Treatment of clonal hematopoiesis of undetermined potential (CHIP) with lymphocyte antigen 75 (LY75), cluster of differentiation 164 (CD164), or poly(ADP-ribose) polymerase 1 (PARP1) inhibitors

Abstract

Provided herein are methods for treating subjects with clonal hematopoiesis of undetermined potential (CHIP) with lymphocyte antigen 75 (LY75), cluster of differentiation 164 (CD164), or poly(ADP-ribose) polymerase 1 (PARP1) inhibitors, and methods for identifying subjects at high risk for developing CHIP.

Description

[Technical field]

[0001] Sequence Listing Reference This application contains a Sequence Listing that has been filed electronically as an XML file entitled 381203582SEQ, created on September 11, 2022, and is 1,547 kilobytes in size. This Sequence Listing is incorporated herein by reference.

[0002] The present disclosure relates generally to the treatment of subjects with clonal hematopoiesis of indeterminate potential (CHIP) with lymphocyte antigen 75 (LY75), cluster of differentiation 164 (CD164), or poly(ADP-ribose) polymerase 1 (PARP1) inhibitors, and to methods for identifying subjects at high risk for developing CHIP. [Background technology]

[0003] CHIP is a genetically defined phenotype that reflects age-related changes to hematopoietic stem cells (HSCs). As people age, their HSCs accumulate mutations (so-called somatic mutations, i.e. mutations acquired after birth) as a result of DNA replication errors and DNA damage repair. Thus, the prevalence increases with age, being around 10% in people aged 70-80 years. Patients undergoing molecular genetic investigations for cytopenias (anemia, leukopenia, thrombocytopenia) are most likely to receive this diagnosis. Some of these mutations confer a proliferation advantage, increasing the proliferation of these cells compared to other cells, increasing the frequency of these mutations, accumulating further mutations, and inducing neoplastic changes. A subset of genes are strongly remutated with clonal hematopoiesis and are considered "CHIP genes" including DNA methyltransferase 3 alpha (DNMT3A), Tet methylcytosine dioxygenase 2 (TET2), ASXL transcription factor 1 (ASXL1), Janus kinase 2 (JAK2), and splicing factor 3B subunit 1 (SF3B1). CpG=>TpG mutations are very common in CHIP. In addition to the identification in blood DNA of specific recurrent mutations, the clinical definition of CHIP requires the absence of dysplasia and leukemia (<20% blasts). CHIP is associated with an increased risk of hematologic cancers such as myeloid or lymphoid neoplasms, and atherosclerotic cardiovascular disease such as coronary heart disease, myocardial infarction, and severe calcific aortic stenosis.

[0004] LY75 is an endocytic receptor that captures antigens from the extracellular space and directs them to specialized antigen processing compartments for antigen processing, presentation, and cross-presentation. LY75 can cause decreased proliferation of B lymphocytes. LY75 is expressed on human dendritic cells, monocytes, B cells, T cells, NK cells, and thymic epithelial cells.

[0005] CD164 is an adhesion glycoprotein expressed by HSCs and bone marrow stromal cells that acts as a regulator of hematopoiesis. CD164 belongs to the sialomucin family of secreted or membrane-bound mucins that regulate HSC proliferation, adhesion, and migration.

[0006] PARP1 is a DNA repair protein involved in PAR polymerization and recruits a series of repair molecules to support single- and double-strand repair, as well as chromatin remodeling in the context of NER. PARP1 modifies various nuclear proteins by poly(ADP-ribosyl)ation of glutamic acid, aspartic acid, serine, or tyrosine residues. The modifications are DNA-dependent and are involved in the regulation of various important cellular processes, such as differentiation, proliferation, and tumor transformation, as well as the regulation of molecular events involved in the recovery of cells from DNA damage. Summary of the Invention

[0007] The present disclosure provides a method for preventing or reducing the occurrence of CHIP in a subject, comprising administering to the subject an LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0008] The disclosure also provides a method of treating a subject with a therapeutic agent that prevents or reduces the onset of CHIP, wherein the subject has or is at risk of developing CHIP, the method comprising obtaining or obtaining a biological sample from the subject, performing or having a sequence analysis performed on the biological sample, determining whether the subject has an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule by determining whether the subject has a genotype that includes an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule, and administering or continuing to administer to the subject who is of the LY75 reference type, CD164 reference type, and / or PARP1 reference type a therapeutic agent that prevents or reduces the onset of CHIP at a standard dose, and / or administering to the subject an LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof. administering or continuing to administer a therapeutic agent that prevents or reduces the onset of CHIP to a subject who is heterozygous for an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule at an amount equal to or less than a standard dose, and / or administering an LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof, to a subject who is homozygous for an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule at an amount equal to or less than a standard dose, wherein the presence of a genotype having an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule indicates a reduced risk of the subject developing CHIP.

[0009] The present disclosure also provides a method for identifying a subject at increased risk of developing CHIP, the method comprising determining or having determined the presence or absence of an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule in a biological sample obtained from the subject, wherein if the subject is of the LY75 reference type, CD164 reference type, and / or PARP1 reference type, the subject has an increased risk of developing CHIP, and if the subject is heterozygous or homozygous for the LY75 variant nucleic acid molecule, CD164 variant nucleic acid molecule, and / or PARP1 variant nucleic acid molecule, the subject has a reduced risk of developing CHIP.

[0010] The present disclosure also provides therapeutic agents for preventing or reducing CHIP for use in preventing or reducing CHIP in a subject identified as having an LY75 variant genomic nucleic acid molecule, a CD164 variant genomic nucleic acid molecule, and / or a PARP1 variant genomic nucleic acid molecule, an LY75 variant mRNA molecule, a CD164 variant mRNA molecule, and / or a PARP1 variant mRNA molecule, or an LY75 variant cDNA molecule, a CD164 variant cDNA molecule, and / or a PARP1 variant cDNA molecule.

[0011] The present disclosure also provides an LY75 inhibitor for use in preventing or reducing CHIP in a subject that is a) a reference type for an LY75 genomic nucleic acid molecule, an LY75 mRNA molecule, or an LY75 cDNA molecule, or b) heterozygous for i) an LY75 variant genomic nucleic acid molecule, ii) an LY75 variant mRNA molecule, or iii) an LY75 variant cDNA molecule.

[0012] The present disclosure also provides a CD164 inhibitor for use in preventing or reducing CHIP in a subject who a) is reference type for a CD164 genomic nucleic acid molecule, a CD164 mRNA molecule, or a CD164 cDNA molecule, or b) is heterozygous for i) a CD164 variant genomic nucleic acid molecule, ii) a CD164 variant mRNA molecule, or iii) a CD164 variant cDNA molecule.

[0013] The present disclosure also provides PARP1 inhibitors for use in preventing or reducing CHIP in a subject that is a) a reference type for a PARP1 genomic nucleic acid molecule, a PARP1 mRNA molecule, or a PARP1 cDNA molecule, or b) heterozygous for i) a PARP1 variant genomic nucleic acid molecule, ii) a PARP1 variant mRNA molecule, or iii) a PARP1 variant cDNA molecule.

[0014] The present disclosure also provides a method for identifying a subject at risk of developing lung cancer, the method comprising determining or having determined the presence or absence of one or more somatic CHIP mutations in DNA methyltransferase 3 alpha (DNMT3A) and / or ASXL transcription factor 1 (ASXL1) in a biological sample taken from the subject, wherein if the subject has a somatic CHIP mutation in DNMT3A and / or ASXL1, the subject has an increased risk of developing lung cancer, and if the subject does not have a somatic CHIP mutation in DNMT3A and / or ASXL1, the subject does not have an increased risk of developing lung cancer.

[0015] The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate several features of the present disclosure.

[0016] The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee. [Brief description of the drawings]

[0017] [Figure 1-1] LY75 burden masked analysis of CHIP risk is shown. [Figure 1-2] LY75 burden masked analysis of CHIP risk is shown. [Figure 2-1] The effect of the ly75 locus stratified by CHIP mutation carriers is shown. [Figure 2-2] The effect of the ly75 locus stratified by CHIP mutation carriers is shown. [Figure 2-3] The effect of the ly75 locus stratified by CHIP mutation carriers is shown. [Diagram 3] Shown is the CHIP-negative malignant blood LY75-CD302 mask. [Figure 4] Figure 1 shows that the PARP1:226367601:A:C missense variant is significantly associated with CHIP. [Diagram 5] We show that PARP missense variants are significantly associated with CHIP. [Figure 6-1] This indicates that CHIP carriers are at increased risk of developing solid tumors. [Figure 6-2] This indicates that CHIP carriers are at increased risk of developing solid tumors. [Figure 7-A] Functional modeling of identified CHIP-GWAS loci is shown; Panels A and B show systematic tracking of the percentage of HDR and indels in PARPi-treated cells; Cells were treated with PARPi for 8 days and then subjected to Sanger sequencing across each locus to determine population dynamics; (Panel A) RPE-1 hTERT cells with CRISPR-mediated knock-in of the DNMT3A-R882H allele. [Figure 7-B] Functional modeling of identified CHIP-GWAS loci is shown; Panels A and B show systematic tracking of the percentage of HDR and indels in PARPi-treated cells; Cells were treated with PARPi for 8 days and then subjected to Sanger sequencing across each locus to determine population dynamics; (Panel B) CRISPR-mediated TET2 deficiency in HEK293T cells. [Figure 8] Forest plot reflecting the protective association of two LY75 missense variants (rs78446341-A, rs147820690-T) with DNMT3A-CHIP across all CHIP phenotypes in the UKB and GHS cohorts. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0018] Various terms relating to aspects of the present disclosure are used throughout the specification and claims. Unless otherwise indicated, such terms are to be given their ordinary meaning in the art. Other terms that are specifically defined are to be interpreted in a manner consistent with the definitions set forth herein.

[0019] Unless expressly stated otherwise, no method or embodiment set forth herein is intended to be construed as requiring that its steps be performed in a particular order. Thus, unless specifically stated by a method claim in the claims or description that the steps should be limited to a particular order, no order is intended to be imposed in any respect. This also applies to any possible implicit criteria of interpretation, including logical matters regarding the arrangement of steps or work flow, general meanings derived from grammatical construction or punctuation, or the number or type of embodiments described herein.

[0020] As used herein, the singular forms "a," "an," and "the" include plural referents unless the context clearly indicates otherwise.

[0021] As used herein, the term "about" means that a cited numerical value is approximate and that small variations do not significantly affect the practice of the disclosed embodiments. When a numerical value is used, unless otherwise indicated by context, the term "about" means that the numerical value can vary by ±10% and remain within the range of the disclosed embodiments.

[0022] As used herein, the term "comprising" may in certain embodiments be replaced with "consisting of" or "consisting essentially of," as desired.

[0023] As used herein, the term "isolated" in reference to a nucleic acid molecule or polypeptide means that the nucleic acid molecule or polypeptide is in a state other than its natural environment, e.g., apart from blood and / or animal tissue. In some embodiments, an isolated nucleic acid molecule or polypeptide is substantially free of other nucleic acid molecules or other polypeptides, particularly other nucleic acid molecules or polypeptides of animal origin. In some embodiments, the nucleic acid molecule or polypeptide may be in a highly purified form, i.e., greater than 95% pure or greater than 99% pure. When used in this context, the term "isolated" does not exclude the presence of the same nucleic acid molecule or polypeptide in alternative physical forms, such as dimers or alternatively phosphorylated or derivatized forms.

[0024] As used herein, the terms "nucleic acid," "nucleic acid molecule," "nucleic acid sequence," "polynucleotide," or "oligonucleotide" can include polymeric forms of nucleotides of any length, can include DNA and / or RNA, and can be single-stranded, double-stranded, or multistranded. A strand of a nucleic acid also refers to its complementary strand.

[0025] As used herein, the term "subject" includes any animal, including mammals. Mammals include, but are not limited to, farm animals (e.g., horses, cows, pigs), pet animals (e.g., dogs, cats), laboratory animals (e.g., mice, rats, rabbits), and non-human primates. In some embodiments, the subject is a human. In some embodiments, the human is a patient of a physician.

[0026] In accordance with the present disclosure, it has been observed that LY75 variant nucleic acid molecules, CD164 variant nucleic acid molecules, and PARP1 variant nucleic acid molecules (regardless of whether these variants are homozygous or heterozygous in a particular subject) are associated with a reduced risk of developing CHIP or a CHIP-related disorder. The identification by the present disclosure of an association of additional variants with a masking gene burden indicates that one or more of LY75, CD164, and PARP1 are, by themselves (and not in linkage disequilibrium with a variant of another gene), responsible for the protective effect in CHIP and CHIP-related disorders.

[0027] Thus, a subject who is an LY75 reference type or heterozygous for an LY75 variant nucleic acid molecule may be treated with an LY75 inhibitor, a subject who is an CD164 reference type or heterozygous for a CD164 variant nucleic acid molecule may be treated with a CD164 inhibitor, and a subject who is an PARP1 reference type or heterozygous for a PARP1 variant nucleic acid molecule may be treated with a PARP1 inhibitor, thereby preventing or inhibiting CHIP, inhibiting or preventing a CHIP-associated disorder, reducing or preventing symptoms thereof, and / or inhibiting or preventing the onset of symptoms. It is also contemplated that such a subject with CHIP may be further treated with a therapeutic agent that treats or inhibits CHIP or a CHIP-associated disorder.

[0028] For the purpose of this disclosure, any particular subject, for example, a human, can be categorized as having one of three LY75 genotypes: i) LY75 reference type; ii) heterozygous for LY75 variant nucleic acid molecule, or iii) homozygous for LY75 variant nucleic acid molecule.If the subject does not have a copy of LY75 variant nucleic acid molecule, the subject is LY75 reference type.If the subject has a single copy of LY75 variant nucleic acid molecule, the subject is heterozygous for LY75 variant nucleic acid molecule.

[0029] In any of the embodiments described herein, the LY75 variant nucleic acid molecule is any nucleic acid molecule (such as a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule) that is a missense variant, a splice site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, an in-frame indel variant, or a variant that encodes a truncated LY75 polypeptide.In any of the embodiments described herein, the LY75 variant nucleic acid molecule can also be any nucleic acid molecule (such as a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule) that encodes an LY75 polypeptide with partial loss of function, complete loss of function, predicted partial loss of function, or predicted complete loss of function.Subjects that have an LY75 polypeptide with partial loss of function (or predicted partial loss of function) are hypomorphic for LY75.If a subject has two copies (same or different) of an LY75 variant nucleic acid molecule, the subject is homozygous for the LY75 variant nucleic acid molecule.

[0030] For the purpose of this disclosure, any particular subject, for example, human, can be categorized as having one of three CD164 genotypes: i) CD164 reference type; ii) heterozygous for CD164 variant nucleic acid molecule, or iii) homozygous for CD164 variant nucleic acid molecule.If the subject does not have a copy of CD164 variant nucleic acid molecule, the subject is CD164 reference type.If the subject has a single copy of CD164 variant nucleic acid molecule, the subject is heterozygous for CD164 variant nucleic acid molecule.

[0031] In any of the embodiments described herein, the CD164 variant nucleic acid molecule is any nucleic acid molecule (such as a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule) that is a missense variant, a splice site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, an in-frame indel variant, or a variant that encodes a truncated CD164 polypeptide. In any of the embodiments described herein, the CD164 variant nucleic acid molecule can also be any nucleic acid molecule (such as a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule) that encodes a CD164 polypeptide with partial loss of function, complete loss of function, predicted partial loss of function, or predicted complete loss of function. A subject that has a CD164 polypeptide with partial loss of function (or predicted partial loss of function) is hypomorphic for CD164. If a subject has two copies (same or different) of a CD164 variant nucleic acid molecule, the subject is homozygous for the CD164 variant nucleic acid molecule.

[0032] For the purpose of this disclosure, any particular subject, for example, human, can be categorized as having one of three PARP1 genotypes: i) PARP1 reference type; ii) heterozygous for PARP1 variant nucleic acid molecule, or iii) homozygous for CD164 variant nucleic acid molecule.If subject does not have a copy of PARP1 variant nucleic acid molecule, the subject is PARP1 reference type.If subject has a single copy of PARP1 variant nucleic acid molecule, the subject is heterozygous for PARP1 variant nucleic acid molecule.

