule targeting). It is used by itself to treat early-stage breast cancer after surgery (when chemotherapy and trastuzumab were given before surgery, and there was cancer still present at the time of surgery), or to treat advanced breast cancer in women who have already been treated with trastuzumab and chemotherapy. This therapeutic agent is administered intravenously. Trastuzumab deruxtecan is an ADC that includes the HER2-targeted antibody trastuzumab conjugated to the chemotherapeutic agent deruxtecan, which is a Topoisomerase I (TOPI) inhibitor (DNA targeting) similar to irinotecan. It can be used by itself to treat breast cancer that cannot be removed with surgery' or that has spread (metastasized) to another part of the body, typically after at least one other HER2-targeted agent has been tried. This therapeutic agent is administered intravenously. Trastuzumab deruxtecan can also be used to treat HER2-low breast cancers that cannot be removed with surgery or that have spread to another part of the body, typically after chemotherapy has been tried or if the cancer recurs within 6 months of finishing adjuvant chemotherapy. Tisotumab vedotin is an ADC that includes the Tissue factor-targeted antibody tisotumab conjugated to the chemotherapeutic agent MMAE (microtubule targeting). Mirvetuximab soravtansine-gynx is an ADC that includes the FOLRI-targeted antibody mirvetuximab conjugated to the chemotherapeutic agent DM4. a maytansinoid derivative (mi crotub ule targeting).

[0071] ADCs currently in development include ADCs targeting ROR1 (e.g., MK-2140, NBE-002, and CS5001), CRC2 (e.g., TAK-500), CD44 (e.g., bivatuzumab mertansine (BIWI 1), which targets CD44v6), CLDN6 (e.g., TOLR-1-32, andDS-9606), TNFRSF10B (e.g., ObaOl), FN-1 (e.g., PYX-201), FGFR2 (e.g., BAY 1187982), GD2 (e.g., M3554), GPC1, GRPR, ITGN6 (e.g., SGN-B6A), IGF1R (e.g., W0101), MUC1 (e.g., MUC1-C-ADC and DS-3939), CDH3 (e.g., PCA062), PD-L1 (e.g., PF-08046054 / SGN-PDLIV), SSTR2 (e.g., PEN-221), S TEAP1 (e.g., DSTP3086S and DXC008), STEAP2 (e.g, H1H7814N), and TM4SF1 (e.g., AGX101).

[0072] MK-2140 comprises a monoclonal antibody targeting R0R1 (Ziiovertamab vedotin) conjugated to MMAE. NBE-002 comprises a humanized anti-RORl antibody enzymatically-conjugated to the anthracycline PNU-159682 using a sortase A-mediated sitespecific transpeptidation reaction. CS5001 comprises a human anti-RORl monoclonal antibody, a p-glucuronide linker, and a pyrrolobenzodiazepine prodrug, which is only metabolized after reaching a tumor. [0073^       TAK-500 is a CCR2-binding ADC that comprises a STING agonist dazostinag, and is designed to target myeloid cells that express CCR2, thereby inducing activation of IFN response, reprogramming of suppressive intratumoral CCR2+ myeloid cells, and blockade of suppressive tumor-associated macrophage recruitment. |0074| Bivatuzumab mertansine (BIWI 1) comprises a monoclonal antibody targeting isoform 6 of CD-44 (CD44v6) conjugated to a thiol-containing maytansinoid (a highly potent anti-microtubule agent). A clinical trial evaluating BIW11 was terminated due to potent skin toxicity of the drug (Riechelmann et al., Oral Oncol, 2008. 44(9):823-9). Potential improved ADC delivery routes could improve the safety profile of BIWI 1, thereby rendering it a useful anti-cancer therapeutic.

[0075] TORL-1-32 comprises an MMAE moiety conjugated to an anti-CLDN6 fully humanized monoclonal antibody . TORL-1-32 ADC has a favorable safety / tolerability profile and pharmacokinetic (PK) characteristics and has demonstrated preliminary- antitumor activity in patients with heavily-pretreated CLDN6-expressing ovarian and testicular cancers (see, e.g., Konecny et al., ESMO Annals of Oncol. 2024. 54(S2, S551)). DS-9606 comprises a humanized anti-CLDN6 antibody conjugated to modified pyrrol obenzodi azepi ne. DS-9606 has also shown favorable safety and preliminary efficacy results in ovarian, gastric, NSCLC, giant cell tumor, breast, and endometrial cancer patients. Dose-escalation studies investigating with both TORL-1-32 and DS-9606 are currently ongoing (see, e.g., Pate et al., ESMO Annals of Oncol. 2024. 54(S2, S488-489)).

[0076] ObaOl is a. DR-5 (TNFR.SF10) targeting ADC and is an MMAE-conjugated Zaptuzumab. ObaOl promoted pancreatic cancer tumor cell death and displayed potent antitumor activity in mono and combinational (e.g., in combination with gemcitabine) therapies in patient-derived xenograft murine models (Zheng et al., Cell Death A Disease. 2023. 14(295)).

[0077] PYX-201 comprises a fully human anti-extra-domain B splice variant of fibronectin antibody, a cleavable mcValCitPABC linker, and four Auristatin 0101 (AurOlOl, PF-06380101) payload molecules. PYX-201 has been granted a Food and Drug Administration (FDA) fast track designation for the treatment of adult patients with recurrent or metastatic head and neck squamous cell carcinoma (R / M HNSCC) whose disease has progressed following treatment with platinum-based chemotherapy and an anti-PD-(L)! antibody. PYX-201 was shown to inhibit tumor growth in patient-derived xenografts in mice by 90% or more (Severe et al., Cancer Res. 2024, 84(6 Supplement)).

[0078] BAY 1187982 (Aprutumab ixadotin) comprises a fully human anti-FGFR2 monoclonal antibody linked to an auristatin W derivative, toxophore. Aprutumab ixadotin was found to be poorly tolerated in a phase I, first-in-human trial in patients with advanced solid tumors from cancer indications known to be FGFR2-positive.

[0079] M3554 comprises a humanized anti-GD2 antibody linked to exatecan, a Topoisomerase I inhibitor (TOPli) payload, via a cleavable beta-glucuronide linker. A Phase I clinical trial (NCT06641908) is currently ongoing for evaluating the safety and preliminary antitumor activity of M3554 in participants with soft tissue sarcoma (STS) and IDH-wiidtype glioblastoma.

[0080] An anti-GPCl has been created by conjugating a humanized anti-glypican-1 (anti-GPC1) antibody to MMAE (see Uchida et al., Neoplasia. 2024. 50(100982)). This GPC1-ADC was shown to be efficiently internalized by glioblastoma cells lines and potently suppress glioblastoma tumor growth in murine subjects, supporting its potential utility for treating cancer.

[0081] Currently, only peptide drug-conjugates are being developed to target GRPR. For example, 212 Pb-GRPR is a radioligand being developed for therapeutic and diagnostic (e.g., theragnostic) purposes. 212 Pb-GRPR comprises a lead-212 radioisotope conjugated to a GRPR-targeting peptide, GRPR1 (see Saidi et al., J Nud Med. 2024. 165(11)). Nonetheless, GRPR remains a valuable therapeutic target with potential to be targeted with an ADC therapeutic.

[0082] SGN-B6A is an ITGB6-directed vedotin ADC that comprises a monomethyl auristatin E (MMAE) payload. In a phase I study evaluating SGN-B6A in patients with advance solid tumors in NSCLC, head and neck (HNSCC), and esophageal cancer (EC) indications, SGN-B6A demonstrated a manageable safety profile, and preliminary antitumor activity and response durability in dose escalation in a heavily pretreated patient population (see Hollebecque et al., J Clin Oncol. 2023. 41(16_Supplement)).

[0083] W0101 (Lonigutamab Ugodotin) comprises an anti-IGFIR humanized monoclonal antibody conjugated to a dolastatin / auristatin derivative, and is designed to target IGFIR-overexpressing tumors. W0101 has been shown to be effective in inhibiting tumor growth in a preclinicai murine model of breast cancer, and induced potent tumor regression in several other cancer models (see Alda et al., Mol Cancer Ther. 2020. 19(1)).

[0084] MUC1 -targeting ADCs constitute an area of high interest for targeting stromal and difficult to treat tumors, and are likely to be expanded to various metastatic cancer indications in future clinical trials. MUC1-C-ADC comprises an anti-glycosylated Mucin 1 (MUC1) monoclonal antibody (targeting the extracellular domain of MUC1), conjugated to MMAE via vc-PAB linkers. MUC1-C-ADC has been shown to effectively kill metastatic colorectal cancer (mCRC) cells in vitro and inhibit tumor growth in mCRC murine models without adverse effects (e.g., weight loss) (see Raina et al., J Clin Oncol. 2024. 42(16_Suppiement)). A MUC1*-ADC comprising a monoclonal anti-MUCl antibody that recognizes only a conformational epitope created when MUC1 is cleaved by certain tumor-associated enzymes (e.g., MNC2) and a monomethyl auristatins or Topoisomerase 1 inhibitor moiety has also been developed. See Bamdad et a., Cancer Res. 2024. 84(6 Supplement). Pancreatic cancer xenografts in mice were eliminated by MNC2-MMAE, MNC2-Deruxtecan and MNC2-exatecan ADCs, and breast cancer tumor xenografts were inhibited with a MNC2-Deruxtecan ADC). DS-3939 is another MUC1-targeting ADC, which has recently entered a Phase I clinical trial for locally advanced, metastatic, or unresectable urothelial, non-small cell lung, breast, ovarian, biliary tract, or pancreatic cancers. DS-3939 comprises a humanized anti-TA-MUC1 antibody attached to a number of topoisomerase I inhibitor payloads (an exatecan derivative, DXd) via tetrapeptide-based cleavable linkers.

[0085] PCA062 is a P-cadherin-targeting ADC, and has been evaluated in HNSCC, EC, and triple-negative, Cadherin-3 positive breast cancer patients for safety and preliminary efficacy. High incidence of adverse events and limited antitumor activity led to termination of the clinical trial evaluating PCA062. To supplement efficacy of a P-cadherin-only ADC, bi specific P-cadherin and CDH17 ADC conjugated to MMAE has been developed, and shown to lead to tumor regression in a CRC xenograft mouse model (Synan et al., biorXiv, 2024. 590291).

[0086] PF-08046054 / SGN-PDL1V is an investigational ADC comprising a monoclonal anti-PD-Ll antibody conjugated to MMAE via a protease-cleavable mc-vc (maieimidocaproyl-valine-citrulline) linker. Patients with advanced solid tumors are currently being enrolled in a Phase 1 clinical trial to test, the safety and preliminary efficacy of PF-08046054 / SGN-PDL1V alone or in combination with pembrolizumab (NCT05208762).

[0087] PEN-221 is an emtansine-conjugated, SSTR2-targeting .ADC, which has been investigated in a Phase 2 clinical trial in a patient population with advanced GI mid-gut neuroendocrine tumors. PEN-221 was shown to be w'ell-tolerated by patients, and exceeded clinical efficacy goals for Clinical benefit Rate and median progression-free survival (see Halperin et al., J Clin Oncol. 2021.39(15_Supplement). PEN-221 may also have potential utility in treating SSTR2-positive SCLC.

[0088] STEAP1 is a promising ADC target, due to its high expression in prostate cancer. DSTP3086S is an ADC that comprises a humanized anti-STEAPl monoclonal antibody conjugated to MMAE. DSTP3086S was evaluated in patients with metastatic castration-resistant prostate cancer and was shown to be tolerated by patients at a dose level that provides beneficial anti-tumor activity, indicating the potential benefit of treating STEAP1-expressing metastatic castration-resistant prostate cancer with a STEAP1 -targeting ADC (Danila et al., J Clin Oncol. 2019. 37(36)). DXC008 is another STEAP1 -targeting ADC, comprising an antibody having high binding affinity to PSMA conjugated to a tubulysin B analogue. DXC008 was shown to be well-tolerated in preclinical investigations in mice and non-human primates, and result in durable antitumor response in murine prostate cancer xenograft models (Yang et ah, Cancer Res. 2024. 84(6_Supplem ent)).

[0089] H1H7814N is an early-development ADC comprising an anti-STEAP2 monoclonal antibody that is conjugated to either auristatin or a maytansinoid. H1H7814N has show'll preliminary anti-tumor activity in murine models of prostate cancer, when compared to an unconjugated anti-STEAP2 antibody.

[0090] AGX101 is a first-in-class anti-TM4SFl ADC comprising a conjugated tubulin inhibitor, and targets nuclear membranes of cancer cells to deliver payloads directly to the nucleus. AGX101 has shown potent anti-tumor activity in colon and pancreatic cancer murine xenografts and a favorable safety profile in animal studies (see Jami net et al. J Clin Oncol. 2024. 43 (4_Supplement)). A phase 1 clinical trial is currently ongoing to test the safety and efficacy of A.GX101 in patients with unresectable, locally advanced, or metastatic solid tumors.

[0091] Exemplary agents that target DLL3 are known in the art and are described, e.g., in Rudin, Charles M., et al. “Emerging therapies targeting the delta-like ligand 3 (DLL3) in small cell lung cancer." Journal of Hematology & Oncology 16.1 (2023): 66. Exemplary agents targeting DLL3 include ADCs (e.g., Rova-T, an ADC comprising a DLL3-specific humanized monoclonal antibody (SC16) conjugated to a membrane-permeable pyrrolobenzodiazepine (PBD) dimer toxin (warhead) via a lysosomal, protease-sensitive dipeptide linker; and SC-002, a bioengineered, DLL3-directed antibody-drug conjugate (ADC) that delivers the cytotoxic pyrrolobenzodiazepine (PBD) dimer warhead, SC-DR002, to cells expressing DLL3).

[0092] In some embodiments, where a method of the present disclosure detects or quantifies a high level of activity (relative to a reference) and / or detects an increase in the level of activity (e.g., relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of a gene encoding an ADC target, this may be used io select an ADC or radioligand for that ADC target as an ADC therapy or radioligand for a subject.

[0093] In some embodiments, where a method of the present disclosure predicts high levels of ADC target expression (relative to a reference) and / or detects an increase in .ADC target expression (e.g., relative to a prior measurement during treatment) this may be used to select an ADC or radioligand for that ADC target as an ADC therapy radioligand for a subject. In some embodiments, ADC selection is based on an assessment of ADC target status using a method of the present disclosure in combination with IHC testing. Genes That Modulate ADC response / resistance

[0094] In some embodiments, the methods of the present disclosure use epigenomic differences (alone or in combination with each other and / or with other biomarkers) that are associated with genes that modulate ADC response / resi stance to select subjects for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), to identify subpopulations of subjects that respond to treatment with an agent that is directed to an ADC target antigen (e.g., ADCs or radioligands), to monitor subjects during treatment with an agent that is directed to an ADC target antigen (e.g., ADC therapy or radioligand), etc.

[0095] As used herein, a “gene that modulates ADC response / resistance / ’ refers to a gene encoding a protein that has an activity that can modulate ADC efficacy. Without limitation, examples of proteins having an activity that can modulate ADC response / resi stance include proteins that can interfere with ADC internalization, proteins that can interfere with pathway signaling, proteins that increase stability of an ADC target antigen, proteins involved in lysosomal transport, proteins involved in a DNA damage repair pathway, and proteins that function as a drug efflux pump.

[0096] Exemplary genes that modulate ADC response / resistance (and the proteins they encode) include SH3GL1 (Endophilin A2), HSP90AA1 (HSP90), SLC46A3, CCNB1 (Cyclin Bl), SLFN11, ABCB1 (MDR1), ABCG2 (BCRP), and TUBB3 (Class III beta-tubulin). In some embodiments, epigenomic differences (alone or in combination with each other and / or with other biomarkers) associated with these genes may be used in combination with epigenomic differences (or other biomarkers, e.g., HER2 IHC test resuits) associated with a gene for an ADC target antigen (e.g., ERRB2 gene encoding HER2).

[0097] Endophilin A2 is a scaffolding protein involved in clathrin-mdependent endocytosis. Reduced EndophilinA2 expression has been shown to decrease HER2 internalization, reduce downstream signaling, and decrease the migratory potential of the BRCA cells. A decrease in Endophilin A2 results in reduced cytotoxicity of HER2-targeted ADCs (e.g., trastuzumab emtansine) against HER2-positive cells. See Baldassarre et al., Breast Cancer Res (2017) 19:110 which is incorporated herein by reference in its entirety. In some embodiments, where a method of the present disclosure predicts low levels of Endophilin A2 expression (relative to a reference) and / or detects a decrease in Endophilin A2 expression (e.g., relative to a prior measurement during treatment) this may be used to select a therapy other than a HER2-targeted ADC for a subject. In some embodiments, where a method of the present disclosure predicts high levels of Endophilin A2 expression (relative to a reference) and / or detects an increase in Endophilin A2 expression (e.g., relative to a prior measurement during treatment) this may be used to select a HER2-targeted ADC (e.g., trastuzumab emtansine) as an ADC therapy for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g., relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of SH3GL1. In some embodiments, IIER2-targeted .ADC selection is also based on an assessment of HER2 status using a method of the present disclosure and / or based on IHC testing.

[0098] HSP90 is a chaperone protein that is important for HER2 stability (by preventing ubiquitination). Increase in HSP90 results in more stable HER2, reduced internalization and reduced ADC efficacy. See Li et al., Cancer Discov (2020) 10(5):674-687 which is incorporated herein by reference in its entirety. In some embodiments, where a method of the present disclosure predicts low levels of HSP90 expression (relative to a reference) and / or detects a decrease in HSP90 expression (e.g., relative to a prior measurement during treatment) this may be used to select a HER2-targeted ADC (e.g., trastuzumab emtansine) as an ADC therapy for a subject. In some embodiments, where a method of the present disclosure predicts high levels of HSP90 expression (relative to a reference) and / or detects an increase in HSP90 expression (e.g., relative to a prior measurement during treatment) this may be used to select a therapy other than a HER.2-targeted ADC for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g., relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of HSP90AA1. In some embodiments, HER2-targeted ADC selection is also based on an assessment of HER2 status using a method of the present disclosure and / or based on IHC testing.

[0099] SLC46A3 is a lysosomal membrane transporter protein relevant for efflux of maytansine-based catabolites from the lysosome. Loss / decrease in SLC46A3 has been shown to lead to accumulation of maytansine-based catabolites in lysosomes resulting in resistance to the HER2-targeted ADC trastuzumab emtansine. See Li et al., Mol Cancer Th er (2018) 17(7): 14411453 which is incorporated herein by reference in its entirety. In some embodiments, where a method of the present disclosure predicts low levels of SLC46A3 expression (relative to a reference) and / or detects a decrease in SLC46A3 expression (e.g., relative to a prior measurement during treatment) this may be used to select a therapy other than a HER2-targeted ADC for a subject. In some embodiments, where a method of the present disclosure predicts high levels of SLC46A3 expression (relative to a reference) and / or detects an increase in SLC46A3 expression (e.g., relative to a prior measurement during treatment) this may be used to select a HER2-targeted ADC (e.g., trastuzumab emtansine) as an ADC therapy for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g., relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of SLC46A3. In some embodiments, HER2-targeted ADC selection is also based on an assessment of HER2 status using a method of the present disclosure and / or based on IHC testing.

[0100] Cyclin Bl is essential for mitosis / rnitotic catastrophe. Reduced CCNB1 has been shown to result in resistance to the HER2-targeted ADC trastuzumab emtansine. See Sabbaghi et al., Clin Cancer Res (2017) 23(22):7006-7019 which is incorporated herein by reference in its entirety. In some embodiments, where a method of the present disclosure predicts low levels of Cyclin B1 expression (relative to a reference) and / or detects a decrease in Cyclin Bl expression (e.g., relative to a prior measurement during treatment) this may be used to select a therapy other than a HER2-targeted ADC for a subject. In some embodiments, where a method of the present disclosure predicts high levels of Cyclin Bl expression (relative to a reference) and / or detects an increase in Cyclin Bl expression (e.g., relative to a prior measurement during treatment) this may be used to select a HER2-targeted ADC (e.g., trastuzumab emtansine) as an ADC therapy for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g, relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of CCNB1. In some embodiments, HER2-targeted ADC selection is also based on an assessment of HER2 status using a method of the present disclosure and / or based on IHC testing.

[0101] SLFNI1 is a DNA / RNA helicase important in DNA damage response and replication stress. SLFNI1 sensitizes cells to a broad range of anti-cancer drugs including platinum derivatives (cisplatin and carboplatin), inhibitors of topoisomerases (camptothecin, irinotecan, topotecan, doxorubicin, daunorubicin, mitoxantrone and etoposide), DNA synthesis inhibitors (gemcitabine, cytarabine, hydroxyurea and nucleoside analogues), and poly(ADPribose) polymerase (PARP) inhibitors (olaparib, rucaparib, niraparib and talazoparib). In the ADC context, increased levels of SLFNI 1 are predictive of response to Topoisomerase I (TOPI) inhibitor payloads. See Murai et al., Pharmacol Ther (2020) 201:94-102 and Coleman et al., British Journal of Cancer (2021) 124:857-859 which are both incorporated herein by reference in their entirety. In some embodiments, where a method of the present disclosure predicts low7 levels of SLFN11 expression (relative to a reference) and / or detects a decrease in SLFN I 1 expression (e.g., relative to a prior measurement during treatment) this may be used to select an ADC with a payload other than one of the aforementioned anti-cancer drugs, e.g., an ADC with a payload other than a TOPI inhibitor payload (e.g., an ADC with a payload other than camptothecin, topotecan, or irinotecan) for a subject. In some embodiments, where a method of the present disclosure predicts high levels of SLFNI 1 expression (relative to a reference) and / or detects an increase in SLFNI 1 expression (e.g., relative to a prior measurement during treatment) this may be used to select an ADC with one of the aforementioned anti-cancer drugs, e.g., an ADC with a TOPI inhibitor payload (e.g., an ADC with an camptothecin, topotecan, or irinotecan payload) for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g., relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of SLFN11,

[0102] Multi-Drug Resistance Protein 1 (MDR1) is a drug efflux pump with MMAE as a substrate. Increased expression of MDR1 results in reduced sensitivity to ADCs with MMAE payloads. See Liu-Kreyche et al., Front Pharmacol (2019) 10:749 and Aldonza et al., Oncotarget (2016) 7(23):34395-34419 which are both incorporated herein by reference in their entirety. In some embodiments, where a method of the present disclosure predicts low levels of MDR1 expression (relative to a reference) and / or detects a decrease in MDR1 expression (e.g., relative to a prior measurement during treatment) this may be used to select an ADC with an MMAE payload for a subject. In some embodiments, where a method of the present disclosure predicts high levels of MDR1 expression (relative to a reference) and / or detects an increase in MDR1 expression (e.g., relative to a prior measurement during treatment) this may be used to select an ADC with a pay load other than MMAE for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g., relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of ABCB1.

[0103] BCRP is a drug efflux pump. Increased expression results in reduced sensitivity to ADC payloads. See Chang et al., Mol Cancer Ther (2016) 15(8): 1910-1919 which is incorporated herein by reference in its entirety. In some embodiments, where a method of the present disclosure predicts high levels of BCRP expression (relative to a reference) and / or detects an increase in BCRP expression (e.g., relative to a prior measurement during treatment) this may be used to combine ADC therapy with a BCRP inhibitor, e.g., Ko 143 (see .Allen et al., Mol Cancer Ther (2002) 1:417-425), YHO-13351 (see Yamazaki etal., Mol Cancer Ther (2011) 10:1252-1263), FTC (see Rabindran et al., Cancer Res (2000) 60:47-50), cyclosporine A (see Qadir et al., Clin Cancer Res (2005) 11:2320-2326, or GF120918 (see de Bruin et al., Cancer Lett (1999) 146:117-126) for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g, relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of ABCG2.

[0104] Class III beta-tubulin is a microtubule protein. Increased expression is associated with resistance to microtubule-targeting agents (e.g., MMAE). See Kanakkanthara and Miller, Biochim Biophys Rev Cancer (2021) 1876(2): 188607 which is incorporated herein by reference in its entirety. In some embodiments, where a method of the present disclosure predicts low levels of Class III beta-tubulin expression (relative to a reference) and / or detects a decrease in Class III beta-tubulin expression (e.g., relative to a prior measurement during treatment) this may be used to select an ADC with microtubule-targeting agent (e.g., MMAE) payload for a subject. In some embodiments, where a method of the present disclosure predicts high levels of Class III beta-tubulin expression (relative to a reference) and / or detects an increase in Class III betatubulin expression (e.g., relative to a prior measurement during treatment) this may be used to select an ADC with a payload other than a microtubule-targeting agent (e.g, MMAE) for a subject. In some embodiments, the selection is based in part on detecting or quantifying a level of activity (relative to a reference) and / or detecting an increase or decrease in the level of activity (e.g, relative to a prior measurement during treatment) at one or more genomic loci associated with a promoter or an enhancer of TUBB3. Subjects and Samples

[0105] A sample analyzed using methods, kits and systems provided herein can be any biological sample including any processed sample that includes circulating tumor DNA (ctDNA) derived from a biological sample. In various embodiments, a sample analyzed using methods, kits and systems provided herein can be a sample obtained from a mammalian subject. In various embodiments, a sample analyzed using methods, kits and systems provided herein can be a sample obtained from a human subject.

[0106] In various instances, a human subject is a subject diagnosed or seeking diagnosis as having, diagnosed as, or seeking diagnosis as at risk of having, and / or diagnosed as or seeking diagnosis as at immediate risk of having cancer, e.g, breast cancer, small cell lung cancer (SCLC) or non-small cell lung cancer (NSCLC), neuroendocrine prostate cancer (NEPC). prostate adenocarcinoma (PRAD), etc. In various instances, a human subject is a subject identified as needing treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand). In certain instances, a human subject is a subject identified as needing ADC therapy or radioligand screening by a medical practitioner. (0107] The subject may not have undergone previous treatments for cancer, such as the treatments recited in this disclosure. In other embodiments, the subject has undergone previous treatments for cancer, such as the treatments recited in this disclosure.

[0108] In various embodiments a subject has one or more biomarkers and / or risk factors for cancer, e.g., breast cancer, small cell lung cancer (SCLC) or non-small cell lung cancer (NSCLC), neuroendocrine prostate cancer (NEPC), prostate adenocarcinoma (PRAD), etc. In certain embodiments, a human subject is identified as in need of ADC therapy or radioligand screening based on an initial cancer diagnosis, e.g., a breast cancer, small cell lung cancer (SCLC) or non-small cell lung cancer (NSCLC), neuroendocrine prostate cancer (NEPC), prostate adenocarcinoma (PRAD), etc. diagnosis. In various instances, a human subject is a subject not yet diagnosed as having, not at risk of having, not at immediate risk of having, not diagnosed as having, and / or not seeking diagnosis for a cancer. Genetic factors may also contribute to cancer risk, as evidenced by individuals with a family history of cancer.

[0109] In various embodiments, a sample from a subject, e.g., a human can be obtained from a liquid biopsy. In certain embodiments, a sample and / or reference is obtained from serum, plasma, or urine. In certain embodiments, the sample is serum. In certain embodiments, a sample comprises circulating tumor DN.A (ctDNA). In certain embodiments, a sample is derived from about 1 mL of blood obtained from the subject. In certain embodiments, a sample is derived from about 0.5-2 mL of blood obtained from the subject, e.g., about 0.5 to 1.75 mL, about 0.5 to 1.5 mL, about 0.75 to 1.25 mL or about 0.9 to 1.1 mL of blood.

[0110] In various embodiments, a sample is a sample of cell-free DNA (cfDNA). cfDNA is typically found in human biofluids (e.g, plasma, serum, or urine) in short, doublestranded fragments. The concentration of cfDNA is typically low, but can significantly increase under particular conditions, including without limitation pregnancy, autoimmune disorders, myocardial infarction, and cancer. Circulating tumor DNA (ctDNA) is the component of cell-free DNA specifically derived from cancer cells. ctDNA can be present in human biofluids bound to leukocytes and erythrocytes or not bound to leukocytes and erythrocytes. Various tests for detection of tumor-derived ctDNA are based on detection of genetic or epigenetic modifications that are characteristic of cancer (e.g., of a relevant cancer). Genetic or epigenetic factors characteristic of cancer can include, without limitation, oncogenic or cancer-associated mutations in tumor-suppressor genes, activated oncogenes, chromosomal disorders, histone modifications (e.g., histone methylation and / or histone acetylation), chromatin accessibility, binding of one or more transcription factors and / or DNA methylation. |01111 In various embodiments, ctDNA comprises less than 30%, less than 20%, or less than 10% of the cfDNA in the liquid biopsy sample obtained from the subject, e.g., less than 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2% or less than 1% of the cfDNA in the sample. In some embodiments, the percentage of ctDNA in the liquid biopsy sample is assessed using ichorCNA which estimates the percentage of ctDNA in a sample probabilistically (see Adalsteinsson et al., Nat Commun (2017) 8(1):1324 the entire contents of which are incorporated herein by reference).

[0112] cfDN A and ctDNA can provide a real-time or nearly real time metric of status of a source tissue. ctDNA and ctDNA demonstrate a half-life in blood of about 2 hours, such that a sample taken at a given time provides a. relatively timely reflection of the status of a source tissue.

[0113] Various methods of isolating nucleic acids from a sample (e.g, of isolating cfDNA from blood or plasma) are known in the art. Nucleic acids can be isolated using, without limitation, standard DNA purification techniques, by direct gene capture (e.g., by clarification of a sample to remove assay-inhibiting agents and capturing a target nucleic acid, if present, from the clarified sample with a capture agent to produce a capture complex and isolating the capture complex to recover the target nucleic acid).

[0114] Reagents and protocols for obtaining and analyzing cfDNA and ctDNA, such as circulating in blood or other tissue, are commercially available as described in the Examples and well-known in the art (see, for example, Anker et al., Cancer and Metastasis Rev (1999) 18:6573; Wua et al., Clin Chim Acta (2002) 321:77-87: Fiegl et al., Cancer Res (2005) 15:1141-1145; Pathak et al., Clin Chem (2006) 52:1833-1842; Schwarzenbach et al., Clin Cancer Res (2009) 15:1032-1038; Schwarzenbach et al, Nat Rev Cancer (2011) 11:426-437) the contents of each of which is separately incorporated herein by reference in their entirety).

[0115] In various embodiments, samples can be collected from individuals repeatedly over a period of time (e.g, once daily, weekly, monthly, annually, biannuahy, etc.). In various embodiments, such samples can be used to verify results from earlier detections and / or to identify an alteration in biological pattern because of, for example, disease progression, resistance to therapy, treatment, remission, and the like. For example, subject samples can be taken and monitored every month, every two months, or combinations of one, two, or threemonth intervals according to the present disclosure. In various embodiments, samples can be collected for monitoring over time beginning at or at certain clinically determined stages, such as at resistance to a therapy, before radiographic progression, after radiographic progression, and / or at tissue biopsy. In addition, results from samples obtained at different points in time can be conveniently compared with each other, as well as with those of normal controls during the monitoring period, thereby providing the subject’s own values, as an internal, or personal, control for long-term monitoring.

[0116] Samples include materials prepared by processes including, without limitation, steps such as concentration, dilution, adjustment of pH, removal of high abundance polypeptides (e.g., albumin, gamma globulin, and transferrin, etc.), addition of preservatives, addition of calibrants, addition of protease inhibitors, addition of denaturants, desalting, concentration and / or extraction of sample nucleic acids, and / or amplification of sample nucleic acids (e.g., by PCR or other nucleic acid amplification techniques). Samples also include materials prepared by techniques that isolate, e.g., nucleosomes or transcription factors and / or nucleic acids associated with nucleosomes or transcription factors.