[0033] In any of the embodiments described herein, the PARP1 variant nucleic acid molecule is any nucleic acid molecule (such as genomic nucleic acid molecule, mRNA molecule, or cDNA molecule) that is a missense variant, a splice site variant, a stop-gain variant, a start-loss variant, a stop-loss variant, a frameshift variant, an in-frame indel variant, or a variant that encodes a truncated PARP1 polypeptide.In any of the embodiments described herein, the PARP1 variant nucleic acid molecule can also be any nucleic acid molecule (such as genomic nucleic acid molecule, mRNA molecule, or cDNA molecule) that encodes a PARP1 polypeptide with partial loss of function, complete loss of function, predicted partial loss of function, or predicted complete loss of function.Subjects that have a PARP1 polypeptide with partial loss of function (or predicted partial loss of function) are hypomorphic for PARP1.When a subject has two copies (same or different) of the PARP1 variant nucleic acid molecule, the subject is homozygous for the PARP1 variant nucleic acid molecule.

[0034] For subjects genotyped or determined to be LY75, CD164, and PARP1 reference types, such subjects are at increased risk of developing CHIP and CHIP-related disorders, such as hematological cancers, myeloid neoplasms, lymphoid neoplasms, atherosclerotic cardiovascular disease, coronary heart disease, myocardial infarction, and / or severe calcific aortic stenosis. For subjects genotyped or determined to be heterozygous for LY75, CD164, and PARP1 reference types, or one or more LY75, CD164, or PARP1 variant nucleic acid molecules, such subjects can be treated with an LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0035] In any of the embodiments described herein, the subject that is prevented or reduced by administering LY75 inhibitor, CD164 inhibitor, or PARP1 inhibitor, or any combination thereof, can be any subject that is at risk of developing CHIP, including but not limited to subjects that have a CHIP-related disorder.Furthermore, in some embodiments, the subject is at risk of developing CHIP.In some embodiments, the administration of LY75 inhibitor, CD164 inhibitor, or PARP1 inhibitor, or any combination thereof, can be performed to prevent the development of additional CHIP or CHIP-related disorder in subjects that already have CHIP or CHIP-related disorder.

[0036] In any of the embodiments described herein, the LY75 variant nucleic acid molecule can be any nucleic acid molecule (e.g., a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule, etc.) that encodes an LY75 variant polypeptide having partial loss of function, complete loss of function, predicted partial loss of function, or predicted complete loss of function. In some embodiments, the LY75 variant nucleic acid molecule that encodes a predicted loss-of-function polypeptide of LY75 is associated with a reduced in vitro response to an LY75 ligand compared to a reference LY75. In some embodiments, the LY75 variant nucleic acid molecule that encodes a predicted loss-of-function polypeptide of LY75 is an LY75 variant that results in, or is predicted to result in, a truncation of the LY75 polypeptide compared to a human reference genomic sequence.

[0037] In any of the embodiments described herein, the CD164 variant nucleic acid molecule can be any nucleic acid molecule (e.g., a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule, etc.) that encodes a CD164 variant polypeptide with partial loss of function, complete loss of function, predicted partial loss of function, or predicted complete loss of function. In some embodiments, the CD164 variant nucleic acid molecule that encodes a predicted loss-of-function polypeptide of CD164 is associated with a reduced in vitro response to CD164 ligand compared to a reference CD164. In some embodiments, the CD164 variant nucleic acid molecule that encodes a predicted loss-of-function polypeptide of CD164 is a CD164 variant that results or is predicted to result in a truncation of the CD164 polypeptide compared to a human reference genomic sequence.

[0038] In any of the embodiments described herein, the PARP1 variant nucleic acid molecule can be any nucleic acid molecule (such as a genomic nucleic acid molecule, an mRNA molecule, or a cDNA molecule) that encodes a PARP1 variant polypeptide with partial loss of function, complete loss of function, predicted partial loss of function, or predicted complete loss of function. In some embodiments, the PARP1 variant nucleic acid molecule that encodes a predicted loss-of-function polypeptide of PARP1 is associated with a reduced in vitro response to a PARP1 ligand compared to a reference PARP1. In some embodiments, the PARP1 variant nucleic acid molecule that encodes a predicted loss-of-function polypeptide of PARP1 is a PARP1 variant that causes or is predicted to cause a truncation of PARP1 polypeptide compared to a human reference genomic sequence.

[0039] In some embodiments, the LY75, CD164, or PARP1 variant nucleic acid molecule is a variant that is predicted to be damaging by an in vitro predictive algorithm, such as Polyphen, SIFT, or a similar algorithm.

[0040] In some embodiments, the LY75 variant nucleic acid molecule is a variant that causes or is predicted to cause a nonsynonymous amino acid substitution in an LY75 nucleic acid molecule, the allele frequency of which is less than 1 in 100 alleles in the population to which the subject is selected. In some embodiments, the LY75 variant nucleic acid molecule is any rare variant (allele frequency <0.1%; or 1 in 1,000 alleles), or any splice site, stop-gain, start-loss, stop-loss, frameshift, in-frame indel, or other frameshift LY75 variant.

[0041] In any of the embodiments described herein, the predicted loss-of-function polypeptide of LY75 can be any LY75 polypeptide having a partial loss-of-function, a complete loss-of-function, a predicted partial loss-of-function, or a predicted complete loss-of-function.

[0042] In any of the embodiments described herein, the LY75 variant nucleic acid molecule may have variation at a location on chromosome 2, using the nucleotide sequence of the LY75 reference genomic nucleic acid molecule (SEQ ID NO:1; ENSG00000054219.11, chr2:159,803,355-159,904,756 or within the GRCh38 / hg38 human genome assembly) as the reference sequence. There are numerous genetic variants within LY75 that cause subsequent changes in the LY75 polypeptide sequence, including but not limited to rs78446341 (GRCh38 / hg38 chr2:159,834,145:G:A) and rs147820690 (GRCh38 / hg38 chr2:159,878,663:C:T).

[0043] In some embodiments, the CD164 variant nucleic acid molecule is a variant that causes or is predicted to cause a nonsynonymous amino acid substitution in a CD164 nucleic acid molecule, the allele frequency of which is less than 1 in 100 alleles in the population to which the subject is selected. In some embodiments, the CD164 variant nucleic acid molecule is any rare variant (allele frequency <0.1%; or 1 in 1,000 alleles), or any splice site, stop-gain, start-loss, stop-loss, frameshift, in-frame indel, or other frameshift CD164 variant.

[0044] In any of the embodiments described herein, the predicted loss-of-function polypeptide of CD164 can be any CD164 polypeptide having a partial loss of function, a complete loss of function, a predicted partial loss of function, or a predicted complete loss of function.

[0045] In any of the embodiments described herein, the CD164 variant nucleic acid molecule may have a variation at a location on chromosome 6, using the nucleotide sequence of the CD164 reference genomic nucleic acid molecule (SEQ ID NO:55; ENSG00000135535.17, chr6:109,366,514 to 109,381,739 within the GRCh38 / hg38 human genome assembly) as the reference sequence. There are numerous genetic variants within CD164 that cause subsequent changes in the CD164 polypeptide sequence, including but not limited to rs3799840 (GRCh38 / hg38 chr6:109381443A:T).

[0046] In some embodiments, the PARP1 variant nucleic acid molecule is a variant that causes or is predicted to cause a nonsynonymous amino acid substitution in a PARP1 nucleic acid molecule, the allele frequency of which is less than 1 in 100 alleles in the population to which the subject is selected. In some embodiments, the PARP1 variant nucleic acid molecule is any rare variant (allele frequency <0.1%; or 1 in 1,000 alleles), or any splice site, stop-gain, start-loss, stop-loss, frameshift, in-frame indel, or other frameshift PARP1 variant.

[0047] In any of the embodiments described herein, the predicted loss-of-function polypeptide of PARP1 can be any PARP1 polypeptide having a partial loss-of-function, a complete loss-of-function, a predicted partial loss-of-function, or a predicted complete loss-of-function.

[0048] In any of the embodiments described herein, the PARP1 variant nucleic acid molecule can have a variation in location on chromosome 1, using the nucleotide sequence of the PARP1 reference genomic nucleic acid molecule (SEQ ID NO:113; ENSG00000143799.14, chr1:226,360,691 to 226,408,093 within the GRCh38 / hg38 human genome assembly) as the reference sequence. There are a number of genetic variants within PARP1 that cause subsequent changes in the PARP1 polypeptide sequence, including but not limited to s1136410 (GRCh38 / hg38 chr1:226367601:A:G), rs2793379 (GRCh38 / hg38 chr1:226408985:T:A), rs2570367 (GRCh38 / hg38 chr1:226414809T:C), rs1433574 (GRCh38 / hg38 chr1:226421638:A:C), and rs2039925 (GRCh38 / hg38chr1:226422811:C:G).

[0049] Any one or more (i.e., any combination) of LY75, CD164, or PARP1 variant nucleic acid molecules can be used in any of the methods described herein to determine whether a subject is at increased risk of developing CHIP or a CHIP-related disorder.A particular combination of variants can form a mask for use in statistical analysis of a particular correlation between any one or more of LY75, CD164, or PARP1 and reduced risk of developing CHIP.

[0050] In any of the embodiments described herein, the CHIP or CHIP-related disorder is a hematological cancer, a myeloid tumor, a lymphoid tumor, an atherosclerotic cardiovascular disease, a coronary heart disease, a myocardial infarction, and / or severe calcific aortic stenosis. In some embodiments, the CHIP or CHIP-related disorder is a hematological cancer. In some embodiments, the CHIP or CHIP-related disorder is a myeloid tumor. In some embodiments, the CHIP or CHIP-related disorder is a lymphoid tumor. In some embodiments, the CHIP or CHIP-related disorder is atherosclerotic cardiovascular disease. In some embodiments, the CHIP or CHIP-related disorder is a coronary heart disease. In some embodiments, the CHIP or CHIP-related disorder is a myocardial infarction. In some embodiments, the CHIP or CHIP-related disorder is severe calcific aortic stenosis.

[0051] Symptoms of myeloid tumors include, but are not limited to, fever, bone pain, lethargy and fatigue, shortness of breath, paleness, frequent infections, easy bruising, and abnormal bleeding, such as frequent nosebleeds and bleeding gums.

[0052] Symptoms of lymphatic tumors include, but are not limited to, painless swelling of lymph nodes in the neck, armpits, or groin, persistent fatigue, fever, night sweats, shortness of breath, unexplained weight loss, and itchy skin.

[0053] Symptoms of coronary heart disease include, but are not limited to, angina, cold sweats, dizziness, lightheadedness, nausea or indigestion, neck pain, shortness of breath (especially with activity), sleep problems, and weakness.

[0054] Symptoms of myocardial infarction include, but are not limited to, chest pressure or tightness; pain in the chest, back, jaw, and other areas of the upper body that lasts for more than a few minutes or that comes and goes; shortness of breath, sweating, nausea, vomiting, anxiety, coughing, dizziness, and fast heart rate.

[0055] Symptoms of severe calcific aortic stenosis include, but are not limited to, abnormal heart sounds heard through a stethoscope (heart murmurs), chest pain (angina) or tension (with activity), feeling faint or dizzy or fainting (with activity), shortness of breath (especially with activity), fatigue (especially with increased activity), fluttery heart rate (palpitations), small appetite (mainly in children with aortic stenosis), and low body weight (mainly in children with aortic stenosis).

[0056] It has also been observed according to the present disclosure that the CHIP somatic mutation in either DNMT3A or ASXL1 is associated with the increased risk of developing lung cancer.Therefore, the subject with the CHIP somatic mutation in either DNMT3A or ASXL1 can be monitored more frequently for lung cancer pathology (such as by more frequent chest X-rays), treatment with palliatives, or smoking cessation procedures, so as to prevent or delay the development of lung cancer.

[0057] In any of the embodiments described herein, the DNMT3A or ASXL1 somatic mutation is any mutation that is a missense mutation, a splice site mutation, a stop-gain mutation, a start-loss mutation, a stop-loss mutation, a frameshift mutation, an in-frame indel mutation, or a mutation that results in a truncated DNMT3A or ASXL1 polypeptide.In any of the embodiments described herein, the DNMT3A or ASXL1 somatic mutation can also be any mutation that results in a DNMT3A or ASXL1 polypeptide with partial loss of function, complete loss of function, predicted partial loss of function, or predicted complete loss of function.

[0058] In any of the embodiments described herein, the DNMT3A mutation may include a mutation at a location on chromosome 2, using the nucleotide sequence of the DNMT3A reference genomic nucleic acid molecule (SEQ ID NO:212; ENSG00000119772.17, chr2:25,227,855 to 25,342,590 in the GRCh38 / hg38 human genome assembly) as the reference sequence.

[0059] In any of the embodiments described herein, the ASXL1 mutation may include a mutation at a location on chromosome 20, using the nucleotide sequence of the ASXL1 reference genomic nucleic acid molecule (SEQ ID NO:267; ENSG00000171456.20, chr20:32,358,330 to 32,439,260 within the GRCh38 / hg38 human genome assembly) as the reference sequence.

[0060] The present disclosure provides a method for preventing or reducing the occurrence of CHIP in a subject, comprising administering to the subject an LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0061] The present disclosure also provides a method of treating a subject having or at risk of developing a hematological cancer, the method comprising administering to the subject an LY75 inhibitor, or a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0062] The present disclosure also provides a method of treating a subject having or at risk of developing a myeloid tumor, the method comprising administering to the subject an LY75 inhibitor, or a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0063] The present disclosure also provides a method of treating a subject having or at risk of developing a lymphoid tumor, the method comprising administering to the subject an LY75 inhibitor, or a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0064] The present disclosure also provides a method of treating a subject having or at risk of developing atherosclerotic cardiovascular disease, the method comprising administering to the subject an LY75 inhibitor, or a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0065] The present disclosure also provides a method of treating a subject having or at risk of developing coronary heart disease, the method comprising administering to the subject an LY75 inhibitor, or a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0066] The present disclosure also provides a method of treating a subject who has or has had a myocardial infarction or is at risk of developing a myocardial infarction, the method comprising administering to the subject an LY75 inhibitor, or a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0067] The present disclosure also provides a method of treating a subject having or at risk of developing severe calcific aortic stenosis, the method comprising administering to the subject an LY75 inhibitor, or a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof.

[0068] In some embodiments, the LY75 inhibitor comprises an inhibitory nucleic acid molecule. Examples of inhibitory nucleic acid molecules include, but are not limited to, antisense nucleic acid molecules, small interfering RNA (siRNA), and short hairpin RNA (shRNA). Such inhibitory nucleic acid molecules can be designed to target any region of the LY75 nucleic acid molecule. In some embodiments, the antisense RNA, siRNA, or shRNA hybridizes with a sequence in the LY75 genomic nucleic acid molecule or mRNA molecule in the cells of the subject and reduces the expression of the LY75 polypeptide. In some embodiments, the LY75 inhibitor comprises an antisense molecule, which hybridizes with the LY75 genomic nucleic acid molecule or mRNA molecule in the cells of the subject and reduces the expression of the LY75 polypeptide. In some embodiments, the LY75 inhibitor comprises an siRNA, which hybridizes with the LY75 genomic nucleic acid molecule or mRNA molecule in the cells of the subject and reduces the expression of the LY75 polypeptide. In some embodiments, an LY75 inhibitor comprises an shRNA, which hybridizes to an LY75 genomic nucleic acid molecule or mRNA molecule and reduces expression of an LY75 polypeptide in a subject's cells.

[0069] In some embodiments, the CD164 inhibitor comprises an inhibitory nucleic acid molecule. Examples of inhibitory nucleic acid molecules include, but are not limited to, antisense nucleic acid molecules, small interfering RNA (siRNA), and short hairpin RNA (shRNA). Such inhibitory nucleic acid molecules can be designed to target any region of the CD164 nucleic acid molecule. In some embodiments, the antisense RNA, siRNA, or shRNA hybridizes to a sequence in a CD164 genomic nucleic acid molecule or mRNA molecule in a subject's cells and reduces the expression of a CD164 polypeptide. In some embodiments, the CD164 inhibitor comprises an antisense molecule, which hybridizes to a CD164 genomic nucleic acid molecule or mRNA molecule in a subject's cells and reduces the expression of a CD164 polypeptide. In some embodiments, the CD164 inhibitor comprises an siRNA molecule, which hybridizes to a CD164 genomic nucleic acid molecule or mRNA molecule in a subject's cells and reduces the expression of a CD164 polypeptide. In some embodiments, the CD164 inhibitor comprises an shRNA molecule, which hybridizes with a CD164 genomic nucleic acid molecule or mRNA molecule and reduces expression of a CD164 polypeptide in cells of a subject.

[0070] In some embodiments, the PARP1 inhibitor comprises an inhibitory nucleic acid molecule. Examples of inhibitory nucleic acid molecules include, but are not limited to, antisense nucleic acid molecules, small interfering RNA (siRNA), and short hairpin RNA (shRNA). Such inhibitory nucleic acid molecules can be designed to target any region of the PARP1 nucleic acid molecule. In some embodiments, the antisense RNA, siRNA, or shRNA hybridizes to a sequence in the PARP1 genomic nucleic acid molecule or mRNA molecule in the cells of the subject, and reduces the expression of the PARP1 polypeptide. In some embodiments, the PARP1 inhibitor comprises an antisense molecule, which hybridizes to the PARP1 genomic nucleic acid molecule or mRNA molecule in the cells of the subject, and reduces the expression of the PARP1 polypeptide. In some embodiments, the PARP1 inhibitor comprises an siRNA molecule, which hybridizes to the PARP1 genomic nucleic acid molecule or mRNA molecule in the cells of the subject, and reduces the expression of the PARP1 polypeptide. In some embodiments, the PARP1 inhibitor comprises an shRNA, which hybridizes with a PARP1 genomic nucleic acid molecule or mRNA molecule and reduces expression of a PARP1 polypeptide in a cell of a subject.

[0071] The inhibitory nucleic acid molecule may comprise RNA, DNA, or both RNA and DNA. The inhibitory nucleic acid molecule may also be linked or fused to a heterologous nucleic acid sequence, for example in a vector, or a heterologous label. For example, the inhibitory nucleic acid molecule may be present as an exogenous donor sequence in or containing a vector that contains the inhibitory nucleic acid molecule and the heterologous nucleic acid sequence. The inhibitory nucleic acid molecule may also be linked or fused to a heterologous label. The label may be directly detectable (e.g., a fluorophore) or indirectly detectable (e.g., a hapten, an enzyme, or a fluorophore quencher). Such labels may be detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Such labels include, for example, radioactive labels, pigments, dyes, chromogens, spin labels, and fluorescent labels. The label may also be, for example, a chemiluminescent substance, a metal-containing substance, or an enzyme, where an enzyme-dependent secondary generation of a signal occurs. The term "label" may also refer to a "tag" or hapten that can be selectively attached to a binding molecule such that the binding molecule is subsequently added with a substrate and used to generate a detectable signal. For example, biotin can be used as a tag with an avidin or streptavidin conjugate of horseradish peroxidase (HRP) to bind to the tag and tested using a colorimetric (e.g., tetramethylbenzidine (TMB)) or fluorogenic substrate to detect the presence of HRP. Exemplary labels that can be used as tags to facilitate purification include, but are not limited to, myc, HA, FLAG or 3xFLAG, 6xHis or polyhistidine, glutathione-S-transferase (GST), maltose binding protein, epitope tags, or the Fc portion of an immunoglobulin. Numerous labels include, for example, particles, fluorophores, haptens, enzymes, and their colorimetric, fluorogenic, and chemiluminescent substrates, as well as other labels.

[0072] In any of the embodiments described herein, any of the inhibitory nucleic acid molecules can be formulated as a component of a lipid nanoparticle and delivered to a cell by the lipid nanoparticle.

[0073] Inhibitory nucleic acid molecules can include, for example, nucleotides, or non-natural or modified nucleotides, such as, for example, nucleotide analogs or nucleotide substitutes. Such nucleotides include nucleotides that contain modified bases, sugars, or phosphate groups, or nucleotides that incorporate non-natural moieties into their structure. Examples of non-natural nucleotides include, but are not limited to, dideoxynucleotides, biotinylated nucleotides, aminated nucleotides, deaminated nucleotides, alkylated nucleotides, benzylated nucleotides, and fluorophore-labeled nucleotides.

[0074] The inhibitory nucleic acid molecule may contain one or more nucleotide analogs or nucleotide substitutes. A nucleotide analog is a nucleotide that contains a modification to either the base, sugar, or phosphate moiety. Modifications to the base moiety include, but are not limited to, natural and synthetic modifications of A, C, G, and T / U, as well as various purine or pyrimidine bases, such as, for example, pseudouridine, uracil-5-yl, hypoxanthine-9-yl (I), and 2-aminoadenine-9-yl. Modified bases include 5-methylcytosine, ... (5-me-C), 5-hydroxymethylcytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyluracil and cytosine, 6-azouracil, cytosine and thymine, 5-uracil (pseudouracil), 4 -thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo (e.g., 5-bromo), 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine, 7-methyladenine, 8-azaguanine, 8-azaadenine, 7-deazaguanine, 7-deazaadenine, 3-deazaguanine, and 3-deazaadenine.

[0075] Nucleotide analogs may include modifications of the sugar moiety. Modifications to the sugar moiety include, but are not limited to, natural modifications of ribose and deoxyribose, as well as synthetic modifications. Sugar modifications include, but are not limited to, the following modifications at the 2' position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S-, or N-alkynyl; or O-alkyl-O-alkyl, where alkyl, alkenyl, and alkynyl are substituted or unsubstituted C 1~10 Alkyl or C 2~10 Alkenyl, and C 2~10 Exemplary 2' sugar modifications include -O[(CH2) n O] m CH3, -O(CH2) n OCH3, -O(CH2) n NH2, -O(CH2) n CH3, -O(CH2) n -ONH2 and -O(CH2) n ON [(CH2) nOther modifications at the 2' position include, but are not limited to, C 1~10 Examples of suitable substituents include, but are not limited to, alkyl, substituted lower alkyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN, CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, RNA cleaving groups, reporter groups, intercalators, groups for improving the pharmacokinetic properties of oligonucleotides, or groups for improving the pharmacodynamic properties of oligonucleotides, and other substituents with similar properties. Similar modifications may be made at other positions on the sugar, particularly the 3' position of the sugar in the 3' terminal nucleotide or 2'-5' linked oligonucleotides, and the 5' position of the 5' terminal nucleotide. Modified sugars can also include those containing modifications at the bridging ring oxygen, such as CH2 and S. Nucleotide sugar analogs can also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar.

[0076] Nucleotide analogs can also be modified at the phosphate moiety. Modified phosphate moieties include, but are not limited to, those in which the linkage between two nucleotides can be modified to contain phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkyl phosphotriesters, methyl phosphonates and other alkyl phosphonates including 3'-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3'-amino phosphoramidates and aminoalkyl phosphoramidates, thionophosphoramidates, thionoalkyl phosphonates, thionoalkyl phosphotriesters, and boranophosphates. Such phosphate or modified phosphate linkages between two nucleotides can be via 3'-5' or 2'-5' linkages, and the linkages can contain reverse polarity such as 3'-5' to 5'-3' or 2'-5' to 5'-2'. Various salts, mixed salts, and free acid forms are also included. Nucleotide substitutes also include peptide nucleic acids (PNAs).

[0077] In some embodiments, the antisense nucleic acid molecule is a gapmer, whereby the first 1-7 nucleotides of the 5'-end and the 3'-end, respectively, have a 2'-methoxyethyl (2'-MOE) modification. In some embodiments, the first 5 nucleotides of the 5'-end and the 3'-end, respectively, have a 2'-MOE modification. In some embodiments, the first 1-7 nucleotides of the 5'-end and the 3'-end are RNA nucleotides. In some embodiments, the first 5 nucleotides of the 5'-end and the 3'-end are RNA nucleotides. In some embodiments, each of the internucleotide backbone linkages is a phosphorothioate linkage.

[0078] In some embodiments, the siRNA molecule has terminal modification.In some embodiments, the 5'-end of the antisense strand is phosphorylated.In some embodiments, a 5'-phosphate analog that cannot be hydrolyzed, such as 5'-(E)-vinyl-phosphonate, is used.

[0079] In some embodiments, the siRNA molecule has a backbone modification. In some embodiments, modified phosphodiester groups linking successive ribose nucleosides have been shown to increase the stability and bioavailability of siRNA in vivo. The non-ester group (-OH, =O) of the phosphodiester bond can be replaced with sulfur, boron, or acetate to obtain phosphorothioate, boranophosphate, and phosphonoacetate linkages. In addition, the phosphodiester group can be replaced with a phosphotriester to facilitate cellular uptake of the siRNA and retention in serum components by removing its negative charge. In some embodiments, the siRNA molecule has a sugar modification. In some embodiments, the sugar is deprotonated (a reaction catalyzed by exonucleases and endonucleases), whereby the 2'-hydroxyl can act as a nucleophile and attack the adjacent phosphorus in the phosphodiester bond. Such alternatives include 2'-O methyl, 2'-O-methoxyethyl, and 2'-fluoro modifications.

[0080] In some embodiments, the siRNA molecule has base modifications, in some embodiments, the bases may be replaced with modified bases such as pseudouridine, 5'-methylcytidine, N6-methyladenosine, inosine, and N7-methylguanosine.

[0081] In some embodiments, siRNA molecules are bound to lipid.Lipid can be bound to 5'-end or 3'-end of siRNA, and can improve their bioavailability in vivo by associating with serum lipoprotein.Representative lipids include, but are not limited to, cholesterol and vitamin E, and fatty acids such as palmitic acid and tocopherol.

[0082] In some embodiments, an exemplary siRNA has the following formula: Sense: mN * mN * / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / * mN * / 32FN / Antisense: / 52FN / * / i2FN / * mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN / i2FN / mN * N * N where "N" is a base; "2F" is a 2'-F modification; "m" is a 2'-O-methyl modification; "I" is an internal base; * " are phosphorothioate backbone linkages.

[0083] The present disclosure also provides a vector comprising any one or more of the inhibitory nucleic acid molecules. In some embodiments, the vector comprises any one or more of the inhibitory nucleic acid molecules and a heterologous nucleic acid. The vector can be a viral vector or a non-viral vector capable of transporting the nucleic acid molecule. In some embodiments, the vector is a plasmid or a cosmid (such as a circular double-stranded DNA to which additional DNA segments can be ligated). In some embodiments, the vector is a viral vector to which additional DNA segments can be ligated into the viral genome. Expression vectors include, but are not limited to, plasmids, cosmids, retroviruses, adenoviruses, adeno-associated viruses (AAV), plant viruses such as cauliflower mosaic virus and tobacco mosaic virus, yeast artificial chromosomes (YACs), Epstein-Barr (EBV) derived episomes, and other expression vectors known in the art.

[0084] The present disclosure also provides compositions comprising any one or more of the inhibitory nucleic acid molecules. In some embodiments, the composition is a pharmaceutical composition. In some embodiments, the composition comprises a carrier and / or excipient. Examples of carriers include, but are not limited to, poly(lactic acid) (PLA) microspheres, poly(D,L-lactic-co-glycolic acid) (PLGA) microspheres, liposomes, micelles, reverse micelles, lipid cochleates, and lipid microtubules. The carrier may comprise a buffered salt solution such as PBS, HBSS, and the like.

[0085] In some embodiments, the LY75 inhibitor, CD164 inhibitor, or PARP1 inhibitor comprises a nuclease agent that induces one or more nicks or double-strand breaks in the recognition sequence(s), or a DNA-binding protein that binds to the recognition sequence in the LY75, CD164, or PARP1 genomic nucleic acid molecule. The recognition sequence can be located in the coding region of the LY75 gene, CD164 gene, or PARP1 gene, or in a regulatory region that affects the expression of the gene. The recognition sequence of the DNA-binding protein or nuclease agent can be located in an intron, exon, promoter, enhancer, regulatory region, or any non-protein coding region. The recognition sequence can include or be close to the start codon of the LY75 gene, CD164 gene, or PARP1 gene. For example, the recognition sequence can be located about 10, about 20, about 30, about 40, about 50, about 100, about 200, about 300, about 400, about 500, or about 1,000 nucleotides from the start codon. As another example, two or more nuclease agents can be used, each of which targets a nuclease recognition sequence that includes or is adjacent to a start codon. As another example, two nuclease agents can be used, one of which targets a nuclease recognition sequence that includes or is adjacent to a start codon, and the other of which targets a nuclease recognition sequence that includes or is adjacent to a stop codon, and cleavage by these nuclease agents can result in the deletion of the coding region between the two nuclease recognition sequences. Any nuclease agent that induces a nick or double-strand break at the desired recognition sequence can be used in the methods and compositions disclosed herein. Any DNA binding protein that binds to the desired recognition sequence can be used in the methods and compositions disclosed herein.

[0086] Suitable nuclease agents and DNA binding proteins for use herein include, but are not limited to, zinc finger proteins or zinc finger nuclease (ZFN) pairs, transcription activator-like effector (TALE) proteins or transcription activator-like effector nucleases (TALEN), or clustered regularly interspaced short palindromic repeats (CRISPR) / CRISPR-associated (Cas) systems. The length of the recognition sequence can vary, but includes, for example, recognition sequences that are about 30-36 bp for zinc finger proteins or ZFN pairs, about 15-18 bp for each ZFN, about 36 bp for TALE proteins or TALEN, and about 20 bp for CRISPR / Cas guide RNA.

[0087] In some embodiments, the CRISPR / Cas system can be used to modify LY75, CD164, and / or PARP1 genomic nucleic acid molecules in cells. The methods and compositions disclosed herein can employ the CRISPR-Cas system by utilizing a CRISPR complex (comprising a guide RNA (gRNA) complexed with a Cas protein) for site-specific cleavage of LY75, CD164, and / or PARP1 nucleic acid molecules.

[0088] Cas proteins generally contain at least one RNA recognition or binding domain that can interact with gRNA. Cas proteins can also contain nuclease domains (e.g., DNase or RNase domains), DNA binding domains, helicase domains, protein-protein interaction domains, dimerization domains, and other domains. Suitable Cas proteins include, for example, wild-type Cas9 proteins and wild-type Cpf1 proteins (e.g., FnCpf1). Cas proteins can have full cleavage activity to generate double-stranded breaks in LY75, CD164, or PARP1 genomic nucleic acid molecules, or can be nickases that generate single-stranded breaks in LY75, CD164, or PARP1 genomic nucleic acid molecules. Additional examples of Cas proteins include Cas1, Cas1B, Cas2, Cas3, Cas4, Cas5, Cas5e (CasD), Cas6, Cas6e, Cas6f, Cas7, Cas8a1, Cas8a2, Cas8b, Cas8c, Cas9 (Csn1 or Csx12), Cas10, Cas10d, CasF, CasG, CasH, Csy1, Csy2, Csy3, Cse1 (CasA), Cse2 (CasB), Cse3 (CasE), Cas proteins include, but are not limited to, Cse4 (CasC), Csc1, Csc2, Csa5, Csn2, Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1, Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csx1, Csx15, Csf1, Csf2, Csf3, Csf4, and Cu1966, as well as homologs or variants thereof. Cas proteins can also be operably linked to heterologous polypeptides as fusion proteins. For example, Cas proteins can be fused to a cleavage domain, an epigenetic modification domain, a transcriptional activation domain, or a transcriptional repressor domain. Cas proteins can be provided in any form. For example, the Cas protein can be provided in the form of a protein, e.g., a Cas protein complexed with a gRNA.Alternatively, the Cas protein can be provided in the form of a nucleic acid molecule, e.g., RNA or DNA, encoding the Cas protein.

[0089] In some embodiments, targeted genetic modification of LY75 genomic nucleic acid molecule can be caused by contacting a cell with Cas protein and one or more gRNAs that hybridize with one or more gRNA recognition sequences in the target genomic locus of LY75 genomic nucleic acid molecule.For example, LY75 gRNA recognition sequence can be located in the region of SEQ ID NO:1. The gRNA recognition sequence can include or be adjacent to the start codon of LY75 genomic nucleic acid molecule or the stop codon of LY75 genomic nucleic acid molecule.For example, the gRNA recognition sequence can be located about 10, about 20, about 30, about 40, about 50, about 100, about 200, about 300, about 400, about 500, or about 1,000 nucleotides away from the start codon or the stop codon.