[0117] Removal from a sample of proteins that are not desirable for a relevant purpose or context (e.g., high abundance, uninformative, or undetectable proteins) can be achieved using high affinity reagents, high molecular weight filters, ultracentrifugation and / or electrodialysis. High affinity reagents include antibodies or other reagents (e.g., aptamers) that selectively bind to high abundance proteins. Sample preparation can also include ion exchange chromatography, metal ion affinity chromatography, gel filtration, hydrophobic chromatography, chromatofocusing, adsorption chromatography, isoelectric focusing and related techniques. Molecular weight filters include membranes that separate molecules based on size and molecular weight. Such filters may further employ reverse osmosis, nanofiltration, ultrafiltration and microfiltration. Ultracentrifugation is the centrifugation of a sample at about 15,000-60,000 rpm while monitoring with an optical system the sedimentation (or lack thereof) of particles. Electrodialysis is a procedure which uses an electromembrane or serai permeable membrane in a process in which ions are transported through semi-permeable membranes from one solution to another under the influence of a potential gradient. Since the membranes used in electrodi alysis may have the ability to selectively transport ions having positive or negative charge, reject ions of the opposite charge, or to allow species to migrate through a semipermeable membrane based on size and charge, it renders electrodialysis useful for concentration, removal, or separation of electrolytes. [011§]        Separation and purification in the present disclosure may include any procedure known in the art, such as capillary electrophoresis (e.g., in capillary or on-chip) or chromatography (e.g., in capillary, column or on a chip). Electrophoresis is a method that can be used to separate ionic molecules under the influence of an electric field. Electrophoresis can be conducted in a gel, capillary, or in a microchannel on a chip. Examples of gels used for electrophoresis include starch, acrylamide, polyethylene oxides, agarose, or combinations thereof. A gel can be modified by its cross-linking, addition of detergents, or denaturants, immobilization of enzymes or antibodies (affinity electrophoresis) or substrates (zymography) and incorporation of a pH gradient. Examples of capillaries used for electrophoresis include capillaries that interface with an electrospray.

[0119] Capillary' electrophoresis (CE) is preferred for separating complex hydrophilic molecules and highly charged solutes. CE technology can also be implemented on microfluidic chips. Depending on the types of capillary and buffers used, CE can be further segmented into separation techniques such as capillary zone electrophoresis (CZE), capillary isoelectric focusing (CIEF), capillary' isotachophoresis (CITP) and capillary electrochromatography (CEC). An embodiment to couple CE techniques to electrospray ionization involves the use of volatile solutions, for example, aqueous mixtures containing a volatile acid and / or base and an organic such as an alcohol or acetonitrile.

[0120] Capillary isotachophoresis (CITP) is a technique in which the analytes move through the capillary at a constant speed but are nevertheless separated by their respective mobilities. Capillary' zone electrophoresis (CZE), also known as free-solution CE (FSCE), is based on differences in the electrophoretic mobility of the analytes, determined by the charge on the analytes, and the frictional resistance the analytes encounter during migration, which is often directly proportional to the size of the analytes. Capillary isoelectric focusing (CIEF) allows weakly-ionizable amphoteric molecules, to be separated by electrophoresis in a pH gradient. CEC is a hybrid technique between traditional high performance liquid chromatography (HPLC) and CE. [01211 Separation and purification techniques used in the present disclosure can include any chromatography procedures known in the art. Chromatography can be based on the differential adsorption and elution of certain analytes or partitioning of analytes between mobile and stationary phases. Different examples of chromatography include, but not limited to, liquid chromatography (LC), gas chromatography (GC), high performance liquid chromatography (HPLC), etc.

[0122] In some embodiments, whole blood is collected from a subject, and a plasma layer is separated by centrifugation. cfDNA may be then extracted from the plasma using methods known in the art. Histone Modifications, Chromatin Accessibility'- and Transcription Factor Binding

[0123] Histone methylation is understood to increase or decrease expression of associated coding sequences, depending on which histone residue is methylated. Histone methylation is an essential modification that can cause monomethylation (mel), dimethylation (me2), and trimethylation (me3) of several amino acids, thus directly affecting heterochromatin formation, gene imprinting, X chromosome inactivation, and gene transcriptional regulation. Histone methyltransferases promote monomethylation, dimethylation, or trimethylation of histones while histone demethylases promote demethylation of histones. In general, lysine (Lys or K), arginine (Arg or R), and rarely histidine (His or H) are the most common histone methyl acceptors. Histone methylation only occurs at specific lysine and arginine sites of histone H3 and H4. In histone H3, lysine 4, 9, 26, 27, 36, 56, and 79 and arginine 2, 8, and 17 can be methylated. By comparison, histone H4 has fewer methylation sites, in which only lysine 5, 12, and 20 and arginine .3 can be methylated. Histone methylation is often associated with transcriptional activation or inhibition of downstream genes. The methylation of histone H3K4, R8, R17, K26, K36, K79, H4R3, and K12 can activate gene transcription. However, the methylation of histone H3K9, K27, K56, H4K5, and K20 can inhibit gene transcription. Thus, for example, H3K4 methylation generally activates gene expression, while H3K27 methylation generally represses gene expression.

[0124] Histone acetylation occurs predominantly at lysine residues and is generally understood to increase expression of associated coding sequences. Without wishing to be bound by any theory, acetylation of lysine residues is thought to neutralize lysine’s positive charge and thereby cause histones to drift away from DNA, which has a. negative charge. The released structure facilitates access to transcriptional machinery such as transcription factors and RNA polymerase II. Histone acetylation and deacetylation are generally catalyzed by histone acetyltransferases (HATs) and HDACs, respectively. Acetyl-CoA can be a source and co-factor of acetylation. In regulatory regions, HATs can acetylate histones and recruit HAT-containing complexes to activate the transcriptional process. For instance, H3K9ac and H3K27ac levels can be associated with promoter and enhancer activities. Furthermore, H3K27ac enhances not only the kinetics of transcriptional activation, but also accelerates the transition of RNA polymerase II from the initiation state to the elongation state.

[0125] Differential modification of a genomic locus (e.g., differential histone methylation and / or differential histone acetylation) can refer to, or be determined by or detected as, a comparative difference or change in modification status of one or more genomic loci between a first sample, condition, disease, or state and a second or reference sample, condition, disease, or state. Those of skill in the art will appreciate that a reference is typically produced by measurement using a methodology identical, similar, or comparable to that by which a compared non-reference measurement was taken.

[0126] Chromatin accessibility can refer to the degree to which nuclear macromolecules are able to physically contact DNA and is determined in part by the occupancy and modification status of nucleosomes. Modified histones can regulate chromatin accessibility through a variety of mechanisms, such as altering transcription factor (TF) binding through steric hindrance and modulating nucleosome affinity for active chromatin remodelers. The topological organization of nucleosomes across the genome is non-uniform: while histones can be densely arranged within facultative and constitutive heterochromatin, histones can be depleted at regulatory loci, including within enhancers, insulators and transcribed gene bodies. Active regulatory elements of the genome are generally accessible.

[0127] Differential accessibility of a genomic locus can refer to, or be determined by or detected as, a comparative difference or change in modification status of one or more genomic loci between a first sample, condition, disease, or state and a second or reference sample, condition, disease, or state. Those of skill in the art will appreciate that a reference is typically produced by measurement using a methodology identical, similar, or comparable to that by which a compared non-reference measurement was taken.

[0128] A reference can be a value or set of values that are predetermined or derived from a sample or set of samples. A reference can be a sample or set of samples. A reference value can be a predetermined threshold value, a value that varies in accordance with circumstances (e.g., according to patient subpopulation, age, weight, or other variables), or a ratio. Reference ratios can be ratios relating to the modification and / or accessibility of multiple loci within individual samples and / or references, or across or between samples and / or references. In various embodiments, a reference can have or represent a normal, non-diseased state In some embodiments, such as for staging of disease or for evaluating the efficacy of treatment, a reference can have or represent a diseased state, e.g., a cancer, stage of cancer, or subtype of cancer. In some embodiments, a reference can represent a particular level of ADC target expression based on IHC testing, e.g., ADC target-positive or ADC target-negative cancer.

[0129] In certain instances, a. reference is a non-contemporaneous sample from the same source, e.g., a prior sample from the same source, e.g., from the same subject. In certain instances, a reference for the modification status of one or more genomic loci (e.g., one or more differentially modified genomic loci) can be the modification status of the one or more genomic loci (e.g., one or more differentially modified genomic loci) in a sample (e.g., a sample from a subject), or a plurality of samples, known to represent a particular state (e.g., ADC targetpositive or ADC target-negative cancer). In certain instances, a reference for the accessibility status of one or more genomic loci (e.g., one or more differentially accessible genomic loci) can be the accessibility status of the one or more genomic loci (e.g., one or more differentially accessible genomic loci) in a sample (e.g., a sample from a subject), or a plurality of samples, known to represent a particular state (e.g., ADC target-positive or ADC target-negative cancer).

[0130] In some illustrative but non-limiting embodiments of the present disclosure differential modification or differential accessibility can refer to a differential (e.g., between a sample and a reference) with an absolute log2(fold-change) that is greater than or equal to 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0 or more, or any range in between, inclusive, e.g., as measured according to an assay provided herein. [0131 ] Enhancers are genomic loci that can be differentially modified or differentially accessible in and / or between conditions, diseases, and other states. Enhancers are cis-acting DNA regulatory regions that are thought to bind trans-acting proteins that contribute to expression patterns of associated genes. Chromatin ImmunoPrecipitation sequencing (ChlP-seq) of histone modifications (e.g., acetylation) have identified millions of enhancers in mammalian genomes. The number of active enhancers in any given cell type is estimated to be in the tens of thousands. Certain transcription factors (TFs), sometimes referred to as ‘'master' transcription factors, associate with active enhancers with important impacts on gene expression and cell function. Certain such transcription factors preferentially associate with enhancers that regulate genes required for establishing cell identity and function, including enhancer domains known as “super-enhancers”. Moreover, master TFs can participate in inter-connected auto-regulatory circuitries or “cliques” that are self-reinforcing, show marked cell selectivity, and function to maintain cell state and / or cell survival. Techniques for Detecting and Quantifying Histone Modifications and Transcription Factor Binding

[0132] Various techniques of molecular biology are well known in the art and / or disclosed in the present application for detecting and quantifying histone modifications and / or transcription factor binding. In some embodiments, the methods, kits and systems of present disclosure involve the detection and quantification of histone modifications and / or transcription factor binding in samples, e.g., in liquid biopsy samples including cfDNA such as plasma samples including cfDNA. Chromatin ImmunoPrecipitation (ChIP) is one technique of molecular biology useful in detecting and quantifying histone modifications and transcription factor binding in samples. CUT&RUN or CUT&Tag are other more recent techniques that can also be used to detect and quantify histone modifications and transcription factor binding sites. ChlP-chip, ChlP-exo, ChIP Re-ChIP, and ChlPmentation are other alternative techniques that could be used.

[0133] ChIP can involve various steps including one or more of fixation, sonication, immunoprecipitation, and analysis of the immunoprecipitated DNA. ChIP has become a very widely used tissue-based technique for determining the in vivo location of binding sites of various transcription factors and histones. Because the proteins are captured at the sites of their binding with DNA, ChIP helps to detect DNA-protein interactions that take place in living cells. More importantly, ChIP can be coupled to many commonly used molecular biology techniques such as PCR and real-time PCR, PCR with single-stranded conformational polymorphism, Southern blot analysis, Western blot analysis, cloning, and microarray. ’The resulting versatility has increased the potential of this technique. |'0.l34'| ChIP of tissue samples usually involves cross-linking of the chromatin-bound proteins by formaldehyde, followed by sonication or nuclease treatment to obtain small DNA fragments. Immunoprecipitation can be then carried out using specific antibodies to the DNA-binding protein of interest. The DNA can be then released from the proteins and analyzed using various methods. ChIP has also been used to study RNA-protein interactions. X-ChIP methods utilize fixed chromatin fragmented by sonication, while the N-ChIP methods utilize native chromatin, which can be unfixed and nuclease digested.

[0135] The first step of the technique can be the cross-linking of DNA. and proteins. Formaldehyde is one of the most used cross-linking agents. One advantage of using formaldehyde can be the ease of reversibility of the cross-links and its ability to form bonds that span approximately 2 angstroms. This means that formaldehyde can bind molecules in close association with each other. Generally, formaldehyde can be added to the medium in the cell culture flask or plate. It enters the cells through the cell membrane and cross-links the proteins to the chromatin. Formaldehyde fixation of tumor tissues has also been done. Other crosslinking agents that have been used include chemicals such as methylene blue and acridine orange, cisplatin, dimethylarsinic acid, potassium chromate, and ultraviolet (UV) light and lasers.

[0136] Harvested chromatin can be sonicated in one or more sonication cycles. DNA can be typically broken into to 100-500 bp fragments to pinpoint the location of the DNA sequence of interest. An alternative to sonication can be nuclease digestion of the chromatin, e.g., in N-ChlP methods. Purification of chromatin can be achieved using a cesium chloride (CsCl) gradient centri fugati on.

[0137] Chromatin can be immunoprecipitated using one or more antibodies that bind a target epitope. For example, an antibody used in ChIP can selectively bind a particular transcription factor or one or more particular histone modifications, such as one or more particular histone acetylation modifications or histone methylation modifications. In some embodiments, an antibody used to bind a target epitope can be a “pan” antibody (e.g., a panacetylation antibody, a pan-methylation antibody, an antibody that binds a group of histone modifications associated with increased transcription activation, and / or an antibody that binds a group of histone modifications associated with increased transcription repression). The antibody against the protein of interest is allowed to bind to the protein-DNA complex, and the complex can be then precipitated. Immunosorbants commonly used to separate the antigen-antibody complex from the lysate include salmon sperm DNA-protein A-Sepharose®, protein G, magnetic beads, and other engineered immunoprecipitation systems known to those of skill in the art.

[0138] Immunoprecipitated DNA can be eluted. Once the DNA of interest is isolated, many detection and quantification methods can be used to study the isolated gene fragments. Commonly utilized methods include PCR, real-time PCR, slot blot hybridization, microarray techniques, and deep or next-generation sequencing. ChlP-seq combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. ChlP-seq can be used to map DNA-binding proteins, e.g., transcription factor binding sites and histone modifications in a genome-wide manner.

[0139] Cell-free Chromatin ImmunoPrecipitation sequencing (cf'ChlP-seq) involves applying ChlP-seq to samples that include cell-free DNA, e.g., liquid biopsy samples including cfDNA such as plasma samples including cfDNA (e.g., see Sadeh et al., NatBiotechnol (2021) 39: 586-598 and Jang et al., Life Sci Alliance (2023) 6(12):e202302003 the entire contents of each of which are incorporated herein by reference). In some embodiments, cfChlP-seq uses antibodies or antibody fragments that bind specific histone modifications (e.g., H3K4me3 and / or H3K27ac) and / or transcription factors that are coupled (covalently or non-covalently) to beads, e.g., magnetic beads such as Dynabeads® magnetic beads and incubated with a volume, e.g., about 1 mL of thawed plasma obtained from a subject. Without limitation, exemplary antibodies that bind H3K4me3 include PA5-27029 (available from Thermo Fisher Scientific in Waltham, MA) and C15410003 (available from Diagenode in Denville, NJ) and exemplary antibodies that bind H3K27ac include ab21623 or ab4729 (both available from Abeam in Cambridge, UK) and Cl5210016 (available from Diagenode in Denville, NJ).

[0140] In some embodiments, the antibodies or antibody fragments can be covalently coupled to beads, e.g., epoxy beads. In some embodiments, the antibodies or antibody fragments can be non-covalently coupled to beads, e.g., Protein A or Protein G beads such as Dynabeads® Protein A or Dynabeads® Protein G beads. After washing, a cfDNA library' is then typically prepared from the captured cfDNA. Library7 preparation can be done on-bead or after releasing the captured cfDNA by digestion of bound histones, e.g., using proteinase K. The cfDNA library is then sequenced to generate reads of captured cfDNA sequences, e.g., by next-generation sequencing (NGS) as is known in the art. The reads are then analyzed, e.g., aligned and counted using standard bioinformatic techniques as is known in the art. A cfChlP-seq bioinformatic pipeline can include, e.g., alignment of sequence reads to a reference genome with BWA or Bowtie2. Aligned reads can be used to call and quantify peaks as compared to a reference.

[0141] CUT&Tag involves antibody-based binding of a target protein, e.g., transcription factor or histone modification of interest, where antibody incubation is directly followed by the shearing of the chromatin and library preparation (see Kaya-Okur et al., Nat Comm (2019) 10:1930). CUT&Tag assays take advantage of a Tn5 transposase that is fused with Protein A to direct the enzyme to the antibody bound to its target on chromatin. Tn5 transposase is preloaded with sequencing adapters (generating the assembled pA-Tn5 adapter transposome) to carry' out antibody-targeted tagmentation. In a typical CUT&Tag assay samples are incubated with an antibody immobilized on Concanavalin A-coated magnetic beads to facilitate subsequent washing steps. Cells can be incubated with a primary antibody specific for the target protein of interest followed by incubation with a secondary / antibody. Samples can then be incubated with assembled transposomes, wdiich consist of Protein A fused to the Tn5 transposase enzyme that is conjugated to NGS adapters. After incubation, unbound transposome can be washed away using stringent conditions. Tn5 is a Mg2 -dependent enzyme so \lg? can be added to activate the reaction, which results in the chromatin being cut close to the protein binding site and simultaneous addition of the NGS adapter DNA sequences. Chromatin cleavage and library preparation can be achieved in one single step.

[0142] CUT&RUN is an epigenomic profiling strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases specific protein-DNA complexes into the supernatant for paired-end DNA sequencing (see Skene and Henikoff, Elife (2017) 6:1-35, Skene et al., Nat Protoc (2018) 13:1006-1019). As only targeted fragments enter into solution, and the vast majority of DNA is left behind, CUT&RUN has low background levels. In an example CUT&RUN assay, a sample is incubated with an antibody or antibody fragment that binds the target protein, e.g., transcription factor or histone modification of interest. The sample is then incubated with Protein-A-MNa.se after which CaCh can be added to initiate the calcium dependent nuclease activity of MNase to cleave the DNA around the target protein. The protein-A-MNase reaction can be quenched by adding chelating agents (EDTA and EGTA). Cleaved DNA fragments are then liberated, extracted, and used to construct a sequencing library. Techniques for Detecting and Quantifying Chromatin Accessibility 10143 J Various techniques of molecular biology are well known in the art and / or disclosed in the present application for detecting and quantifying chromatin accessibility. In some embodiments, the methods, kits and systems of the present disclosure involve the detection and quantification of chromatin accessibility in samples, e.g., in liquid biopsy samples including cfDNA such as plasma samples including cfDNA. ATAC-seq (Assay of Transpose Accessible Chromatin sequencing), NOMe-seq (Nucleosome Occupancy and Methylome sequencing), FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory' Elements sequencing), MNase-seq (Micrococcal Nuclease digestion with sequencing), and DNase hypersensitivity assays are exemplary' techniques of molecular biology useful in detecting and quantifying chromatin accessibility in samples. Sono-Seq is another alternative method that could be used (see .Auerbach et al., Proc Natl Acad USA (2009) 106(35):14926-14931). Fragmentomics-based methods are yet another method that can be used to assess chromatin accessibility (see Ding, Spencer C., and YM Dennis Lo. "Cell-free DNA fragmentomics in liquid biopsy." Diagnostics 12.4 (2022): 978).

[0144] DNase hypersensitivity assays can use the non-specific DNA endonuclease Deoxyribonuclease I (DNase I), which selectively digests accessible DNA regions. DNase I hypersensitivity sites (DBS) identified by DNase-seq include open chromatin regulatory regions. A typical DNase hypersensitivity assay can include a first step in which nuclei are isolated from cells using lysis buffer, and nuclei are digested using DNase I. DNA fragment sizes are measured to identify optimal digestion using gel electrophoresis. Biotinylated linkers can be ligated to the ends of digested DNA after polishing to make blunt ends, and the DNA can then be isolated. DNA with biotinylated linker can be digested by restriction endonuclease Mmel and captured by streptavidin coated Dynabeads® to generate short tags to which a second sequencing adaptor can be ligated. A second linker can be ligated and amplified to generate a library for sequencing. A DNase-seq bioinformatic pipeline can include, e.g., alignment of sequence reads to a reference genome with BWA or Bowtie2. Aligned reads can be used to call and quantify peaks as compared to a reference.

[0145] MNase-seq determines chromatin accessibility with micrococcal nuclease (MNase) that preferentially digests nucleosome-free, protein-unbound DNA. A typical MNase- seq assay can include a first step in which nuclei are isolated from either native or crosslinked chromatin and digested using MNase with titration. In vivo formaldehyde crosslinking step that is designed to capture the interaction between proteins and DNA. This crosslinking allows bound proteins to shield their associated DNA from digestion by MNase. Following crosslinking, samples are digested with MNase, which can be specifically activated by addition of Ca2+ to the buffer. Digestion can be halted by chelating the reaction, at which point the samples are RNase treated, crosslinks are reversed, and proteins are digested away from the chromatin. DNA can then be isolated via a phenol-chloroform extraction. Uncut DNA is purified and mononucleosome bands are isolated and excised through gel electrophoresis. Isolated DNA can be amplified by adding adapters to generate a library, and sequenced. MNase-seq primarily sequences regions of DNA bound by histones or other proteins. Therefore, it indirectly determines which regions of DNA are accessible by directly determining which regions are bound to nucleosomes or proteins.

[0146] FAIRE-seq is a method in which nucleosome-depleted regions of DNA (NDRs) are isolated from chromatin. A typical FAIRE-seq assay can include a first step in which cells are fixed using formaldehyde so that histones are crosslinked to interacting DNA. Crosslinked chromatin can then be sheared by sonication that generates protein-free DN A and protein-crosslinked DNA fragments. Protein-free DNA can be isolated using a phenol-chloroform extraction: DNA crosslinked with protein stays in organic phase, while protein-free DNA stays in aqueous phase. Highly crosslinked DNA remains in the organic phase and the noncrosslinked DNA is pulled to the aqueous phase. Non-crosslinked DNA from the aqueous phase can then be amplified and sequenced. Reads enriched in the sequencing pool tend to have lower nucleosome and transcription factor binding and are therefore inferred to come from accessible regions.

[0147] NOMe-seq is a method to identify nucleosome-depleted regions of DNA (NDRs) with M.CviPI methyltransferase that methylates cytosine in GpC dinucleotides not protected by nucleosomes or other proteins. Unlike CmpG, GpCm in the human genome does not occur naturally in most cell types. GpC'" levels at. open chromatin regions can be compared to background signals and used to detect and quantify NDRs. A typical NOMe-seq protocol can include a step in which samples are treated with M.CviPI and S-adenosylhomocysteine (SAM) to methylate accessible GpC sites. M.CviPI treated DNA can be sheared using a sonicator, so that DNA fragments can be sequenced. DNA is treated with bisulfite, which converts unmethylated cytosine to uracil using sodium bisulfite, while methylated cytosine is unaffected. A library is generated using adapters and sequenced. Accessible chromatin is expected to have high levels of GpCm but low levels of CmpG. Therefore, NOMe-seq identifies NDRs using the two separate methylation analyses that serve as independent (but opposite) measures, providing matched chromatin designations for each regulatory element.

[0148] ATAC-seq uses hyperactive Tn5 transposase that preferentially cuts accessible chromatin regions and simultaneously inserts adapters to the fragmented region (Buenrostro et al., Nat Methods (2013) 10(12):1213-1218 the entirety of which is incorporated herein by reference). A typical ATAC-seq assay can include a first step in which samples are incubated with Tn5 transposase. DNA can then be isolated and purified. DNA fragmented and tagged by Tn5 transposase can be purified and then amplified to generate a library and sequenced for analysis.

[0149] “Fragmentomics” or a “fragmentomics assay” refers to methods that use certain size and sequence characteristics of cfDNA to gain insight into the epigenetic state of cells at the time their genomic DNA was released into the extracellular environment. Without wishing to be bound by theory, upon release of genomic DNA from a cell into the extracellular environment, nucleases rapidly cleave the genomic DNA into short fragments. The cleavage pattern and sequences of the fragments reflect the positioning of nucleosomes genome-wide at the point of cell death, and by finding nucleosomes that are consistently genomically positioned across cancer cells (i.e. many of the circulating tumor DNA. fragments that map to that small region of the genome have the same start and end positions or similar fragment length characteristics) fragmentomics attempts to infer the location of stably positioned nucleosomes at regulatory' sites, and thus to infer where the active regulatory sites are in a given cell type. Accordingly, analysis of cfDNA fragmentation patterns can be used to infer characteristics of the cells at the time they released genomic DNA. Examples of metrics commonly measured in fragmentomics include fragment size, preferred ends, end motifs, single-stranded jagged ends, and nucleosomal footprints. Approaches for measuring fragmentomics metrics include, e.g., qPCR, electron microscopy, single molecule sequencing, and next-generation sequencing. A relationship between fragmentomic metrics and histone modifications (h3K4me3 and H3K27ac) has been established. See Bai, Jinyue, et al. "Histone modifications of circulating nucleosomes are associated with changes in cell-free DNA fragmentation patterns." Proceedings of the National Academy of Sciences 121.42 (2024): e2404058121. Exemplary Genomic Loci

[0150] The present disclosure includes the identification of exemplary genomic loci that are differentially modified and / or differentially accessible in samples from different cancer patients (e.g., different breast cancer patients, different SCLC patients or different NSCLC patients) and / or samples from cancer patients (e.g., breast cancer patients, SCLC patients or NSCLC patients) and samples from healthy volunteers. The present disclosure also includes the identification of exemplary genomic loci that are differentially modified and / or differentially accessible depending on ADC target status. See Table 1 which shows exemplary genomic coordinates of H3K4me3 regions associated with genes that encode ADC target antigens, Table 2 which show's exemplary genomic coordinates of H3K4me3 regions associated with genes that modulate ADC response / resistance, Table 3 which shows exemplary genomic coordinates of H3K27ac regions associated with genes that encode ADC target antigens, Table 4, which show's exemplary' genomic coordinates of H3K4me3, H3K27ac, or DNA methylation regions associated with genes that encode ADC target antigens, Table 5, which shows exemplary genomic coordinates of H3K4me3 methylation regions associated with DLL 3, Table 6, which shows exemplary genomic coordinates ofH3K4me3, H3K27ac, or DNA methylation regions associated with DLL3 or genes whose expression levels are correlated with expression level of DLL3. The chromosomal coordinates in Tables 1-6 are based on human genome build hg!9.

[0151] The present disclosure is not limited to methods that use the exact same chromosomal coordinates that are recited in Tables 1-6. The present disclosure encompasses methods that use any of the genomic loci in Tables 1-6 and also subregions thereof, / .e., references herein to methods that involve detecting and / or quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci of Tables 1-6 encompasses methods that detect these marks anywhere within these genomic loci including within any subregions. For example, where Table 1 references chrl :59,039,915-59,043,420 as a genomic locus for detecting and / or quantifying H3K4me3 modification, this encompasses methods that detect and / or quantify H3K4me3 modification at any position or sub-region of chrl :59,039,915-59,043,420, e.g., methods that detect and / or quantify H3K4me3 modification within chrl :59,039,915-59,043,420, etc. In some embodiments, a subregion may span at least 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500 or at least 3000 contiguous base pairs that are located between the lower and upper coordinates of a genomic locus recited in Tables 1-6. In some embodiments, a subregion may span less than 100, 200, 300, 400, 500, 600, 700, 800, 900, 1000, 1500, 2000, 2500 or at least 3000 contiguous base pairs that are located between the lower and upper coordinates of a genomic locus recited in Tables 1-6. In some embodiments, a subregion may have the same central coordinate as a genomic locus recited in Tables 1-6. In some embodiments, a subregion may have a different central coordinate as a genomic locus recited in Tables 1-6. It is also to be understood that the lower / upper coordinates of the genomic loci in Tables 1-6 are approximate and that the present disclosure encompasses methods where any one or more of the genomic loci are expanded by increasing the size of the genomic locus by 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40% or up to 50% in one or both directions.

[0152] In some embodiments a classifier is generated using a set of differentially modified and / or differentially accessible genomic loci that are correlated with ADC targetpositive status and a set of differentially modified and / or differentially accessible loci that are correlated with ADC target-negative status (e.g. based on IHC testing). Sequence reads that fall into each selected genomic locus are analyzed and counted, e.g., as described herein including the Examples. In some embodiments, counts from genomic loci that are correlated with ADC target-positive status are aggregated and counts from genomic loci that are correlated with ADC target-negative status are aggregated. In some embodiments, a ratio of the aggregated ADC target-positive and ADC target-negative counts is used to determine ADC target status. Other ways of using the genomic loci and related sequencing data to generate and apply a classifier to determine .ADC target status are described herein and known in the art, e.g., without limitation, methods that use a learning statistical classifier system or a combination of learning statistical classifier systems.

[0153] In some embodiments, exemplary genomic loci from Table 1, 2, 3, 4, or 5 are used in a monomodai classifier, e.g., a classifier that uses a single histone modification (e.g., H3K4me3 or H3K27ac) or only DNA methylation for purposes of determining ADC target status or status of a gene the expression of which is associated with responsiveness / resistance to an ADC treatment. In some embodiments, exemplary genomic loci from Table 1, 2, 3, 4, 5, and / or 6 are used in combination in a multimodal classifier, e.g., a classifier that uses more than one histone modification (e.g., H3K4me3 and H3K27ac) or more than one histone modification (e.g., H3K4me3 and H3K27ac) and DNA methylation at one or more genomic loci for purposes of determining ADC target status.

[0154] In some embodiments, exemplary genomic loci from Table 6 associated with DLLS, RAB3IP, PAKS, ITPRIPL2, or any combination thereof are used in a monomodal or multimodal classifier for purposes of determining DLL3 status. In some embodiments, exemplary genomic loci from Table 6 associated with DLLS are used in a monomodal or multimodal classifier for purposes of determining DLL3 status. In some embodiments, exemplary genomic loci from Table 6 associated with RAB31P are used in a monomodal or multimodal classifier for purposes of determining DLLS status. In some embodiments, exemplary' genomic loci from Table 6 associated with PAKS are used in a monomodal or multimodal classifier for purposes of determining DLL3 status. In some embodiments, exemplary genomic loci from Table 6 associated with ITPR1PL2 are used in a monomodal or multimodal classifier for purposes of determining DLL3 status.

[0155] In some embodiments, exemplary genomic loci from Table 1, Table 3, Table 5, or Table 6 associated with DLLS are used in a monomodal or multimodal classifier that also uses one or more genomic loci associated with RAB3IP, PAK5, or ITPRIPL2, or any combination thereof for purposes of determining DLL3 status. In some embodiments, exemplary genomic loci associated with RAB3IP, PAK5, or 1TPRIPL2, or any combination thereof are provided in Table 6.