[0090] In some embodiments, targeted genetic modification of CD164 genomic nucleic acid molecule can be caused by contacting cells with Cas protein and one or more gRNAs that hybridize with one or more gRNA recognition sequences in the target genomic locus of CD164 genomic nucleic acid molecule. For example, CD164 gRNA recognition sequence can be located in the region of SEQ ID NO: 55. The gRNA recognition sequence can include or be adjacent to the start codon of CD164 genomic nucleic acid molecule or the stop codon of CD164 genomic nucleic acid molecule. For example, the gRNA recognition sequence can be located about 10, about 20, about 30, about 40, about 50, about 100, about 200, about 300, about 400, about 500, or about 1,000 nucleotides away from the start codon or the stop codon.

[0091] In some embodiments, targeted genetic modification of PARP1 genomic nucleic acid molecule can be caused by contacting cells with Cas protein and one or more gRNAs that hybridize with one or more gRNA recognition sequences in the target genomic locus of PARP1 genomic nucleic acid molecule.For example, PARP1 gRNA recognition sequence can be located in the region of SEQ ID NO: 113. The gRNA recognition sequence can include or be close to the start codon of PARP1 genomic nucleic acid molecule or the stop codon of PARP1 genomic nucleic acid molecule.For example, the gRNA recognition sequence can be located about 10, about 20, about 30, about 40, about 50, about 100, about 200, about 300, about 400, about 500, or about 1,000 nucleotides away from the start codon or the stop codon.

[0092] The gRNA recognition sequence in the target genomic locus in the LY75, CD164, or PARP1 genomic nucleic acid molecule is located near a protospacer adjacent motif (PAM) sequence, which is a 2-6 base pair DNA sequence that immediately follows the DNA sequence targeted by the Cas9 nuclease. A canonical PAM is the sequence 5'-NGG-3', where "N" is any nucleobase followed by two guanine ("G") nucleobases. The gRNA can transport Cas9 anywhere in the genome for gene editing, but editing cannot occur at sites other than the site where Cas9 recognizes the PAM. 5'-NGA-3' can also be a non-canonical PAM that is highly efficient for human cells. Generally, the PAM is about 2-6 nucleotides downstream of the DNA sequence targeted by the gRNA. The PAM can be adjacent to the gRNA recognition sequence. In some embodiments, the gRNA recognition sequence can be adjacent to the PAM at the 3' end. In some embodiments, the gRNA recognition sequence can be adjacent to the PAM at the 5' end. For example, the cleavage site of the Cas protein can be about 1 to about 10 base pairs, about 2 to about 5 base pairs, or 3 base pairs upstream or downstream of the PAM sequence. In some embodiments (e.g., when using Cas9 from S. pyogenes or a closely related Cas9), the PAM sequence of the non-complementary strand can be 5'-NGG-3', where N is any DNA nucleotide and is immediately 3' to the gRNA recognition sequence of the non-complementary strand of the target DNA. Thus, the PAM sequence of the complementary strand is 5'-CCN-3', where N is any DNA nucleotide and is immediately 5' to the gRNA recognition sequence of the complementary strand of the target DNA.

[0093] gRNA is an RNA molecule that binds to Cas protein and targets Cas protein to a specific location in LY75, CD164 or PARP1 genomic nucleic acid molecule.Exemplary gRNA is an effective gRNA that induces Cas enzyme to bind to or cleave LY75, CD164 or PARP1 genomic nucleic acid molecule, and gRNA comprises a DNA targeting segment that hybridizes with gRNA recognition sequence in LY75, CD164 or PARP1 genomic nucleic acid molecule.Exemplary gRNA comprises a DNA targeting segment that hybridizes with gRNA recognition sequence present in LY75, CD164 or PARP1 genomic nucleic acid molecule that includes or is adjacent to start codon or stop codon. For example, a gRNA can be selected to hybridize with a gRNA recognition sequence located about 5, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 100, about 200, about 300, about 400, about 500, or about 1,000 nucleotides away from a start codon, or with a gRNA recognition sequence located about 5, about 10, about 15, about 20, about 25, about 30, about 35, about 40, about 45, about 50, about 100, about 200, about 300, about 400, about 500, or about 1,000 nucleotides away from a stop codon. Suitable gRNAs can include about 17 to about 25 nucleotides, about 17 to about 23 nucleotides, about 18 to about 22 nucleotides, or about 19 to about 21 nucleotides. In some embodiments, the gRNA can include 20 nucleotides.

[0094] Examples of suitable gRNA recognition sequences located within the human LY75 reference gene are shown in Table 1 as SEQ ID NOs: 152-171. [Table 1]

[0095] Examples of suitable gRNA recognition sequences located within the human CD164 reference type gene are shown in Table 2 as SEQ ID NOs: 172-191. [Table 2]

[0096] Examples of suitable gRNA recognition sequences located within the human PARP1 reference gene are shown in Table 3 as SEQ ID NOs: 192-211. [Table 3]

[0097] The Cas protein and gRNA form a complex, and the Cas protein cleaves the target LY75, CD164, or PARP1 genomic nucleic acid molecule. The Cas protein can cleave the nucleic acid molecule at a site inside or outside the nucleic acid sequence present in the target LY75, CD164, or PARP1 genomic nucleic acid molecule to which the DNA targeting segment of the gRNA binds. For example, the formation of a CRISPR complex (including the gRNA hybridized with the gRNA recognition sequence and complexed with the Cas protein) can cause one or both strand cleavage within or near (e.g., within 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, or 50 or more base pairs) the nucleic acid sequence present in the LY75, CD164, or PARP1 genomic nucleic acid molecule to which the DNA targeting segment of the gRNA binds.

[0098] Such a method may result in an LY75 genomic nucleic acid molecule in which, for example, the region of SEQ ID NO:1 is disrupted, the start codon is disrupted, the stop codon is disrupted, or the coding sequence is disrupted or deleted. Optionally, the cell can be further contacted with one or more additional gRNAs that hybridize with additional gRNA recognition sequences in the target genomic locus of the LY75 genomic nucleic acid molecule. By contacting the cell with one or more additional gRNAs (such as a second gRNA that hybridizes with a second gRNA recognition sequence), cleavage by the Cas protein can generate two or more double-strand breaks or two or more single-strand breaks. CD164 and PARP1 genomic DNA can be targeted in a similar manner.

[0099] In some embodiments, the prevention and / or reduction methods further comprise detecting the presence or absence of an LY75 variant nucleic acid molecule in a biological sample from the subject. In some embodiments, the prevention and / or reduction methods further comprise detecting the presence or absence of a CD164 variant nucleic acid molecule in a biological sample from the subject. In some embodiments, the prevention and / or reduction methods further comprise detecting the presence or absence of a PARP1 variant nucleic acid molecule in a biological sample from the subject.

[0100] The present disclosure also provides a method of treating a subject with a therapeutic agent that treats or inhibits CHIP, the subject being at risk of developing CHIP or a CHIP-related disorder. In some embodiments, the method includes obtaining or obtaining a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has an LY75 variant nucleic acid molecule by determining whether the subject has a genotype that includes an LY75 variant nucleic acid molecule. In some embodiments, the method further includes administering or continuing to administer a therapeutic agent that prevents or reduces the onset of CHIP, which is LY75, to the subject at a standard dose, and / or administering an LY75 inhibitor to the subject. In some embodiments, the method further includes administering or continuing to administer a therapeutic agent that prevents or reduces the onset of CHIP at or below a standard dose, and / or administering an LY75 inhibitor to the subject who is heterozygous for the LY75 variant nucleic acid molecule. In some embodiments, the methods further include administering or continuing to administer to a subject who is heterozygous for an LY75 variant nucleic acid molecule a therapeutic agent that prevents or reduces the occurrence of CHIP at the same or a lesser amount than a standard dose, and / or administering an LY75 inhibitor to the subject.

[0101] The present disclosure also provides a method of treating a subject with a therapeutic agent that treats or suppresses CHIP, the subject being at risk of developing CHIP or a CHIP-related disorder. In some embodiments, the method includes obtaining or obtaining a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a genotype that includes a CD164 variant nucleic acid molecule, thereby determining whether the subject has a CD164 variant nucleic acid molecule. In some embodiments, the method further includes administering or continuing to administer a therapeutic agent that prevents or reduces the onset of CHIP, which is CD164, to the subject at a standard dose, and / or administering a CD164 inhibitor to the subject. In some embodiments, the method further includes administering or continuing to administer a therapeutic agent that prevents or reduces the onset of CHIP at a standard dose or less, and / or administering a CD164 inhibitor to the subject who is heterozygous for the CD164 variant nucleic acid molecule. In some embodiments, the method further includes administering or continuing to administer to a subject who is heterozygous for a CD164 variant nucleic acid molecule a therapeutic agent that prevents or reduces the onset of CHIP at the same or a lesser amount than a standard dose, and / or administering a CD164 inhibitor to the subject.

[0102] The present disclosure also provides a method of treating a subject with a therapeutic agent that treats or suppresses CHIP, the subject being at risk of developing CHIP or a CHIP-related disorder. In some embodiments, the method includes taking or taking a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a genotype that includes a PARP1 variant nucleic acid molecule, thereby determining whether the subject has a PARP1 variant nucleic acid molecule. In some embodiments, the method further includes administering or continuing to administer a therapeutic agent that prevents or reduces the onset of CHIP, which is PARP1, to the subject at a standard dose, and / or administering a PARP1 inhibitor to the subject. In some embodiments, the method further includes administering or continuing to administer a therapeutic agent that prevents or reduces the onset of CHIP at a standard dose or less, and / or administering a PARP1 inhibitor to the subject who is heterozygous for a PARP1 variant nucleic acid molecule. In some embodiments, the method further includes administering or continuing to administer to a subject who is heterozygous for the PARP1 variant nucleic acid molecule a therapeutic agent that prevents or reduces the onset of CHIP at the same or a lesser amount than a standard dose, and / or administering a PARP1 inhibitor to the subject.

[0103] In some embodiments, the method further comprises administering or continuing to administer to the subject homozygous for the LY75 variant nucleic acid molecule a therapeutic agent that prevents or reduces the occurrence of CHIP at a dose equal to or less than a standard dose. The presence of a genotype with the LY75 variant nucleic acid molecule indicates that the subject has a low risk of developing CHIP or a CHIP-related disorder. In some embodiments, the subject is of the LY75 reference type. In some embodiments, the subject is heterozygous for the LY75 variant nucleic acid molecule.

[0104] In some embodiments, the method further comprises administering or continuing to administer to the subject who is homozygous for CD164 variant nucleic acid molecule a therapeutic agent that prevents or reduces the occurrence of CHIP at a dose equal to or less than a standard dose. The presence of a genotype with CD164 variant nucleic acid molecule indicates that the subject has a low risk of developing CHIP or CHIP-related disorder. In some embodiments, the subject is of CD164 reference type. In some embodiments, the subject is heterozygous for CD164 variant nucleic acid molecule.

[0105] In some embodiments, the method further comprises administering or continuing to administer to the subject who is homozygous for PARP1 variant nucleic acid molecule a therapeutic agent that prevents or reduces the occurrence of CHIP at the same or less than standard dose.The presence of the genotype with PARP1 variant nucleic acid molecule indicates that the subject has a low risk of developing CHIP or CHIP-related disorder.In some embodiments, the subject is PARP1 reference type.In some embodiments, the subject is heterozygous for PARP1 variant nucleic acid molecule.

[0106] For subjects who are genotyped or determined to be either heterozygous for an LY75 reference type, or an LY75 variant nucleic acid molecule, such subjects can be administered an LY75 inhibitor as described herein.

[0107] For subjects who are genotyped or determined to be heterozygous for a CD164 reference type, or a CD164 variant nucleic acid molecule, such subjects can be administered a CD164 inhibitor as described herein.

[0108] For subjects who are genotyped or determined to be heterozygous for a PARP1 reference type, or a PARP1 variant nucleic acid molecule, such subjects can be administered a PARP1 inhibitor as described herein.

[0109] For subjects who have been genotyped or determined to be heterozygous for either or both of an LY75 reference type and a CD164 reference type, or for an LY75 reference type and a CD164 variant nucleic acid molecule, or for a CD164 reference type and an LY75 variant nucleic acid molecule, or for both an LY75 variant nucleic acid molecule and a CD164 variant nucleic acid molecule, such subjects can be administered an LY75 inhibitor, a CD164 inhibitor, or both, as described herein.

[0110] For subjects who have been genotyped or determined to be heterozygous for either or both of the LY75 reference type and the PARP1 reference type, or heterozygous for the LY75 reference type and a PARP1 variant nucleic acid molecule, or heterozygous for the PARP1 reference type and an LY75 variant nucleic acid molecule, or heterozygous for both an LY75 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, such subjects can be administered an LY75 inhibitor, a PARP1 inhibitor, or both, as described herein.

[0111] For subjects who have been genotyped or determined to be heterozygous for either or both of the CD164 reference type and the PARP1 reference type, or heterozygous for the CD164 reference type and a PARP1 variant nucleic acid molecule, or heterozygous for the PARP1 reference type and a CD164 variant nucleic acid molecule, or heterozygous for both a CD164 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, such subjects can be administered a CD164 inhibitor, a PARP1 inhibitor, or both, as described herein.

[0112] For subjects who have been genotyped or determined to be heterozygous for any of the LY75, CD164, and PARP1 reference types, or heterozygous for both the LY75 reference type and a CD164 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, or heterozygous for both the CD164 reference type and a LY75 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, or heterozygous for the PARP1 reference type and both a LY75 variant nucleic acid molecule and a CD164 variant nucleic acid molecule, or heterozygous for an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and a PARP1 variant nucleic acid molecule, such subjects can be administered an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof, as described herein.

[0113] Detecting the presence or absence of one or more LY75, CD164, or PARP1 variant nucleic acid molecules in a biological sample from a subject and / or determining whether a subject has one or more LY75, CD164, or PARP1 variant nucleic acid molecules can be performed by any of the methods described herein. In some embodiments, these methods can be performed in vitro. In some embodiments, these methods can be performed in situ. In some embodiments, these methods can be performed in vivo. In any of these embodiments, the nucleic acid molecules can be present in cells taken from the subject.

[0114] In some embodiments, if the subject is LY75 reference type, the therapeutic agent for preventing or reducing the occurrence of CHIP is administered to the subject at a standard dose. In some embodiments, if the subject is heterozygous for the LY75 variant nucleic acid molecule, the therapeutic agent for preventing or reducing the occurrence of CHIP is administered to the subject at a dose equal to or less than the standard dose.

[0115] In some embodiments, if the subject is CD164 reference type, the therapeutic agent that prevents or reduces the occurrence of CHIP is administered to the subject at a standard dose. In some embodiments, if the subject is heterozygous for a CD164 variant nucleic acid molecule, the therapeutic agent that prevents or reduces the occurrence of CHIP is administered to the subject at a dose that is equal to or less than the standard dose.

[0116] In some embodiments, if the subject is PARP1 reference type, the therapeutic agent for preventing or reducing the occurrence of CHIP is administered to the subject at a standard dose.In some embodiments, if the subject is heterozygous for PARP1 variant nucleic acid molecule, the therapeutic agent for preventing or reducing the occurrence of CHIP is administered to the subject at a dose equal to or less than the standard dose.

[0117] In some embodiments, the methods of prevention and / or reduction include detecting the presence or absence of a loss-of-function polypeptide predicted by LY75 in a biological sample from a subject. In some embodiments, if the subject does not have a loss-of-function polypeptide predicted by LY75, a standard dose of a therapeutic agent that prevents or reduces the onset of CHIP is administered to the subject. In some embodiments, if the subject has a loss-of-function polypeptide predicted by LY75, a dose of a therapeutic agent that prevents or reduces CHIP is administered to the subject at the same or a lower dose than the standard dose.