[0156] In some embodiments, exemplary genomic loci from Table 1 associated with DLLS are used in a monomodal or multimodal classifier that also uses one or more genomic loci from Table 6 associated with RAB3IP, PAK5, or ITPRIPL2, or any combination thereof for purposes of determining DLL3 status. In some embodiments, exemplary' genomic loci from Table 3 associated with DLLS are used in a monomodal or multimodal classifier that also uses one or more genomic loci from Table 6 associated with BAB3JP, PAKS, or ITPR1PL2, or any combination thereof for purposes of determining DLL3 status. In some embodiments, exemplary-' genomic loci from Table 5 associated with DLLS are used in a monomodal or multimodal classifier that also uses one or more genomic loci from Table 6 associated with RAB3IP, PAK.5, or ITPRIPL2, or any combination thereof for purposes of determining DLL3 status. In some embodiments, exemplary genomic loci from Table 6 associated with DLLS are used in a monomodal or multimodal classifier that also uses one or more genomic loci from Table 6 associated with RAB3IP, PAK5, or ITPRIPL2, or any combination thereof for purposes of determining DLLS status. Differential H3K4me3 modification

[0157] Genomic loci demonstrating differential H3K4 methylation (in particular H3K4 trimethylation, H3K4me3) in samples from different cancer patients (e.g., different breast cancer patients, different SCLC patients, different NSCLC patients, different NEPC patients, or different PRAD patients) and / or samples from cancer patients (e.g., breast cancer patients, SCLC patients, NSCLC patients, NEPC patients, or PRAD patients) and samples from healthy volunteers are provided in Tables 1-2 and 4-6 which show the chromosomal coordinates of each genomic locus. The chromosomal coordinates are based on human genome build hg!9. [015S]        A person of skill in the art will recognize that the methods disclosed herein do not require that even,' genomic locus listed in Tables 1-2 and 4-6be assessed for H3K4me3 modification. Instead, a subset of loci may be assessed for H3K4me3 modification. Subsets of the genomic loci of Tables 1-2 and 4-6can be selected (e.g., for use in determining ADC target status) based on the type of ADC screening required (e.g., the ADC target or ADC targets of interest), based on various performance criteria, e.g., to select genomic loci that demonstrate differential modification with a particular level of statistical significance, progression free survival (PFS) of subjects, from whom the sample is obtained or derived, and / or a particular threshold of differential between relevant states (e.g., a measured log2(fold-change)). Subsets of the genomic loci may also be selected based on an algorithm, e.g., during the process of obtaining a classifier. Those of skill in the art will appreciate that such subsets of loci of Tables 1-2 and 4~6and loci included in such subsets, are together, individually, and / or in randomly selected subsets, at least as informative (e.g., as statistically significant and / or reliable) for uses disclosed herein, e.g., for determining ADC target status.

[0159] In various embodiments, a sample or subject from whom the sample is obtained or derived, is determined to have a particular ADC target status (e.g., ADC target-positive) if (i) at least 1, 2, 3, 4, 5 or more loci identified in Tables 1,2, 4, 5, or 6 (or any subset thereof), (ii) at least 10%, 25%, 50%, 60%, 75%, 80%, 90% or more of the loci identified in Tables 1, 2, 4, 5, or 6 (or any subset thereof), or (iii) a majority or all of the 1 oci identified in Tables 1, 2, 4, 5, or 6 (or any subset thereof) are differentially H3K4me3 modified as compared to a reference (e.g., a sample from an ADC target-negative subject or healthy volunteer or a sample from a subject who responded positively or poorly to treatment with an ADC).

[0160] In various embodiments, differentially H3K4me3 modified refers to a methylation status characterized by an increase or decrease in a value measuring methylation (e.g., of read counts and / or normalized read counts for a given genomic locus), and / or a mean, median and / or mode thereof, and / or a log thereof (e.g, log base 2 (log2)), of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, 2-fold, 3-fold, 4fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40fold, 45-fold, 50-fold, or greater, or any range in between, inclusive, such as 1% to 50%, 50% to 2-fold, 25% to 50-fold, 25% to 30-fold, 25% to 20-fold, 25% to 16-fold, 30% to 16-fold, 50% to 16-fold, 70% to 16-fold, 2-fold to 16-fold, 2.2-fold to 16-fold, 2.6-fold to 16-fold, 3-fold to 16fold, 3.4-fold to 16-fold, 4-fold to 16-fold, 4.5-fold io 16-fold, 5.2-fold to 16-fold, 6-fold to 16fold, 7-fold to 16-fold, or 8-fold to 16-fokl, as compared to a reference, optionally where the statistical significance of the increase or decrease is at least 5e-2, le-2, 5e-3, 1 e-3, 5e-4, le-4, 5e-5, le-5, 5e-6, or 1 e-6. In various embodiments, an increase or decrease in a value measuring methylation can be, or is expressed as, a log2(fold-change), e.g., a log2(fold-change) of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, or greater, or any range in between, inclusive, such as an increase or decrease of 0.1-fold to 10fold, 0.2-fold to 5-fold, 0.2-fold to 4.0-fold, 0.4-4.0-fold, 0.4-fold to 4.0-fold, 0.6-fold to 4.0-fold, 0.8-fold to 4.0-fold, 1.0-fold to 4.0-fold. 1.2-fold to 4.0-fold. 1.4-fold to 4.O-fold, 1.6-fold to 4.0-fold, 1.8-fold to 4.0-fold, 2.0-fold to 4.0-fold, 2.2-fold to 4.0-fold, 2.4-fold to 4.0-fold, 2.6-fold to 4.0-fold, 2.8-fold to 4.0-fold, or 3.0-fold, to 4.0-fold, optionally where the statistical significance of the increase or decrease is at least 5e-2, le-2, 5e-3, I e-3, 5e-4, le-4, 5e-5, le-5, 5 e-6, or le-6. Differential H3K2 7ac modification

[0161] Genomic loci demonstrating differential H3K27 acetylation (H3K27ac) in samples from different cancer patients (e.g., different breast cancer patients, different SCLC patients, different NSCLC patients, different NEPC patients, or different PRAD patients) and / or samples from cancer patients (e.g., breast cancer patients, SCLC patients, NSCLC patients, NEPC patients, or PRAD patients) and samples from healthy volunteers are provided in Tables 3, 4 and 6, which show the chromosomal coordinates of each genomic locus. The chromosomal coordinates are based on human genome build hg!9.

[0162] A person of skill in the art will recognize that the methods disclosed herein do not require that every genomic locus listed in Tables 3, 4 and 6be assessed for H3K27ac modification. Instead, a subset of loci may be assessed for H3K27ac modification. Subsets of the genomic loci of Tables 3, 4 and 6can be selected (e.g., for use in determining ADC target status or the status of one or more genes that modulate .ADC response / resistance) based on the type of ADC screening required (e.g., the ADC target or ADC targets of interest), based on various performance criteria., e.g., to select genomic loci that demonstrate differential modification with a particular level of statistical significance and / or a particular threshold of differential between relevant states (e.g, a measured log2(fold-change)). Subsets of the genomic loci may also be selected based on an algorithm, e.g., during the process of obtaining a classifier. Those of skill in the art will appreciate that such subsets of loci of Tables 3, 4 and 6, and loci included in such subsets, are together, individually, and / or in randomly selected subsets, at least as informative (e.g., as statistically significant and / or reliable) for uses disclosed herein, e.g., for determining ADC target status or the status of one or more genes that modulate ADC response / resistance.

[0163] In various embodiments, a sample or subject from whom the sample is obtained or derived, is determined to have a particular ADC target status (e.g., ADC target-positive) if (i) at least 1, 2, 3, 4, 5 or more loci identified in Table 3, 4, or 6 (or any subset thereof), (ii) at least 10%, 25%, 50%, 60%, 75%;, 80%, 90% or more of the loci identified in Tables 3, 4, or 6 (or any subset thereof), or (iii) a majority or all of the loci identified in Tables 3, 4, or 6 (or any subset thereof) are differentially H3K27ac modified as compared to a reference (e.g., a sample from an ADC target-negative subject or healthy volunteer).

[0164] In various embodiments, a sample or subject from whom the sample is obtained or derived, is determined to have a particular ADC target status (e.g., ADC target-positive) if at least 1, 2, 3, 4, 5 or more loci identified in Table 4 or 6 (or any subset thereof) are differentially H3K27ac modified as compared to a reference (e.g., a. sample from an ADC target-negative subject or healthy volunteer). [0.165] In various embodiments, differentially H3K27ac modified refers to an acetylation status characterized by an increase or decrease in a value measuring acetylation (e.g., of read counts and / or normalized read counts for a given genomic locus), and / or a mean, median and / or’ mode thereof, and / or a log thereof (e.g., log base 2 (log2)), of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, 2-fold, 3-fold, rifold, 5-fold, 6-fokl, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40fold, 45-fold, 50-fold, or greater, or any range in between, inclusive, such as 1% to 50%, 50% to 2-fold, 25% to 50-fold, 25% to 30-fold, 25% to 20-fold, 25% to 16-fold, 30% to 16-fold, 50% to 16-fold, 70% to 16-fold, 2-fold to 16-fold, 2.2-fold to 16-fold, 2.6-fold to 16-fold, 3-fold to 16fold, 3.4-fold to 16-fold, 4-fold to 16-fold, 4.5-fold to 16-fold, 5.2-fold to 16-fold, 6-fold to 16fold, 7-fold to 16-fold, or 8-fold to 16-fold, as compared to a reference, optionally where the statistical significance of the increase or decrease is at least 5e-2, le-2, 5e-3, le-3, 5e-4, le-4, 5e-5, le-5, 5e-6, or le-6. In various embodiments, an increase or decrease in a value measuring acetylation can be, or is expressed as, a log2(fold-change), e.g., a. Iog2(fold-change) of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, or greater, or any range in between, inclusive, such as an increase or decrease of 0.1 -fold to 10fold, 0.2-fold to 5-fold, 0.2-fold to 4.0-fold, 0.4-4.0-fold, 0.4-fold to 4.0-fold, 0.6-fold to 4.0-fold, 0.8-fold to 4.0-fold, 1.0-fold to 4.0-fold, 1.2-fold to 4.0-fold, 1 4-fold to 4.0-fold, 1.6-fold to 4.0-fold, 1.8-fold to 4.0-fold, 2.0-fold to 4.0-fold, 2.2-fold to 4.0-fold, 2.4-fold to 4.0-fold, 2.6-fold to 4.0-fold, 2.8-fold to 4.0-fold, or 3.0-fold to 4.0-fold, optionally where the statistical significance of the increase or decrease is at least 5e-2, le-2, 5e-3, le-3, 5e-4, le-4, 5e-5, le-5, 5e-6, or le-6. Differential DNA methylation

[0166] Genomic loci demonstrating differential DNA methylation status in samples from different cancer patients (e.g., different breast cancer patients, different SCLC patients, different NSCLC patients, different NEPC patients, or different PRAD patients) and / or samples from cancer patients (e.g., breast cancer patients, SCLC patients, NSCLC patients, NEPC patients, or PRAD patients) and samples from healthy volunteers are provided in Table 4, which show the chromosomal coordinates of each genomic locus. The chromosomal coordinates are based on human genome build hg!9.

[0167] A person of skill in the art will recognize that the methods disclosed herein do not require that every MBD analyte genomic locus listed in Table 4 be assessed for DNA methylation. Instead, a subset of MBD loci may be assessed for DNA methylation. Subsets of the MBD genomic loci of Table 4 can be selected (e.g., for use in determining ADC target status) based on various performance criteria, e.g., to select genomic loci that demonstrate differential modification with a particular level of statistical significance and / or a particular threshold of differential between relevant states (e.g., a measured log2(fold-change)). Subsets of the genomic loci may also be selected based on an algorithm, e.g., during the process of obtaining a classifier. Those of skill in the art will appreciate that such subsets of loci of Table 4, and loci included in such subsets, are together, individually, and / or in randomly selected subsets, at least as informative (e.g., as statistically significant and / or reliable) for uses disclosed herein, e.g., for use in determining ADC target status.

[0168] In various embodiments, a. sample or subject from whom the sample is obtained or derived, is determined to have a particular ADC target status (e.g., ADC target-positive) if (i) at least 1, 2, 3, 4, 5 or more loci identified in Table 4 (or any subset thereof), (ii) at least 10%, 25%, 50%, 60%, 75%, 80%, 90% or more of the loci identified in Table 4 (or any subset thereof), or (iii) a majority or all of the loci identified in Table 4 (or any subset thereof) are differentially DNA methylated as compared to a reference (e.g., a sample from an ADC targetnegative subject or healthy volunteer or a sample from a subject who responded positively or poorly to treatment with an ADC).

[0169] In various embodiments, differentially DNA methylated refers to a methylation status characterized by an increase or decrease in a value measuring methylation (e.g., of read counts and / or normalized read counts for a given genomic locus), and / or a mean, median and / or mode thereof, and / or a log thereof (e.g., log base 2 (log2)), of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, 2-fold, 3-fold, 4fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, 25-fold, 30-fold, 35-fold, 40fold, 45-fold, 50-fold, or greater, or any range in between, inclusive, such as 1% to 50%, 50% to 2-fold, 25% to 50-fold, 25% to 30-fold, 25% to 20-fold, 25% to 16-fold, 30% to 16-fold, 50% to 16-fold, 70% to 16-fold, 2-fold to 16-fold, 2.2-fold to 16-fold, 2.6-fold to 16-fold, 3-fold to 16fold, 3.4-fold to 16-fold, 4-fold to 16-fold, 4.5-fold to 16-fold, 5.2-fold to 16-fold, 6-fold to 16fold, 7-fold to 16-fold, or 8-fold to 16-fold, as compared to a reference, optionally where the statistical significance of the increase or decrease is at least 5e-2, le-2, 5e-3, le-3, 5e-4, le-4, 5e-5, le-5, 5e-6, or le-6. In various embodiments, an increase or decrease in a value measuring methylation can be, oris expressed as, a log2(fold-change), e.g., a log2(fold-change) of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 75%, 100%, 2-fold, 3-fold, 4-fold, 5-fold, 6-fold, 7-fold, 8-fold, 9-fold, 10-fold, 15-fold, 20-fold, or greater, or any range in between, inclusive, such as an increase of 0.1-fold to 10-fold, 0.2-fold to 5-fold, 0.2-fold to 4.0-fold, 0.4-4.0-fold, 0.4-fold to 4.0-fold, 0.6-fold to 4.0-fold, 0.8-fold to 4.0-fold, 1.0-fold to 4.0-fold. 1.2-fold to 4.0-fold. 1.4-fold to 4.0-fold, 1.6-fold to 4.0-fold, 1.8-fold to 4.0-foid, 2.0-fold to 4.0-fold, 2.2-fold to 4.O-fold, 2.4-fold to 4.0-fold, 2.6-fold to 4.0-fold, 2.8-fold to 4.0-fold, or 3.0-fold to 4.0-fold, optionally where the statistical significance of the increase or decrease is at least 5e-2, le-2, 5e-3, le-3, 5e-4, le-4, 5e-5, le-5, 5e-6, or le-6. Differential chromatin accessibility or transcription factor binding

[0170] Genomic loci provided in 'fables 1-6 can also demonstrate differential chromatin accessibility or transcription factor binding in ADC target-positive cancer (e.g., based on IHC testing) vs. ADC target-negative cancer (e.g., based on IHC testing) or a cancer that expresses a marker of ADC response / resistance vs. one that does not.

[0171] In various embodiments, without wishing to be bound by any particular scientific theory, histone methylation (e.g., H3K4me3) corresponds and / or is correlated with chromatin accessibility. In various embodiments, without wishing to be bound by any particular scientific theoiyy histone acetylation (e.g., H3K27ac) corresponds and / or is correlated with chromatin accessibility. In various embodiments, without wishing to be bound by any particular scientific theory, DNA methylation corresponds and / or is correlated with chromatin accessibility.

[0172] In some embodiments, without wishing to be limited to any particular scientific theora, chromatin accessibility corresponds and / or is correlated with H3K4me3 modifications. As a result, in some embodiments, ADC target status may be determined by detecting and quantifying chromatin accessibility at one or more genomic loci in Tables 1, 2 and 4-6in accordance with the section above discussing exemplary genomic ioci with differential H3K4me3 modifications. 10173J In some embodiments, without wishing to be limited to any particular scientific theory, chromatin accessibility corresponds and / or is correlated with H3K27ac modifications. As a result, in some embodiments, ADC target status .may be determined by detecting and quantifying chromatin accessibility at one or more genomic loci in Table 3, 4 or 6 in accordance with the section above discussing exemplary genomic loci with differential H3K27ac modifications.

[0174] In some embodiments, without wishing to be limited to any particular scientific theory, chromatin accessibility corresponds and / or is correlated with DNA methylation. As a result in some embodiments, ADC target status may be determined by detecting and quantifying chromatin accessibility at one or more genomic loci in Table 4 in accordance with the section above discussing exemplary genomic loci with differentially methylated DNA.

[0175] In various embodiments, without wishing to be bound by any particular scientific theory, histone methylation (e.g., H3K4me3) corresponds and / or is correlated with transcription factor binding. In various embodiments, without wishing to be bound by any particular scientific theory, histone acetylation (e.g., H3K27ac) corresponds and / or is correlated with transcription factor binding. In various embodiments, without wishing to be bound by any particular scientific theory, DNA methylation corresponds and / or is correlated with transcription factor binding.

[0176] In some embodiments, without wishing to be limited to any particular scientific theory, binding of RNA pol II corresponds and / or is correlated with H3K4me3 modifications. As a result, in some embodiments, ADC target status may be determined by detecting and quantifying binding of RNA pol IT at. one or more genomic loci in Tables 1, 2, or 4-6 in accordance with the section above discussing exemplary genomic loci with differential H3K4me3 modifications.

[0177] In some embodiments, without wishing to be limited to any particular scientific theory', binding of p300, mediator complex, cohesin complex or RNA pol II corresponds and / or is correlated with H3K27ac modifications. As a result, in some embodiments, ADC target status may be determined by detecting and quantifying binding of p300, mediator complex, cohesin complex or RNA pol II at one or more genomic loci in Tables 3, 4, or 6 in accordance with the section above discussing exemplary' genomic loci with differential H3K2.7ac modifications.

[0178] In some embodiments, without wishing to be limited to any particular scientific theory, binding of FOXA1, ESRI, PR, MYC, ENI, F0XM1, KLF4, AP-2, RARa, or RUNX1 corresponds and / or is correlated with histone methylation (e.g., H3K4me3) or histone acetylation (e.g., H3K27ac). As a result, in some embodiments, ADC target status may be determined by detecting and quantifying binding of F0XA1, ESRI, PR, MYC, ENI, FOXMI, KLF4, AP-2, RARa, RUNX1 at one or more genomic loci in Tables 1-36 in accordance with the sections above discussing exemplary' genomic loci with differential histone methylation (e.g, H3K4me3), histone acetylation (e.g., H3K27ac), or DNA methylation. Applications

[0179] Methods, kits and systems of the present disclosure include analysis of differentially modified and / or differentially accessible genomic loci to determine the ADC target status of a cancer. Methods, kits and systems of the present disclosure can be used in any of a variety of applications. For example, methods, kits and systems of the present disclosure can be used in detecting and / or treating cancers based on ADC target status. Methods, kits and systems of the present disclosure can also be used to detect or determine response / resistance of a cancer, e.g., breast cancer, SCLC, NSCLC, NEPC, PRAD or other cancer to a therapy or transformation from one cancer subtype to another.

[0180] In various embodiments, methods, kits and systems of the present disclosure can be applied to an asymptomatic human subject. As used herein, a subject can be referred to as “asymptomatic” if the subject does not report, and / or demonstrate by non-invasively observable indicia (e.g., without one, several, or all of device-based probing, tissue sample analysis, bodily fluid analysis, surgery, or cancer screening), sufficient characteristics of cancer to support a medically reasonable suspicion that the subject is likely suffering from cancer, e.g., breast cancer, SCLC, NSCLC, NEPC, PRAD or other cancer. [0181J        In various embodiments, methods, kits and systems of the present disclosure can be applied to a symptomatic human subject. As used herein, a subject can be referred to as “symptomatic” if the subject report, and / or demonstrates by non-invasively observable indicia (e.g., without one, several, or all of device-based probing, tissue sample analysis, bodily fluid analysis, surgery, or cancer screening), sufficient characteristics of cancer to support a medically reasonable suspicion that the subject is likely suffering from cancer, e.g., breast cancer, SCLC, NSCLC, NEPC, PRAD or other cancer. For example, in various embodiments a sample from a subject, optionally where the subject has a cancer that is of unknown ADC target status, can be assayed according to one or more embodiments of the present disclosure to determine if the cancer is .ADC target-positive or ADC target-negative. In various embodiments a sample from a subject, where the subject has a cancer that is known or suspected of being ADC target-positive (or ADC target-negative), can be assayed according to one or more embodiments of the present disclosure to determine if the cancer is in fact ADC target-positive (or ADC target-negative).

[0182] In some embodiments, methods, kits and systems of the present disclosure can be used to determine that a subject has an ADC target-positive cancer, optionally an ADC targetpositive cancer that correlates with an ADC target-positive classification based on IHC testing. In some embodiments, methods, kits and systems of the present disclosure can be used to determine that a subject has an ADC target-negative cancer, optionally an ADC target-negative cancer that correlates with an ADC target-negative classification based on IHC testing.

[0183] In some embodiments, methods, kits and systems of the present disclosure can be used to validate or confirm a prior determination that a subject has an ADC target-positive cancer. In some embodiments, methods, kits and systems of the present disclosure can be used to validate or confirm a prior determination that a subject has an ADC target-negative cancer.

[0184] In some embodiments, methods, kits and systems of the present disclosure are used to identify and detect new ADC target related categories that are independent of IHC scoring. For example, instead of training a classifier on samples from cohorts that were defined based on ADC target IHC testing, classifiers are trained on samples from cohorts that are defined based on whether they respond or do not respond to a particular ADC for a given ADO' target. The resulting classifiers are then used to identify subjects that are more likely to respond to the particular .ADC independent of any IHC scoring. It is therefore to be understood that the term ‘"ADC target status” as used herein is not limited to ADC target-positive and ADC targetnegative or the traditional ADC target scoring based on IHC testing but can encompass any ADC target related categories including whether a subject will or will not respond to a particular ADC for a given ADC target and / or whether ADC-target expression is equal to or greater than a certain reference (e.g., a reference described herein, including, e.g., a predetermined threshold, a measurement from a liquid biopsy sample, a normalized value, a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have undetectable or low expression of the ADC target based on 1HC testing, or a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to be cancer free). [01 §5]       In various embodiments ADC target status determination in accordance with the present disclosure is performed once for a given subject or multiple times for a given subject. In various embodiments, ADC target status determination in accordance with the present disclosure is performed on a regular basis, e.g., every six months, annually, every two years, every three years, every four years, every five years, or every ten years.

[0186] In various embodiments, methods, kits and systems disclosed herein provide a determination of ADC target status. In other instances, methods, kits and systems disclosed herein will be indicative of ADC target status but not definitive for ADC target status. In various instances in which methods, kits and systems of the present disclosure are used to determine .ADC target status, the same can be followed by a further confirmatory assay, which further assay can confirm, support, undermine, or reject a determination resulting from a prior determination, e.g., a determination in accordance with the present disclosure. As used herein, a confirmatory assay can be an ADC target test that is currently recognized by medical practitioners, e.g., ADC target scoring based on IHC testing.

[0187] In various embodiments, ADC target status determination according to one or more methods, kits and / or systems disclosed herein is followed by treatment of cancer. In various embodiments, treatment of cancer includes administration of a therapeutic regimen including one or more cancer therapies provided herein, including without limitation one or more of treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy), surgery / , radiation, endocrine therapy, chemotherapy, and / or immunotherapy. In various embodiments, treatment of cancer includes administration of a therapeutic regimen including one or more treatments provided herein as available, appropriate, and / or preferred for a particular ADC target, status.

[0188] In various embodiments, methods, kits and systems can be used to determine whether a particular subject and / or cancer is likely to be and / or is characterized as responsive to treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy). In some such embodiments, methods, kits and systems can be followed by treatment of the subject with an agent that is directed to an ADC target antigen (e.g., an ADC therapy).

[0189] In some embodiments, differential epigenomic modifications and / or differential chromatin accessibility of chromatin in one or more genomic loci of a promoter or enhancer associated with one or more genes encoding an ADC target antigen can be used to determine the likelihood of a subject responding to treatment with an agent that is directed to an .ADC target antigen (e.g., an ADC therapy).

[0190] In various embodiments, methods, kits and systems can be used to determine whether a particular subject and / or cancer is likely to be and / or is characterized as resistant to, non-responsive to, or not recommended treatment with an agent that is directed to an ADC target antigen (e.g., an .ADC therapy). In some such embodiments, methods, kits and systems can be followed by treatment with one or more of surgery and / or radiation, endocrine therapy (if positive for a hormone receptor such as estrogen receptor), chemotherapy and immunotherapy instead of .ADC therapy.

[0191] In some embodiments, the likelihood of a particular subject and / or cancer to be characterized as resistant to, non-responsive to, or not recommended for treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy) is associated with ADC target status (e.g., expression).

[0192] In some embodiments, differential epigenomic modifications and / or differential chromatin accessibility of chromatin in one or more genomic loci of one or more promoter or enhancer regions associated with one or more genes encoding an ADC target antigen are associated with the likelihood of a particular subject and / or cancer to be characterized as resistant to, non-responsive to, and / or not recommended for treatment with an agent that is directed to the .ADC target antigen (e.g., an ADC therapy).

[0193] As used herein, “an agent that is directed to an ADC target antigen” refers to an agent that comprises a moiety that has previously been shown to associate with (e.g., as determined using a suitable binding assay) a given ADC target antigen, hi some embodiments, an agent directed to an .ADC target antigen is an ADC. In some embodiments, an agent directed to an ADC target antigen is a radioligand, e.g., an antibody or antibody fragment, peptide or small molecule ligand that (i) associates with the ADC target, antigen and (ii) is linked to a chelator that is bonded to a radioisotope.

[0194] Responsiveness can refer to the ability or likelihood of a therapy to cause a reduction in tumor size or inhibit tumor growth or metastasis. Responsiveness can refer to improvement in prognosis (e.g., increased time to cancer recurrence or increased life expectancy, e.g., overall survival, recurrence-free survival, metastasis-free survival, progression-free survival, or disease-free survival). Responsiveness can refer to achievement of a treatment benefit, including e.g., improvement in one or more symptoms of cancer, e.g., breast cancer, gastric / gastroesophageal cancer, colorectal cancer, prostate cancer, or lung cancer. Responsiveness can be measured quantitatively (e.g., as in the case of tumor size; as in the case of measurement of histone modification, chromatin accessibility, transcription factor binding, or D\A methylation at one or more genomic loci; or as in the calculation of clinical benefit (CBR)), or qualitatively (e.g, by measures such as “pathological complete response” (pCR), “clinical complete remission” (cCR), “clinical partial remission” (cPR), “'clinical stable disease” (cSD), “clinical progressive disease” (cPD), or other qualitative criteria). Resistance can refer to the inability or unli kelihood of a therapy to achieve a. desired therapeutic effect (e.g., a reduction in tumor size, improvement in prognosis, or other treatment benefit such as, e.g., improvement in one or more symptoms of cancer) in a subject and / or cancer. Resistance includes both acquired and natural resistance. Tn certain embodiments, resistance includes the extent to which one or more desired therapeutic benefits results from administration of a therapy to a subject and / or cancer is less than that expected and / or achieved in a reference (e.g., less than 90%, 80%, 70%, 60%, 50%, 40%, 30%, 20%, or 10% of benefit achieved in a reference).

[0195] In various embodiments, methods, kits and systems can be used to detect the clinical efficacy of a course of therapy for cancer, e.g., breast cancer, gastric / gastroesophageal cancer, colorectal cancer, prostate cancer, or lung cancer. For example, methods and / or compositions of the present disclosure could be used to determine the presence, absence, or ADC target status of a cancer in a subject over the course of treatment. Methods and / or compositions of the present disclosure could be used in conjunction with, or confirmed by, other means of determining the presence, absence, or ADC target status of a cancer including, for example measurements of tumor size or character by techniques such as CT, PET, mammogram, ultrasound, palpation, histology, caliper measurement after biopsy or surgical resection, or by various qualitative, quantitative, or semi quantitative scoring systems including without limitation based on IHC testing, residual cancer burden (Symmans et al., J Clin Oncol (2007) 25:4414-4422, incorporated by reference herein in its entirety) or Miller-Payne score (Ogston et al., Breast (2003) 12:320-327, incorporated by reference herein in its entirety) in a qualitative fashion like “pathological complete response” (pCR), “clinical complete remission” (cCR), “clinical partial remission” (cPR), “clinical stable disease” (cSD), “clinical progressive disease” (cPD).

[0196] In some embodiments, methods, kits and systems for ADC target status determination provided herein can inform treatment and / or payment (e.g., reimbursement for or reduction of cost of medical care, such as detecting or treatment) decisions and / or actions, e.g., by individuals, healthcare facilities, healthcare practitioners, health insurance providers, governmental bodies, or other parties interested in healthcare cost.

[0197] In some embodiments, methods, kits and systems for ADC target status determination provided herein can inform decision making relating to whether health insurance providers reimburse a healthcare cost payer or recipient (or not), e.g., for (1) ADC target status determination itself (e.g., reimbursement for detecting otherwise unavailable, available only for periodic / regular detecting, or available only for temporally- and / or incidentally" motivated detecting); and / or for (2) treatment, including initialing, maintaining, and / or altering therapy, e.g., based on the determined ADC target status. For example, in some embodiments, methods, kits and systems for ADC target status determination provided herein are used as the basis for, to contribute to, or support a determination as to whether a reimbursement or cost reduction will be provided to a healthcare cost payer or recipient. In some instances, a party seeking reimbursement, or cost reduction can provide results of ADC target status determination conducted in accordance with the present disclosure together with a request for such reimbursement or reduction of a healthcare cost. In some instances, a party making a determination as to whether or not to provide a reimbursement or reduction of a healthcare cost will reach a determination based in whole or in part upon receipt and / or review of results of ADC target status determination conducted in accordance with the present disclosure.

[0198] In various embodiments, ADC target status determination using methods, kits and systems disclosed herein can be used in classifying subjects, samples, and / or tumors (e.g., breast, gastric / gastroesophageal, colorectal, prostate, or lung cancer subjects, samples, and / or tumors). In various embodiments, methods, kits and systems disclosed herein can be used to generate a set. of subjects, samples, and / or tumors identified according to the present methods, kits and systems each classified as corresponding to a particular ADC target status, and optionally using two or more of such classified subjects, samples, and / or tumors to identify biomarkers that distinguish the classes (i.e., distinguish the subjects, samples, and / or tumors according to their class, e.g., according to their ADC target status). 10199 J For illustration purposes and without limitation, in an exemplary assay of the present disclosure, a sample obtained from a subject (e.g., a liquid biopsy sample including cfDNA, e.g., a plasma sample including cfDNA) is analyzed by ChlP-seq for a histone modification (e.g., H3K4me3 and / or H3K27ac). ChlP-seq sequence reads are aligned to human genome build hg!9, e.g., using the Burrows-Wheeler Aligner (BWA). Non-uniquely mapping and redundant reads are optionally discarded. To provide one example of peak calling, MACS v2.1.1.20140616 can be used for ChlP-seq peak calling with a q-value (FDR) threshold of 0.01. ChlP-seq data quality can optionally be evaluated by any of one or more of a variety of measures, including total peak number, FRiP (fraction of reads in peak) score, number of high-confidence peaks (e.g., enriched > ten-fold over background), and percent of peak overlap with “blacklist” DHS peaks derived from the ENCODE project (Amemiya et al., Sci Rep (2019) 9(1):9354). If the ChlP-seq data quality is below a particular threshold the data may be discarded and the assay repeated. ChlP-seq peaks that overlap with selected genomic loci that are differentially modified as provided herein for the relevant histone modification (Tables 1-6) can then be used to determine ADC target status or status of one or more genes that modulate ADC response / resistance, The number of reads overlapping the selected genomic loci for the relevant histone modification are summed, e.g., in some embodiments all the genomic loci that are differentially modified with an absolute log2(fold-change) > 4.0 are selected. In some embodiments, the average number of reads in the local background of each ChlP-seq peak is subtracted to improve signal to noise. The data is then log2-transformed and quantile normalized to match the distribution of the data used to train the classifier. The normalized data is then used as input into a classifier that was trained using the same histone modification and selected genomic loci. The classifier then uses the inputted data to determine ADC target status of the subject’s cancer. It will be appreciated that this or similar approaches can be applied to assays of the present disclosure that quantify chromatin accessibility and / or transcription factor binding.

[0200] For the avoidance of any doubt, those of skill in the art will appreciate from the present disclosure that methods, kits and systems for ADC target status determination of the present disclosure are at least for in vitro use. A ccordingly, all aspects and embodiments of the present disclosure can be performed and / or used at least in vitro. [ 02011 Those of skill in the art will also appreciate that, in certain embodiments, methods of the present disclosure can be implemented on and / or in conjunction with a computer program and computer system. In some embodiments, methods of the present disclosure can be implemented on and / or in conjunction with a non-transitory computer readable storage medium encoded with the computer program, wherein the program comprises instructions that when executed by one or more processors cause the one or more processors to perform operations to perform the method. A computer system can also store and manipulate data generated by methods of the present disclosure that comprise a plurality of genomic locus modification status and / or accessibility status changes / profiles, which data can be used by a computer system in implementing methods disclosed herein. In certain embodiments, a computer system (i) receives modification status and / or accessibility status data; (ii) stores the data; and (iii) compares the data in any number of ways described herein (e.g., analysis relative to appropriate references), e.g., to determine ADC target status. In certain embodiments, a computer system (i) compares the genomic locus modification and / or accessibility status to a reference; and (ii) outputs an indication of whether the modification status and / or accessibility status of the genomic locus is significantly different from the reference and / or provides a determination regarding ADC target status.

[0202] Numerous types of computer systems can be used to implement methods of the present disclosure according to knowledge possessed by a skilled artisan in the bioinformatics and / or computer arts. Several software components can be loaded into memory during operation of such a computer system. The software components can comprise both software components that are standard in the art and components that are special to the present disclosure (e.g., dCHIP software described in Lin et al., Bioinformatics (2004) 20:1233-1240, incorporated herein by reference in its entirety; radial basis machine learning algorithms (RBM) known in the art). Methods of the present disclosure can also be programmed or modeled in mathematical software packages that allow symbolic entry of equations and high-level specification of processing, including specific algorithms to be used, thereby freeing a user of the need to procedurally program individual equations and algorithms. Such packages include, e.g., Matlab from Mathworks (Natick, MA), Mathematica from Wolfram Research (Champaign, IL), S-Plus from MathSoft (Seattle, WA). R from R Foundation for Statistical Computing (Vienna, .Austria), Python from Python Software Foundation (Wilmington, DE), or Perl from Perl Foundation (Holland, MI). In certain embodiments, a computer system comprises a database for storage of genomic locus modification status and / or accessibility status data. Such stored profiles can be accessed and used to perform comparisons of interest at a later point in time. In addition to the exemplary program structures and computer systems described herein, other, alternative program structures and computer systems will be readily apparent to the skilled artisan, [0203J As demonstrated in the Examples, various algorithms can be applied to the comparison, between samples and references, of the modification status and / or accessibility status of genomic loci that are differentially modified in different ADC target states. In various embodiments, an algorithm can be a single learning statistical classifier system. Other suitable statistical algorithms are well known to those of skill in the art. For example, learning statistical classifier systems include a machine learning algorithmic technique capable of adapting to complex datasets (e.g., a panel of genomic loci of interest) and making decisions based upon such datasets. In some embodiments, a single learning statistical classifier system such as a classification tree (e.g., random forest) is used. In other embodiments, a combination of 2, 3, 4, 5, 6, 7, 8, 9, 10, or more learning statistical classifier systems are used, preferably in tandem. Examples of learning statistical classifier systems include, but are not limited to, those described in the Examples and also those using inductive learning (e.g., decision / classification trees such as random forests, classification and regression trees (C&RT), boosted trees, etc.), Probably Approximately Correct. (PAC) learning, connectionist learning (e.g., neural networks (NN), artificial neural networks (ANN), neuro fuzzy networks (NFN), network structures, perceptrons such as multi-layer perceptrons, multi-layer feed-forward networks, applications of neural networks, Bayesian learning in belief networks, etc.), reinforcement learning (e.g., passive learning in a known environment such as naive learning, adaptive dynamic learning, and temporal difference learning, passive learning in an unknown environment, active learning in an unknown environment, learning action-value functions, applications of reinforcement learning, etc.), and genetic algorithms and evolutionary programming. Other learning statistical classifier systems include support vector machines (e.g.. Kernel methods), multivariate adaptive regression splines (MARS), Levenberg-Marquardt algorithms, Gauss-Newton algorithms, mixtures of Gaussians, gradient descent algorithms, and learning vector quantization (LVQ). In certain embodiments, methods of the present disclosure can include sending classification results to a. medical practitioner, e.g., an oncologist.

[0204] In various embodiments, the area under the receiver operating characteristic (AUROC) for determining if a subject has a particular ADC target status (e.g., an ADC targetpositive cancer vs. an ADC target-negative cancer) is greater than 0.5 (e.g., greater than 0.55, greater than 0.6, greater than 0.65, greater than 0.7, greater than 0.75, greater than 0.8, greater than 0.85, greater than 0.9, or greater than 0.95). Formulation and Administration of ADC Therapy

[0205] The present disclosure includes methods where an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) is administered to a subject based on the ADC target status of a cancer (e.g., breast cancer, SCLC, NSCLC, etc.). In general, the agent that is directed to an ADC target antigen provided herein will be available, appropriate, and / or preferred for the determined ADC target status. Those of skill in the art will be aware of recommended and / or governmentally approved formulations and / or dosages for various ADC therapies provided herein.

[0206] The present disclosure includes pharmaceutical compositions for delivery' of one or more ADCs to a subject. As disclosed herein, a pharmaceutical composition may be in any form known in the art, including formulations for administration according to any route known in the art. A suitable means of administration can be selected based on the age and condition of a subject.

[0207] Pharmaceutical composition forms of the present disclosure can include, e.g., liquid, semi-solid and solid dosage forms. Pharmaceutical composition forms of the present disclosure can include, e.g., liquid solutions (e.g., injectable and infusible solutions), dispersions or suspensions, tablets, pills, powders, and liposomes. Selection or use of any particular form may depend, in part, on the intended mode of administration and therapeutic application. Accordingly, the compositions can be formulated for administration by a parenteral mode (e.g., intravenous, subcutaneous, intraperitoneal, or intramuscular injection) or a non-parenteral mode. As used herein, parenteral administration refers to modes of administration other than enteral and topical administration, usually by injection or infusion.

[0208] In some embodiments, the compositions provided herein are present in unit dosage form, which unit dosage form can be suitable for self-administration. Such a unit, dosage form may be provided within a container, e.g., a pill, vial, cartridge, prefilled syringe, or disposable pen. A pharmaceutical composition of the present disclosure can be in an injectable or infusible form. For example, the present disclosure includes sterile formulations for injection or infusion, which can be formulated in accordance with conventional pharmaceutical practices. Sterile solutions can be prepared by incorporating a composition described herein in the required amount in an appropriate solvent with one or a combination of ingredients enumerated above, as required, followed by filter sterilization. Solutions can be formulated, e.g., using distilled water, physiological saline, or an isotonic solution containing glucose and other supplements such as D-sorbitol, D-mannose, D-mannitol, or sodium chloride as an aqueous solution for injection, optionally in combination with a suitable solubilizing agent, for example, an alcohol such as ethanol and / or a polyalcohol such as propylene glycol or polyethylene glycol, and / or a nonionic surfactant such as polysorbate 80™ or HCO-50, and the like. In the case of sterile powders for the preparation of sterile injectable solutions, methods for preparation include vacuum drying and freeze-drying that yield a powder of a composition described herein plus any additional desired ingredient (see below) from a previously sterile-filtered solution thereof. The proper fluidity of a solution can be maintained, for example, by the use of a coating such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. Prolonged absorption of injectable compositions can be brought about by including in the composition a reagent that delays absorption, for example, monostearate salts, and gelatin. In particular instances, a pharmaceutical composition can be formulated, for example, as a buffered solution at a suitable concentration and suitable for storage, e.g., at 2-8°C fo.g., 4°C).

[0210] In various embodiments, a pharmaceutical composition of the present disclosure can be formulated as a solution, microemulsion, dispersion, liposome, or other ordered structure suitable for stable storage at high concentration. Generally, dispersions are prepared by incorporating a composition described herein into a. sterile vehicle that contains a basic dispersion medium and the required other ingredients from those enumerated above.

[0211] In various instances, a pharmaceutical composition can be formulated to include a pharmaceutically acceptable carrier or excipient. Examples of pharmaceutically acceptable carriers include, without limitation, any and all solvents, dispersion media, coatings, antibacterial and antifungal agents, isotonic and absorption delaying agents, and the like that are physiologically compatible. 102121 In certain embodiments, compositions can be formulated with a carrier that will protect the ADC against rapid release, such as a controlled release formulation, including implants and microencapsulated delivery systems. Biodegradable, biocompatible polymers can be used, such as ethylene vinyl acetate, polyanhydrides, polyglycolic acid, collagen, polyorthoesters, and polylactic acid. Many methods for the preparation of such formulations are known in the art. See, e.g., J. R. Robinson (1978) “'Sustained and Controlled Release Drug Delivery Systems,” Marcel Dekker, Inc., New York.

[0213] Route of administration can be parenteral, for example, administration by injection. Administration by injection can be by intravenous injection, intramuscular injection, intraperitoneal injection, subcutaneous injection. Administration can be systemic or local. In certain embodiments, a composition described herein can be therapeutically delivered to a subject by way of local administration. As used herein, “local administration” or “local delivery',” can refer to delivery that does not rely upon transport of the composition or ADC to its intended target tissue or site via the vascular system. For example, the composition may be delivered by injection or implantation of the composition or ADC or by injection or implantation of a device containing the composition or ADC. In certain embodiments, following local administration in the vicinity of a target tissue or site, the composition or ADC, or one or more components thereof, may diffuse to an intended target tissue or site that is not the site of administration.

[0214] A pharmaceutical composition can be administered parenterally in the form of an injectable formulation comprising a sterile solution or suspension in water or another pharmaceutically acceptable liquid. For example, a pharmaceutical composition can be formulated by suitably combining the therapeutic molecule with pharmaceutically acceptable vehicles or media, such as sterile water and physiological saline, vegetable oil, emulsifier, suspension agent, surfactant, stabilizer, flavoring excipient, diluent, vehicle, preservative, binder, followed by mixing in a unit dose form required for generally' accepted pharmaceutical practices. Examples of oily liquid include sesame oil and soybean oil, and it may be combined with benzyl benzoate or benzyl alcohol as a solubilizing agent. Other items that may be included are a buffer such as a phosphate buffer, or sodium acetate buffer, a soothing agent such as procaine hydrochloride, a stabilizer such as benzyl alcohol or phenol, and an antioxidant. The formulated injection can be packaged in a suitable ampule.

[0215] In various embodiments, subcutaneous administration can be accomplished by means of a device, such as a syringe, a prefilled syringe, an auto-injector (e.g., disposable or reusable), a pen injector, a patch injector, a wearable injector, an ambulatory syringe infusion pump with subcutaneous infusion sets, or other device for combining with a ADC for subcutaneous injection.

[0216] An injection system of the present disclosure may employ a delivery pen as described in U.S. Pat. No. 5,308,341. Pen devices, most commonly used for self-delivery of insulin to patients with diabetes, are well known in the art. Such devices can include at least one injection needle, are typically pre-filled with one or more therapeutic unit doses of a solution that includes the ADC and are useful for rapidly delivering solution to a subject with as little pain as possible. One medication delivery pen includes a vial holder into which a vial of a therapeutic or other medication may be received. The pen may be an entirely mechanical device or it may be combined with electronic circuitry7 to accurately set and / or indicate the dosage of medication that is injected into the user. See, e.g., U.S. Pat, No. 6,192,891. In some embodiments, the needle of the pen device is disposable and the kits include one or more disposable replacement needles. Pen devices suitable for delivery of any one of the presently featured compositions are also described in, e.g., U.S. Pat, Nos. 6,277,099, 6,200,296; and 6,146,361, the disclosures of each of which are incorporated herein by reference in their entirety. A microneedle-based pen device is described in, e.g., U.S. Pat. No. 7,556,615, the disclosure of which is incorporated herein by reference in its entirety. See also the Precision Pen Injector (PPI) device, MOLLY™, manufactured by Scandinavian Health Ltd.

[0217] In some embodiments, a composition can be formulated for storage at a temperature below 0°C (e.g, -20°C or -80°C). In some embodiments, the composition can be formulated for storage for up to 2 years (e.g., one month, two months, three months, four months, five months, six months, seven months, eight months, nine months, 10 months, 11 months, 1 year, or 2 years) at 2-8°C (e.g-, 4 C} Thus, in some embodiments, the compositions described herein are stable in storage for at least 1 year at 2-8°C (e.g., 4°C).

[0218] A pharmaceutical composition can include a therapeutically effective amount of a ADC described herein. Such effective amounts can be readily determined by one of ordinary skill in the art. A therapeutically effective amount can be an amount at which any toxic or detrimental effects of the composition are outweighed by therapeutically beneficial effects. In some embodiments, a dose can also be chosen to reduce or avoid production of antibodies or other host immune responses against an ADC. Those of skill in the art will appreciate that data obtained from cell culture assays and animal studies can be used in formulating a range of dosage for use in humans. In various embodiments, the amount of active ingredient included in a pharmaceutical composition is such that a suitable dose within the designated range can be administered to subjects. The dose and method of administration can vary depending on weight, age, condition, and other characteristics of a patient, and can be suitably selected as needed by those skilled in the art.

[0219] Pharmaceutical compositions including certain ADCs can be administered as a fixed dose, or in a milligram per kilogram (mg / kg) dose. While in no way intended to be limiting, an exemplary' single dose of certain pharmaceutical compositions described herein can include certain ADCs as described herein in an amount equal to, e.g., 0.001 to 1000 mg / kg, 11000 mg / kg, 1-100 mg / kg, 0.5-50 me / ks, 0.1-100 ms / ke, 0.5-25 mg / kg. 1-20 mg / kg, and 1-10 mg / kg body weight. Exemplary dosages of a composition described herein include, without limitation, 0.1 mg / kg, 0.5 mg / kg, 1 mg / kg, 2 mg / kg, 4 mg / kg, 8 mg / kg, or 20 mg / kg. The present disclosure is not limited to such ranges or dosages.

[0220] The present disclosure further includes methods of preparing pharmaceutical compositions of the present disclosure and kits including pharmaceutical compositions of the present disclosure.

[0221] In various embodiments, ADCs of the present disclosure can be administered to a subject in a course of treatment that further includes administration of one or more additional therapeutic agents or therapies that are not .ADCs (e.g., surgery or radiation). Combination therapies of the present disclosure can include simultaneous exposure of a subject to therapeutic agents of two or more therapeutic regimens.

[0222] In certain embodiments, an ADC as described herein can be administered together with (e.g., at the same time and / or in the same composition as) an additional agent or therapy. In certain embodiments, an ADC of the present disclosure can be administered separately from an additional therapeutic agent or therapy (e.g., at a different time and / or in a different composition than the additional therapeutic agent or therapy). Dosing regimens of an ADC and one or more additional therapeutic agents with which it is administered in combination can be coordinated or independently determined. In various embodiments, an additional therapeutic agent or therapy administered in combination with an ADC as described herein can be administered at the same time as the ADC, on the same day as the ADC, or in the same week as the ADC. In various embodiments, an additional therapeutic agent or therapy administered in combination with an ADC as described herein can be administered such that administration of the ADC and the additional therapeutic agent or therapy are separated by one or more hours before or after, one or more days before or after, one or more weeks before or after, or one or more months before or after administration of the ADC. In various embodiments, the administration frequency and / or dosage of one or more additional therapeutic agents can be the same as, similar to, or different from the administration frequency of the ADC. In some embodiments, the two or more regimens can be administered simultaneously; in some embodiments, such regimens can be administered sequentially (e.g., all “doses” of a first regimen are administered prior to administration of any doses of a second regimen); in some embodiments, such therapeutic agents are administered in overlapping dosing regimens.

[0223] In certain embodiments, administration of an ADC can be to a subject having previously received, scheduled to receive, or in the course of a treatment regimen including an additional cancer therapy. Administration of an ADC can, in some instances, improve delivery or efficacy of another therapeutic agent or therapy with which it is administered in combination.

[0224] It is contemplated that therapeutic agent combination therapies can demonstrate synergy and / or greater-than-additive effects between an ADC and one or more additional therapeutic agents with which it is administered in combination. An ADC can be administered in any effective amount as determined independently or as determined by the joint action of the ADC and any of one or more additional therapeutic agents or therapies administered. Administration of the ADC may, in some embodiments, reduce the therapeutically effective dosage, required dosage, or administered dosage of the additional therapeutic agent or therapy relative to a reference regimen for administration of additional therapeutic agent or therapy or therapy absent the ADC. In certain embodiment, a composition described herein can replace or augment other previously or currently administered therapy. For example, upon treating with an ADC, administration of one or more additional therapeutic agents or therapies can cease or diminish, e.g., be administered at lower levels. Kits

[0225] The present disclosure includes kits for detecting modification and / or accessibility of one or more genomic loci. In some embodiments, the present disclosure provides kits for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci. Kits of the present disclosure can include, e.g., reagents such as buffers and / or antibodies useful in the detection and quantification of histone modifications. In certain embodiments, a kit of the present disclosure can include at least one antibody that selective binds a histone modification selected from H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, H3K4me1, H3K4me2, or H3K4me3, or pan acetylation. In certain embodiments, a kit of the present disclosure can include at least one antibody that selective binds H3K4me3 modifications. In certain embodiments, a kit of the present disclosure can include at least one antibody that selective binds H3K27ac modifications. A kit of the present disclosure can include instructional materials disclosing or describing the use of the kit in a method of determining ADC target status and / or treatment disclosed herein. In various embodiments, a kit of the present disclosure can include one or more ADCs or other therapeutic agents useful in the treatment of cancer, e.g, as disclosed herein, optionally in combination with instruction materials for treatment of cancer, e.g., breast cancer, SC 1.( NSCLC, etc. based on ADC target status.

[0226] In some embodiments, a kit of the present disclosure comprises reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci, wherein the one or more genomic loci are selected from Tables 1-6.

[0227] In some embodiments, the kit comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1. In some embodiments, the kit comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2. In some embodiments, the kit comprises reagents for quantifying H3K27ac modifications for at. least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3. In some embodiments, the kit comprises reagents for quantifying H3K27ac or H3K4me3 modifications or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4. In some embodiments, the kit comprises reagents for quantifying H3K4me3 modifications for 1 or 2 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 5. In some embodiments, the kit comprises reagents for quantifying H3K27ac or H3K4me3 modifications or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6. In some embodiments, the kit comprises one or more antibodies for use in ChlP-seq, optionally wherein the one or more antibodies specifically bind H3K4me3- or H3K27ac-modified histones.

[0228] In some embodiments, the kit comprises reagents for isolation of cell-free DNA (cfDNA) from a liquid biopsy sample. In some embodiments, the kit comprises reagents for library^ preparation for sequencing. In some embodiments, the kit comprises reagents for sequencing. In some embodiments, the kit comprises instructions for determining if a subject has an ADC target-positive cancer. Systems

[0229] The present disclosure includes systems for detecting modification and / or accessibility of one or more genomic loci. In some embodiments, the present disclosure provides systems for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci. Systems of the present disclosure can include a sequencer configured to generate a sequencing dataset from a sample, and a non-transitory computer readable storage medium and / or a computer system.

[0230] In some embodiments, the non-transitory computer readable storage medium is encoded with a computer program, wherein the program comprises instructions that when executed by one or more processors cause the one or more processors to perform operations to perform a method of the present disclosure.

[0231] In some embodiments, the computer system comprises a memory and one or more processors coupled to the memory, wherein the one or more processors are configured to perform a method of the present disclosure.

[0232] In some embodiments, the sequencer is configured to generate a Whole Genome Sequencing (WGS) dataset from the sample. In some embodiments, the system also includes a sample preparation device configured to prepare the sample for sequencing from a biological sample, optionally a liquid biopsy sample. The sample preparation device may include reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci in cell-free DNA (cfDNA) from the biological sample, optionally the liquid biopsy sample.

[0233] Systems of the present disclosure can include, e.g., reagents such as buffers and / or antibodies useful in the detection and quantification of histone modifications. In certain embodiments, a system of the present disclosure can include at least one antibody that selective binds a histone modification selected from H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, H3K4mel, H3K4me2, or H3K4me3, or pan acetylation. In certain embodiments, a system of the present disclosure can include at least one antibody that selective binds H3K4me3 modifications. In certain embodiments, a system of the present disclosure can include at least one antibody that selective binds H3K27ac modifications. A system of the present disclosure can include instructional materials di sclosing or describing the use of the system in a method of determining ADC target status and / or treatment disclosed herein.

[0234] In some embodiments, a system of the present disclosure comprises reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci, wherein the one or more genomic loci are selected from Tables 1-6.

[0235] In some embodiments, the system comprises reagents for quantifying H3K4me3 modifications for at least 1,2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1. In some embodiments, the system comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2, In some embodiments, the system comprises reagents for quantifying H3K27ac modifications for at least 1,2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3. In some embodiments, the system comprises reagents for quantifying H3K27ac or H3K4me3 modifications or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 2.5 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4. In some embodiments, the system comprises reagents for quantifying H3K4me3 modifications for 1 or 2 genomic ioci that are located within one or more regions defined by pairs of genomic coordinates in Table 5. In some embodiments, the system comprises reagents for quantifying H3K4me3 or H3K27ac modifications for 1, 2, 3, 4, 5, 10, 15, or 16 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6. In some embodiments, the system comprises one or more antibodies for use in ChlP-seq, optionally wherein the one or more antibodies specifically bind H3K4me3- or H3K27ac-modified histones or methylated DNA. In some embodiments, the system comprises one or more methyl binding domains (MBDs) for use in MBD-seq.

[0236] In some embodiments, the system comprises reagents for isolation of cell-free DNA (cfDNA) from a. liquid biopsy sample. In some embodiments, the sequencer comprises reagents for library' preparation for sequencing. In some embodiments, the sequencer comprises reagents for sequencing. In some embodiments, the system comprises instructions for determining if a subject has an ADC target-positive cancer. Definitions

[0237] “A ” or “An”: The articles “a” and “an” are used herein to refer to one or to more than one (i.e., to at least one) of the grammatical object of the article. By way of example, “an element” refers to one element or more than one element.

[0238] About: The term “about”, when used herein in reference to a value, refers to a value that is similar, in context, to the referenced value. In general, those skilled in the art, familiar with the context, will appreciate the relevant degree of variance encompassed by “about” in that context. For example, in some embodiments, the term “about” can encompass a range of values that within 25%, 20%, 19%, 18%, 17%, 16%, 15%, 14%, 13%, 12%, 11%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or within a fraction of a percent, of the referenced value.

[0239] “Accessibility Status” or “Chromatin Accessibility Status”: As used herein, “accessibility status” or “chromatin accessibility status” of a genomic locus refers to the frequency with which DNA sequences corresponding to the genomic locus are identified in an assay for detection of accessible chromatin. Accessibility status can be determined by various assays known in the art, including without limitation ChiP-seq as one example. Where two samples are separately analyzed by the same assay or comparable assays for detection of accessible DNA sequences, differences in chromatin accessibility status of genomic loci can be detected. Accessibility status can be compared to a standard or reference. A sample that has an accessibility status that differs in accessibility status from a. standard or reference can be referred to as differentially modified. Suitable assays for determining chromatin accessibility are known in the art. Exemplary assays include ATAC-seq (Assay of Transpose Accessible Chromatin sequencing), NOMe-seq (Nucleosome Occupancy and Methylome sequencing), FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing), MNase-seq (Micrococcal Nuclease digestion with sequencing), a DNase hypersensitivity assay, and / or a fragmentomics assay.

[0240] Administration: As used herein, the term “administration’’ typically refers to the administration of a disease appropriate treatment. In some embodiments, the disease appropriate treatment may comprise administering a composition to a subject, for example to achieve delivery' of an agent that is, is included in, or is otherwise delivered by, the composition. In some embodiments, the disease appropriate treatment may comprise administering an appropriate surgical procedure or radiological procedure, optionally in combination with administration of a composition. [0241 ] Agent: As used herein, the term “agent” may refer to any chemical or physical entity, including without limitation any of one or more of an atom, e.g., a radioactive atom, molecule, compound, conjugate, polypeptide, polynucleotide, polysaccharide, lipid, cell, or combination or complex thereof.

[0242] Antibody: As used herein, the term “antibody” refers to a polypeptide that includes one or more canonical immunoglobulin sequence elements sufficient to confer specific binding to a particular antigen (e.g, a heavy chain variable domain, a light chain variable domain, and / or one or more CDRs). Thus, the term antibody includes, without limitation, human antibodies, non-human antibodies, synthetic and / or engineered antibodies, fragments thereof, and agents including the same. Antibodies can be naturaliv occurring immunoglobulins foe;, generated by an organism reacting to an antigen). Synthetic, non-naturally occurring, or engineered antibodies can be produced by recombinant engineering, chemical synthesis, or other artificial systems or methodologies known to those of skill in the art.

[0243] As is well known in the art, typical human immunoglobulins are approximately 150 kD tetrameric agents that include two identical heavy (H) chain polypeptides (about 50 kD each) and two identical light (L) chain polypeptides (about 25 kD each) that associate with each other to form a structure commonly referred to as a “Y-shaped” structure. Typically, each heavy chain includes a. heavy chain variable domain (VH) and a heavy chain constant domain (CH). The heavy chain constant domain includes three CH domains: CHI, CH2 and CH3. A short region, known as the “switch”, connects the heavy chain variable and constant regions. The “hinge” connects CH2 and CH3 domains to the rest of the immunoglobulin. Each light chain includes a light chain variable domain (AX) and a light chain constant domain (CL), separated from one another by another “switch” Each variable domain contains three hypervariable loops known as “complement determining regions” (CDR1, CDR2, and CDR3) and four somewhat invariant “framework” regions (FR1, FR2, FR3, and FR4). In each VH and VL, the three CDRs and four FRs are arranged from amino-terminus to carboxy-terminus in the following order: FR1, CDR1, FR2, CDR2, FR3, CDR3, and FR4. The variable regions of a heavy and / or a. light chain are typically understood to provide a binding moiety that can interact with an antigen. Constant domains can mediate binding of an antibody to various immune system cells (e.g.. effector cells and / or cells that mediate cytotoxicity), receptors, and elements of the complement system. Heavy and light chains are linked to one another by a single disulfide bond, and two other disulfide bonds connect the heavy chain hinge regions to one another, so that the dimers are connected to one another and the tetramer is formed. When natural immunoglobulins fold, the FR regions form the beta sheets that provide the structural framework for the domains, and the CDR loop regions from both the heavy and light chains are brought together in threedimensional space so that they create a single hypervariable antigen binding site located at the tip of the Y structure.

[0244] In some embodiments, an antibody is a polyclonal, monoclonal, monospecific, or multispecific antibody (e.g., a bispecific antibody). In some embodiments, an antibody includes at least one light chain monomer or dimer, at least one heavy chain monomer or dimer, at least one heavy chain-light chain dimer, or a tetramer that includes two heavy chain monomers and two light chain monomers. Moreover, the term “antibody” can include (unless otherwise stated or clear from context) any art-known constructs or formats utilizing antibody structural and / or functional features including without limitation intrabodies, domain antibodies, antibody mimetics, Zybodies®, Fab fragments. Fab’ fragments, F(ab’)2 fragments, Fd’ fragments, Fd fragments, isolated CDRs or sets thereof, single chain antibodies, single-chain Fvs (scFvs), di sulfide-linked Fvs (sdFv), polypeptide-Fc fusions, single domain antibodies (e.g., shark single domain antibodies such as IgNAR or fragments thereof), cameloid antibodies, camelized antibodies, masked antibodies (e.g., Probodies®), affybodies, anti-idiotypic (anti-Id) antibodies (including, e.g.., anti-anti-Id antibodies), Small Modular ImmunoPharmaceuticals (SMIPs), single chain or Tandem diabodies (TandAb®), VHHs, Anticalins®, Nanobodies®, minibodies, BiTE®s, ankyrin repeat proteins or DARPINs®, Avimers®, DARTs, TCR-like antibodies, Adnectins®, Affilins®, Trans-bodies®, Affibodies®, TrimerX®, MicroProteins, Fynomers®, Centyrins®, KALBITOR®s, chimeric antigen receptors (CARs), engineered T-cell receptors (TCRs), and antigen-binding fragments of any of the above.

[0245] In various embodiments, an antibody includes one or more structural elements recognized by those skilled in the art as a complementarity determining region (CDR) or variable domain. In some embodiments, an antibody can be a covalently modified (“conjugated”) antibody (e.g., an antibody that includes a polypeptide including one or more canonical immunoglobulin sequence elements sufficient to confer specific binding to a particular antigen, where the polypeptide is covalently linked with one or more of a therapeutic agent, a detectable moiety, another polypeptide, a glycan, or a polyethylene glycol molecule). In some embodiments, antibody sequence elements are humanized, primatized, chimeric, etc., as is known in the art.

[0246] An antibody including a heavy chain constant domain can be, without limitation, an antibody of any known class, including but not limited to, IgA, secretory IgA, IgG, IgE and IgM, based on heavy chain constant domain amino acid sequence (e.g., alpha (a), delta (5), epsilon (s), gamma (y) and mu (u)). IgG subclasses are also well known to those in the art and include but are not limited to human IgGl, IgG2, IgG3 and IgG4. “Isotype” refers to the Ab class or subclass (e.g., IgM or IgGl) that is encoded by the heavy chain constant region genes. As used herein, a “light chain” can be of a distinct type, e.g., kappa (k) or lambda (X), based on the amino acid sequence of the light chain constant domain. In some embodiments, an antibody has constant region sequences that are characteristic of mouse, rabbit, primate, or human immunoglobulins. Naturally produced immunoglobulins are glycosylated, typically on the CH2 domain. As is known in the art, affmitv and / or other bindins attributes of Fc regions for Fc receptors can be modulated through glycosylation or other modification. In some embodiments, an antibody may lack a covalent modification (e.g., attachment of a glycan) that it would have if produced naturally. In some embodiments, antibodies produced and / or utilized in accordance with the present invention include glycosylated Fc domains, including Fc domains with modified or engineered glycosylation.

[0247] In some embodiments, an antibody can be specific for a particular histone modification (e.g., an antibody can bind one histone modification, e.g., H3K27ac with a higher affinity than other histone modifications, under conditions that are commonly used in ChlP-seq experiments). In some embodiments, an antibody is specific for an H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac, H3K4mel, H3K4me2, or H3K4me3 modification. In some embodiments, an antibody is specific for an H3K27ac modification. In some embodiments, an antibody is specific for an H3K4me3 modification. [0248} In some embodiments, an antibody is a “pan” antibody. As used herein, the term pan antibody refers to an antibody that, can bind a group of histone modifications having one or more features that are similar. In some embodiments, a pan antibody is a pan-methylation antibody (e.g., an antibody that can bind a histone, e.g., H3 that comprises at least one methylated lysine, wherein the at least one methylated lysine can be at any one of a plurality of amino acid positions, e.g., in some embodiments, a pan-methylation antibody can bind an H3 protein comprising a methylated lysine at any position). In some embodiments, a pan antibody is a pan-acetylation antibody (e.g., an antibody that can bind a histone, e.g., H3 that comprises at least one acetylated lysine, wherein the at least one acetylated lysine can be at any one of a plurality of amino acid positions, e.g., a pan-acetylation antibody can bind an H3 protein comprising an acetylated lysine at any position). In some embodiments, a pan antibody can bind one or more histone modifications that are associated with transcription activation. In some embodiments, a pan antibody can bind one or more histone modifications that are associated with transcription silencing.

[0249] Antibody fragment: As used herein, an “antibody fragment” refers to a portion of an antibody or antibody agent as described herein, and typically refers to a portion that includes an antigen-binding portion or variable region thereof. An antibody fragment can be produced by any means. For example, in some embodiments, an antibody fragment can be enzymatically or chemically produced by fragmentation of an intact antibody or antibody agent. Alternatively, in some embodiments, an antibody fragment can be recombinantly produced, ?.e., by expression of an engineered nucleic acid sequence. In some embodiments, an antibody fragment can be wholly or partially synthetically produced. In some embodiments, an antibody fragment (particularly an antigen-binding antibody fragment) can have a length of at least about 50, 60, 70, 80, 90, 100, 110, 120, 130, 140, 150, 160, 170, 180, 190 amino acids or more, in some embodiments at least about 200 amino acids.