[0118] In some embodiments, the methods of prevention and / or reduction include detecting the presence or absence of a loss-of-function polypeptide predicted by CD164 in a biological sample from a subject. In some embodiments, if the subject does not have a loss-of-function polypeptide predicted by CD164, a standard dose of a therapeutic agent that prevents or reduces the onset of CHIP is administered to the subject. In some embodiments, if the subject has a loss-of-function polypeptide predicted by CD164, a dose of a therapeutic agent that prevents or reduces CHIP is administered to the subject at the same or a lower standard dose.

[0119] In some embodiments, the methods of prevention and / or reduction include detecting the presence or absence of a PARP1 predicted loss-of-function polypeptide in a biological sample from a subject. In some embodiments, if the subject does not have a PARP1 predicted loss-of-function polypeptide, a standard dose of a therapeutic agent that prevents or reduces the onset of CHIP is administered to the subject. In some embodiments, if the subject has a PARP1 predicted loss-of-function polypeptide, a dose of a therapeutic agent that prevents or reduces CHIP is administered to the subject at the same or a lower dose than the standard dose.

[0120] The present disclosure also provides a method of treating a subject with a therapeutic agent for treating or suppressing a blood cancer, the subject having CHIP. In some embodiments, the method includes determining whether the subject has an LY75 variant nucleic acid molecule by taking or taking a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has an LY75 variant nucleic acid molecule. If the subject does not have an LY75 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent for treating or suppressing a blood cancer at a standard dose, and / or an LY75 inhibitor is administered to the subject. If the subject has an LY75 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent for treating or suppressing a blood cancer at a standard dose or less, and / or an LY75 inhibitor is administered to the subject. The presence of an LY75 variant nucleic acid molecule indicates that the subject is at a low risk of developing a blood cancer. In some embodiments, the subject has an LY75 variant nucleic acid molecule. In some embodiments, the subject does not have an LY75 variant nucleic acid molecule.

[0121] The present disclosure also provides a method of treating a subject with a therapeutic agent that treats or inhibits a blood cancer, the subject having CHIP. In some embodiments, the method includes determining whether the subject has a CD164 variant nucleic acid molecule by taking or taking a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a CD164 variant nucleic acid molecule. If the subject does not have a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent that treats or inhibits a blood cancer at a standard dose, and / or a CD164 inhibitor is administered to the subject. If the subject has a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent that treats or inhibits a blood cancer at a standard dose or less, and / or a CD164 inhibitor is administered to the subject. The presence of a CD164 variant nucleic acid molecule indicates that the subject is at a low risk of developing a blood cancer. In some embodiments, the subject has a CD164 variant nucleic acid molecule. In some embodiments, the subject does not have a CD164 variant nucleic acid molecule.

[0122] The present disclosure also provides a method of treating a subject with a therapeutic agent for treating or suppressing a blood cancer, the subject having CHIP. In some embodiments, the method includes determining whether the subject has a PARP1 variant nucleic acid molecule by taking or taking a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a PARP1 variant nucleic acid molecule. If the subject does not have a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent for treating or suppressing a blood cancer at a standard dose, and / or a PARP1 inhibitor is administered to the subject. If the subject has a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent for treating or suppressing a blood cancer at a standard dose or less, and / or a PARP1 inhibitor is administered to the subject. The presence of a PARP1 variant nucleic acid molecule indicates that the subject is at a low risk of developing a blood cancer. In some embodiments, the subject has a PARP1 variant nucleic acid molecule. In some embodiments, the subject does not have a PARP1 variant nucleic acid molecule.

[0123] In some embodiments, when a subject has both an LY75 variant nucleic acid molecule and a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a standard or lesser dose of a therapeutic agent to treat or suppress a hematological cancer, and / or the subject is administered an LY75 inhibitor, or a CD164 inhibitor, or both.

[0124] In some embodiments, when a subject has both an LY75 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent to treat or suppress a hematological cancer at or below a standard dose, and / or the subject is administered an LY75 inhibitor, or a PARP1 inhibitor, or both.

[0125] In some embodiments, when a subject has both a CD164 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent to treat or suppress a hematological cancer at or below a standard dose, and / or the subject is administered a CD164 inhibitor, or a PARP1 inhibitor, or both.

[0126] In some embodiments, if a subject has an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent to treat or suppress a hematological cancer at or below a standard dose, and / or the subject is administered an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof.

[0127] The present disclosure also provides a method of treating a subject with a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease, the subject having CHIP. In some embodiments, the method includes obtaining or obtaining a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has an LY75 variant nucleic acid molecule by determining whether the subject has an LY75 variant nucleic acid molecule. If the subject does not have an LY75 variant nucleic acid molecule, administer or continue to administer a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease at a standard dose to the subject, and / or administer an LY75 inhibitor to the subject. If the subject has an LY75 variant nucleic acid molecule, administer or continue to administer a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease at a standard dose or less, and / or administer an LY75 inhibitor to the subject. The presence of an LY75 variant nucleic acid molecule indicates that the subject has a low risk of developing atherosclerotic cardiovascular disease. In some embodiments, the subject has an LY75 variant nucleic acid molecule. In some embodiments, the subject does not have an LY75 variant nucleic acid molecule.

[0128] The present disclosure also provides a method of treating a subject with a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease, the subject having CHIP. In some embodiments, the method includes determining whether the subject has a CD164 variant nucleic acid molecule by taking or taking a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a CD164 variant nucleic acid molecule. If the subject does not have a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease at a standard dose, and / or a CD164 inhibitor is administered to the subject. If the subject has a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease at a standard dose or less, and / or a CD164 inhibitor is administered to the subject. The presence of a CD164 variant nucleic acid molecule indicates that the subject is at a low risk of developing atherosclerotic cardiovascular disease. In some embodiments, the subject has a CD164 variant nucleic acid molecule.In some embodiments, the subject does not have a CD164 variant nucleic acid molecule.

[0129] The present disclosure also provides a method of treating a subject with a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease, the subject having CHIP. In some embodiments, the method includes taking or taking a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a PARP1 variant nucleic acid molecule by determining whether the subject has a PARP1 variant nucleic acid molecule. If the subject does not have a PARP1 variant nucleic acid molecule, administer or continue to administer a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease at a standard dose to the subject, and / or administer a PARP1 inhibitor to the subject. If the subject has a PARP1 variant nucleic acid molecule, administer or continue to administer a therapeutic agent for treating or suppressing atherosclerotic cardiovascular disease at a standard dose or less, and / or administer a PARP1 inhibitor to the subject. The presence of a PARP1 variant nucleic acid molecule indicates that the subject has a low risk of developing atherosclerotic cardiovascular disease. In some embodiments, the subject has a PARP1 variant nucleic acid molecule. In some embodiments, the subject does not have a PARP1 variant nucleic acid molecule.

[0130] In some embodiments, when a subject has both an LY75 variant nucleic acid molecule and a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a standard or lesser amount of a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease, and / or the subject is administered an LY75 inhibitor, or a CD164 inhibitor, or both.

[0131] In some embodiments, if a subject has both an LY75 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a standard or lesser amount of a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease, and / or the subject is administered an LY75 inhibitor, or a PARP1 inhibitor, or both.

[0132] In some embodiments, if a subject has both a CD164 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease at or below a standard dose, and / or the subject is administered a CD164 inhibitor, or a PARP1 inhibitor, or both.

[0133] In some embodiments, if a subject has an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease at or below a standard dose, and / or the subject is administered an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof.

[0134] In some embodiments, the subject is heterozygous for an LY75 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at the same or less than a standard dose, and is administered an LY75 inhibitor.

[0135] In some embodiments, the subject is heterozygous for a CD164 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at the same or less than a standard dose, and a CD164 inhibitor is administered.

[0136] In some embodiments, the subject is heterozygous for a PARP1 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at the same or less than a standard dose, and is administered a PARP1 inhibitor.

[0137] In some embodiments, the subject is heterozygous for both an LY75 variant nucleic acid molecule and a CD164 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP as described herein at or below a standard dose, and is administered an LY75 inhibitor, a CD164 inhibitor, or both.

[0138] In some embodiments, the subject is heterozygous for both an LY75 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP as described herein at or below a standard dose, and is administered an LY75 inhibitor, a PARP1 inhibitor, or both.

[0139] In some embodiments, the subject is heterozygous for both a CD164 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP as described herein at or below a standard dose, and is administered a CD164 inhibitor, a PARP1 inhibitor, or both.

[0140] In some embodiments, the subject is heterozygous for an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and a PARP1 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the development of CHIP as described herein at or below a standard dose, and is administered an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof.

[0141] The present disclosure also provides a method for preventing a subject from developing CHIP by administering a therapeutic agent that prevents or reduces the onset of CHIP. In some embodiments, the method includes determining whether the subject has an LY75 variant nucleic acid molecule by taking or having taken a biological sample from the subject, performing or having performed a sequence analysis on the biological sample, and determining whether the subject has an LY75 variant nucleic acid molecule. If the subject does not have an LY75 variant nucleic acid molecule, administer or continue to administer a therapeutic agent that prevents or reduces the onset of CHIP to the subject at a standard dose, and / or administer an LY75 inhibitor to the subject. If the subject has an LY75 variant nucleic acid molecule, administer or continue to administer a therapeutic agent that prevents or reduces the onset of CHIP to the subject at a standard dose or less, and / or administer an LY75 inhibitor to the subject.

[0142] The present disclosure also provides a method for preventing a subject from developing CHIP by administering a therapeutic agent that prevents or reduces the development of CHIP. In some embodiments, the method includes determining whether the subject has a CD164 variant nucleic acid molecule by collecting or collecting a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a CD164 variant nucleic acid molecule. If the subject does not have a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent that prevents or reduces the development of CHIP at a standard dose, and / or a CD164 inhibitor is administered to the subject. If the subject has a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent that prevents or reduces the development of CHIP at a standard dose or less, and / or a CD164 inhibitor is administered to the subject.

[0143] The present disclosure also provides a method for preventing a subject from developing CHIP by administering a therapeutic agent that prevents or reduces the onset of CHIP. In some embodiments, the method includes determining whether the subject has a PARP1 variant nucleic acid molecule by collecting or collecting a biological sample from the subject, performing or performing a sequence analysis on the biological sample, and determining whether the subject has a PARP1 variant nucleic acid molecule. If the subject does not have a PARP1 variant nucleic acid molecule, administer or continue to administer a therapeutic agent that prevents or reduces the onset of CHIP to the subject at a standard dose, and / or administer a PARP1 inhibitor to the subject. If the subject has a PARP1 variant nucleic acid molecule, administer or continue to administer a therapeutic agent that prevents or reduces the onset of CHIP to the subject at a standard dose or less, and / or administer a PARP1 inhibitor to the subject.

[0144] In some embodiments, when a subject has both an LY75 variant nucleic acid molecule and a CD164 variant nucleic acid molecule, the subject is administered or continues to be administered a standard or lesser amount of a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease, and / or the subject is administered an LY75 inhibitor, or a CD164 inhibitor, or both.

[0145] In some embodiments, if a subject has both an LY75 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a standard or lesser amount of a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease, and / or the subject is administered an LY75 inhibitor, or a PARP1 inhibitor, or both.

[0146] In some embodiments, if a subject has both a CD164 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease at or below a standard dose, and / or the subject is administered a CD164 inhibitor, or a PARP1 inhibitor, or both.

[0147] In some embodiments, if a subject has an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and a PARP1 variant nucleic acid molecule, the subject is administered or continues to be administered a therapeutic agent to treat or inhibit atherosclerotic cardiovascular disease at or below a standard dose, and / or the subject is administered an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof.

[0148] The presence of one or more LY75, CD164 or PARP1 variant nucleic acid molecules indicates that the subject has a low risk of developing CHIP or CHIP-related disorder.In some embodiments, the subject has one or more LY75, CD164 or PARP1 variant nucleic acid molecules.In some embodiments, the subject does not have one or more LY75, CD164 or PARP1 variant nucleic acid molecules.

[0149] Detecting the presence or absence of one or more LY75, CD164, or PARP1 variant nucleic acid molecules in a biological sample from a subject and / or determining whether a subject has one or more LY75, CD164, or PARP1 variant nucleic acid molecules can be performed by any of the methods described herein. In some embodiments, these methods can be performed in vitro. In some embodiments, these methods can be performed in situ. In some embodiments, these methods can be performed in vivo. In any of these embodiments, the polypeptide can be present in a cell obtained from the subject.

[0150] In any embodiment described herein with respect to nucleic acid molecules, similar methods are encompassed for polypeptides.

[0151] In some embodiments, the LY75 inhibitor is a small molecule. In some embodiments, the LY75 inhibitor is an inhibitory nucleic acid molecule.

[0152] In some embodiments, the CD164 inhibitor is a small molecule. In some embodiments, the CD164 inhibitor is atorvastatin. In some embodiments, the CD164 inhibitor is an inhibitory nucleic acid molecule.

[0153] In some embodiments, the PARP1 inhibitor is a small molecule.In some embodiments, the PARP1 inhibitor is rucaparib, olaparib, veliparib ABT-888, veliparib, INO-1001, MK4827, CEP-9722, BMN-673, iniparib, AG-14361, NMS-P118, BYK204165, 4-hydroxyquinazoline, pamiparib, E7449, A-966492, niraparib, moltaparib or ME0238.In some embodiments, the PARP1 inhibitor is an inhibitory nucleic acid molecule.

[0154] Examples of therapeutic agents that treat or inhibit myeloid tumors include arsenic trioxide, azacitidine, cerbidine (daunorubicin hydrochloride), cyclophosphamide, cytarabine, daunorubicin hydrochloride, daunorubicin hydrochloride and cytarabine liposome, daurismo (glasdegib maleate), dexamethasone, doxorubicin hydrochloride, enasidenib mesylate, gemtuzumab ozogamicin, gilteritinib fumarate, glasdegib maleate, idamycin These include, but are not limited to, pfs (idarubicin hydrochloride), idarubicin hydrochloride, idhifa (enasidenib mesylate), ivosidenib, midostaurin, mitoxantrone hydrochloride, mylotarg (gemtuzumab ozogamicin), onureg (azacitidine), prednisone, rubidomycin (daunorubicin hydrochloride), rydapt (midostaurin), tabloid (thioguanine), thioguanine, tibsovo (ivosidenib), trisenox (arsenic trioxide), venclexta (venetoclax), venetoclax, vincristine sulfate, vyxeos (daunorubicin hydrochloride and cytarabine liposomal), and xospata (gilteritinib fumarate).

[0155] Examples of therapeutic agents that treat or inhibit lymphatic tumors include acalabrutinib, alemtuzumab, arzerra (ofatumumab), bendamustine hydrochloride, bendeka (bendamustine hydrochloride), calquence (acalabrutinib), campath (alemtuzumab), chlorambucil, copiktra (duvelisib), cyclophosphamide, dexamethasone, duvelisib, fludarabine phosphate, gazyva (obinutuzumab), ibrutinib, idelalisib, imbruvica (ibrutinib), leukeran (chlorambucil), obinutuzumab, ofatumumab, prednisone, rituxan (rituximab), rituxan These include, but are not limited to, hycela (rituximab and human hyaluronidase), rituximab, rituximab and human hyaluronidase, trenda (bendamustine hydrochloride), truxima (rituximab), venclexta (venetoclax), venetoclax, and zydelig (idelalisib).

[0156] Examples of therapeutic agents for treating or inhibiting coronary heart disease include, but are not limited to, angiotensin-converting enzyme (ACE) inhibitors (such as benazepril, captopril, enalapril, fosinopril, lisinopril, moexipril, perindopril, quinapril, ramipril, or trandolapril), beta-blockers (such as acebutolol, atenolol, betaxolol, bisoprolol, bisoprolol / hydrochlorothiazide, metoprolol tartrate, metoprolol succinate, nadolol, pindolol, propranolol, solotol, or timolol), calcium channel blockers (such as amlodipine, diltiazem, felodipine, isradipine, nicardipine, nifedipine, nisoldipine, olverapamil), metformin, and nitrates (such as nitroglycerin).