[0250] Associated with: Two events or entities are “associated” with one another, as that term is used herein, if the presence, level and / or form of one is correlated with that of the other. For example, a particular entity (e.g., an epigenetic profile comprising one or more histone modifications at a set of genomic loci, etc.) is considered to be associated with a particular disease, disorder, or condition, if its presence, level and / or form correlates with incidence of and / or susceptibility to the disease, disorder, or condition (e.g., across a relevant population). To give another example, a genomic loci can be considered to be associated with an enhancer or a promoter of a gene if it exhibits certain physical and / or functional properties, including, e.g., physical proximity to the gene and / or a correlation between the level of one or more epigenetic modifications associated with promoter or enhancer activity (whether positively or negatively) and expression of the gene. In some embodiments, two or more entities are physically “associated” with one another if they interact, directly or indirectly, so that they are and / or remain in physical proximity with one another. In some embodiments, two or more entities that are physically associated with one another are covalently linked to one another; in some embodiments, two or more entities that are physically associated with one another are not covalently linked to one another but are non-covalently associated, for example by means of hydrogen bonds, van der Waals interaction, hydrophobic interactions, magnetism, or a combination thereof.

[0251] “Between” or “From”: As used herein, the term “between” refers to content that falls between indicated upper and lower, or first and second, boundaries, inclusive of the boundaries. Similarly, the term “from”, when used in the context of a range of values, indicates that the range includes content that falls between indicated upper and lower, or first and second, boundaries, inclusive of the boundaries.

[0252] Biological Sample: As used herein, the term “biological sample” typically refers to a sample obtained or derived from a biological source (e.g, a tissue or organism or cell) of interest, as described herein. In some embodiments, a. biological source is or includes an organism, such as a human subject. In some embodiments, a biological sample is or includes a biological tissue or fluid. In some embodiments, a biological sample can be or include cells, tissue, or bodily fluid. “Bodily fluids” refer to fluids that are excreted or secreted from the body as well as fluids that are normally not (e.g., blood, serum, plasma, Cowper’s fluid or preejaculate fluid, chyle, chyme, stool, interstitial fluid, intracellular fluid, lymph, menses, saliva, sebum, semen, serum, sweat, synovial fluid, tears, urine, vitreous humor, vomit). In some embodiments, a biological sample can be or include blood, blood components, cell-free DNA (cfDNA), circulating-tumor DNA (ctDNA), ascites, biopsy samples, surgical specimens, cellcontaining body fluids, sputum, saliva, feces, urine, cerebrospinal fluid, peritoneal fluid, pleural fluid, lymph, gynecological fluids, secretions, excretions, skin swabs, vaginal swabs, oral swabs, nasal swabs, washings or lavages such as a ductal lavages or bronchoalveolar lavages, aspirates, scrapings, or bone marrow. In some embodiments, a biological sample is a liquid biopsy sample obtained from a bodily fluid. In some embodiments, a biological sample is or includes DNA obtained from a single subject or from a plurality of subjects. A biological sample can be a “primary sample” obtained directly from a biological source or can be a “processed sample”, i.e., a. sample that was derived from a primary sample, e.g., via dilution, purification, mixing with one or more reagents, or any other processing step(s) as described herein. A biological sample can also be referred to as a “sample.”

[0253] Blood component: As used herein, the term “blood component” refers to any component of whole blood, including red blood cells, white blood cells, plasma, platelets, endothelial cells, mesothelial cells, epithelial cells, cell-free DNA (cfDNA), and circulatingtumor DNA (ctDNA). Blood components also include the components of plasma, including proteins, metabolites, lipids, nucleic acids, and carbohydrates, and any other cells that can be present in blood, e.g., due to pregnancy, organ transplant, infection, injury', or disease.

[0254] Cancer: As used herein, the terms “cancer,” “malignancy,” “tumor,” and “carcinoma,” are used interchangeably to refer to a disease, disorder, or condition in which cells exhibit or exhibited relatively abnormal, uncontrolled, and / or autonomous growth, so that they display or displayed an abnormally elevated proliferation rate and / or aberrant growth phenotype. In some embodiments, a cancer can include one or more tumors. In some embodiments, a cancer can be or include cells that are precancerous (e.g., benign), malignant, pre-metastatic, metastatic, and / or non-metastatic. In some embodiments, a cancer can be or include a solid tumor. 10255| Combination therapy: As used herein, the term “combination therapy” refers to administration to a subject of two or more therapeutic agents or therapeutic regimens such that the two or more therapeutic agents or therapeutic regimens together treat a disease, condition, or disorder of the subject. In some embodiments, the two or more therapeutic agents or therapeutic regimens can be administered simultaneously, sequentially, or in overlapping dosing regimens. Those of skill in the art will appreciate that combination therapy includes but does not require that the two therapeutic agents or therapeutic regimens be administered together in a single composition, nor at the same time.

[0256] Corresponding tot As used herein, the term “corresponding to” may be used to designate the position / identity of a structural element in a compound or composition through comparison with an appropriate reference compound or composition. For example, in some embodiments, a monomeric residue in a polymer (e.g., an amino acid residue in a polypeptide or a nucleic acid residue in a polynucleotide) may be identified as “corresponding to” a residue in an appropriate reference polymer. For example, those of skill in the art appreciate that residues in a provided polypeptide or polynucleotide sequence are often designated (e.g., numbered or labeled) according to the scheme of a related reference sequence (even if, e.g., such designation does not reflect literal numbering of the provided sequence). By way of illustration, if a reference sequence includes a particular amino acid motif at positions 100-110, and a second related sequence includes the same motif at positions 110-120, the motif positions of the second related sequence can be said to “correspond to” positions 100-110 of the reference sequence. Those of skill in the art appreciate that corresponding positions can be readily identified, e.g., by alignment of sequences, and that such alignment is commonly accomplished by any of a variety of known tools, strategies, and / or algorithms, including without limitation software programs such as, for example, BLAST, CS-BLAST, CUDASW++, DIAMOND, FASTA, GGSEARCH / GL SEARCH, Genoogle, HMMER, HHpred / HHsearch, IDF, Infernal, KLAST, USEARCH, parasail, PSI-BLAST, PSI-Search, ScalaBLAST, Sequilab, SAM, SSEARCH, SWAPHI, SWAPHI-LS, SWIMM, or SWIPE. Two sequences can be identified as corresponding if they are identical or if they share substantial identity, e.g, at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identity, e.g., over a length of at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500 or more residues. In various embodiments, a nucleic acid sequence can correspond to a sequence that is identical or substantially identical (e.g., at least 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% identical) to the complement of the nucleic acid sequence, e.g., over a length of at least 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 200, 300, 400, 500 or more nucleic acid residues. {0257] “Diagnosing”, “Detecting”, “Determining” or “Screeningfor”: As used herein, “diagnosing”, “detecting”, “determining'', “screening for” the presence of a condition or disease, or a related state (e.g., responsiveness of a cancer to one or more ADC therapies) includes the act, process, and / or outcome of determining whether, and / or the qualitative of quantitative probability that, a. subject has or will develop the condition, disease, or related state. In some instances, diagnosing can include a determination relating to prognosis and / or likely response to one or more general or particular therapeutic agents or regimens.

[0258] Differentially accessible: As used herein, the term “differentially accessible” describes a genomic locus for which chromatin accessibility status differs between a first condition or sample and a second condition or sample (e.g., a standard or reference). A differentially accessible genomic locus can include a greater or smaller measured accessibility under a selected condition of interest, such as disease state, as compared to a reference state, such as healthy state.

[0259] Differentially mollified: As used herein, the term “'differentially modified” describes a genomic locus for which histone modification status differs between a first condition or sample and a second condition or sample (e.g., a standard or reference). A differentially modified genomic locus can include a greater or smaller number or frequency of histone modification under a selected condition of interest, such as a disease state, as compared to a reference state, such as healthy state.

[0260] Gene: As used herein, the term “gene” refers to a DNA sequence in a chromosome encoding a gene product (e.g., an RNA product and / or a polypeptide product). In some embodiments, a gene includes a coding sequence (e.g., a sequence encoding a particular gene product), in some embodiments, a gene includes a non-coding sequence. In some embodiments, a gene may include both coding (e.g., exonic) and non-coding (e.g., intronic) sequences. In some embodiments, a gene may include one or more regulatory elements (e.g. promoters, silencers, termination signals) that, for example, may control or impact one or more aspects of gene expression (e.g., cell-type-specific expression). [02611 Identity: As used herein, the term “identity” refers to the overall relatedness between polymeric molecules, e.g., between nucleic acid molecules (e.g., DNA molecules) and / or between polypeptide molecules. Methods for the calculation of a percent identity as between two provided sequences are known in the art. The term “% sequence identity” refers to a. relationship between two or more sequences, as determined by comparing the sequences. In the art, “identity” also means the degree of sequence relatedness between protein and nucleic acid sequences as determined by the match between strings of such sequences. “Identity” (often referred to as “similarity”) can be readily calculated by known methods, including those described in: Computational Molecular Biology (Lesk, A. M. ed.) Oxford University Press, NY (1988); Biocomputing: Informatics and Genome Projects (Smith, D. W. ed.) Academic Press, NY (1994): Computer Analysis of Sequence Data, Part I (Griffin, A. M. and Griffin, H. G. eds.) Humana Press, NJ (1994); Sequence Analysis in Molecular Biology (Von Heijne, G. ed.) Academic Press (1987); and Sequence Analysis Primer (Gribskov, M. and Devereux, J. eds.) Oxford University Press, NY (1992), each of which are separately incorporated by reference in their entirety. Preferred methods to determine identity are designed to give the best match between the sequences tested. Methods to determine identity and similarity are codified in publicly available computer programs. For example, calculation of the percent identity of two nucleic acid or polypeptide sequences can be performed by aligning the two sequences (or the complement of one or both sequences) for optimal comparison purposes (e.g., gaps can be introduced in one or both of a first and a second sequences for optimal alignment and nonidentical sequences can be disregarded for comparison purposes). The nucleotides or amino acids at corresponding positions are then compared. When a position in the first sequence is occupied by the same residue (e.g., nucleotide or amino acid) as the corresponding position in the second sequence, then the molecules are identical at that position. The percent identity between the two sequences is a function of the number of identical positions shared by the sequences, optionally accounting for the number of gaps, and the length of each gap, which may need to be introduced for optimal alignment of the two sequences. The comparison of sequences and determination of percent identity between two sequences can be accomplished using a computational algorithm, such as BLAST (basic local alignment search tool). Sequence alignments and percent identity calculations may be performed using the Megalign program of the LASERGENE bioinformatics computing suite (DNASTAR, Inc., Madison, Wisconsin). Multiple alignment of the sequences can also be performed using the Clustal method of alignment (Higgins and Sharp, Comp Appl Biosci (1989) 5(2): 151-153), incorporated by reference herein in its entirety, with default parameters (GAP PEN ALT Y= 10, GAP LENGTH PENALTY=10). Relevant programs also include the GCG suite of programs (Wisconsin Package Version 9.0, Genetics Computer Group (GCG), Madison, Wisconsin), BLASTP, BLASTN, BLASTX (Altschul etai., J Mol Biol (1990) 215:403-410); DNASTAR (DNASTAR, Inc., Madison, Wisconsin); and the FASTA program incorporating the SmithWaterman algorithm (Pearson, Comput Methods Genome Res [Proc Int Symp] (1994), Meeting Date 1992, 111-120. Eds. Suhai, Sandor. Plenum, New York, NY' (the contents of each of which is separately incorporated herein by reference in its entirety). Within the context of this disclosure, it will be understood that where sequence analysis software is used for analysis, the results of the analysis are based on the “default values” of the program referenced. “Default values” will mean any set of values or parameters, which originally load with the software when first initialized.

[0262] “Improve” “increase^ “inhibit,” or “reduce”: As used herein, the terms “improve”, “increase”, “inhibit”, and “reduce”, and grammatical equivalents thereof, indicate qualitative or quantitative difference from a reference.

[0263] “Modification Status” or “Histone Modification Status”: As used herein, “modification status” or “histone modification status” of a genomic locus refers to the frequency with which DNA sequences corresponding to the genomic locus are identified in an assay for detection of DNA sequences associated with histones bearing one or more histone modifications (e.g., one or more particular histone modifications) and / or the density (e.g., the measured density) of histone modifications (e.g., one or more particular histone modifications) corresponding to the genomic locus. Modification status can be determined by various assay s known in the art, including without limitation ChlP-seq as one example. Other well-known assays include CUT&RUN (Cleavage Under Targets and Release Using Nuclease) sequencing and CUT&Tag (Cleavage Under Targets and Tagmentation). Where two samples are separately analyzed by the same assay or comparable assays for detection of DNA sequences associated with histones bearing one or more histone modifications (e.g., one or more particular histone modifications), differences in modification status of genomic loci can be detected. Modification status can be compared to a standard or reference. A sample that has a modification status that differs in modification status or histone modification status from a standard or reference can be referred to as differentially modified.

[0264] Regulatory sequence: As used herein in the context of expression of a nucleic acid coding sequence, a regulatory sequence is a nucleic acid sequence that controls expression of a coding sequence, e.g., a promoter sequence or an enhancer sequence. In some embodiments, a regulatory sequence can control or impact one or more aspects of gene expression (e.g., cell-type-specific expression, inducible expression, etc.).

[0265] Subject: As used herein, the term “subject” refers to an organism, typically a mammal (e.g., a human). In some embodiments, a subject is suffering from a disease, disorder or condition (e.g., breast cancer, small cell lung cancer or SCLC, non-small cell lung cancer or NSCLC, neuroendocrine prostate cancer or NEPC, prostate adenocarcinoma or PRAD, etc.). In some embodiments, a subject is susceptible to a disease, disorder, or condition In some embodiments, a subject displays one or more symptoms or characteristics of a disease, disorder or condition. In some embodiments, a subject is not suffering from a disease, disorder or condition. In some embodiments, a subject does not display any symptom or characteristic of a disease, disorder, or condition. In some embodiments, a subject has one or more features characteristic of susceptibility to or risk of a disease, disorder, or condition. In some embodiments, a subject is a subject that has been tested for a disease, disorder, or condition, and / or to whom therapy has been administered. In some instances, a human subject can be interchangeably referred to as a “patient” or “individual”. References herein to a subject that is a “cancer patient” or a “breast cancer patient”, etc. are not intended to limit the subject to a subject that has been diagnosed with cancer, breast cancer, etc. and is intended to encompass any of the aforementioned subjects.

[0266] Therapeutic agent: As used herein, the term “therapeutic agent” refers to any agent that elicits a desired pharmacological effect when administered to a subject. In some embodiments, an agent is considered to be a therapeutic agent if it demonstrates a statistically significant effect across an appropriate population. In some embodiments, the appropriate population can be a population of model organisms or a human population. In some embodiments, an appropriate population can be defined by various criteria, such as a certain age group, gender, genetic background, preexisting clinical conditions, etc. in some embodiments, a therapeutic agent is a substance that can be used for treatment of a disease, disorder, or condition (e.g., breast cancer, small cell lung cancer or SCLC, non-small cell lung cancer or NSCLC, neuroendocrine prostate cancer orNEPC, prostate adenocarcinoma or PRAD, etc.). In some embodiments, a therapeutic agent is an agent that has been or is required to be approved by a government agency before it can be marketed for administration to humans. In some embodiments, a therapeutic agent is an agent for which a medical prescription is required for administration to humans. In some embodiments, a therapeutic agent is an ADC.

[0267] Therapeutically effective amount: As used herein, “therapeutically effective amount” refers to an amount that produces the desired effect for which it is administered. In some embodiments, the term refers to an amount that is sufficient, when administered to a population suffering from or susceptible to a disease, disorder, and / or condition {e.g., breast cancer, small cell lung cancer or SCLC, non-small cell lung cancer or NSCLC, neuroendocrine prostate cancer or NEPC, prostate adenocarcinoma, or PRAD, etc.) in accordance with a therapeutic dosing regimen, to treat the disease, disorder, and / or condition. In some embodiments, a therapeutically effective amount is one that reduces the incidence and / or severity of, and / or delays onset of, one or more symptoms of the disease, disorder, and / or condition. Those of ordinary skill in the art will appreciate that the term “therapeutically effective amount” does not in fact require successful treatment be achieved in a particular individual. Rather, a therapeutically effective amount may be that amount that provides a particular desired pharmacological response in a significant, number of subjects when administered to patients in need of such treatment. In some embodiments, reference to a therapeutically effective amount may be a reference to an amount as measured in one or more specific tissues (e.g., a tissue affected by the disease, disorder or condition) or fluids (e.g, blood, saliva, serum, sweat, tears, urine, etc.). Those of ordinary skill in the art will appreciate that, in some embodiments, a therapeutically effective amount of a particular agent or therapy may be formulated and / or administered in a single dose. In some embodiments, a therapeutically effective amount of a particular agent or therapy may be formulated and / or administered in a plurality of doses, for example, as part of a dosing regimen.

[0268] Treatment: As used herein, the term “treatment” (also “treat” or “treating”) refers to administration of a therapy that partially or completely alleviates, ameliorates, relieves, inhibits, delays onset of, reduces severity of, and / or reduces incidence of one or more symptoms, features, and / or causes of a particular disease, disorder, or condition, or is administered for the purpose of achieving any such result. In some embodiments, such treatment can be of a subject who does not exhibit signs of the relevant disease, disorder, or condition and / or of a subject who exhibits only early signs of the disease, disorder, or condition (e.g., breast cancer, small cell lung cancer or SCLC, non-small cell lung cancer or NSCLC, neuroendocrine prostate cancer or NEPC, prostate adenocarcinoma or PRAD, etc,). Alternatively, or additionally, such treatment can be of a subject who exhibits one or more established signs of the relevant disease, disorder and / or condition. In some embodiments, treatment can be of a subject who has been diagnosed as suffering from the relevant disease, disorder, and / or condition. In some embodiments, treatment can be of a subject known to have one or more susceptibility factors that are statistically correlated with increased risk of development of the relevant disease, disorder, or condition. A “prophylactic treatment” includes a treatment administered to a subject who does not display signs or symptoms of a condition to be treated or displays only early signs or symptoms of the condition to be treated such that treatment is administered for the purpose of diminishing, preventing, or decreasing the risk of developing the condition. Thus, a prophylactic treatment functions as a preventative treatment against a condition. A “therapeutic treatment” includes a treatment administered to a subject who displays symptoms or signs of a condition and is administered to the subject for the purpose of reducing the severity or progression of the condition. EXAMPLES Example 1: Materials and Methods

[0269] This Example describes the materials and methods that were used to generate sequencing data that was then used in Example 2 to identify promoter (H3K4me3) and enhancer (H3K27ac) epigenomic activation signals at select genes for ADC target antigens or genes that modulate ADC response / resistance. Materials Plasma samples

[0270] Plasma samples (from cancer patients and healthy volunteers) were collected from commercial biobanks and stored at -80°C until use. The percentage of ctDNA in the plasma samples from cancer patients was assessed using ichorCNA which estimates the percentage of ctDNA in a sample probabilistically (see Adalsteinsson et al., Nat Commun (2017) 8(1):1324 the entire contents of which are incorporated herein by reference). Plasma samples from cancer patients with at least 5.5% ctDNA were used in the Examples described herein. Methods Chromatin immiinoprecipitation (ChIP) [0271 ]       Chromatin immunoprecipitation (ChIP) for histone marks (H3K4me3 and H3K27ac) in plasma samples was performed using methods similar to those previously described in Sadeh et al., Nat Biotechnol (2021) 39:586-598; Jang et al., Life Sci Alliance (2023) 6( 12):e202302003; and Baca et al., Nat Medicine (2023) 29:2737-2741. Briefly, about 1 mL frozen plasma was thawed and then prepared for ChIP. The thawed plasma was incubated with antibodies that bind H3K4me3 modifications or H3K27ac modifications that were previously conjugated to magnetic epoxy beads (Invitrogen) with constant mild shaking overnight. The beads were then washed and rinsed. Sequencing libraries were generated from purified immunoprecipitated sample DNA and then sequenced. ChlP-seq data analysis

[0272] ChlP-sequencing reads were aligned to the human genome build hg!9 using the Burrows-Wheeler Aligner (BWA) version 0.7.15. Non-uniquely mapping and redundant reads were discarded. MACS v2.2.7.1 was used for peak calling with a q-value (FDR) threshold of 0.01. Data quality was evaluated by a variety of measures, including total peak number, FrIP (fraction of reads in peak) score, number of high-confidence peaks (enriched > ten-fold over background), and percent of peak overlap with “■blacklist” DHS peaks derived from the ENCODE project (Amemiya et al., Sci Rep (2019) 9(1):9354). Peaks were assessed for overlap with gene features and CpG islands using annotatr. IGV was used to visualize normalized read counts at specific genomic loci. Overlap of peaks was assessed using BEDTooN and the GenomicRanges package in Bioconductor. Peaks were considered overlapping if they shared one or more nucleotide. Example 2: Identification of promoter and enhancer epigenomic activation signals at select genes for ADC target antigens or genes that modulate ADC response / resistance

[0273] To identify promoter (H3K4me3) epigenomic activation signals at select genes for ADC target antigens or genes that modulate ADC response / resistance we defined a peak within + / - Ikb of the transcription site (TSS) for each gene. If there was no peak, the entire region within + / - Ikb of the TSS was used. If there were multiple peaks or multipie TSSs the peak with the largest differential between samples from cancer patients and healthy volunteers was selected. For simplicity, these peaks or regions are called “regions of interest” below. Exemplary genomic coordinates of the H3K4me3 regions of interest for select genes for ADC target antigens are provided in Table 1. Exemplary' genomic coordinates of the H3K4me3 regions of interest for select genes that modulate ADC response / resistance are provided in Table 2. As a control, H3K4me3 epigenomic activation signals were also measured at housekeeping genes using a similar approach. Table 1: Exemplary' genomic coordinates of H3K4me3 regions of interest for select genes for ADC target antigens. Indication Gene (Target) Genomic coordinates Breast cancer TACSTD2 (TROP2) chr1:5 9,03 9,915 -5 9,043,420 Breast cancer VTCN1 (B7H4) chrl :117,751,175-117,754,040 Breast cancer NECTIN4 chrl :161,055,227-161,059,566 Breast cancer ERBB3 (HER3) chr!2:56,472,803-56,476,077 Breast cancer ERBB2 (HER2) chr 17:3 7,85 5,644-3 7,858,603 Breast cancer EPHA5 chr4:66533810-66536825 Breast cancer ROR2 chr9:94,710,609-94,713,185 Breast cancer F3 (Tissue factor) chrl :95,006,236-95,008,261 Breast cancer FOLRI chrl 1:71,903,170-71,904,632 Breast cancer CD276 (B7H3) chr 15:73,976,174-73,978,243 Breast cancer MSLN (Mesothelin) chrfo 809.511-812,651 Breast cancer SLC39A6 (LIV-1) chrl 8:33,708,080-33,711,701 Breast cancer LY75 (CD205) chr2:160,759,912-160,761,807 Breast cancer CDH6 (Cadherin-6) chr5:31,193,280-31,195,577 Breast cancer KAAGS (Kidney associated antigen 1) chr6:24,3 57,5 70-24,3 5 8,734 Breast cancer TPBG (51'4) chr6:83,072,566-83,076,13 3 Breast cancer MET (HGF receptor) chr7:1 16,311,271-116,314,304 SCLC TACSTD2 (TROP2) chr1:59,040,748-59,043,452 SCLC F0LH1 (PSMA) chrl 1:49,228,902-49,230,855 SCLC NCAM1 (CD56) chr 11:112,831,765-112,8 3 5 J 07 SCLC ERBB3 (HER3) chrl 2:56,472,687-56,476,022 SCLC CD276 (B7H3) chrl 5:73,976,062-73,978,323 SCLC MSLN (Mesothelin) chrl6:809,357-812,589 SCLC SEZ6 chrl 7:27,3 3 0,915-27,3 3 3,747 SCLC DLL3 chr 19:3 9,988,419-3 9,990,492 SCLC FAP (FAP-alpha) chr2:163,098,569-163,100,102 NSCLC TACSTD2 (TROP2) chrl :59,040,748-59,043,452 NSCLC F3 (Tissue factor) chrl :95,006,162-95,008,600 NSCLC NECTIN4 chrl :161,056,326-161,059,765 NSCLC FOLRI chr 11:71,902,93 3 -71,903,696 NSCLC ERBB3 (HER3) chr!2:56,472,687-56,476,022 NSCLC CD276 (B7H3) chrl 5:73,976,062-73,978,323 NSCLC ERBB2 (HER2) chrl7:37,855,636-37,858,255 NSCLC AXL (UFO) chr 19:41,724,440-41,727,245 NSCLC CEACAMS chr 19:42,212,213-42,216,598 NSCLC TFRC (CD71) chr3:195,807,254-195,809,869 NSCLC SLC34A2 (NaPi2b) chr4:25,656,062-25,658,914 NSCLC PTK7 (CCK4) chr6:43,043,653 -43,045,93 5 NSCLC GPNMB (NMB) chr7:23,286,381-23,288,213 NSCLC EGFR chr7:55,086,035-55,090,115 NSCLC MET (HGF receptor) chr7:116,311,591 -116,314,204 NSCLC R0R2 chr9:94,710,429-94,713,216 Table 2: Exemplary genomic coordinates of H3K4me3 regions of interest for select genes that modulate ADC response / resistance. Indication Gene (Protein) Genomic coordinates Breast cancer SH3GL1 (Endophilin A2) chrl 9:43,99,000-4,401,200 Breast cancer HSP90AA1 (HSP90) chr!4:102,604,000-102,606,200 Breast cancer SLC46A3 chrl 3:29,290,000-29,295,000 Breast cancer ABCB1 (MDR1) chr7:87,220,000-87,260,500 Breast cancer ABCG2 (BCRP) chr4:89,077,500-89,081,500 Breast cancer SLFN11 chr!7:33,698,000-33,704,000 Breast cancer CCNB1 (Cyd in Bi ; chr5:68,461,000-68,465,000 SCLC (Fig. 54) SH3GL1 (Endophilin A2) chr!9:4,399,000-4,401,200 SCLC (Fig. 54) HSP90AA1 (HSP90) chrl4:l 02,604,000-102,606,200 SCLC (Fig. 54) SLC46A3 chr 13:29,290,000-29,295,000 SCLC (Fig. 54) ABCB1 (AIDRI) chr7:87,220,000-87,260,500 SCLC (Fig. 54) ABCG2 (BCRP) chr4:89,077,500-89,081,500 SCLC (Fig. 54) SLFN11 chrl 7:33,698,000-33,704,000 SCLC (Fig. 54) CCNB1 (CyclinBl) chr5:68,461,000-68,465,000 SCLC (Fig. 53) SLFNH chr 17:3 3,697,511 -3 3,704,214 SCLC (Fig. 53) TUBB3 (Class III betatubulin) chrl 6:89,987,582-89,991,834 SCLC (Fig. 53) CCNB1 (Cyclin Bl) chr5:68,459,974-68,465,020 SCLC (Fig. 53) ABCG2 (BCRP) chr4:89,078,504-89,081,880 SCLC (Fig. 53) ABC Bl (MDR1) chr7:87,228,250-87,231,219 NSCLC SH3GL1 (Endophilin A2) chr 19:4,399,000-4,401,200 NSCLC HSP90AA1 (HSP90) chr14:102,604,000-102,606,200 NSCLC SLC46A3 chr 13:29,290,000-29,295,000 NSCLC ABCB1 (MDR1) chr7:87,220,000-87,260,500 NSCLC ABCG2 (BCRP) chr4:89,077,500-89,081,500 NSCLC SLFN11 chr!7:33,698,000-33,704,000 NSCLC CCNB1 (CyclinBl) chr5:68,461,000-68,465,000

[0274] To identify enhancer (H3K27ac) epigenomic activation signals at select genes for ADC target antigens we defined a peak within + / - lOkb of the transcription site (TSS) for each gene. If there was no peak, the entire region within + / - lOkb of the TSS was used. If there were multiple peaks or multiple TSSs the peak with the largest differential between samples from cancer patients and healthy volunteers was selected. For simplicity, these peaks or regions are called “regions of interest” below. Exemplary genomic coordinates of the H3K27ac regions of interest for select genes for ADC target antigens are provided in Table 3. As a control, H3K27ac epigenomic activation signals were also measured at housekeeping genes using a similar approach. Table 3: Exemplary genomic coordinates of H3K27ac regions of interest for select genes for ADC target antigens. Indication Gene (Target) Genomic coordinates Breast cancer TACSTD2 (TROP2) chrl :59,039,637-59,043,945 Breast cancer VTCN1 (B7H4) chrl: 117,751,834-117,754,613 Breast cancer NECTIN4 chrl :161,052,126-161,057,049 Breast cancer ERBB3 (HER3) chrl 2:56,472,605-56,478,146 Breast cancer ERBB2 (HER2) chrl7:37,859,023-37,864,576 Breast cancer EPHA5 chr4:66,526,213 -66,546,214 Breast cancer ROR2 chr9:94,707,398-94,708,365 Breast cancer F3 (Tissue factor) chrl :95,005,901-95,008,635 Breast cancer FOLRI chrl 1:71,910,584-71,911,554 Breast cancer CD276 (B 7FI 3) chrl5:73,975,752-73,978,782 Breast cancer MS LN (Mesothelin) chrl 6:801,799-802,240 Breast cancer SLC39A6 (LIV-1) chr 18:3 3,708,3 96-3 3,711,5 60 Breast cancer LY75 (CD205) chr2:160,759,445-160,762,503 Breast cancer CDH6 (Cadherin-6) chr5:31,187,037-31,187,53 7 Breast cancer KAAG1 (Kidney associated antigen 1) chr6 24.360,161-24,361,281 Breast cancer TPBG (5T4) chr6:83,073,089-83,075,684 Breast cancer MET (HGF receptor) chr7:116,310,986-116,313,609 SCLC TACSTD2 (TR0P2) chrl :59,039,532-59,043,865 SU1.C FOLH 1 (PSMA) chrl 1:49,229,019-49,230,275 SCLC NCAM1 (CD56) chrl 1:112,832,023-112,835,433 SCLC ERBB3 (HER3) chrl2:56,472,568-56,477,378 SCLC CD276 (B7H3) chr!5:73,975,958-73,978,165 SCLC MSLN (Mesothelin) chrl6:801,195-802,413 SCLC SEZ6 chr 17:27,323,2 84-2 7,3 27,03 2 SCLC DLL3 chrl 9:39,988,066-39,990,472 SCLC FAP (FAP-alpha) chr2:163,100,818-163,102,765 NSCLC TACSTD2 (TROP2) chrl :59,039,532-59,043,865 NSCLC F3 (Tissue factor) chrl :95,006,534-95,008,785 NSCLC NECTIN4 chr 1:161,052,370-161,054,583 NSCLC FOLRI chrl 1:71,906,482-71,907,263 NSCLC ERBB3 (HER3) chrl 2:56,472,568-56,477,378 NSCLC CD276 (B7H3) chr!5:73,975,958-73,978,165 NSCLC ERBB2 (HER2) chr 17:3 7,859,129-3 7,863,93 7 NSCLC AXL (UFO) chrl9:41,731,678-41,732,870 NSCLC CEACAM5 chr!9:42,210,536-42,215,398 NSCLC TFRC (CD71) chr3:195,806,219-195,810,076 NSCLC SLC34A2 (NaPi2b) chr4:25,648,085-25,668,086 NSCLC PTK7 (CCK4) chr6:43,043,211 -43,045,8 52 NSCLC GPNMB (NMB) chr7:23,285,885-23,288,750 NSCLC EGFR chr7:55,085,919-55,088,964 NSCLC MET (HGF receptor) chr7:116,311,3 63-116,314,002 NSCLC R0R2 chr9:94,710,93 3-94,712,974 NEPC / PRAD AR chrX: 66,678,734-66,865,332 NEPC / PRAD KLK3 chr!9:51,356,740-51,362,589 NEPC / PRAD KLK2 Chr 19:51,3 74,684-51,381,812 NEPC / PRAD STEAP1 Chr7:89,778,795-89,789,153 NEPC / PRAD DLL3 Chr 19:3 9,98 5,409-3 9,994,931 NEPC / PRAD SEZ6 Chrl7:27,305,415-27,356,950 NEPC / PRAD SSTR2 Chrl 7:71,156,347-71,167,970 NEPC / PRAD CHGA Chr 14:93,3 84,482-93,3 96,617 NEPC / PRAD GAPDH Chr12:6,641,904-6,645,758

[0275] A consensus map of all peaks (by MACS) was created by taking the union of all base pairs covered by any peak in any of the cancer patient or healthy volunteer plasma samples. This set of regions was then combined with the set of “regions of interest” defined above to produce a set of “enriched regions”. The number of sequencing fragments (reads) overlapping each enriched region (by at least 1 bp) were quantified for each analyte. Counts of reads in all enriched regions between experiments (any region called a peak in at least one sample) were quantile normalized together. Quantile normalized counts of reads in the regions of interest were corrected for local ChlP-seq background to improve signal-to-noise. Promoter and enhancer epigenomic activation signals were ctDNA corrected independently. To correct for ctDNA% we used the ichorCNA estimated values for each sample and regressed the log of the normalized, corrected counts against logit-transformed estimated ctDNA% with standard linear regression, and then subtracted the estimated percent of each count due to ctDNA% based on its regression weight. Corrected enhancer and promoter counts were summed for each gene to produce an integrated activation score. The mean and standard-deviation of the summed enhancer and promoter counts within the healthy volunteers were used to calculate a z-score for each patient sample, which was then logged and 0-1 scaled for the final activation score.

[0276] Fig. 1 (left-hand image) shows a qualitative track view' displaying promoter (H3K4me3) signals across breast cancer-relevant ADC target antigens (plus housekeeping genes GAPDH and ACTBY Row's represent select breast cancer patient plasma samples sorted by ichorCNA ctDNA fraction estimate or healthy volunteer plasma samples. Fig. I (right-hand image) shows a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for each ADC target antigen. Patient-specific epigenomic activation scores for each gene are represented on a white (low') to dark (high) gradient.

[0277] Figs. 2-8 show trend lines and confidence intervals for promoter signals (H3K4me3; left graph) and enhancer signals (H3K27ac; right graph) based on ctDNA% for individual breast cancer-relevant ADC target antigens.

[0278] Fig. 9 (left-hand image) shows a. qualitative track view' displaying promoter (H3K4me3) signals across SCLC-relevant ADC target antigens (plus housekeeping genes GAPDH ACTS'). Rows represent select SCLC patient plasma samples sorted by ichorCNA ctDNA fraction estimate or healthy volunteer plasma samples. Fig. 9 (right-hand image) shows a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for each ADC target antigen. Patient-specific epigenomic activation scores for each gene are represented on a white (low) to dark (high) gradient.

[0279] Figs. 10-18 show trend lines and confidence intervals for promoter signals (H3K4me3; left graph) and enhancer signals (H3K27ac; right graph) based on ctDNA% for individual SCLC-relevant ADC target antigens.

[0280] Fig. 19 (left-hand image) shows a qualitative track view displaying promoter (H3K4me3) signals across NSCLC-relevant ADC target antigens (plus housekeeping genes GAPDH and ACTS). Rows represent select NSCLC patient plasma samples sorted by ichorCNA. ctDN.A fraction estimate or healthy volunteer plasma samples. Fig. 19 (right-hand image) show’s a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for each ADC target antigen. Patient-specific epigenomic activation scores for each gene are represented on a white (low) to dark (high) gradient.

[0281] Figs. 20-35 show' trend lines and confidence intervals for promoter signals (H3K4me3, left graph) and enhancer signals (H3K27ac; right graph) based on ctDNA.% for individual NSCLC-relevant ADC target antigens.

[0282] Figs. 36-51 show additional data obtained for breast cancer-relevant ADC target antigens using breast cancer patient plasma samples and healthy volunteer plasma samples. Each figure is for a different ADC target antigen identified in the top left-hand comer of the figure (e.g., TROP2 in Figure 35, ROR2 in Figure 36, etc.). In each figure, the left-hand image show's a qualitative track view displaying promoter (H3K4me3) signals for the gene encoding the relevant ADC1 target antigen and other transcripts of interest in breast cancer for context (HEP2, EOXA1 and MYC) plus housekeeping genes (GAPDH and ACTB) as controls. Rows represent select breast cancer patient plasma samples sorted by ichorCNA ctDNA .fraction estimate or healthy volunteer plasma samples. The ER and HER2 status (based on IHC) is also shown for each sample. Blue boxes identify samples for which ER status was unknown. In each figure, the central image shows a quantitative heatmap of normalized and ctDNA-corrected epigenomic activation score (combining enhancer and promoter signals) for the ADC target antigen compared to the other transcripts of interest in breast cancer (HER2, F0XA1 and MYC}. Patientspecific epigenomic activation scores for each gene are represented on a gradient (regressed out. and scaled to the min and the max of the .ADC target antigen in these samples). In each figure, the right-hand images show trend lines and confidence intervals for the promoter signal (H3K4me3; top graph) and enhancer signal (H3K27ac; bottom graph) based on ctDNA% for the relevant ADC target antigen. Without limitation, the results in Figs. 36-51 show that epigenomic signals associated with the VTCN1, NECHN4, ERBB2, EPHA5, ROR2, CDH6 and MET genes produce the greatest differentiation among breast cancer patients and / or between breast cancer patients and healthy volunteers. Epigenomic signals associated with the TACSTD2, ERBB3, F3, CD276, LY75 and KAAG2 genes also show some useful differentiation.

[0283] Fig. 52 shows trend lines and confidence intervals for the promoter signal (H3K4me3; top graph) and enhancer signal (H3K27ac; bottom graph) based on ctDNA% for the other transcripts of interest in breast cancer for context (HER2, FOXA1 and MYC).

[0284] Fig. 53 shows promoter epigenomic activation signals at select genes known to modulate ADC response / resistance in SCLC patient plasma samples. Altered expression of these genes could impart payload resistance (SLFNM: topoisomerase inhibitor resistance, TUBB3: microtubule inhibitor resistance, CCNBT) or induce payload efflux (increase in drug efflux pumps ABCG2, ABC BE).

[0285] Fig. 54 shows promoter epigenomic activation signals at select genes known to modulate ADC response / resistance in breast, NSCLC and SCLC patient plasma samples. Altered expression of these genes could impair / ADC internalization (chaperone proteins Endophilin A2, HSP90), disrupt lysosomal processing (SLC46A3), induce payload efflux (increase in drug efflux pumps ABCG2, ABCBT) or impart payload resistance (SLENH: topoisomerase inhibitor resistance, CCEBE)

[0286] Fig. 55 (left-hand image) shows a qualitative track view displaying histone modification signal across NEPC and PRAD-relevant ADC target antigens (plus housekeeping genes GAPDH and ACTS) in plasma samples obtained from patients with NEPC or PRAD or healthy subjects. Rows represent select NEPC or PRAD patient plasma samples sorted by ichorCNA ctDNA fraction estimate or healthy volunteer plasma, samples. Right-hand top plot shows H3K27ac signal at an enhancer region associated with AR in plasma samples obtained from AR+ / NE- PRAD subjects. Also shown is a measure of H3K27ac signal at the locus, which demonstrates an ability to detect increased H3K27ac signal at the AR locus in prostate cancer patients as compared to healthy subjects. Right-hand bottom plot shows H3K27ac signal at an enhancer region associated with DLL3 in NE4- tumors. Also shown is a measure of H3K27ac signal at the locus, which demonstrates an ability to detect increased H3K27ac signal at the DLL3 locus in NEPC subjects as compared to PRAD subjects. In some embodiments, a method described herein comprises quantifying, at one or more genomic loci in a plasma sample obtained from a subject with prostate cancer, optionally in cell-free DNA (cfDNA), one or more histone modifications, wherein the one or more genomic loci are associated with a promoter or an enhancer of a gene encoding an ADC target antigen. In some embodiments, the one or more genomic loci are associated with an enhancer and are located within + / - lOkb of the transcription site (TSS) of a gene encoding an ADC target antigen

[0287] Among other things, the present disclosure described a method of treating prostate cancel’, where the method comprises determining the expression status of one or more ADC targets by quantifying one or more H3K27ac modifications at one or more enhancers of a gene encoding an ADC target antigen (e.g., one or more PRAD / NEPC associated target loci listed in Table 3). Example 3: Correlation Between Predicted Expression and Measured Expression in Cell Lines

[0288] The present Example provides data demonstrating that technologies described herein can be used to predict expression of certain ADC targets. In particular, the present Example provides data demonstrating that loci described herein can be used to predict of each of the targets indicated in Fig. 56(A), including HER2, B7-H4, ER, NECTIN4, MET, MUC1, TMRSF1, P-CAD, HER3, IB-6, EGFR, TF, R0R2, AXL, NaPi2b, FGFR2, EPHA5, GD2, GRPR, GPC-1, TROP2, LIV1, PTK-7, and RORl. Predictive ability was shown in both (1) simulated plasma samples (breast cancer cell line sequencing data diluted in silico with sequencing data from plasma samples obtained from healthy subjects), and (2) plasma samples from patients with cancer.

[0289] RNA-seq, ChlP-Seq, and MBD-seq assays were performed for a number of relevant cancer cell lines to measure RNA expression and determine H3K4me3-, H3K27ac-, and DNAme- modification patterns.

[0290] Table 4 provides genomic loci, each one of which was shown to have the indicated epigenetic modifications correlate with expression of the indi cated target of interest. These loci were determined using breast cancer cell lines and were obtained by analyzing loci within a gene of interest and within 200 kB of the gene of interest.

[0291] Fig. 56(A) provides spearman correlations coefficients (determined by comparing predicted expression vs. measured expression as determined by RNA-seq) plotted against AUC for a number of targets. These values were obtained using simulated 10% ctDNA breast cancer plasma samples (generated by diluting in silica breast cancer cell line sequencing data with sequencing data from the plasma of healthy patients). As shown, strong predictive performance was observed for a number of genes, including HER2, B7-H4, ER, NECT1N4, MET, and EGFR. These results demonstrate that loci described herein can be used to predict expression of genes that are clinically actionable.

[0292] Fig. 56(B) show's predicted and measured expression levels of B7-H4 (VTCN1) in 35 different breast cancer cell lines. As shown, a strong correlation was observed between measured and predicted expression, demonstrating the robustness of technologies described herein and their ability to accurately predict expression across a range of biological conditions.

[0293] Fig. 56(C) shows Spearman correlation coefficient values (determined by comparing predicted and measured expression) measured at different tumor fractions (ctDNA) in simulated plasma samples for 9 different targets. Simulated plasma samples were generated by diluting breast cancer cell line data, in silico with sequencing data from healthy plasma samples. This data demonstrates that technologies described herein can predict ADC target expression with high accuracy even at lower ctDNA levels.

[0294] Lastly, the foci described in Table 4 were used to predict target expression in plasma samples obtained from breast cancer patients. These predicted expression levels were then compared to expression levels that were measured using RNA-seq in matched tumor biopsy (tissue) samples. Results are shown in Fig. 57. As shown, a strong correlation between predicted and actual expression was observed in patient plasma samples, again confirming the ability of technologies described herein to predict target expression, and demonstrating that results obtained using simulated plasma sample correspond with those obtained in patient plasma samples. Example 4: Prediction of DLL3 Expression using a Single Gene Model and a Multigene Model

[0295] The present Example provides data demonstrating that loci described herein can be used to accurately predict DLL3 expression. The present Example provides results from two models --- a “Single Gene Model,” which incorporated loci that are proximal to the DLLS gene, and a “Multigene Model,” which incorporated loci that are proximal to the DLLS gene and loci proximal to other genes whose expression correlated with that of DLL3. In the present Example, “proximal” refers to loci within a gene or within 200 kB of a gene.

[0296] The loci used in the single gene model are shown in Table 5, below. Table 5: Loci Proximal to DLLS, in Which Epigenetic Modifications Correlate with DLL3 Expression Chr Start End Gene Analyte chr 19 39990062 39991061 DLL3 H3K4me3 chr 19 40319062 40320061 DLL3 H3K4me3

[0297] The genes shown to correlate with DLL3 expression were RAB31P (RAB3 A Interacting Protein), PAK5 (p21 (RAC1) activated kinase 5), and ITPR1PL2 (ITPRIP like 2). Proximal regions to each of these genes andDZZd, which were used in the multigene model are shown in Table 6, below. Table 6: Loci Proximal to DLLS, RAB3IP, PAK5 and ITPRIPL2, in Which Epigenetic Modifications Correlate with DLL3 Expression Chr Start End Gene Analyte chr 19 39990062 39991061 DLL3 H3K4me3 chr 19 40319062 40320061 DLL3 H3K4me3 chr 12 70091133 70092132 RAB3IP H3K4me3 chr 12 70092133 70093132 RAB3IP H3K4me3 chr 12 70135133 70136132 RAB3IP H3K4me3 chr 12 70406133 70407132 RAB3IP H3K4me3 chr20 9818072 9819071 PAK5 H3K4me3 chr 16 18995335 18996334 ITPRIPL2 H3K27ac chr 16 19008335 19010334 ITPRIPL2 H3K27ac chr 16 19119335 19120334 ITPRIPL2 H3K27ac chr 16 19123335 19124334 ITPRIPL2 H3K27ac chr 16 19133335 19134334 ITPRIPL2 H3K27ac chr 16 19144335 19145334 ITPRIPL2 H3K27ac chr 16 19214335 19215334 ITPRIPL2 H3K27ac chr 16 19421335 19423334 ITPRIPL2 H3K27ac chr 16 19440335 19441334 ITPRIPL2 H3K27ac

[0298] In each of Tables 5 and 6, “Chr.,” “Start,” and “End” refer to the genomic position (positions shown relative to the hgl9 genome), “Gene” refers to the gene that the indicated loci is proximal to, and “analyte” refers to the epigenetic modification at the loci that correlates with DLL3 expression.

[0299] hi silica samples were prepared and DLL3 expression levels predicted using the multi gene model and the single gene model. Predicted values were compared against actual expression values and Pearson’s coefficients were determined. Results are shown in Fig. 58. As shown, both the single gene and the multigene model accurately predicted DLL3 expression. The Multigene Model provided improved precision as compared to the Single Gene model, as a higher correlation with 30% ctDNA predictions was maintained at lower ctDNA%. DLL3 expression prediction was also found to correspond with models predicting likelihood of a subject having SCLC (data not shown), as expected, and further demonstrating that DLL3 models provided herein can accurately predict DLL3 expression. Example 5: Predicting Expression of NEPC and PRAD Markers in Patient Plasma Samples

[0300] The present Example provides further data demonstrating that technologies provided herein can be used to measure expression of ADC targets. In particular, the present Example demonstrates that technologies described herein can be used to measure expression of DLLS, SEZ6, and CHGA in subjects having NEPC or PRAD.

[0301] Plasma samples were obtained from subjects with NEPC or PRAD. DLL3, SEZ6, and CHGA are markers of NEPC and are not highly expressed in PRAD. Promoter regions having H3K4me3 signal that correlated with expression of each of these markers was determined. For each sample, promoter (H3K4me3) signal at each of these promoter regions was measured and corrected for ctDNA%. Results are provided in Fig. 59(A). As shown, promoter signal for each of DLL 3, SEZ6, and CHGA was increased in NEPC subjects as compared to PRAD subjects, demonstrating that technologies provided herein can be used to measure expression of each of these targets in subjects with prostate cancer. Expression of KLK3 and KLK2 was also measured as control, as these genes are expressed in PRAD but not NEPC. Both KLK2 and KLK3 expression was found to be elevated in PRAD as compared to NEPC, again demonstrating that technologies provided herein can be used to measure ADC target expression.

[0302] As DLLS, SEZ6, and CHGA are each markers of NEPC, they can also be used to classify subjects as having NEPC or PRAD, which can be useful, e.g., for diagnosing a subject, informing therapy selection, and / or monitoring disease progression. A score for distinguishing PRAD and NEPC was developed by combining DLL3, SEZ6, and CHGA promoter signal. Results are provided in Fig. 59(B). As shown, a clear difference in NEPC / PRAD score was observed in the two patient populations, demonstrating that technologies provided herein can be used to classify NEPC and PRAD subjects. Also, as shown, several subjects were found to have elevated DLL3 / SEZ6 / CHGA promoter signal, despite having been diagnosed with PRAD. This result suggests that epigenetic markers may provide an alternative and / or complementary method for diagnosing subjects that, in some embodiments, may provide more accurate results as compared to histology-based methods for diagnosing subjects. TABLES