[0157] Examples of therapeutic agents that treat or inhibit myocardial infarction include antiplatelet anticoagulants (such as aspirin, clopidogrel, prasugrel, ticagrelor, dipyridamole, or integrin), angiotensin-converting enzyme (ACE) inhibitors (such as benazepril, captopril, enalapril, fosinopril, lisinopril, moexipril, perindopril, quinapril, ramipril, or trandolapril), beta-blockers (acebutolol, atenolol, In some embodiments, the therapeutic agent may be an agonist, such as, but not limited to, an anticoagulant, such as ribavirin, betaxolol, bisoprolol, bisoprolol / hydrochlorothiazide, metoprolol tartrate, metoprolol succinate, nadolol, pindolol, propranolol, solotol, or timolol), a vasodilator (such as hydralazine or minoxidil), or a thrombolytic agent (such as streptokinase, reteplase, alteplase, urokinase, or tenecteplase).

[0158] Examples of therapeutic agents that treat or inhibit severe calcific aortic stenosis include angiotensin-converting enzyme (ACE) inhibitors (benazepril, captopril, enalapril, fosinopril, lisinopril, moexipril, perindopril, quinapril, ramipril, or trandolapril), beta-blockers (acebutolol, atenolol, betaxolol, bisoprolol, bisoprolol / hydrochlorothiazide, metoprolol tartrate, metoprolol succinate, nadolol, pindolol, diuretics (such as chlorothiazide, chlorthalidone, hydrochlorothiazide, indapamide, metolazone, bumetanide, ethacrynic acid, furosemide, torsemide, amiloride, eplerenone, spironolactone, or triamterene), and antiarrhythmics (such as amiodarone, flecainide, ibutilide, lidocaine, procainamide, propafenone, quinidine, or tocainide).

[0159] In some embodiments, for subjects who are heterozygous for LY75 variant nucleic acid molecules, heterozygous for CD164 variant nucleic acid molecules, or heterozygous for PARP1 variant nucleic acid molecules, the dose of a therapeutic agent that prevents or reduces CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, or about 90% (i.e., less than the standard dose) compared to subjects who are LY75, CD164, and PARP1 reference types (subjects who may receive a standard dose). In some embodiments, the dose of a therapeutic agent that prevents or reduces CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, or about 50%. Additionally, a subject who is heterozygous for an LY75 variant nucleic acid molecule, who is heterozygous for a CD164 variant nucleic acid molecule, or who is heterozygous for a PARP1 variant nucleic acid molecule may be administered less frequently compared to a subject who is of the LY75, CD164, and PARP1 reference types.

[0160] In some embodiments, the dose of a therapeutic agent for preventing or reducing CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, about 50% for a subject who is homozygous for an LY75 variant nucleic acid molecule compared to a subject who is heterozygous for an LY75 variant nucleic acid molecule. In some embodiments, the dose of a therapeutic agent for preventing or reducing CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, or about 50%. Furthermore, the dose of a therapeutic agent for preventing or reducing CHIP in a subject who is homozygous for an LY75 variant nucleic acid molecule can be administered less frequently compared to a subject who is heterozygous for an LY75 variant nucleic acid molecule.

[0161] In some embodiments, the dose of a therapeutic agent for preventing or reducing CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, about 50% for a subject who is homozygous for a CD164 variant nucleic acid molecule compared to a subject who is heterozygous for a CD164 variant nucleic acid molecule. In some embodiments, the dose of a therapeutic agent for preventing or reducing CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, or about 50%. Furthermore, the dose of a therapeutic agent for preventing or reducing CHIP in a subject who is homozygous for a CD164 variant nucleic acid molecule can be administered less frequently compared to a subject who is heterozygous for a CD164 variant nucleic acid molecule.

[0162] In some embodiments, the dosage of the therapeutic agent for preventing or reducing CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, about 50% for the subject who is homozygous for PARP1 variant nucleic acid molecule compared to the subject who is heterozygous for PARP1 variant nucleic acid molecule. In some embodiments, the dosage of the therapeutic agent for preventing or reducing CHIP can be reduced by about 10%, about 20%, about 30%, about 40%, or about 50%. Furthermore, the dosage of the therapeutic agent for preventing or reducing CHIP in the subject who is homozygous for PARP1 variant nucleic acid molecule can be administered less frequently compared to the subject who is heterozygous for PARP1 variant nucleic acid molecule.

[0163] Administration of the therapeutic agent for preventing CHIP and / or LY75 inhibitor, or CD164 inhibitor, PARP1 inhibitor, or any combination thereof can be repeated, for example, after 1 day, 2 days, 3 days, 5 days, 1 week, 2 weeks, 3 weeks, 1 month, 5 weeks, 6 weeks, 7 weeks, 8 weeks, 2 months, or 3 months. Repeated administration can be the same dose or different doses. Administration can be repeated 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more times. For example, according to a particular dosing regimen, a subject can be treated for an extended period of time, for example, 6 months, 1 year, or more.

[0164] Administration of the therapeutic agent for preventing CHIP and / or the LY75 inhibitor, or the CD164 inhibitor, the PARP1 inhibitor, or any combination thereof can be by any suitable route, including, but not limited to, parenteral, intravenous, oral, subcutaneous, intraarterial, intracranial, intrathecal, intraperitoneal, topical, intranasal, or intramuscular. Pharmaceutical compositions for administration are desirably sterile, substantially isotonic, and manufactured under GMP conditions. Pharmaceutical compositions can be provided in unit dosage form (i.e., a single dose for administration). Pharmaceutical compositions can be formulated using one or more physiologically and pharmacologic acceptable carriers, diluents, excipients, or adjuvants. The formulation depends on the route of administration selected. The term "pharmaceutical acceptable" means that the carrier, diluent, excipient, or adjuvant is compatible with the other ingredients of the formulation and is not substantially deleterious to the recipient thereof.

[0165] As used herein, the terms "treat", "treating", and "treatment", as well as "prevent", "prevention", and "prevention" refer to eliciting a desired biological response, such as a therapeutic effect and a preventative effect, respectively. In some embodiments, the therapeutic effect includes one or more of the following after administration of the agent or a composition comprising the agent: reduction / alleviation of CHIP, reduction / alleviation of the severity of CHIP (e.g., reduction or inhibition of onset of CHIP), reduction / alleviation of symptoms and CHIP-related effects, delay in onset of symptoms and CHIP-related effects, reduction in the severity of symptoms of CHIP-related effects, reduction in the number of symptoms and CHIP-related effects, reduction in the latency of symptoms and CHIP-related effects, improvement of symptoms and CHIP-related effects, reduction in secondary symptoms, reduction in secondary infections, prevention of recurrence of CHIP, reduction in the number or frequency of recurrent episodes, increase in the latency period between symptomatic episodes, increase in the time to persistent progression, rapid recovery, or increase in the effectiveness of or reduction in resistance to alternative treatments, and / or increase in the survival time of the affected host animal. A prophylactic effect can include complete or partial avoidance / suppression, or delay (e.g., complete or partial avoidance / suppression or delay, etc.) of the onset / progression of CHIP following administration of a treatment protocol, and extending the survival time of an affected host animal. Treating CHIP includes treating a subject already diagnosed with any form of CHIP at any clinical stage or clinical manifestation, delaying the onset or progression or progression or worsening of symptoms or signs of CHIP, and / or preventing and / or reducing the severity of CHIP.

[0166] In any of the embodiments described herein, for subjects with a loss-of-function variant of TET2 (e.g., due to the presence of indels, TET2 somatic mutation deficiency, etc.), the methods of treatment and prevention exclude treatment with a PARP1 inhibitor. Such subjects can be treated with other methods described herein.

[0167] The present disclosure also provides a method for identifying a subject at high risk of developing CHIP. In some embodiments, the method includes determining or having determined the presence or absence of LY75 variant nucleic acid molecule, CD164 variant nucleic acid molecule, and / or PARP1 variant nucleic acid molecule in a biological sample taken from the subject. If the subject lacks LY75, CD164, and / or PARP1 variant nucleic acid molecule (i.e., the subject is genotypically classified as LY75, CD164, and / or PARP1 reference type), the subject's risk of developing CHIP increases. If the subject has one or more of LY75 variant nucleic acid molecule, CD164 variant nucleic acid molecule, and / or PARP1 variant nucleic acid molecule (i.e., the subject is heterozygous or homozygous for one or more of LY75, CD164, or PARP1 variant nucleic acid molecule), the subject's risk of developing CHIP decreases.

[0168] Having a single copy of the LY75 variant nucleic acid molecule, a subject is more protected from developing CHIP than if they have no copy of the LY75 variant nucleic acid molecule. Having a single copy of the CD164 variant nucleic acid molecule, a subject is more protected from developing CHIP than if they have no copy of the CD164 variant nucleic acid molecule. Having a single copy of the PARP1 variant nucleic acid molecule, a subject is more protected from developing CHIP than if they have no copy of the PARP1 variant nucleic acid molecule.

[0169] Without intending to be limited to any particular theory or mechanism of action, it is believed that a single copy of an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, or a PARP1 variant nucleic acid molecule (i.e., heterozygous for one or more of LY75, CD164, or PARP1 variant nucleic acid molecules) may protect a subject from developing CHIP and CHIP-related disorders, and that carrying two copies of an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, or a PARP1 variant nucleic acid molecule (i.e., homozygous for one or more of LY75, CD164, or PARP1 variant nucleic acid molecules) may be more protective against developing CHIP and CHIP-related disorders compared to a subject having a single copy of the corresponding LY75, CD164, or PARP1 variant nucleic acid molecule.

[0170] Thus, in some embodiments, a single copy of an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, or a PARP1 variant nucleic acid molecule may not completely protect a subject from developing CHIP and CHIP-related disorders, but may instead provide partial or incomplete protection. Without wishing to be bound by any particular theory, there may be additional factors or molecules involved in the development of CHIP and CHIP-related disorders that are still present in a subject having a single copy of one or more of LY75, CD164, or PARP1 variant nucleic acid molecules, and therefore may provide less than complete protection from developing CHIP and CHIP-related disorders.

[0171] Determining whether a subject has one or more of LY75, CD164, or PARP1 variant nucleic acid molecules can be performed by any of the methods described herein. In some embodiments, these methods can be performed in vitro. In some embodiments, these methods can be performed in situ. In some embodiments, these methods can be performed in vivo. In any of these embodiments, the nucleic acid molecule can be present in a cell taken from the subject.

[0172] In some embodiments, when a subject is identified as being at high risk of developing CHIP, a therapeutic agent that prevents or reduces the development of CHIP, as described herein, and / or a LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof, is administered to the subject. For example, when a subject is an LY75 reference type and is therefore at high risk of developing CHIP, a LY75 inhibitor is administered to the subject. Furthermore, when a subject is a CD164 reference type and is therefore at high risk of developing CHIP, a CD164 inhibitor is administered to the subject. Furthermore, when a subject is a PARP1 reference type and is therefore at high risk of developing CHIP, a PARP1 inhibitor is administered to the subject. In some embodiments, such a subject is also administered a therapeutic agent that prevents or reduces the development of CHIP.

[0173] In some embodiments, such subject is also administered a therapeutic agent that prevents or reduces the occurrence of CHIP. In some embodiments, if the subject is homozygous for one or more of LY75, CD164 or PARP1 variant nucleic acid molecules, the therapeutic agent that prevents or reduces the occurrence of CHIP is administered to the subject at a dose equal to or less than the standard dose.

[0174] In some embodiments, if the subject is heterozygous for LY75 variant nucleic acid molecule, the therapeutic agent that prevents or reduces the occurrence of CHIP is administered or continues to be administered to the subject at a dose equal to or less than standard dose, and also administers a LY75 inhibitor.In some embodiments, if the subject is heterozygous for CD164 variant nucleic acid molecule, the therapeutic agent that prevents or reduces the occurrence of CHIP is administered or continues to be administered to the subject at a dose equal to or less than standard dose, and also administers a CD164 inhibitor.In some embodiments, if the subject is heterozygous for PARP1 variant nucleic acid molecule, the therapeutic agent that prevents or reduces the occurrence of CHIP is administered or continues to be administered to the subject at a dose equal to or less than standard dose, and also administers a PARP1 inhibitor.

[0175] In some embodiments, the subject is heterozygous for both an LY75 variant nucleic acid molecule and a CD164 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at the same or less than a standard dose, and is administered an LY75 inhibitor, a CD164 inhibitor, or both.

[0176] In some embodiments, the subject is heterozygous for both an LY75 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at an amount equal to or less than a standard dose, and is administered an LY75 inhibitor, a PARP1 inhibitor, or both.

[0177] In some embodiments, the subject is heterozygous for both a CD164 variant nucleic acid molecule and a PARP1 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at the same or less than a standard dose, and is administered a CD164 inhibitor, a PARP1 inhibitor, or both.

[0178] In some embodiments, the subject is heterozygous for an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and a PARP1 variant nucleic acid molecule, and the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at an amount equal to or less than the standard dose, and is administered an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof.

[0179] In some embodiments, the subject is LY75, CD164, and PARP1 reference type. In some embodiments, the subject is heterozygous for one or more of LY75, CD164, or PARP1 variant nucleic acid molecules. In some embodiments, the subject is homozygous for one or more of LY75, CD164, or PARP1 variant nucleic acid molecules.

[0180] The present disclosure also provides a method for identifying a subject at high risk of developing lung cancer. In some embodiments, the method includes determining or having determined the presence or absence of a CHIP somatic mutation in DNMT3A and / or ASXL1 in a biological sample taken from the subject. If the subject lacks a CHIP somatic mutation in DNMT3A and / or ASXL1, the subject's risk of developing lung cancer is not increased. If the subject has a CHIP somatic mutation in DNMT3A and / or ASXL1, the subject's risk of developing lung cancer is increased. In some embodiments, the subject is a smoker. In some embodiments, the subject is a non-smoker. In some embodiments, the CHIP somatic mutation is in DNMT3A. In some embodiments, the CHIP somatic mutation is in ASXL1. A subject who does not have an increased risk of developing lung cancer because of lacking a CHIP somatic mutation in DNMT3A and / or ASXL1 may still be at increased risk compared to the average individual due to reasons such as smoking, inhalation of toxic chemicals at work, urban pollution, etc.

[0181] Determining whether a subject has one or more somatic CHIP mutations in DNMT3A and / or ASXL1 can be performed by any of the methods described herein. In some embodiments, these methods can be performed in vitro. In some embodiments, these methods can be performed in situ. In some embodiments, these methods can be performed in vivo. In any of these embodiments, a nucleic acid molecule having a somatic CHIP mutation in DNMT3A and / or ASXL1 can be present in a cell taken from the subject.

[0182] In some embodiments, if a subject is identified as being at high risk for developing lung cancer, the subject may be subjected to enhanced monitoring, lifestyle changes, and / or reduced exposure to harmful substances. For example, the subject may be monitored more frequently for lung cancer pathology and / or symptoms. In some embodiments, such subjects may be subjected to more frequent chest x-rays, etc., compared to subjects who are not at such increased risk for developing lung cancer. In some embodiments, the subject may be further monitored for lung cancer-associated somatic mutations (EGFR mutations, KRAS mutations, etc.) using DNA from sputum and / or blood (i.e., more frequent cell-free DNA testing / monitoring). In some embodiments, enhanced surveillance options may include earlier monitoring with magnetic resonance imaging (MRI). In some embodiments, such subjects who are smokers may be initiated into smoking cessation procedures. In some embodiments, lifestyle changes may include reduced exposure to environmental risk factors selected from secondhand smoke, radon, and workplace smoking exposure. In some embodiments, the harmful substance is selected from asbestos, arsenic, nickel, chromium, beryllium, cadmium, silica, diesel exhaust, tar, or soot, or any combination thereof.In some embodiments, such subject can be treated with a therapeutic agent for palliative or preventive treatment.In some embodiments, subject can be administered a therapeutically effective amount of erlotinib, 5-(p-methoxyphenyl)-1,2-dithiol-3-thione, deguelin, or iloprost, or any combination thereof.

[0183] In some embodiments, the subject has a somatic CHIP mutation in DNMT3A and / or ASXL1.In some embodiments, the subject does not have a somatic CHIP mutation in DNMT3A and / or ASXL1.