[0303] Table 4 describes loci with epigenetic modification levels that correlate with expression of certain ADC targets. “Target Name” indicates an ADC target, “Gene” indicates a gene in which the indicated epigenetic modification is correlated with expression, “Direct of Effect” refers to whether the association is positive or negative (meaning whether epigenetic modifications increase or decrease as expression increases), “Chromosome No.,” “Start,” and “End” provide the genomic location of the loci, and “Width” refers to the length of the genomic loci. For all of the provided genomic loci, sequence location is shown relative to the positive strand of the hgl9 genome. Assays described herein, however, can use sequence reads from the positive and / or negative strands. Tabie 4: Exemplary Genomic Loci With Epigenetic Modifications That Correlate With Expression of ADC Targets of Interest Gene Analyte Direction of Effect Chromosome No. Start End Width Target Name AXI. H3K4™e3 PC'S chrl 9 41698321 41698712 392 AXL AXL H3K4me3 POS dr!9 41724227 41727980 3754 AXL AXL I13K4me3 POS chrl9 41729389 41729353 470 .AXL AXL H?.K4me3 POS chr!9 41732920 41733139 220 AXL. .AXL H3K4me3 PC'S chrl 9 41836833 41837114 282 AXL AXL H3K27ac chrl 9 41698938 41699373 436 AXL AXL H3K27«o POS chrl9 41723894 41733253 9360 AXL AXL H3K27ac POS chrl 9 41735224 41735716 493 .AXL, AXL H3K27ao POS chrl 9 41736702 41737193 492 AXL AXL H3K27ac chrl 9 41897620 41898115 496 AXL AXL MBD POS chrl 9 41712593 41713535 993 AXL AXL AXL MBD MBD POS PC'S chrl 9 chrl 9 41715077 41738700 41716070 41739187 994 483 AXL, AXI. AXL MBD dr] 9 41743561 41743961 401 AXL AXL MBD POS chrl 9 41758726 41759098 373 AXL AXL MBD POS chrl 9 41831432 41834868 3437 A.XL AXL MBD POS chrl 9 41844385 41844878 494 axl AXL MBD POS chrl 9 41845373 41845S67 495 AXL AXL MBD POS chrl 9 41846856 41847350 495 AXL AXL MBD POS chrl 9 418d7845 4]848338 494 AXL, 'AXL MBD POS chrl 9 41850317 41851798 1482 AXL AXL MBD POS chrl 9 41853777 41854764 988 AXL .XXL MBD POS chrl 9 41855260 41855753 494 AXL AXL MBD POS chrl 9 41867576 41868059 484 AXL, AXL MBD PC'S chrl 9 41872898 41873381 484 AXL AXL MBD dr] 9 41895267 41895731 465 AXL AXL MBD POS chrl 9 41902159 41902637 479 AXL AXL. MBD POS chrl 9 41932820 41933287 468 AXL, .'XXI.. MBD POS chrl 9 41933756 41934223 468 AXL AXL MBD POS chrl 9 41937500 41937968 469 AXI. AXL MBD POS chrl 9 41942909 41943315 407 AXL AXL MBD NEG chrl 9 41595775 41596710 936 AXL AXI. MBD NEG chrl 9 41731547 41732632 1036 AXI. AXL MBD NEG chrl 9 41829468 41829958 491 AXL AXL MBD NEG chrl 9 41830941 41831431 491 AXL B4GALNTI H3K4sc3 POS chrl 2 57848948 57849064 117 GD2 E4GALNTI H3K4me3 POS chrl 2 58005974 58006342 369 GD2 B4GALNT1 H3K4me3 POS dr] 2 58016493 58016889 397 GD2 B4GALNT1 H3K4me3 POS chrl 2 58025253 58025520 268 GD2 B4GALNTI H3K4me3 POS chrl 2 58119137 58120049 913 GD2 B4GALNT1 H3K4me3 POS chrl 2 58120610 58121752 1143 GD2 B4GALNT1 H3K4me3 chrl 2 58130867 58131311 445 GD2 B4GALNT1 H3K4me3 POS dr 12 58132722 58133100 379 GD2 E4GALNU H3K4w.e3 POS chrl 2 58144718 58144992 275 GD2 B4GALNT1 H3K4oie3 POS chrl 2 58164780 58165057 273 GD2 B4GALNT1 H3K27ao dr] 2 57848405 57849392 988 GD2 B4GALNT1 I-13K27ac POS chrl 2 58023884 53024341 458 GD2 B4GALNT1 H3K27ac POS chrl 2 58025718 58027552 1835 GD2 B4GALNTI H3K27ao PGS chrl 2 58116746 58117736 991 GD2 B4GALNT1 GGK27ao PGS chrl 2 58119224 58121701 2478 GD2 B4GALNT1 H3K27ao POS dirl 2 58159547 58160033 487 GD2 B4GALNTI II3K27ac POS chrl2 58161009 53161495 487 GD2 B4GALNTI MBD POS chrl 2 57825547 57825926 380 GD2 E4GALNTI MBD PUS chrl 2 57873699 57874196 498 GD2 B4GALNT1 MBD POS chrl 2 57907963 57908413 451 GD? B4GALNT1 MBD POS chrl 2 57910669 57911119 451 GD2 B4GALNTI MBD POS chrl2 57915166 579161-5 950 GD2 B4GALNTI MBD POS chrl 2 57956555 57956771 217 GD2 B4GALNTI MBD POS Girl 2 57962339 57962769 43 ■ GD2 B4GALNT1 MBD POS chrl 2 58011572 58012069 498 GD2 B4GALNTI E4GALNTI MBD MBD POS POS chrl 2 chrl 2 58020197 3SUZU / ZZ 58020532 58022290 1569 GD2 B4GALNT1 MBD POS dr] 2 58142639 58142999 36i GD2 B4GAL.A11 MBD POS chrl 2 58189838 58190279 GD2 B4GALNT1 MBD POS chrl 2 58194227 58394549 323 GD2 E4GALNT1 MBD NEG chrl 2 57870219 57870715 497 GD2 B4GALNT1 MBD NEG chrl 2 57943272 57944765 1494 Grp B4GALNT1 MBD NEG chrl 2 58025604 58026883 1280 GD2 B4GALNT1 MBD NEG chrl 2 58150348 58150814 467 GD2 CCR2 H3K4me3 POS chr3 46204704 46206123 1420 CCR2 CCR2 H3K27ao POS dir3 46204332 46205790 1459 UCR2 CCR2 H3K27ac POS chrl 46468349 46468832 484 CCR2 CCR2 H3K27ac POS chr3 46469802 46471737 1936 CCR2 CD274 lBK4mc3 POS chr9 5510050 5512138 2089 PD-L1 CD274 H3K27ac POS dr9 5433308 5434756 ■449 PD-Ll CD274 H3K27ac POS chr9 5508714 5509179 466 PD-L1 CD274 H3K27ac POS chr9 5511702 5512659 958 PD-Ll CD274 H3K27ao POS chr9 5621096 5621569 474 PD-Ll CD274 H3K27ac POS chr9 5622045 5622992 948 PD-Ll CD274 H3K27ac POS chr9 5632241 5632696 456 PD-Ll CD274 MBD POS chr9 5304268 5305000 733 PD-Ll CD274 MBD POS chr9 5339634 5340091 458 PD-Ll CD274 MBD POS chr9 5379837 5380574 738 PD-Ll CD274 MBD POS chr9 5394174 5394588 415 PD-Ll CD274 MBD POS chr9 5417552 5417893 342 PD-Ll UDz / 4 MBD POS chr9 5482264 5482942 679 PD-Ll 6792.74 MBD POS dir9 5487017 54S74SS 472 PD-1.1 CD274 MBD POS chr9 5487732 5488194 463 PD-Ll CD274 MBD POS chr9 5515689 5516623 935 PD-Ll CD274 MBD POS chr9 5619199 5619656 458 PD-Ll CD274 MBD POS chr9 5626110 5626908 799 PD-Ll CD276 H3K4me3 POS chrl 5 73978301 73979397 1097 B7-M3 CD276 H3K4w.e3 POS chrl 5 74024268 74025054 787 B7-H3 CD276 H3K4«-.e3 POS chrl 5 74045436 74045854 419 B7-H3 CD276 H3K27ac POS chrl 5 73976223 73980105 3883 B7-H3 CD276 H3K27ac POS chrl 5 73981076 73981561 486 B7-H3 CD276 H3K27ac POS chr 15 73988185 73990653 2469 137-1-13 CD276 H3K27ao PGS chrlS 73991642 73992135 494 B7-H3 CD276 H3K27aa PGS chrl 5 73994605 73995098 494 B7-H3 CD276 H3K27ao POS chrl 5 73996086 73996579 494 B7-H3 CD276 I13K27ac POS chrlS 74089489 74090485 997 B7-II3 CD276 H3K27ac POS chrl 5 74091482 “MrjQJi .jT] 2990 B7-H3 CD276 H3K27ac PC'S chrlS 74101948 74103442 1495 B7-H3 CD276 MBD POS chrl 5 73805365 73805594 230 B7-H3 CD276 MBD POS chrl 5 73988540 73989025 486 B7-H3 CD276 MHD POS chrl 5 7-40.43873 74045691 1819 137-113 CD44 H3K4me3 POS chrll 35103724 35104617 894 CD44 CD44 H3K4me3 POS chrll 35166638 35167040 403 CD44 CD44 H3K27ac POS chrl 1 35019586 35020082 497 CD44 CD44 H3K27ac POS chrll 35029527 35033503 3977 CD44 CD44 H3K27ac POS chrll 35034001 35034497 497 CD44 CD44 H3K27ao POS chrll 35034995 35035988 994 CD44 CD44 H3K27ac POS chrll 35061939 35062936 998 CD44 CD44 H3K27ao POS chrll 35099402 35099891 490 CD44 CD44 H3K27ac PUS chrll 35103318 35106743 3426 CD44 CD44 H3K27ac POS chrl 1 35107234 35107722 489 CD44 CD44 H3K27ac POS chrll 35108702 35111149 2448 CD44 CD44 H3K27ac POS chrll 35119318 35123166 3849 CD44 CD44 H3K27ao POS chrll 35125092 35125572 481 CD44 CD44 H3K27ao POS chrll 35137029 35137525 497 GD44 CD44 H3K27ac POS chrll 35201364 35202360 1497 CD44 CD44 H3K27ac POS chrll 35203860 35205855 1996 CD44 CD44 H3K27ac POS chrll 35209351 35209849 499 CD44 CD44 H3K27ac POS chrll 35212346 35212844 499 631744 CD44 H3K27ac POS chrll 35213844 35214342 499 CD44 (7).-14 H3K27ac POS chrll 35239640 35240106 467 CD44 CD44 H3K27ao POS chrll 35240575 35241042 468 CD44 CD44 H3K27ac POS chrl 1 35241511 35241978 468 CD44 CD44 I-I3K27ac POS chrll 35358362 35359774 1413 CD44 CD-14 MED POS chrll 35149761 35150218 458 UD44 ('D-D AIRD POS chrl 1 35169086 35169961 876 CD44 0044 MBO POS chrll 35259743 35260198 456 CD44 CD44 MBD POS chrll 35261570 35262483 914 CD44 CD44 MBO POS chrll 35439973 35440877 905 CD44 CD44 MBD POS chrll 35453679 35453975 297 CD44 COM3 H3K4me3 POS chrl 6 68562467 6856281S 352 P-CAD CDH3 H3K4me3 POS chrl 6 68678092 68678539 448 P-CAD CDH3 H3K4me3 POS chrl 6 6868021.5 68681888 1674 P-CAD CDH3 H3K4me3 POS chrl 6 68692191 68692545 4^5 P-CAD CDH3 H3K4me3 POS chrl 6 68770475 68770832 358 P-CAD CDH3 H3K4me3 POS chrl 6 68778101 68779584 1484 P-CAD CDH3 H3K27ac POS chrl 6 68508698 68509629 932 P-CAD CDH3 H3K27ac POS chrl 6 68512892 68513357 466 P-CAD COM3 H3K27ac POS chrl 6 68524489 68525984 1496 P-CAD CDH3 H3K27ac POS chrl 6 68526483 68526981 499 P-CAD CDH3 H3K27ac POS chrl 6 68669804 68671303 1500 P-CAD CDH3 H3K27ac PGS chrl 6 68674804 68675803 1000 P-CAD CDH3 H3K27ac PGS ohri6 68678304 68681303 3000 P-C AD CDH3 H3K27ao POS chrl 6 68685304 68686303 1000 P-CAD CDII3 I13K27ac POS chrlS 68689303 6869oj02 4000 P-CAD CDH3 H3K27ac POS chrlS 68698303 68703802 5500 P-CAD CDH3 H3K27ac PUS chrlS 68706303 68706802 500 P-CAD COM3 H3K27ac POS chrl 6 68708802 68710801 2l>00 P-CAD CDH3 H3K27ac POS chrlS 68712302 68712801 500 P-CAD CDH3 H3K27ac POS chi-16 68714302 68714801 500 P-CAD CDH3 H3K27ao POS chrl 6 68719302 68720301 1000 P-CAD CDH3 H3K27ao POS chrl 6 68740382 68742864 2483 P-CAD CDH3 H3K27ac POS chrlS 68765939 68766436 498 P-CAD CDH3 H3K27ac POS chrl 6 68770422 68772911 2490 P-CAD CDH3 H3K27ac POS chrl 6 68775403 68776896 1494 P-CAD COM3 H3K27ao POS chrl 6 68777893 68779885 1993 P-CAD COM3 H3K27ac POS chrlS. 68780384 63781379 996 P-CAD CDH3 H3K27ao POS chrlS 68787856 68791840 3985 P-CAD CDH3 H3K27ao PUS chrl 6 68793833 68796323 2491 P-CAD COM3 H3K27ac POS chrlS 68811765 68813259 ■495 P-CAD CDH3 H3K27ac POS chrlS 68823720 68825213 1494 P-CAD CDH3 H3K27ac POS chrl 6 68832188 68832685 498 P-CAD CDH3 MBD POS chrl 6 68480452 68481831 1 MU P-CAD CDH3 MBD POS chrl 6 68544196 68544491 296 P-CAD CDH3 MBD POS chrlS 68570111 68570594 484 P-CAD CDH3 MBD POS chrl 6 6857284) 68574172 1332 P-CAD CDI-B MBD POS chrl 6 68675878 68677170 ■ 293 P-CAD CDH3 MBD POS chrl 6 68677802 68678297 496 P-CAD CDH3 MBD POS chrlS 68721854 68722754 901 P-CAD CDH3 MBD POS chrl 6 68731.449 68731833 385 P-CAD CDH3 MBD POS chrl 6 68739220 68739718 499 P-CAD COM3 MBD POS chrlS 68745203 68745626 424 P-CAD CDH3 MBD POS chrl 6 68747908 68748360 453 P-CAD CDH3 MBD POS chrlo 68786772 68787760 989 P-CAD CDH3 MBD POS chrl 6 68799139 68799601 463 P-CAD COM3 MBD POS chrl 6 68800528 68800990 463 P-CAD COM3 MBD POS chrl 6 68825956 68826814 859 P-CAD CDH3 MBD POS chrl 6 68838040 68838461 422 P-CAD CDH3 MBD POS chrl 6 68847532 68848013 482 P-CAD COM3 MBD POS chrl 6 68882704 68883156 453 P-CAD CDH3 MBD NEG chrl 6 68678298 68678793 496 P-CAD CDH3 MBD NEG chrl 6 68679786 68680281 496 P-CAD CDH6 MBD POS chr5 31193172 3H93597 426 CDH6 CDH6 MBD POS chr5 31505887 31506351 465 CDH6 CDH6 MBD POS chr5 31508898 31509339 442 CDH6 CDH6 MBD NEG chrS 31194024 31195302 1279 CDH6 CEACAM5 H3K4me3 POS chrl 9 42212577 42213507 931 CEACAM5 CEACAM5 H3K4me3 POS chrl 9 42213973 42215834 ■862 CEACAM5 CEACAM5 H3K4me3 POS chrl 9 42254081 42254519 439 CE / iCAMS CEACAM5 H3K4me3 POS chrl 9 42258961 42263397 4437 CEACAM5 CEACAM5 H3K4me3 PGS chrl9 42349133 42349573 441 CEACAM5 CEACAM5 H3K27ac PGS chrl 9 42211383 42212878 1496 CEACAM5 CEACAM5 H3K27ac POS dr] 9 42237544 42240024 2481 CEACAM5 CEACAM5 II3K27ac POS chrl9 42252920 42256225 3306 CEACAM5 CEACAM5 H3K27ac POS chrl9 42257642 42258114 473 CEACAM5 CEACAM5 H3K27ac PC'S chrl 9 42276255 ■42z,83z,2z, 6968 CEACAM5 CEACAM5 H3K27ac POS chrl 9 42283720 42284217 498 CEACAM5 CEACAM5 H3K27ac POS chrl9 42290688 42291185 498 CEACAM5 CEACAM5 H3.K2,7ac POS chrl9 42292181 42293176 996 CEACAM5 CEACAM5 H3K27ao POS chrl 9 42295167 42296660 1494 CEACAM5 CEACAM5 H3K27ac POS chrl 9 42349092 42349504 413 CEACAM5 CEACAM5 H3K27ac POS chrl 9 42408853 42409325 473 CF.ACAM5 CEACAM5 MBD POS chrl 9 42028319 42028788 470 CEACAM5 CEACAM5 MBD POS chrl 9 42070537 42071032 496 CEACLAM5 CEACAM5 MBD POS dr!9 42150384 42151098 715 CEACAM5 CEACAM5 MBD POS chrl 9 42270493 42270957 465 CEACAM5 CEACAM5 MBD POS chrl 9 42289684 42290640 957 CEACAM5 CEACAM5 MBD POS chrl 9 42312503 42313372 870 CEACAM5 CEACAM5 MBD POS chrl 9 42386432 42386925 494 CEAC.AM5 CEACAM5 MBD POS chrl 9 42431571 42432948 1378 CEACAM5 CEACAM5 MBD NEG chrl9 42365586 42366493 908 CEACAAD CEACAM5 MBD NEG chrl 9 42387420 42387914 495 CEACAM5 CLDN6 H3K4me3 POS drl 6 2905997 2906485 489 CLDN6 CLDNS K3K4:ne3 POS clirlS 2924203 2924995 793 CLDNS CLDN6 H3K4me3 POS chrl 6 2934307 2934664 358 CLDN6 CLDN6 H3K4me3 POS chrl 6 2963212 2963567 356 CLDN6 CLDN6 H3K4me3 POS dr] 6 3012501 3012947 447 CLDN6 CLEW H3K4me3 POS chrl 6 3015927 3016616 690 CLDN6 CLDNS H3K4nw3 POS chrlo 3039530 3043394 3865 CL.DM6 CLDN6 H3K4me3 POS chrl 6 3044362 3045327 966 CLDN6 CLDNS H3K4mc3 POS chrl 6 3220285 3220722 438 CLDN6 CLDNS II3K4me3 POS chrl 6 32’G 799 3222166 368 CLDN6 CLDN6 H3K4me3 POS chrlo 3239345 3239826 482 CL.DN6 CLDN6 IT3K4me3 POS chrl 6 3240791 3242237 : 447 CJDN6 CLDN6 H3K27ac POS chrl 6 2905632. 2907118 1487 CLDN6 CLEW H3K27ac POS chrlS 2924224 2925102 879 CLDN6 CLDNS H3K27ac POS chrl 6 2946340 2950306 3967 CLDN6 CLEW H3K27ao POS chrl 6 2965554 2966995 1442 CLEW Cl ,DN6 H3K27ac POS chrl 6 2969878 481 C1.DN6 CLDNS l-I3K27ac POS chrl 6 3009182 3009680 499 CLDN6 CLDN6 H3K27ac POS chrl 6 3010679 3011177 499 CL.DN6 CLDN6 H3K27ao POS chrl 6 3011677 3020659 8983 CLDN6 CLEW H3K27ac POS dr] 6 3026648 3027645 998 CLDN6 CLEW H3K27ac POS chrl 6 3048472 3048962 491 CLDN6 CLEW H.3K27ac POS chrlo 3053377 3053867 491 CLDN6 CLDN6 H3K27ac POS chrl 6 3078398 3078879 482 CLDN6 CLDNS H3K27ao POS dr! 6 3149622 3150111 490 CLDN6 CLDN6 H3L127aG POS chrlS 3150601 3151090 490 CLDN6 CLDN6 H3K27ac POS chrl 6 3155496 3157453 1958 CLDN6 CLDNb H3K27ao BOS chrl 6 3I6I37G 3162348 979 CLDN6 CLDN6 D3K27ao POS chrl 6 3181943 3183436 1494 CLDN6 CLDN6 H3K27ac POS chrl 6 3201735 3202223 489 CLDN6 CLDN6 I13K27ac POS chrlS 3206627 3207116 490 CLDN6 CLDN6 H3K27ac POS chrl 6 3210545 36]?4?7 1878 CLDN6 CLDN6 H3K27ac POS chr 16 3216080 3217020 941 CLDN6 CLDN6 H3K27ac POS chrl 6 3217491 3219372 1882 CLDN6 CLDN6 H3K27ac POS chrl 6 3232448 3232936 489 CLDN6 CLDN6 H3K27ac POS chi'16 3238686 3239181 496 CLDN6 CLDN6 H3K27ao POS chrl 6 3241165 3242156 992 CLDN6 CLDN6 MBD POS chrl 6 2892276 2892727 452 CLDN6 CLDN6 MBD POS chrlS 3079369 3079756 388 CLDN6 CLDNb CLDNb MBD MBD POS POS chrl 6 chrl 6 3201579 3209005 3209468 1448 464 CLDN6 CLDN6 CLDN6 MBD POS chrl 6 3224424 3225881 ■458 CLDN6 CLDN6 MBD POS chrlS. 3232875 3234830 1956 CLDN6 CLDN6 MBD POS chrl 6 3237765 3239231 1467 CM7N6 CLDN6 MBD NEG chr 16 3012925 3013368 444 CLDN6 DLL,3 H3K4me3 POS chrl 9 39924837 39925204 368 DM- DLL3 H3K4me3 POS chrl 9 39934413 39934912 500 DLL3 DLL3 H3K4me3 POS chrl 9 39972689 39973010 a a DI.L3 DLL3 H3K4me3 POS chrl 9 39988307 39990315 2009 DLL3 DLL3 H3K4me3 POS chrl 9 39998479 39998953 475 DLL, 3 DLL3 H3K4ine3 POS chrl 9 40005310 40006591 1282 DLLS DLL3 H3K27ac POS chrl 9 3981021) 39811192 982 DLL3 DLLS H3K27ac POS chrl 9 39934036 39934525 490 DLLG DLL3 MB.D POS chrl 9 39949306 39949799 494 DLL, 3 DLL3 MBD POS chrl 9 39988687 39989624 938 DLL3 DLL3 MED POS chrl 9 40018289 40018740 452 DLL3 DLL3 MBD NEG chrl 9 39824759 39825249 491 DLL3 DLL, 3 MBD NEG- ON 9 39990094 39990562 469 DLL, 3 DLL3 MBD NEG chrl 9 39997268 39998120 853 DLL3 DLLS MBD NEG chrl 9 40050279 40050640 362 D1.L3 EGFR FI3K4^e3 POS ohr7 54898873 54899790 91 8 EGFP. EGFR H3K4me3 POS chr7 54900250 54901167 918 EGFR EGFR H3K4a;e3 POS chr7 55088679 55090335 1657 EGFR EGFR H3K4me3 POS chr7 55153982 55154905 924 EGFR EGFR IBK27ac POS chr7 54898604 54900045 1442 EGFR FGFR H3K27ac POS dir7 54900526 54901006 481 EGFR EGFR H3K27ac POS chr7 55000838 55001248 411 EGFR EGFR H3K27ac POS chr7 55013866 55015346 1481 EGFR EGFR H3K27ao POS chr? 55034932 55036322 1391 EGFR EGFR H3K27ac POS chr7 55053182 55054118 937 EGER EGFR H3K27ac POS chrl' 55086326 55090700 4375 EGFR EGFR H3K27ac POS chr7 55092I6G 55095075 2916 EGFR EGFR D3K27ac POS chr? 55101396 55101881 486 EGFR EGFR F{3K27ac POS chr7 55111304 55112801 ■498 EGFR EGFR F13K27ac POS chr7 55113801 55116797 2997 EGFR EGFR H3K27ac POS chr7 55118297 55123790 5494 EGFR EGFR H3K27ao PGS chr7 55128787 55129285 499 EGFR EGFR D3K27ao PGS ohr7 55131284 55135279 3996 EGFR EGFR H3K27ac POS vbr7 55140276 55142772 2497 EGER EGFR I13K27ac POS chr7 55146270 55146763 499 EGER EGFR EGK27ac POS chr7 55153263 55155260 1998 EGFR EGFR H3K27ac PC'S chi 7 55164252 55164751 500 EGFR EGFR H3K27aa POS chr7 55176281 55181734 5454 EGFR EGFR FI3K27ac POS chr7 55186197 55190658 4462 EGFR EGFR H3K27ac POS chr7 55192146 55193137 992 EGFR EGFR H3K27ao POS chr7 55193634 55194128 495 EGFR EGFR H3K27ao POS chr7 55195121 55202557 7437 EGFR EGFR FI3K27ac POS chr7 5524992! 55250419 499 EGFR EGFR EGFR H3K27ac H3K27ac POS POS chr7 chr? 55251417 55252914 55251915 55255905 499 2992 EGFR EGFR EGFR MBD POS chr7 54902982 54903459 478 EGFR EGFR MBD POS chr7 54904417 54905373 957 EGFR EGFR MBD POS chr7 54956061 54957012 952 EGFR EGFR MBD PUS chi 7 55038066 55038885 6ZU EGFR MED POS chr7 55049201 55049657 457 EGFR EGFR MBD POS chr7 55049972 55050392 421 EGFR EGFR MED POS chr7 55085588 55086543 956 EGFR EGFR MBD POS chr7 55089413 55090369 957 EGFR EGFR MBD POS chr7 55105693 55105969 277 EGFR EGFR MBD POS chr7 55108613 55109537 925 EGFR EGFR MBD POS chr7 55110001 55110926 926 EGFR EGFR MBD POS chr7 55112316 55112778 463 EGFR EGFR MBD POS dir7 55122732 55123196 465 EGFR EGFR MBD POS £hr7 55124127 55125057 931 EGFR EGFR MBD POS chr7 55125523 55126453 931 EGFR EGFR MBD POS chr? 55134045 55134485 441 EGFR EGFR MBD POS ^■7 5513492.7 55135367 441 EGFR EGFR MBD POS chr7 55135906 55136334 429 EGFR EGFR MBD POS chr7 55138051 55138909 859 EGFR EGFR MBD POS chr7 55148956 55149429 474 ECSFR EGFR MBD POS chr7 55152566 55153533 968 EGFR EGFR MBD POS chi'7 55161330 55161780 451 EGFR EGFR MBD POS chr7 55163817 55164737 921 EGFR EGFR MBD POS chr? 55168055 55169822 1768 EGFR FGFR MBD POS cbr? 55210958 5521 1212 255 EGFR EGFR MBD POS chr7 55212677 55213119 443 EGFR EGFR MBD POS chr7 55220985 55221395 411. EGFR EGFR MBD POS chr? 55225427 55225876 450 EGFR EGFR MBD POS chr7 552.46978 55247402 42,5 EGFR EGFR MBD POS chr'7 55248254 55248679 426 EGFR EGFR MBD POS c.hi‘7 55250140 55250613 474 EGFR EGFR MBD POS chr 7 55251991 55252340 350 EGFR EGFR MBD POS chr7 55255761 55257728 1968 EGFR EGFR MBD POS chr 7 55262130 55262613 484 EGFR EGFR MBD POS chr7 55269745 55270030 286 EGFR EGFR MBD PGS chr7 55315771 55316065 295 EGFR EGFR MBD POS chr7 55322035 55322530 496 EGFR EGFR MBD POS chr7 5532.3027 55323522 496 EGFR EGFR MBD NEG chr7 55086544 55038934 2391 EGFR EPHA5 H3K4me3 POS chr4 66533670 66535990 2321 EPHA5 EPHA5 H3K4me3 PC'S chr4 66536340 66537045 706 EPHA5 EPHA 5 H3K27ac POS chM 66534268 66536532 2265 EPHA 5 EPHA5 MBD POS chr4 66356150 66356534 385 EPHA5 EPHA5 MBD POS chr4 66533691 66534657 967 EPHA5 EPHA5 MBD POS chr4 66536110 66537077 968 EPHA5 ERB.B2 H3K4me3 POS chrl 7 37689538 37691531 1994 HER? ERBB2 H3K4me3 POS chrl 7 376970!5 37697513 499 HFR2 ERBB? EREB? H3K4me3 H3K4me3 POS POS chrl 7 c hr 17 37704991 37712468 37706485 37713464 1495 997 HER? HER? ERBB2 H3K4me3 POS chrl 7 3772.2935 37723433 499 FER2 ERBB2 H3K4me3 POS chrl7 37723932 3??25925 ■994 HER2 ERBB2 H3Kfee3 POS chrl 7 37726425 -,7777471 997 HER?. ERBB2 H3K4me3 POS chrl? 37728419 37729415 997 HER? ERBB2 H3K4me3 POS chrl 7 37730663 37731656 994 HER2 ERBB2 H3K4me3 POS chrl 7 37734639 37735632 994 HER2 ERBB 2 H3K4mc3 POS chrl 7 37736130 37736626 497 HER? ERBB2 H3K4me3 POS chrl 7 37738118 37738614 497 HER2 ERBB2 H3K4me3 POS chrl 7 37739112 37739608 497 HER2 ERBB2 K3K4:ne3 POS chrl 7 37747562 37749052 1491 1-IER2 ERBB2 H3K4me3 POS chrl 7 37749550 37750046 497 HER? EREB? H3K4me3 POS chrl 7 37751041 37756508 5463 HER? ERBB2 H3K4me3 POS chrl 7 37757006 37759490 2485 HER2 ERBB2 H3K4me3 POS chrl 7 37761479 37766449 4971 HER2 ERBB?. H3.K4nw3 POS chrl 7 37767444 7-7-7-7^40^ 5965 HER? ERBB2 H3K4me3 POS chrl 7 37775194 37780545 5352 HER2 ERBB2 H3K4mc3 POS chrl 7 37781520 37782005 486 HER2 ERBB2 H3K4me3 POS chrl 7 37787186 37792437 s?s? HER2 ERBB? H3K4me3 POS chrl 7 37795145 37798112 2968 HER? ERBB? FBK4nie3 POS chrl 7 37798608 37801576 2969 HER? ERBB2 H3K4me3 POS chrl 7 37802.567 37805535 2969 HER2 ERBB? H3K4ine3 POS chrl 7 37806525 37810978 4454 HER? ERBB2 H3K4me3 POS chrl 7 37811969 37815926 3958 HER?. ERBB? H3K4me3 POS chrl 7 37818896 37823349 4454 HER? FRBB2 H3K4me3 POS chrl 7 3782.6571 37837469 ■ 0899 HF.R2 ERBB2 H3K4me3 POS chrl 7 37839452 37843415 3964 HER2 ERBB? H3K4me3 POS chrl 7 37845501 37845997 497 HER? ERBB2 H3K4me3 POS chrl 7 37848986 37849482 497 HER2 ERBB2 H3K4me3 POS chrl 7 37850977 37855955 4979 HER2 ERBB2 H3K4me3 POS chrl 7 37857813 37869253 11441 HER2 ERBB? H3K4me3 POS chrl 7 37870746 37873730 2985 HER? EREB? H3K4me3 POS chrl? 3 7873223 3 7877212 1990 HER? ERBB2 H3K4me3 POS chrl 7 37878208 37885669 7462 HER2 ERBB2 H3K4me3 POS chrl 7 37887597 37838030 484 HER2 ERBB2 H3K4me3 POS chrl 7 37891476 37893900 2425 HER2 ERBB2 H3K4me3 ROS chrl 7 37896241 37909448 13208 HER?, ERBB2 H3K4me3 POS chrl 7 37911771 37913761 1 QQ1 HER? ERBB2 H3K4me3 POS cbrl7 37917744 37919236 1493 HER2 ERBB2 I13K4me3 POS chrl 7 37921726 37922721 996 11ER2 ERBB2 H3K4me3 POS chrl 7 37923717 3792.421 4 498 HER?. ERBB2 H3K4me3 PC'S chrl? 37925708 37927698 1991 HER? FRBB2 H3K4me3 POS chrl 7 37939646 37940143 498 HE.R2 ERBB2 H3K4me3 POS chrl 7 37944126 37944623 498 HER2 ERBE 2 H3K4mc3 POS chrl 7 3794561.9 37946]]6 498 HER? ERBB2 H3K4me3 POS chrl 7 37968517 37969512 996 HER2 ERBB2 H3K4me3 POS chrl 7 37990917 37991414 498 HER2 FRBB2 H3K4n;e3 POS chrl 7 379924!! 37992907 497 14ER2 ERBE 2 ERBB2 H3K27ac H3K27ac POS POS chrl 7 chrl 7 37689375 37696874 37692374 3000 500 HER? HER2 ERBB2 H3K27ao POS dir] 7 37697874 37698373 500 HER2 ERBB2 H3K27ac POS chrl 7 37699373 37706871 7499 HER2 ERBB2 H3K27ao POS chrl 7 37707872 37710379 2499 HER2 EREB2 H3K27ac PUS chrl 7 37711871 37713870 2000 HER? FRBB2 H3K2?ac POS chrl? 37716870 37718869 2000 HER2 ERBB2 H3K27ac POS chrl 7 37719370 37732866 13497 HER2 ERBE 2 H3K27ac POS chrl 7 37734367 37736366 2000 HER? ERBB2 H3K27ao POS chrl 7 37737366 37737865 500 HER2 ERBB2 H3K27ao POS chrl 7 37743865 37744364 500 HER2 ERBB2 H3K27ac POS chrl 7 37748364 37749363 1000 1-IER2 ERBB2 H3K27ac POS chrl 7 37751364 37753862 2499 HER2 ERBB2 H3K27ac POS chrl 7 37754363 3 / 756362 2000 HER2 ERBB2 H3K27ac POS chrl 7 37756863 37759361 2499 HER2 ERBE 2 H3K27ac POS chrl 7 37761362 37761361 500 HER2 ERBE2 H3K27ac POS chrl 7 37762362 37763860 1499 HER? ERBB2 H3K27ao POS chrl 7 37764361 37766360 2000 HER2 ERBB2 H3K27ac POS chrl7 37767361 37780357 ■2997 HER2 ERBB2 H3K27ac POS chrl 7 37781358 37782357 1000 I-IER2 ERBB2 H3K27ac POS chrl7 37784358 37785357 1000 HER? ERBE2 EI3K?7ao POS chrl 7 37795310 37831688 363?9 HER? ERBB2 H3K27ao POS chrl 7 37837528 37843195 5668 HER2 ERBE 2 H3K27ac POS chrl 7 37845276 37847765 2490 HER2 ERBB2 H3K27ac POS chrl 7 37848762 37885125 36364 HER2 EREB2 H3K27ac POS chrl 7 37887693 37908566 20874 HER? FRBB2 H3K2?ac POS chrl 7 37914659 37915656 998 HF.R2 ERBB2 H3K27ac POS chrl 7 37916655 37919149 2495 1-1ER2 ER BE 2 H3K27ac POS chrl 7 37921.646 37928133 6488 HER? ERBB2 H3K27ao POS chrl 7 37939613 37940111 499 HER2 ERBE2 H3K27ac POS chrl 7 37943606 37944603 998 HER2 ERBB2 H3K27ac POS chrl 7 37945602 37946101 500 HER2 ERBE 2 H3K27ac POS chrl 7 37953588 37954086 499 HER? ERBB2 H3K27ac POS chrl? 37964568 37966064 1497 HER2 ERBB2 H3K27ac POS dir] 7 37968561 37969059 499 HER2 ERBB2 H3K27ac POS chrl 7 37991020 37991513 499 HER2 ERBB2 MBD POS chrl 7 37653090 37653572 483 HER2 ERBB2 MEE POS chrl 7 37661070 37662008 939 HER? ERBB2 MBD POS chrl 7 37662947 37663885 939 HER2 ERBB2 MBD POS chrl 7 37667049 37667411 363 HER2 ERBB2 MBD POS chrl 7 37674789 37675784 996 HER2 ERBB2 MBD POS chrl 7 37694627 37695060 434 HER? ERBB2 MBD PC'S chrl? 37698615 37699033 419 HER? FRBB2 MBD POS chrl? 37703243 37703702 460 HER2 ERBB2 MBD POS chrl 7 37718305 37718790 486 1-IER2 ER BE 2 MBD POS chrl 7 37719278 37719764 487 HER?. ERBB2 MBD POS chrl 7 37721070 37721488 419 HER2 ERBB2 MBD POS chrl 7 37733328 37733802 475 HER? FRBB2 MBD POS chrl 7 37737765 37738599 835 HER2 ERBB2 MBD POS chrl 7 37752443 37753440 998 HER? ERBB2 MBD POS chrl 7 37754938 37756433 1496 HER2 ERBB2 MBD POS chrl 7 37759926 37764415 4490 HER2 ERBB2 MBD POS chrl 7 37765913 37766411 499 HER2 ERBB2 MBD POS chrl 7 37772051 37772,496 446 HER? ERBB2 MBD POS chrl 7 37776480 37776964 485 HER? ERBB2 MBD POS chrl 7 37778906 4777^4^0 485 HER2 ERBB2 MBD POS chrl 7 37782303 37784243 1941 HER2 ER BE 2 MBD POS chrl 7 37789195 37789689 495 HER? ERBB2 MBD POS chrl 7 37792657 37793150 494 HER2 ERBB2 MBD POS chrl 7 37794635 37795128 494 HER? ERBB2 MBD POS chrl 7 37801063 37802051 989 1-IER2 ERBB2 MBD POS chrl 7 37805252 37805639 388 HER? ERBB2 MBD POS chrl 7 37806028 37806416 389 HER? ERBB2 MBD POS chrl 7 37806658 37808613 ■956 HER2 ERBB2 MBD POS chrl 7 37812467 37812914 448 HER2 ERBE2 MBD POS chrl 7 37815519 37816556 1038 HER? ERBB2 MBD POS chrl 7 37817639 37818056 418 HER2 ERBB2 MBD POS chrl 7 37821559 37821973 415 HER2 ERBB2 MBD POS chrl 7 37823351 37825249 1899 HER2 ERBE2 MBD POS chrl 7 37827636 37828469 834 HER? ERBB2 MBD POS chrl 7 37829945 37830347 403 HER? ERBB2 MBD POS chrl 7 37834645 37835122 478 HER2 ERBE 2 MBD POS chrl 7 37836558 37837514 957 HER? ERBB2 MBD POS chrl 7 37839115 37839512 398 HER? ERBB2 MBD POS chrl 7 37839912 37840309 398 HER? EREB2 MBD POS chrl 7 37842032. 37842485 454 HF.R2 ERBB2 MBD POS chrl 7 37846352 37846837 486 HER2 ER BE 2 MBD POS chrl 7 37848786 47849272 487 HER? ERBB2 MBD POS chrl 7 37849760 37850246 487 HER2 ERBB2 MBD POS chrl 7 37852212 37852647 436 HER? ERBB2 MBD POS chrl 7 37853084 37853519 436 HER2 ERBE 2 MBD POS chrl 7 37853869 37854833 965 HER? ERBB2 MBD POS chrl 7 37865042 37866290 1249 PIER? ERBB2 MBD POS chrl 7 37868357 37868809 453 HER2 ERBB2 MBD POS chrl 7 37869718 37870170 453 HER2 ERBB2 MBD POS chrl 7 37870625 37871078 454 HER2 ERBB2 MEE ROS chrl 7 37873880 37874373 494 HER? ERBB2 MBD POS chrl 7 37876846 37877834 989 HER2 ERBB2 MBD POS chrl 7 3787882.3 37879317 495 HER2 ERBB2 MBD POS chrl 7 37882902 37833319 418 HER2 ERBB2 MBD POS chrl 7 37885298 37885750 453 HER?, ERBB2 MBD PC'S chrl? 3 7888046 37888518 473 HER2 FRBB2 MBD POS chrl? 37890886 37891359 474 HER2 ERBB2 MBD POS chrl 7 37897600 37898859 1260 HER2 ERBB2 MBD POS chrl 7 37909486 37909930 445 HER?, ERBB2 MBD POS chrl 7 37910823 37912160 ■ 338 HER2 ERBB2 MBD POS chrl 7 37916470 37916939 470 HER2 FRBB2 MBD POS chrl 7 37917410 37917379 470 HER2 ERBB2 MBD POS chrl 7 37919244 3791968?, 439 HER?, ERBB2 MBD POS chrl 7 37920122 37920560 439 HER2 ERBB2 MBD POS chrl 7 37931654 37932118 465 HER2 ERBB2 MBD POS chrl 7 3 7934910 37935375 466 UER2 ERBB2 MBD POS chrl 7 37935628 37935971 344 HER?, ERBB2 MBD PUS chrl 7 37939859 37940337 479 HER2 ERBB2 MBD POS chrl 7 37944994 37945400 497 HER2 ERBB2 MBD POS chrl 7 37945742 37946218 4 / / HER2 ER BE 2 MBD POS chrl 7 37953000 37953.467 468 HER? ERBB2 MBD POS chrl 7 37958145 37958642 498 HER2 ERBB2 MBD BOS chrl 7 37959639 37960135 497 HER2 ERBB2 MBD POS chrl 7 37970319 37970776 458 1-IER2 ERBB2 MBD POS chrl 7 3798679) 37987243 453 HER?, ERBB2 MBD POS chrl 7 38023292 38023763 472 HER? ERBB2 MBD POS chrl 7 38049940 38050430 491 HER?. ERBB2 MBD POS chrl 7 38065739 38066229 491 HER2 ERBE2 MBD POS chrl 7 38068192 38068682 491 HER? ERBB3 H3K4me3 POS chrl 2 56333863 56334678 816 HER? ERBB3 H3K4mc3 BOS chrl 2 56399880 56400585 796 HER3 ERBB3 H3K4me3 POS chrl 2 56472325 56472659 335 HERS ERBB3 H3K4me3 POS chrl 2 56476428 56477414 987 HERS ER BE 3 H3K4me3 POS chrl 2 56544876 56545167 292 HER3 ERBB3 H3K27ao POS chrl?. 56302.990 56303444 455 HER? ERBB3 H3K27ac POS chrl 2 56333463 56334422 960 HERS ERBB3 H3K27ac POS chrl 2 56348883 56349371 489 HER? ERBB3 H3K27ac POS chrl 2 56350836 56351811 976 HERS ERBB3 H3K27ac POS chrl 2 56407127 56408573 ■ 447 HF.R3 ERBB3 H3K27ac POS chrl 2 56422331 56423304 974 HER3 ER BE 3 H3K27ac POS chrl 2 56442571 56443949 479 HERS ERBB3 H3K27ao POS chrl 2 56471500 56482391 10892 HER? ERBB3 H3K27ac POS chrl?. 56607978 56608455 478 HER? ERBB3 H3K27ac POS chrl 2 56685496 56686448 953 HER3 ERBE 3 MBD POS chrl 2 56325526 56326699 1165 HERS ERBB3 MBD POS chrl 2 a6a234a6 56524140 685 HER3 ERBB3 MBD POS chrl 2 5654092.7 56541386 460 HER3 ERBB3 MBD POS chrl 2 56550456 5633U384 429 HERS ERBB3 MBD NEG chrl2 56434846 56435222 377 HER3 ERBB3 MBD NEG chrl2 56600043 56600493 451 HER3 ERBB3 MBD NEG chrl 2 56661047 56661536 490 JIER3 ERBB3 MBD NEG dir] 2 56687324 56687819 496 HER3 ESRl I13K4me3 BOS chr6 151777858 151778337 480 ER ESR] H3K4me3 POS chr6 151816741 151817152 412 ER ESRl H3K4me3 PC'S chr6 151935644 151938001 2358 ER ESRl H3K4me3 POS chr6 152011379 152011695 337 ER ESRl H3K4me3 POS chr6 152084308 152085248 941 ER ESRI H3K4mc3 POS chr6 152130343 352335604 5262 ER ESRl H3K4me3 POS chr6 152136084 152137039 956 ER ESRl H3K27ac POS chr6 151935984 151937978 3995 ER ESRl l-I3K27ac POS chr6 i 5 i 950946 151951444 499 RR ESR] ESRl H3K27ac H3K27ac POS POS chr6 chr6 151952941 151954438 153953938 151955434 998 997 ER ER ESRl H3K27ac POS chr6 151956932 151957928 997 ER ESRl H3K27ac POS chr6 151968902 151970397 1496 ER ESRI H3K27ao POS chr6 151970897 151971395 499 ER ESRl H3K27ac POS chr6 151973391 151973889 499 ER ■SR1 H3K27ac POS uhr6 151979376 151981370 3995 ER ESRI H3K27ac POS dir6 151982368 151983864 1497 ER ESR1 H3K27ac POS chrl. 151987356 151987854 499 ER ESRl H3K27ao POS chr6 151989351 151991345 1995 ER ESRl H3K27ac POS chr6 152008304 152008802 499 ER ESRI H3K27ac POS ohr6 152009302 152009799 498 ER ESR] H3K27ac POS chr6 152010798 152013790 2993 ER ESRl H3K27ac POS chr6 152023766 152025760 * 995 ER ESRl H3K27ac POS dir 6 152027257 152028254 998 ER ESRl H3K27ac POS chr6 152037218 152037657 440 ER ESR1 H3K27ac POS chr6 152084562 152085046 485 ER ESRI H3K27ao POS chr6 152128191 152137516 9326 ER ESRl H3K27ac POS chr6 152221879 152222373 495 ER ESRI MBD POS chrf. 151796250 151796745 496 ER ESR] MBD POS chrt 151812719 15181317] 453 ER ESRI MBD POS chro 151823712 ]5]824]30 419 ER ESRl MBD POS dir6 151843595 151844070 476 ER ESRl MBD POS ehr6 151853944 151854632 689 ER ESR] MBD POS chr6 151868084 151868550 467 ER ESRl MBD POS chr6 151896436 151896806 371 ER FSR1 MBD POS dir6 151912301 154943128 828 ER ESRl MBD POS chr6 151940531 151940733 203 ER ESR1 MBD POS chr6 151991629 353993295 267 ER ESRl MBD POS chr6 152002182 152003580 ■ 399 ER ESRl MBD POS dir6 152005746 152006094 349 ER ESRI MBD POS dir6 152114209 152114428 220 ER ESR] MBD POS chr6 152261153 152202025 873 ER ESRl MBD POS chr6 152265086 152265868 ER ESRl MBD POS chr6 152348861 152350618 1758 ER ESRl MBD POS chrG 152577465 152577768 304 ER ESRI MBD NEG chr6 152128313 152128789 4' / ' / ER ESR1 MED NEG chrft 152473249 152473690 442 ER ESR I MBD NEG chr6 152622692 152623476 785 ER F3 H3K4me3 POS chrl 95003777 95006071 2295 TF T?-- I13K4me3 POS chrl 95008649 95009983 435 TF Jr 5 H3K4me3 POS chrl 95200591 952,01056 466 TF F3 H3K27ac PC'S chrl 94992852 94993348 497 TF F3 H3K27ac POS chrl 95002805 95003301 497 TF F3 H3K27ac POS chrl 95003800 95004794 995 TF H3K27ac POS chrl 95005293 95008278 2986 TF F3 H3K27ao POS chrl 95009772 95010269 498 TF F3 H3K27ao POS chrl 95045087 95046029 943 TF I?': H3K27ac POS chrl 95082121 95083582 ■462 TF Jr 5 F3 H3K27ac H3K27ac POS POS chrl chrl 95086994 95090405 95089916 95090891 2923 487 TF TF F3 H3K27ao POS chrl 95111006 95112501 1496 TF F3 H3K27ac POS chrl 95113001 95114496 1496 TF F > H3K27ao POS chrl 95192746 951932,1 7 472 TF F3 H3K27ao POS chrl 95193689 95194631 943 TF F3 H3K27ac POS chrl 95200213 95201657 ■445 TF F3 MBD POS chrl 94910836 94911208 373 TF F3 MBD POS chrl 94911538 94911720 183 TF F3 MBD POS chrl 94976887 94977336 450 TF F3 MBD POS chrl 94977731 94978120 390 TF I?': MBD POS chrl 95069909 95070383 475 TF F 5 MBD POS chrl 95095088 95095584 497 TF F3 MBD POS chrl 95118291 95119149 859 TF F3 MBD POS chrl 95121739 95122565 82,7 TF F3 MBD POS chrl 95143877 95144212 336 TF F3 MBD / POS chrl 95181646 95181424 385 TF F3 MBD POS chrl 95183289 95183695 407 TF F3 MBD NEG- chrl 95007901 95008277 377 TF FAP H3K27ac POS chr2 162974595 162975478 884 FAP a" AB MBD POS chr2 163054524 163054754 231 RAP FAP MBD POS chr2 163055657 163055406 350 FAP FAP MBD NEG cbr2 162930308 162931278 971 FAP FGFR2 H3K4ine3 POS chrlO 123333232 12MM615 384 FGFR2 FGFR2 H3K4me3 POS chrlO 123355053 123355522 470 FGFP2, FGFR2 H3K4me3 POS chrl 9 123368127 123368876 750 FGFR2 FGFR2 H3K4me3 POS chrl 0 123494213 123494589 377 FGFR2 FGFR2 H3K27ac POS chrlO 123332573 123333450 878 FGFR2 FGFR2 H3K27ac POS chrlO 123339566 123340968 1403 FGFR2 FGFR2 H3K27ao POS chrlO 123355379 123358699 3321 FGFR2 FGFR2 MBD POS chrl 0 123155879 123156369 491 FGFR2 FGFR2 MBD POS chrlO 123226619 123227089 471 FGFR2 FG6E2 MBD POS chrlO 123229791 123230696 906 FGFR2 FGFR2 MBD POS chrlO 123243915 123244298 384 FMR2 FGFR2 MBD POS chrlO 123244614 123245073 460 FGFR2 FGFR2 MBD POS chrlO 123247313 123247694 382 FGFR2 FGFR2 MBD POS chrlO 123249892 123251291 1400 FGFR2 FGFR 2 MBD BOS chrlO 123252226 123253158 933 FGFR2 FGFR2 MBD POS chrlO 123260480 123260941 462 FGFR2 FGFR?. MBD POS chrlO 123262329 123262791 463 FGFR2 FGFR2 MBD POS chrlO 123264957 123266112 1156 FGFR2 FGFR2 MBD POS chrlO 123274264 1 4. J / . / *♦ / V 4. 499 FGFR?. FGFR2 MBD PC'S chrlO 123285462 123286846 1385 FGFR2 FGFR2 MBD POS chrlO 123293713 123294206 494 FGFR2 FGFR2 MBD POS chrlO 123294701 123295194 494 FGFR2 FGFR2 MBD POS chrlO 123299405 123300326 922 FGFR2 FGFR? MBD POS chrlO 123321898 123322346 449 FGFR2 FGFR2 MBD POS chrl 0 123325989 123326168 180 FGFR2 FGFR2 MBD POS chrlO 123328263 123329129 867 FGFR2 FGFR2 MBD POS chrlO 123341641 1233-12543 903 FGFR?. FGFR2 MBD POS chrl 0 123403374 123403848 475 FGFR2 FGFR?. MBD POS chrlO 123418656 123419135 480 FGFR2 FGFR2 MBD POS chrlO 123422271 123422528 258 FGFR2 FGFR 2 MBD POS chrlO 123458099 123458961 863 FGFR?. FGFR2 MBD POS chrlO 123468582 123469519 938 FGFR2 FGFR2 MBD POS chrlO 123495601 123496042 442 FGFR2 FGFR2 MBD POS chrlO 123497809 123498250 442 FGFR2 FGFR2 MBD NEG chrlO 123356483 123357792 1310 FGER2 FNl H3K4me3 POS chr? 216296406 216296852 447 EDB FNl H3K4me3 POS chr2 246297747 216298641 895 EDB FNl H3K4ine3 POS chr2 216302051 '216302370 320 EDB FNl H3K27ac POS chr2 216192496 21619495’ 2456 EDB FNl H3K27ac POS chr2 216273979 216274473 495 EDB FNl H3K27ac POS chr?. 216297783 216298774 992 EDB FNl H3K27ac POS chr2 216299767 216302246 2480 EDB FNl MBD POS chr2 216188686 216189-45 460 EDB FNl MBD POS chr2 216190528 216191448 921 EDB FN1 MBD POS chr?. 246192370 216192829 460 EDB FNl MBD POS chr2 216211826 216212285 460 EDB FNl MBD POS chr2 21.6213666 216214126 461 EDB FNi MBD POS chr2 216238269 216238720 452 EDB FNl MBD POS chr? 2.162.3962.6 216240530 905 EDB FNl MBD POS chr2 216250655 216251039 385 EDB FNl MBD POS chr2 216257722 216258139 418 EDB FNl MBD POS chr 2 216288533 216288982 450 EDB FNl MBD POS chr?. 2.1632.7393 216327724 332 EDB FNl MBD POS chr2 216409656 216409982 327 EDB FNl MBD POS chr2 216181241 216485325 1085 EDB FNl MBD NEG chr2 216073227 216073562 336 EDB FNl MBD NEG- chr?. 216299752 216300603 852 EDB FOLHl H3K4me3 POS chrl 1 49199301 49199982 682 PSMA FOLHl H3K4me3 POS chrll 49228656 49229051 396 PSMA FOLHl EDR-BhD POS chrl 1 49230533 49230950 418 PSMA FOLHl H3K27ac POS chrll 49229607 49230036 430 PSMA FOLHl MBD POS chrll 49202779 49203115 337 PSMA FOLHJ MBD NEG chrll 49229359 49230119 76 ! PSMA FOLRI H3K4me3 POS chrll 71955066 71955472 407 FRa FOLRi H3K27ac ROS chrl 1 71723768 / 1724260 493 FRa FOLRI H3K27ac POS chrll 71726233 71726725 493 FRa FOLRI II3K27ac POS chrll 71880525 71881913 489 FRa FOLRI H3K27ac POS chrll 71882969 71883457 489 FRa FOLRi H3K27ac POS chrll 71889812 71890299 483 FRa FOLRI H3K27ae POS chrll 71891767 71892255 489 FRa FOLRI H3K27ac POS chrll 71900487 71901959 i 473 FRa FOLRI H3K27ac POS chrll 71902942 71903922 981 FRa FOLRi H3K27ao POS chrll 71906869 71907359 491 FRa FOLRI H3K27ac POS chrll 71950580 71951064 485 FRa FOI.RI Mill) POS chrl 1 7I73H69 71731664 496 FRa FOLRI FOLRi MBD MBD POS POS chrll chrll 71950129 72019544 71951621 72019885 1493 342 FRa FRa FOLRI MBD NEG chrll 71814526 71814983 458 FRa FOLRI MBD NEG chrll 71955605 71956600 996 FRa GPCl H3Kfee3 POS chr2 241190657 241191397 741 GPC-l GPCl B3K4me3 POS ohr2 241194751 241195624 874 GPC-i GPCl H3K4me3 POS vhr2 2.41372744 241374153 1410 GPC-l GPCl H3K4me3 POS chr2 241376923 241378465 1543 GPC-l GPCl H3K4h?c3 POS chr2 241393904 241394375 472 GPC-l GPCl H3K27ao POS chr2 241190026 241191487 1462 GPC-l GPCl H3K27ao POS chr2 241195385 241195872 488 GPC-l GPCl H3K27ac POS chr2 241305439 241305934 496 GPC-l GPCl H3K27ac POS chr2 241308412 241310393 1982 GPC-l GPCl FI3K27ac POS chr2 241324731 241326203 1473 GPC-i GPCl H3I<27ac POS chr?. 241326695 241328657 ■963 GPC-l GPCl H3K27ac POS chr2 241330621 241332093 1473 GPC-' GPCl H3K27ac POS chr2 241332584 241333074 491 GPC-l GPCl H3K27ao POS chr? 241372361 241379855 7495 GPC-i GPCl I-I3K27ac POS chr? 241380356 241383853 3498 GPCl I-I3K27ac POS chr2 241386353 241388351 1999 GPC-l GPCl H3K27ac POS chr2 241389851 241392848 2998 GPC-l GPCl FI3K27ao POS ohr2 241395847 241399844 3998 GPC-l GPCl MBD POS chr?. 241392936 241394294 1359 GPC-l GPCl MBD POS chr2 241561883 241562371 489 GPC-l GPCl MBD NEG chr2 241375618 241376614 997 GPC-l GRPR H3K4me3 POS chrX 16142075 16145349 3275 GRPR GRPR MBD POS chrX 16189452 16189598 147 GRPR GRPR MBD POS chrX 16199181 16199440 260 GRPR GRPR MBD POS chrX 16203250 16203446 197 GRPR IGF1R H3K4me3 POS chr! 5 99092448 99092847 400 IGF-1R IGF1R H3K4me3 POS chrl 5 99196998 99197415 418 IGF-iR 1GF1R H3K4me3 POS chrlS 99198254 99198671 418 1GF-1R 1GF1R H3K4me3 POS chrl 5 99270511 99272246 1736 IGl-IR IGF 1R H3K4«-.e3 POS chrl 5 99295260 99295704 445 IGF-1R IGF1R H3K4me3 POS chrl 5 99352186 99353540 1355 IGF-1R 1GF1R I-DK4uie3 POS chrl 5 99397594 99395724 ii3i IGF-iR IGFIR H3K4me3 POS chrl 5 99411781 99412272 492 IGF-IR IGFIR H3K4me3 BOS chrl 5 99557022 99557447 426 KG-iR IGF 1R POS chrl 5 99198015 99198510 496 IGF-IR IGFIR H3K27ao POS chrl 5 99199008 99199504 497 IGF-IR IGFIR I13K27ac BOS chrl 5 99200996 99201491 496 IGF-IR IGFIR H3K27ac POS chrl 5 99205964 99206957 994 IGF-IR IGFIR H3K27ac PC'S chrlS 99210436 99215403 4968 IGF-IR IGF 1R H3K27ae POS chrl 5 99...