[0184] In any of the embodiments described herein, for subjects who are determined to have an increased risk of developing CHIP, such subjects who also carry a loss-of-function variant of TET2 (e.g., due to the presence of indels; TET2 somatic mutation deficiency) can be subjected to a treatment or prevention regimen that excludes treatment with a PARP1 inhibitor. Such subjects can be treated by other methods described herein. Thus, subjects who have a loss-of-function variant in TET2 and are determined to have an increased risk of developing CHIP can be excluded from the population of subjects suitable for treatment with a PARP1 inhibitor.

[0185] The biological sample for detecting CHIP somatic mutations in DNMT3A and / or ASXL1 can be derived from any cell, tissue, or body fluid from a subject. The biological sample can include any clinically significant tissue, such as lung tissue or lung cells from a biopsy, fine needle aspirate, or a sample of body fluid, such as blood, gingival crevicular fluid, plasma, serum, lymph, ascites, cyst fluid, or urine. In some cases, the sample includes a buccal swab. The biological sample used in the methods disclosed herein can vary based on the assay format, the nature of the detection method, and the tissue, cell, or extract used as the sample. The detection of CHIP somatic mutations in DNMT3A and / or ASXL1 can be performed by the same method as the detection of any variant nucleic acid molecule described herein, using appropriate primers and probes.

[0186] The lung cancer may comprise non-small cell lung cancer, small cell lung cancer, mesothelioma, pulmonary carcinoid tumor, or chest wall tumor. In some embodiments, the lung cancer comprises non-small cell lung cancer. In some embodiments, the lung cancer comprises small cell lung cancer. In some embodiments, the lung cancer comprises mesothelioma. In some embodiments, the lung cancer comprises pulmonary carcinoid tumor. In some embodiments, the lung cancer comprises a chest wall tumor.

[0187] In some embodiments, any of the methods described herein may further comprise determining the subject's burden with one or more of LY75, CD164, or PARP1 variant nucleic acid molecules, and / or one or more of predicted LY75, CD164, or PARP1 loss-of-function variant polypeptides associated with a reduced risk of developing CHIP and CHIP-related disorders. The burden is the sum of all variants of the LY75 gene, CD164 gene, and / or PARP1 gene, and can be performed in an association analysis using CHIP. In some embodiments, the subject is homozygous for one or more LY75 variant nucleic acid molecules associated with a reduced risk of developing CHIP. In some embodiments, the subject is heterozygous for one or more LY75 variant nucleic acid molecules associated with a reduced risk of developing CHIP. In some embodiments, the subject is homozygous for one or more CD164 variant nucleic acid molecules associated with a reduced risk of developing CHIP. In some embodiments, the subject is heterozygous for one or more CD164 variant nucleic acid molecules associated with a reduced risk of developing CHIP. In some embodiments, the subject is homozygous for one or more PARP1 variant nucleic acid molecules associated with a reduced risk of developing CHIP. In some embodiments, the subject is heterozygous for one or more PARP1 variant nucleic acid molecules associated with a reduced risk of developing CHIP.

[0188] The results of the association analysis suggest that LY75, CD164, and / or PARP1 variant nucleic acid molecules are associated with a reduced risk of developing CHIP. If the subject's burden is low, the subject's risk of developing CHIP is high, and the subject is administered or continues to be administered a therapeutic agent that prevents or reduces the development of CHIP at a standard dose, and / or an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof. If the subject's burden is high, the subject's risk of developing CHIP is low, and the subject is administered or continues to be administered a therapeutic agent that prevents or reduces the development of CHIP at the same or lower dose than the standard dose. The higher the burden, the lower the risk of developing CHIP. Alternatively, the genetic burden analysis can include determining whether a CHIP carrier is more likely to have any variants aggregated in the burden framework due to genetic effects.

[0189] In some embodiments, the burden of subjects having one or more of LY75, CD164, and / or PARP1 variant nucleic acid molecules, or any one of the predicted loss-of-function polypeptides of LY75, CD164 predicted loss-of-function polypeptides, and / or PARP1 predicted loss-of-function polypeptides represents a weighted sum of a plurality of any of the LY75, CD164, or PARP1 variant nucleic acid molecules, or predicted loss-of-function polypeptides. In some embodiments, at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 100, at least about 120, at least about 150, at least about 200, at least about 250, at least about 300, at least about 400, at least about 500, at least about 1,000, at least about 10,000, at least about 100,000, or at least 1,000,000 or more genetic variants present in or surrounding the LY75, CD164, or PARP1 gene (up to 10 Mb) are used to calculate the burden, where the genetic burden is the number of alleles multiplied by the estimated association with CHIP or a related outcome for each allele (e.g., a weighted polygenic burden score). This may include any genetic variants that are close to any one of the LY75, CD164, and / or PARP1 genes (up to 10Mb around the gene) that show non-zero association with CHIP-related traits in genetic association analysis, regardless of genome annotation. In some embodiments, if a subject has a load higher than the desired threshold score, the subject's risk of developing CHIP decreases. In some embodiments, if a subject has a load lower than the desired threshold score, the subject's risk of developing CHIP increases.

[0190] In some embodiments, the burdens can be divided into quintiles, such as top quintile, middle quintile, and bottom quintile, with the top quintile of burdens corresponding to the lowest risk group and the bottom quintile of burdens corresponding to the highest risk group. In some embodiments, subjects with larger burdens include the highest weighted burdens, including but not limited to the top 10%, top 20%, top 30%, top 40%, or top 50% burdens from the subject population. In some embodiments, the genetic variants include genetic variants with association with CHIP in the top 10%, top 20%, top 30%, top 40%, or top 50% of the p-value range for association. In some embodiments, each of the identified genetic variants is about 10 -2 Below, about 10 -3 Below, about 10 -4 Below, about 10 -5 Below, about 10 -6 Below, about 10 -7 Below, about 10 -8 Below, about 10 -9 Below, about 10 -10 Below, about 10 -11 Below, about 10 -12 Below, about 10 -13 Below, about 10 -14 Less than or equal to 10 -15 In some embodiments, the identified genetic variants have an association with CHIP with a p-value of 5×10 -8In some embodiments, the identified genetic variants include genetic variants that have an association with CHIP in high-risk subjects with an odds ratio (OR) of about 1.5 or more, about 1.75 or more, about 2.0 or more, or about 2.25 or more, or about 1.5 or more, about 1.75 or more, about 2.0 or more, about 2.25 or more, about 2.5 or more, or about 2.75 or more for the top 20% of the distribution compared to the remainder of the reference population. In some embodiments, the odds ratio (OR) may range from about 1.0 to about 1.5, about 1.5 to about 2.0, about 2.0 to about 2.5, about 2.5 to about 3.0, about 3.0 to about 3.5, about 3.5 to about 4.0, about 4.0 to about 4.5, about 4.5 to about 5.0, about 5.0 to about 5.5, about 5.5 to about 6.0, about 6.0 to about 6.5, about 6.5 to about 7.0, or more than 7.0. In some embodiments, high-risk subjects include subjects with a burden in the bottom decile, quintile, or tertile in the reference population. The burden threshold is determined based on the nature of the intended practical application and the risk difference that is considered meaningful for that practical application.

[0191] In some embodiments, if the subject is identified as being at high risk of developing CHIP, the subject is further administered a therapeutic agent for preventing or reducing CHIP, as described herein, and / or an LY75 inhibitor, a CD164 inhibitor, a PARP1 inhibitor, or any combination thereof.For example, if the subject is an LY75 reference type and therefore at high risk of developing CHIP, the subject is administered an LY75 inhibitor.Further, if the subject is a CD164 reference type and therefore at high risk of developing CHIP, the subject is administered a CD164 inhibitor.Further, if the subject is a PARP1 reference type and therefore at high risk of developing CHIP, the subject is administered a PARP1 inhibitor.

[0192] In some embodiments, such a subject is also administered a therapeutic agent that prevents or reduces the onset of CHIP. In some embodiments, if the subject is heterozygous for LY75 variant nucleic acid molecule, the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at a dose equal to or less than standard dose, and also administered a LY75 inhibitor. In some embodiments, if the subject is heterozygous for CD164 variant nucleic acid molecule, the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at a dose equal to or less than standard dose, and also administered a CD164 inhibitor. In some embodiments, if the subject is heterozygous for PARP1 variant nucleic acid molecule, the subject is further or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at a dose equal to or less than standard dose, and also administered a PARP1 inhibitor.

[0193] In some embodiments, the subject is LY75, CD164, and PARP1 reference type. In some embodiments, the subject is heterozygous for one or more of LY75, CD164, or PARP1 variant nucleic acid molecules. Furthermore, if the subject has a low burden of one or more of LY75, CD164, or PARP1 variant nucleic acid molecules and is therefore at high risk of developing CHIP, the subject is administered a therapeutic agent that prevents or reduces the development of CHIP. In some embodiments, if the subject has a low burden of one or more of LY75, CD164, or PARP1 variant nucleic acid molecules, the subject is administered a therapeutic agent that prevents or reduces the development of CHIP at a dose equal to or higher than the standard dose administered to subjects with a high burden of one or more of LY75, CD164, or PARP1 variant nucleic acid molecules.

[0194] In some embodiments, any of the methods described herein may further comprise determining the subject's burden of having a CHIP somatic mutation in DNMT3A and / or ASXL1 associated with an increased risk of developing lung cancer. The burden is the sum of all somatic mutations in the DNMT3A gene and / or ASXL1 gene, which can be performed in an association study with lung cancer. In some embodiments, the subject has a CHIP somatic mutation in DNMT3A associated with an increased risk of developing lung cancer. In some embodiments, the subject does not have a CHIP somatic mutation in DNMT3A associated with an increased risk of developing lung cancer. In some embodiments, the subject has a CHIP somatic mutation in ASXL1 associated with an increased risk of developing lung cancer. In some embodiments, the subject does not have a CHIP somatic mutation in ASXL1 associated with an increased risk of developing lung cancer.

[0195] The result of the association analysis can show that DNMT3A and / or ASXL1 somatic mutations are associated with an increased risk of developing lung cancer.If the subject has a low burden, the subject's risk of developing lung cancer is not increased.If the subject has a high burden, the subject's risk of developing lung cancer is increased, and the subject can be subjected to any of the treatments described herein related to lung cancer.The higher the burden, the higher the risk of developing lung cancer.

[0196] Representative somatic DNMT3A mutations include the following: [Table 4-1] [Table 4-2] [Table 4-3] [Table 4-4]

Table 4-5

Table 4-6

Table 4-7

Table 4-8

Table 4-9

Table 4-10

Table 4-11

Table 4-12

Table 4-13

Table 4-14

Table 4-15

Table 4-16

Table 4-17

Table 4-18

Table 4-19

Table 4-20

Table 4-21

Table 4-22

Table 4-23

Table 4-24

Table 4-25

Table 4-26

Table 4-27

Table 4-28

Table 4-29

Table 4-30

Table 4-31

Table 4-32

Table 4-33

Table 4-34

Table 4-35

Table 4-36

Table 4-37

Table 4-38

Table 4-39

Table 4-40

Table 4-41

Table 4-42

Table 4-43

Table 4-44

Table 4-45

Table 4-46

Table 4-47

Table 4-48

Table 4-49

Table 4-50

Table 4-51

Table 4-52

Table 4-53

Table 4-54

Table 4-55

Table 4-56

Table 4-57

Table 4-58

Table 4-59

Table 4-60

Table 4-61

Table 4-62

Table 4-63

Table 4-64

Table 4-65

Table 4-66

Table 4-67

Table 4-68

Table 4-69

Table 4-70

Table 4-71

Table 4-72

Table 4-73

Table 4-74

Table 4-75

Table 4-76

Table 4-77

Table 4-78

Table 4-79

Table 4-80

Table 4-81

Table 4-82

Table 4-83

Table 4-84

Table 4-85

Table 4-86

Table 4-87

Table 4-88

Table 4-89

Table 4-90

Table 4-91

Table 4-92

Table 4-93

Table 4-94

Table 4-95

Table 4-96

Table 4-97

Table 4-98

Table 4-99

Table 4-100

Table 4-101

Table 4-102

Table 4-103

Table 4-104

Table 4-105

Table 4-106

Table 4-107

Table 4-108

Table 4-109

Table 4-110

Table 4-111

Table 4-112

Table 4-113

Table 4-114

Table 4-115

Table 4-116

Table 4-117

Table 4-118

Table 4-119

Table 4-120

Table 4-121

Table 4-122

Table 4-123

Table 4-124

Table 4-125

Table 4-126

Table 4-127

Table 4-128

Table 4-129

Table 4-130

Table 4-131

Table 4-132

Table 4-133

Table 4-134

Table 4-135

Table 4-136

Table 4-137

Table 4-138

Table 4-139

Table 4-140

Table 4-141

Table 4-142

Table 4-143

Table 4-144

Table 4-145

Table 4-146

Table 4-147

Table 4-148

Table 4-149

Table 4-150

Table 4-151

Table 4-152

Table 4-153

Table 4-154

Table 4-155

Table 4-156

Table 4-157

Table 4-158

Table 4-159

Table 4-160

Table 4-161

Table 4-162

Table 4-163

Table 4-164

Table 4-165

Table 4-166

Table 4-167

Table 4-168

Table 4-169

Table 4-170

Table 4-171

Table 4-172

Table 4-173

Table 4-174

Table 4-175

Table 4-176

Table 4-177

Table 4-178

Table 4-179

Table 4-180

Table 4-181

Table 4-182

Table 4-183

Table 4-184

Table 4-185

Table 4-186

Table 4-187

Table 4-188

Table 4-189

Table 4-190

Table 4-191

Table 4-192

Table 4-193

Table 4-194

Table 4-195

Table 4-196

[0197] Representative ASXL1 somatic mutations include the following: [Table 5-1] [Table 5-2]

Table 5-3

Table 5-4

Table 5-5

Table 5-6

Table 5-7

Table 5-8

Table 5-9

Table 5-10

Table 5-11

Table 5-12

Table 5-13

Table 5-14

Table 5-15

Table 5-16

Table 5-17

Table 5-18

Table 5-19

Table 5-20

Table 5-21

Table 5-22

Table 5-23

Table 5-24

Table 5-25

Table 5-26

Table 5-27

Table 5-28

Table 5-29

Table 5-30

Table 5-31

Table 5-32

Table 5-33

Table 5-34

Table 5-35

Table 5-36

Table 5-37

Table 5-38

Table 5-39

Table 5-40

Table 5-41

Table 5-42

Table 5-43

Table 5-44

Table 5-45

Table 5-46

Table 5-47

Table 5-48

Table 5-49

Table 5-50

Table 5-51

Table 5-52

Table 5-53

Table 5-54

Table 5-55

Table 5-56

Table 5-57

[0198] In some embodiments, the burden of a subject with any one or more somatic mutations in DNMT3A and / or ASXL1 may represent a weighted sum of any multiple of the DNMT3A and / or ASXL1 somatic mutations. In some embodiments, the burden is calculated using at least about 2, at least about 3, at least about 4, at least about 5, at least about 10, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 100, at least about 120, at least about 150, at least about 200, at least about 250, at least about 300, at least about 400, at least about 500, at least about 1,000, at least about 10,000, at least about 100,000, or at least about 1,000,000 or more mutations present in or surrounding (up to 10 Mb) the DNMT3A gene and / or ASXL1 gene, where the genetic burden is the number of mutations multiplied by the estimated association with lung cancer for each mutation (e.g., a weighted burden score). This may include any somatic mutations proximal to the DNMT3A gene and / or the ASXL1 gene (up to 10 Mb surrounding the gene) that show a non-zero association with lung cancer. In some embodiments, if a subject has a burden higher than the desired threshold score, the subject's risk of developing lung cancer is increased. In some embodiments, if a subject has a burden lower than the desired threshold score, the subject's risk of developing lung cancer is not increased.