Claims

1. A method comprising quantifying, at one or more genomic loci in a biologicai sample, optionally in cell-free DNA (cfDNA) from a liquid biopsy sample, obtained or derived from a subject:(i)     one or more histone modifications,(ii)    DNA methylation,(iii)   chromatin accessibility, and / or(iv)   binding of one or more transcription factors,wherein the one or more genomic loci are:(a) within a gene encoding an ADC target antigen or within a gene that modulates ADC response / resistance; and / or(b) associated with a promoter or an enhancer of:(I) a gene that modulates ADC response / resistance; and / or(II) a gene encoding an ADC target antigen.

2. The method of claim 1, wherein the one or more genomic loci are associated with a promoter and are located within + / - 200 kB (e.g., + / - 10 kB or + / - Ikb) of the transcription site (TSS) of a gene encoding an ADC target antigen or a gene that modulates ADC response / resistance, e.g., a genomic locus that is located within a region defined by a pair of genomic coordinates in Table 1, Table 2, Table 4, Table 5, or Table 6.

3. The method of claim 1 or 2, wherein the one or more genomic loci are associated with an enhancer and are located within + / - 200 kB (e.g., + / - lOkb) of the transcription site (TSS) of a gene encoding an ADC target antigen or a gene that modulates ADC response / resistance, e.g., a genomic locus that is located within a region defined by a pair of genomic coordinates in Table 3, Table 4, Table 5, or Table 6.

4. The method of any one of claims 1-3, wherein the one or more genomic loci are located within + / - 200 kB of the TSS of a gene encoding an ADC target antigen or a gene that modulatesADC response / resistance, e.g., a genomic locus that is located within a region defined by a pair of genomic coordinates in Table 4, Table 5, or Table 6.

5. The method of any one of claims 1-4, wherein the subject is a breast cancer patient and the gene encoding an ADC target antigen is selected from the group consisting otAXL, CCR2, CEACAM5, CD44, CLDN6, DLL3, EGFR, FAP, F0LH1, TNFRSF10B, FN-l, ESRI, FGFR2, B4GALNT1, GPCL GRPR, ITGB6, IGF1R, MUC1, CDH3, CD274, PTK7, SSTR2, STRAP 1, STEAP2, TM4SF1, RORJ, SEZ6, SLC34A2, TACSTD2, VTCN1, NECTIN4, ERBB3, ERBB2, EPHA5, R0R2, F3. FOLRI, CD276, MSLN, SLC39A6, LY75, LY75-CD302, CDH6, KAAG1, TPBG anti MET.

6. The method of claim 5, wherein the subject is a breast cancer patient and the gene encoding an .ADC target antigen is selected from the group consisting of VTCN1, NECTIN4, ERBB2, RPBA5, ROR2. CDH6wAMET.

7. The method of claim 5, wherein the subject is a breast cancer patient and the gene encoding an ADC target antigen is selected from the group consisting of TACSTD2, ERBB3, F3, CD276, LY75 and KAAGE8. The method of any one of claims 1-4, wherein the subject is small cell lung cancer (SCLC) patient and the gene encoding an ADC target antigen is selected from the group consisting of TACSTD2, FOLHL NCAM1, ERBB3, CD276, MSLN, SEZ6, DLLS, and FAP.

9. The method of any one of claims 1-4, wherein the subject is a non-small cell lung cancer (NSCLC) patient and the gene encoding an ADC target antigen is selected from the group consisting of TACSTD2, F3, NECTLN4, FOLRI, ERBB3, CD276, ERBB2, AXL, CEACAM5, TFRC, SLC34A2, PTK7, GPNMB, EGFR, MET and R0R2.

10. The method of any one of claims 1-4, wherein the subject is an NEPC or PRAD patient and the gene encoding an ADC target antigen is selected from the group consisting of AR, STEAP1, CHGA, SEZ6, SSTR2, DLLS, KLK2, and KLK3.

11. The method of any one of claims 1-4, wherein the gene encoding an ADC target gene is DLL312, The method of claim 11, wherein the method further comprises quantifying, in the biological sample, at one or more genomic loci (a) within RAB3IP, PAK5, or ITPRIPL2, or any combination thereof; and / or (b) associated with a promoter or an enhancer ofRAB3IP, PAK5, or ITPRIPL2, or any combination thereof:(i)     one or more histone modifications,(ii)    DNA methylation,(iii)   chromatin accessibility, and / or(i v)   binding of one or more transcription factors.13, The method of claim 12, wherein the one or more genomic loci within RAB3IP, PAK5, or ITPRIPL2, or any combination thereof, and / or associated with a promoter or an enhancer of RAB3IP, PAK5, or ITPRIPL2, or any combination thereof, are located within + / - 200 kB of the TSS of RAB31P, PAK5, or ITPR1PL2, or any combination thereof, e.g., a genomic locus that is defined by a pair of genomic coordinates in Table 6.

14. The method of any one of claims 1-4, wherein the gene that modulates ADC response / resistance is selected from the group consisting of SH3GL1, HSP90AA1, SLC46A3, ABCB1, ABCG2, SLFN11, CCNB1, and TUBB3.

15. The method of claim 14, wherein the subject is a breast cancer patient, optionally wherein the subject is a metastatic breast cancer patient.

16. The method of claim 15, wherein the subject is a breast cancer patient, a small cell lung cancer (SCLC) patient or a non-small cell lung cancer (NSCLC) patient.

17. The method of claim 15, wherein the subject is an ER+ breast cancer patient.

18. The method of any one of claims 1-17, wherein the one or more histone modifications are quantified using a histone modification assay that measures one or more of H3K9ac, H3K14ac, H3K18ac, H3K23ac, H3K27ac. H3K4mel, H3K4me2, H3K4me3, pan-acetylation, and DNAme.19, The method of claim 18, wherein the histone modification assay detects H3K4me3 modifications.

20. The method of claim 18 or 19, wherein the histone modification assay detects H3K27ac modifications.

21. The method of any one of claims 1-20, wherein the histone modification assay is selected from ChlP-seq (Chromatin ImmunoPrecipitation sequencing), CUT&RUN (Cleavage Under Targets and Release Using Nuclease) sequencing, and CUT&Tag (Cleavage Under Targets and Tagmentation) sequencing.

22. The method of any one of claims 1-21, wherein the DNA methylation assay is MeDIP-seq or MBD-seq.

23. The method of any one of claims 1-22, wherein chromatin accessibility is quantified using a chromatin accessibility assay selected from ATAC-seq (Assay of Transpose Accessible Chromatin sequencing), NOMe-seq (Nucleosome Occupancy and Methylome sequencing), FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing), MNase-seq (Micrococcal Nuclease digestion with sequencing), a DNase hypersensitivity assay, and a fragmentomics assay.

24. The method of any one of claims 1-23, wherein the binding of one or more transcription factors is quantified using a transcription factor binding assay that detects binding of one or more of p300, mediator complex, cohesm complex, RNA pol II, FOXAI, ESRI, PR, MYC, ENI, F0XM1, KLF4, AP-2, RA Ra. or RUN XL25. The method of any one of claims 1-24, wherein the transcription factor binding assay is selected from ChlP-seq (Chromatin ImmunoPrecipitation sequencing), CUT&RUN (Cleavage Under Targets and Release Using Nuclease) sequencing, and CUT&Tag (Cleavage Under Targets and Tagmentation) sequencing.

26. The method of any one of claims 1-25, comprising quantifying two or more of the following, each at one or more of the genomic loci in cell-free DNA (cfDNA) from a. liquid biopsy sample obtained or derived from the subject:(i) one or more histone modifications,(ii) DNA methylation,(iii) chromatin accessibility, and(iv) transcription factor binding.27, The method of claim 26, comprising quantifying two or more histone modifications for the same gene.

28. The method of claim 27, comprising quantifying H3K4me3 and H3K27ac modifications for the same gene.

29. The method of claim 26, comprising quantifying one or more histone modifications and DNA methylation for the same gene,30. The1 method of claim 29, comprising quantifying H3K4me3, H3K27ac, and DNA methylation modifications for the same gene.

31. The method of any one of claims 28 or 30, wherein the quantified H3K4me3 and H3K27ac modifications are combined to generate an activation score for the gene.

32. The method of claim 31, wherein the quantified H3K4me3 and H3K27ac modifications are summed, optionally with weighting, to generate an activation score for the gene.

33. The method of claim 30, wherein the quantified H3K4me3, H3K27ac and DNA methylation modifications are combined to generate an activation score for the gene.

34. The method of claim 33, wherein the quantified H3K4me3, H3K27ac, and DNA methylation modifications are summed, optionally with weighting, to generate an activation score for the gene.

35. The method of any one of claims 31-34, wherein the gene encodes an ADC target antigen, optionally wherein the ADC target antigen is TROP2.

36. The method of any one of claims 31-34, wherein the gene modulates ADC respon se / resi stars ce.37, The method of any one of claims 1-36, wherein the liquid biopsy sample is a plasma sample, serum sample, or urine sample.

38. The method of claim 37, wherein the liquid biopsy sample is a plasma sample, optionally a 1 mL plasma sample.

39. The method of any one of claims 1-38, wherein quantification of one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors, at the one or more genomic loci as compared to a reference indicates whether an ADC target is being expressed and / or provides a prediction or measurement of the expression level of the ADC target.

40. The method of claim 39, wherein the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort, of subjects who have previously been determined to have undetectable or low expression of the ADC target based on IHC testing, or to be cancer free.

41. The method of claim 39, wherein the reference is a. predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have high expression of the ADC target based on LHC testing.

42. The method of any one of claims 1-38, wherein quantification of one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors, at the one or more genomic loci as compared to a reference indicates whether a gene that modulates ADC response / resistance is active.

43. The method of claim 42, wherein the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have low or undetectable activity of the gene that modulates ADC response / resistance.

44. The method of claim 42, wherein the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to have high activity of a gene that modulates ADC respon se / resi stan ce.

45. The method of claim 42, wherein the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to respond to treatment with the ADC for the ADC target.

46. The method of any one of claims 1-38, wherein quantification of one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or moretranscription factors, at the one or more genomic loci as compared to a reference indicates whether the subject is likely to respond to treatment with an ADC for the ADC target.

47. The method of claim 46, wherein the reference is a predetermined threshold, a measurement from a liquid biopsy sample, and / or a normalized value, optionally wherein the reference is a measurement from a liquid biopsy sample obtained from a cohort of subjects who have previously been determined to respond to treatment with the ADC for the ADC target.

48. The method of any one of claims 1-47, wherein the method comprises quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1, Table 2, Table 3, Table 4, Table 5, or Table 6.

49. The method of claim 48, wherein the method comprises quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table I50. The method of claim 47 or 49, wherein the method comprises quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2.

51. The1 method of any one of claims 48-50, wherein the method comprises quantifying H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3.

52. The method of any of claims 48-51, wherein the method comprises quantifying H3K27ac or H3K4me3 modifications and / or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4.

53. The method of claim 48-52, wherein the method comprises quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 5.54, The method of any one of claims 48-53, wherein the method comprises quantifying H3K27ac and / or H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6.

55. The method of any one of claims 1-54, wherein the subject has previously been determined to have cancer.

56. The method of claim 55, wherein the subject has previously been determined to have breast cancer, prostate cancer, or lung cancer.

57. The method of claim 56, wherein the lung cancer is SCLC, the prostate cancer is PRAD orNEPC, or the breast cancer is metastatic breast.

58. The method of any one of claims 1-57, further comprising administering an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) to the subject.

59. The method of claim 58, wherein the agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) is selected at least in part based on a quantified level of (i) one or more histone modifications, (ii) DNA methylation, (iii) chromatin accessibility, and / or (iv) transcription factor binding at the one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject.

60. The method of claim 59, wherein the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene encoding a. first ADC target antigen and the selected agent that is directed to an ADC target antigen (e.g., an / ADC therapy or radioligand) targets the first ADC target antigen.

61. The method of claim 59 or 60, wherein the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene that modulates response / resistance to a first ADC and the selected ADC therapy:(i) includes the first ADC if increased activity of a gene associated with improved response to the first ADC is detected; and(ii) does not include the first ADC if increased activity of a gene associated with resistance to the first ADC is detected,62. The method of claim 59 or 60, wherein the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene that modulates response / resistance to a first ADC and the selected ADC therapy:(i) includes the first ADC if increased activity of a gene associated with resistance to the first ADC is not detected; and(ii) does not include the first ADC if increased activity of a gene associated with resistance to the first ADC is detected.

63. The method of any one of claims 58-62, wherein the agent that is directed to an ADC target antigen is an anti-TROP2 ADC and / or comprises a Topoisomerase I (TOPI) inhibitor moiety, optionally wherein the ADC is sacituzumab govitecan (SG).

64. The method of claim 63, wherein the TOPI inhibitor moiety comprises SN-38.

65. A method of treating a subject having cancer with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), the method comprising administering the agent that is directed to the ADC target antigen (e.g., an ADC therapy or radioligand) to the subject that has been selected at least in part based on a quantified level, at one or more genomic loci, of:(i) one or more histone modifications,(ii) DNA methylation,(iii) chromatin accessibility, and / or(iv) transcription factor bindingin cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject,wherein the one or more genomic loci are:(a) within a gene encoding an ADC target antigen or within a gene that modulates ADC response / resistance; and / or(b) are associated with a promoter or an enhancer of:(I) a gene that modulates ADC response / resistance, and / or(II) a gene encoding an ADC target antigen.

66. A. method of determining whether a subject is likely to respond to treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand), comprising quantifying, at one or more genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject:(i) one or more histone modifications,(ii) DNA methylation,(iii) chromatin accessibility, and / or(iv) binding of one or more transcription factors, wherein the one or more genomic loci are:(a) within a gene encoding an ADC target antigen or within a gene that modulates ADC response / resistance; and / or(b) are associated with a promoter or an enhancer of:(I) a gene that modulates ADC response / resistance; and / or(II) a gene encoding an ADC target antigen.

67. The method of claim 65 or 66, wherein the gene that modulates ADC response / resistance is selected from the group consisting of SH3GL1, HSP90AAI, SLC46A3, ABCBJ, ABCG2, SLFNJJ, CCNBJ, and TUBB3.

68. The method of any one of claims 60-67, wherein the first ADC comprises a TOPI inhibitor moiety and / or wherein the first ADC is a TROP2 ADC,69.    The method of claim 68, wherein the TOPI inhibitor moiety comprises SN-38.

70. The method of any one of claims 65-69, wherein the first ADC is sacituzumab govitecan.

71. The method of any one of claims 65-70, wherein the quantification of(i) one or more histone modifications,(ii) DNA methylation,(iii) chromatin accessibility, and / or(iv) transcription factor bindingat one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject was performed using the method of any one of claims 1-57.

72. The method of any one of claims 65-71, wherein the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene encoding a first ADC target antigen and the selected agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) targets the first ADC target antigen.

73. The method of any one of claims 65-72, wherein the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene that modulates response / resistance to an agent that is directed to the first ADC target antigen and the selected / ADC therapy does not include an agent that is directed to the first ADC target antigen.

74. The method of any one of claims 65-73, wherein the quantified level is indicative of activity at one or more genomic loci associated with a promoter or an enhancer of a gene that modulates response / resistance to a first ADC and the selected ADC therapy includes the first ADC.

75. A method of monitoring a subject receiving treatment with an agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) during a treatment period, the method comprising quantifying:(i) one or more histone modifications.(ii) DNA methylation,(iii) chromatin accessibility, and / or(iv) transcription factor binding,at one or more of the genomic loci in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from the subject using the method of any one of claims 1-55 at first and second time points during the treatment period.

76. The method of claim 75, wherein the treatment with the agent that is directed to an ADC target antigen (e.g., an ADC therapy or radioligand) is modified (e.g., the treatment with the agent that is directed to an ADC target antigen (e.g., ADC therapy or radioligand) is discontinued, the agent that is directed to the ADC target antigen (e.g., ADC therapy or radioligand) is changed to a different agent that is directed to the ADC target antigen (e.g., ADC or radioligand), the dose of the agent that is directed to the ADC (e.g., ADC therapy or radioligand) is increased or decreased, or the frequency of administration of the agent directed to the ADC target antigen (e.g., ADC therapy or a radioligand) is increased or decreased after the second time point at least in part based on a quantified level of:(i) one or more histone modifications,(ii) DNA methylation,(iii) chromatin accessibility, and / or(iv) transcription factor bindingat the one or more of the genomic loci in cell-free DNA. (cfDNA) from a liquid biopsy sample obtained or derived from the subject at the second time point.

77. A kit comprising reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility, and / or binding of one or more transcription factors at one or more genomic loci, wherein the one or more genomic loci are located within one or more regions defined by pairs of genomic coordinates in Table 1, Table 2, Table 3, Table 4, Table 5, or Table 6.

78. The kit of claim 77, wherein the kit. comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table I.79, The kit of claim 77, wherein the kit comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2,80. The kit of claim 77, wherein the kit comprises reagents for quantifying H3K27ac modifications for at least 1,2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3.

81. The kit of claim 77, wherein the kit comprises reagents for quantifying H3K4me3 or H3K27ac modifications or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4.

82. The kit of claim 77, wherein the kit comprises reagents for quantifying H3K4me3 modifications for at. least. 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 5.

83. The kit of claim 77, wherein the kit comprises reagents for quantifying H3K4me3 or H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6.

84. The kit of any one of claims 77-83, wherein the kit comprises:(i) one or more antibodies for use in ChlP-seq, optionally wherein the one or more antibodies specifically bind H3K4me3- or H3K27ac-modified histones; or(ii) one or more antibodies for use in MeDIP-seq, optionally wherein the one or more antibodies specifically bind methylated DNA, or a MBD, for use in MBD-seq,85. The kit of any one of claims 77-84, wherein the kit comprises reagents for isolation of cell-free DNA (cfDNA) from a liquid biopsy sample.

86. The kit of any one of claims 77-85, wherein the kit comprises reagents for library preparation for sequencing.

87. The kit of any one of claims 77-86, wherein the kit comprises reagents for sequencing.

88. A non-transilory computer readable storage medium encoded with a computer program, wherein the program comprises instractions that when executed by one or more processors cause the one or more processors to perform operations to perform the method of any one of claims 176.89, A computer system comprising a memory / and one or more processors coupled to the memory, wherein the one or more processors are configured to perform operations to perform the method of any one of claims 1-76.

90. A system comprising a sequencer configured to generate a sequencing dataset from a sample; and the non-transitory computer readable storage medium of claim 88 and / or the computer system of claim 89.

91. The system of claim 90, wherein the sequencer is configured to generate a Whole Genome Sequencing (WGS) dataset from the sample.

92. The system of claim 90 or 91 further comprising a sample preparation device configured to prepare the sample for sequencing from a biological sample, optionally a. liquid biopsysample.

93. The system of claim 92, wherein the sample preparation device comprises reagents for quantifying one or more histone modifications, DNA methylation, chromatin accessibility,and / or binding of one or more transcription factors at one or more genomic loci in cell-free DNA (cfDNA) from the biological sample, optionally the liquid biopsy sample.9-4. The system of claim 93, wherein the one or more genomic loci are located within one or more regions defined by pairs of genomic coordinates in Tables 1-6.

95. The system of claim 94, wherein the device comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 1.

96. The system of claim 94 or 95, wherein the device comprises reagents for quantifying H3K4me3 modifications for at least 1,2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 2.

97. The system of any one of claims 94-96, wherein the device comprises reagents for quantifying H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 3.

98. The system of any one of claims 94-97, wherein the device comprises reagents for quantifying H3K4me3 or H3K27ac modifications or DNA methylation for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 4.

99. The system of any one of claims 94-98, wherein the device comprises reagents for quantifying H3K4me3 modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 5.

100. The system of any one of claims 94-99, wherein the device comprises reagents for quantifying H3K4me3 or H3K27ac modifications for at least 1, 2, 3, 4, 5, 10, 15, 20, or 25 genomic loci that are located within one or more regions defined by pairs of genomic coordinates in Table 6.

101. The system of any one of claims 94-97, wherein the reagents comprise one or more antibodies for use in ChlP-seq, optionally wherein the one or more antibodies specifically bind H3K4me3- or H3K27ac-modified histones.

102. The system of any one of claims 93-101, wherein the device comprises reagents for isolation of cell-free DNA (cfDNA) from the biological sample, optionally the liquid biopsy sample.

103. The system of any one of claims 93-102, wherein the device comprises reagents for library' preparation for sequencing.

104. The system of any one of claims 93-103, wherein the sequencer comprises reagents for sequencing.

Images