[0199] In some embodiments, the burdens can be divided into quintiles, such as top quintile, middle quintile, and bottom quintile, with the bottom quintile of burdens corresponding to the lowest risk group and the top quintile of burdens corresponding to the highest risk group. In some embodiments, subjects with larger burdens include the highest weighted burdens, including but not limited to the top 10%, top 20%, top 30%, top 40%, or top 50% burdens from the subject population. In some embodiments, the somatic mutations include somatic mutations that have an association with lung cancer in the top 10%, top 20%, top 30%, top 40%, or top 50% of the p-value range for the association. In some embodiments, each of the identified somatic mutations is about 10 -2 , about 10 -3 , about 10 -4 , about 10 -5 , about 10 -6 , about 10 -7 , about 10 -8 , about 10 -9 , about 10 -10 , about 10 -11 , about 10 -12 , about 10 -13 , about 10 -14 , or 10 -15 In some embodiments, the identified somatic mutations include those having an association with lung cancer with a p-value of 5×10 -8In some embodiments, the identified somatic mutations include somatic mutations that have an association with lung cancer in high-risk subjects with an odds ratio (OR) of about 1.5 or more, about 1.75 or more, about 2.0 or more, or about 2.25 or more, or about 1.5 or more, about 1.75 or more, about 2.0 or more, about 2.25 or more, about 2.5 or more, or about 2.75 or more for the top 20% of the distribution, relative to the remainder of the reference population. In some embodiments, the OR may range from about 1.0 to about 1.5, about 1.5 to about 2.0, about 2.0 to about 2.5, about 2.5 to about 3.0, about 3.0 to about 3.5, about 3.5 to about 4.0, about 4.0 to about 4.5, about 4.5 to about 5.0, about 5.0 to about 5.5, about 5.5 to about 6.0, about 6.0 to about 6.5, about 6.5 to about 7.0, or more than 7.0. In some embodiments, high-risk subjects include subjects with a burden in the top decile, quintile, or tertile in the reference population. The burden threshold is determined based on the nature of the intended practical application and the risk difference that is considered meaningful for that practical application.

[0200] In some embodiments, if a subject is identified as being at high risk of developing lung cancer, the subject can be subjected to any procedure described herein related to lung cancer.In some embodiments, genetic burden can be replaced by survival analysis, whereby carriers of somatic mutation(s) are testers for determining whether they are more likely or less likely to develop lung cancer over time.

[0201] The genetic burden analysis described herein can also be used as a mask to screen subjects for risk of developing any of the indications.

[0202] The present disclosure also provides a method for detecting the presence or absence of LY75 variant nucleic acid molecules, CD164 variant nucleic acid molecules, and / or PARP1 variant nucleic acid molecules (i.e., genomic nucleic acid molecules, mRNA molecules, or cDNA molecules generated from mRNA molecules) in a biological sample from a subject. It is understood that gene sequences within a population, and the mRNA molecules encoded by such genes, may vary due to polymorphisms, such as single nucleotide polymorphisms. The sequences provided herein for LY75, CD164, and PARP1 variant genomic nucleic acid molecules, LY75, CD164, and PARP1 variant mRNA molecules, and LY75, CD164, and PARP1 variant cDNA molecules are merely exemplary sequences. Other sequences are possible for LY75, CD164, and PARP1 variant genomic nucleic acid molecules, variant mRNA molecules, and variant cDNA molecules.

[0203] The biological sample may be derived from any cell, tissue, or biological fluid of a subject. The biological sample may include any clinically significant tissue of bone marrow sample, tumor biopsy, fine needle aspirate, or bodily fluid sample such as blood, gingival crevicular fluid, plasma, serum, lymph, ascites, cyst fluid, or urine. In some cases, the sample includes a buccal swab. The biological sample used in the methods disclosed herein may vary based on the assay format, the nature of the detection method, and the tissue, cell, or extract used as the sample. The biological sample may be processed differently depending on the assay employed. For example, when detecting any LY75 variant nucleic acid molecule, CD164 variant nucleic acid molecule, and / or PARP1 variant nucleic acid molecule, a pre-processing designed to isolate or enrich the genomic DNA of the biological sample may be used. A variety of techniques may be used for this purpose. When detecting the level of LY75, CD164, and / or PARP1 variant mRNA molecules, a variety of techniques may be used to enrich the biological sample containing mRNA molecules. A variety of methods can be used to detect the presence or levels of mRNA molecules, or the presence of particular variant genomic DNA loci.

[0204] In some embodiments, detecting a predicted loss-of-function polypeptide of LY75 in a subject comprises performing sequence analysis on a biological sample obtained from the subject to determine whether an LY75 genomic nucleic acid molecule in the biological sample, and / or an LY75 mRNA molecule in the biological sample, and / or an LY75 cDNA molecule generated from the mRNA molecule in the biological sample contains one or more variations that cause or are predicted to cause a loss of function (partial or complete).

[0205] In some embodiments, detecting a CD164 variant nucleic acid molecule in a subject comprises performing sequence analysis on a biological sample taken from the subject to determine whether a CD164 genomic nucleic acid molecule in the biological sample, and / or a CD164 mRNA molecule in the biological sample, and / or a CD164 cDNA molecule generated from the mRNA molecule in the biological sample contains one or more variations that cause or are predicted to cause a loss of function (partial or complete).

[0206] In some embodiments, detecting a PARP1 variant nucleic acid molecule in a subject comprises performing sequence analysis on a biological sample taken from the subject to determine whether a PARP1 genomic nucleic acid molecule in the biological sample, and / or a PARP1 mRNA molecule in the biological sample, and / or a PARP1 cDNA molecule generated from the mRNA molecule in the biological sample contains one or more variations that cause or are predicted to cause a loss of function (partial or complete).

[0207] In some embodiments, a method for detecting the presence or absence of an LY75 variant nucleic acid molecule (e.g., a genomic nucleic acid molecule, an mRNA molecule, and / or a cDNA molecule generated from an mRNA) in a subject comprises performing an assay on a biological sample obtained from the subject, the assay determining whether a nucleic acid molecule in the biological sample comprises a particular nucleotide sequence.

[0208] In some embodiments, a method for detecting the presence or absence of a CD164 variant nucleic acid molecule (e.g., a genomic nucleic acid molecule, an mRNA molecule, and / or a cDNA molecule generated from an mRNA) in a subject comprises performing an assay on a biological sample obtained from the subject, the assay determining whether a nucleic acid molecule in the biological sample comprises a particular nucleotide sequence.

[0209] In some embodiments, a method for detecting the presence or absence of a PARP1 variant nucleic acid molecule (e.g., a genomic nucleic acid molecule, an mRNA molecule, and / or a cDNA molecule generated from an mRNA) in a subject comprises performing an assay on a biological sample obtained from the subject, the assay determining whether a nucleic acid molecule in the biological sample comprises a particular nucleotide sequence.

[0210] In some embodiments, the biological sample comprises cells or cell lysates. Such methods can further comprise, for example, obtaining a biological sample from a subject that comprises LY75 genomic nucleic acid molecules or mRNA molecules, CD164 genomic nucleic acid molecules or mRNA molecules, and / or PARP1 genomic nucleic acid molecules or mRNA molecules, and in the case of mRNA, optionally reverse transcribing the mRNA into cDNA. Such assays can comprise, for example, determining the identity of these positions of a particular LY75 nucleic acid molecule, a particular CD164 nucleic acid molecule, and / or a particular PARP1 nucleic acid molecule. In some embodiments, the methods are in vitro methods.

[0211] In some embodiments, the determining, detecting, or sequence analysis step comprises sequencing at least a portion of the nucleotide sequence of an LY75 genomic nucleic acid molecule, an LY75 mRNA molecule, or an LY75 cDNA molecule in the biological sample, wherein the sequenced portion contains one or more mutations that cause or are predicted to cause a loss of function (partial or complete).

[0212] In some embodiments, the determining, detecting, or sequence analysis step comprises sequencing at least a portion of the nucleotide sequence of a CD164 genomic nucleic acid molecule, a CD164 mRNA molecule, or a CD164 cDNA molecule in the biological sample, and the sequenced portion contains one or more mutations that cause or are predicted to cause loss of function (partial or complete).

[0213] In some embodiments, the determining, detecting, or sequence analysis step comprises sequencing at least a portion of the nucleotide sequence of a PARP1 genomic nucleic acid molecule, a PARP1 mRNA molecule, or a PARP1 cDNA molecule in the biological sample, wherein the sequenced portion contains one or more mutations that cause or are predicted to cause a loss of function (partial or complete).

[0214] In some embodiments, the assay comprises sequencing the entire nucleic acid molecule. In some embodiments, only the LY75 genomic nucleic acid molecule is analyzed. In some embodiments, only the LY75 mRNA is analyzed. In some embodiments, only the LY75 cDNA obtained from the LY75 mRNA is analyzed.

[0215] In some embodiments, the assay comprises sequencing the entire nucleic acid molecule. In some embodiments, only the CD164 genomic nucleic acid molecule is analyzed. In some embodiments, only CD164 mRNA is analyzed. In some embodiments, only CD164 cDNA obtained from CD164 mRNA is analyzed.

[0216] In some embodiments, the assay comprises sequencing the entire nucleic acid molecule. In some embodiments, only the PARP1 genomic nucleic acid molecule is analyzed. In some embodiments, only the PARP1 mRNA is analyzed. In some embodiments, only the PARP1 cDNA obtained from the PARP1 mRNA is analyzed.

[0217] Mutation-specific polymerase chain reaction techniques can be used to detect mutations, such as SNPs, in nucleic acid sequences. Mutation-specific primers can be used because DNA polymerase will not extend if there is a mismatch with the template.

[0218] In some embodiments, the nucleic acid molecule in the sample is mRNA, and the mRNA is reverse transcribed into cDNA prior to the amplification step. In some embodiments, the nucleic acid molecule is present in a cell taken from the subject.

[0219] In some embodiments, the assay involves contacting the biological sample with a primer or probe, e.g., a variant-specific primer or variant-specific probe, that specifically hybridizes under stringent conditions to an LY75 variant genomic, mRNA, or cDNA sequence and does not hybridize to the corresponding LY75 reference sequence, and determining whether hybridization occurs.

[0220] In some embodiments, the assay involves contacting the biological sample with a primer or probe, e.g., a variant-specific primer or variant-specific probe, that specifically hybridizes under stringent conditions to a CD164 variant genomic sequence, variant mRNA sequence, or variant cDNA sequence and does not hybridize to the corresponding CD164 reference sequence, and determining whether hybridization occurs.

[0221] In some embodiments, the assay involves contacting the biological sample with a primer or probe, e.g., a mutation-specific primer or a mutation-specific probe, that specifically hybridizes under stringent conditions to a PARP1 variant genomic sequence, variant mRNA sequence, or variant cDNA sequence and does not hybridize to the corresponding PARP1 reference sequence, and determining whether hybridization occurs.

[0222] In some embodiments, the determining, detecting, or sequence analyzing step comprises a) amplifying at least a portion of a nucleic acid molecule encoding an LY75 polypeptide, b) labeling the amplified nucleic acid molecule with a detectable label, c) contacting the labeled nucleic acid molecule with a support comprising a mutation-specific probe, and d) detecting the detectable label.

[0223] In some embodiments, the determining, detecting, or sequence analyzing step comprises: a) amplifying at least a portion of a nucleic acid molecule encoding a CD164 polypeptide; b) labeling the amplified nucleic acid molecule with a detectable label; c) contacting the labeled nucleic acid molecule with a support comprising a mutation-specific probe; and d) detecting the detectable label.

[0224] In some embodiments, the determining, detecting, or sequence analyzing step comprises: a) amplifying at least a portion of a nucleic acid molecule encoding a PARP1 polypeptide; b) labeling the amplified nucleic acid molecule with a detectable label; c) contacting the labeled nucleic acid molecule with a support comprising a mutation-specific probe; and d) detecting the detectable label.

[0225] In some embodiments, the assay involves RNA sequencing (RNA-Seq). In some embodiments, the assay also involves reverse transcribing mRNA into cDNA, for example, by reverse transcription polymerase chain reaction (RT-PCR).

[0226] In some embodiments, the method utilizes probes and primers of sufficient nucleotide length to bind to the target nucleotide sequence and specifically detect and / or identify polynucleotides comprising LY75 variant genomic nucleic acid molecules, variant mRNA molecules, or variant cDNA molecules, and utilizes probes and primers of sufficient nucleotide length to specifically detect and / or identify polynucleotides comprising CD164 variant genomic nucleic acid molecules, variant mRNA molecules, or variant cDNA molecules, and / or PARP1 variant genomic nucleic acid molecules, variant mRNA molecules, or variant cDNA molecules. Hybridization conditions or reaction conditions can be determined by the operator to achieve this result. The nucleotide length may be any length that is sufficient for use in the detection method of choice, including any of the assays described or exemplified herein. Such probes and primers can specifically hybridize to the target nucleotide sequence under highly stringent hybridization conditions. Although probes that are distinct from the target nucleotide sequence and that retain the ability to specifically detect and / or identify the target nucleotide sequence may be designed by conventional methods, the probes and primers may have complete nucleotide sequence identity to consecutive nucleotides within the target nucleotide sequence. The probes and primers can have about 80%, about 85%, about 90%, about 91%, about 92%, about 93%, about 94%, about 95%, about 96%, about 97%, about 98%, about 99%, or 100% sequence identity or complementarity to the nucleotide sequence of the target nucleic acid molecule.

[0227] Exemplary nucleic acid sequencing techniques include, but are not limited to, chain terminator (Sanger) sequencing and dye terminator sequencing. Other methods include nucleic acid hybridization methods other than sequencing (fluorescence in situ hybridization (FISH)), including the use of labeled primers or probes on purified DNA, amplified DNA, and fixed cell preparations. In some methods, the target nucleic acid molecule may be amplified prior to or simultaneously with detection. Illustrative examples of nucleic acid amplification techniques include, but are not limited to, polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA), and nucleic acid sequence-based amplification (NASBA). Other methods include, but are not limited to, ligase chain reaction, strand displacement amplification, and thermophilic SDA (tSDA).

[0228] Hybridization techniques can employ stringent conditions so that the probe or primer specifically hybridizes with its target. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target sequence detectably higher than other non-target sequences, for example, at least 2-fold, at least 3-fold, at least 4-fold or more above background, including more than 10-fold above background. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence detectably higher than other nucleotide sequences at least 2-fold. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence detectably higher than other nucleotide sequences at least 3-fold. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence detectably higher than other nucleotide sequences at least 4-fold. In some embodiments, a polynucleotide primer or probe under stringent conditions will hybridize to its target nucleotide sequence to a detectably greater extent than other nucleotide sequences, more than 10-fold above background. Stringent conditions are sequence-dependent and will be different in different circumstances.

[0229] Suitable stringent conditions that promote DNA hybridization, such as 6x sodium chloride / sodium citrate (SSC) at about 45°C, followed by a 2x SSC wash at 50°C, are known or can be found in Current Protocols in Molecular Biology, John Wiley & Sons, NY (1989), 6.3.1-6.3.6. Typically, stringent conditions for hybridization and detection include conditions in which the salt concentration is less than about 1.5 M NaCl at pH 7.0-8.3. +ion, usually about 0.01 to 1.0 M Na + The conditions will be ionic concentration (or other salts) and temperature of at least about 30° C. for short probes (e.g., 10-50 nucleotides) and at least about 60° C. for longer probes (e.g., more than 50 nucleotides). Stringent conditions may be achieved by the addition of destabilizing agents such as formamide. Optionally, the wash buffer may contain about 0.1% to about 1% SDS. The duration of hybridization is generally less than about 24 hours, usually about 4 to about 12 hours. The duration of the wash period will be at least long enough to reach equilibrium.

[0230] In some embodiments, such isolated nucleic acid molecules comprise at least about 5, at least about 8, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, at least about 25, at least about 30, at least about 35, at least about 40, at least about 45, at least about 50, at least about 55 , at least about 60, at least about 65, at least about 70, at least about 75, at least about 80, at least about 85, at least about 90, at least about 95, at least about 100, at least about 200, at least about 300, at least about 400, at least about 500, at least about 600, at least about 700, at least about 800, at least about 900, at least about 1000, at least about 2000, at least about 3000, at least about 4000, or at least about 5000 nucleotides. In some embodiments, such isolated nucleic acid molecules comprise or consist of at least about 5, at least about 8, at least about 10, at least about 11, at least about 12, at least about 13, at least about 14, at least about 15, at least about 16, at least about 17, at least about 18, at least about 19, at least about 20, at least about 21, at least about 22, at least about 23, at least about 24, or at least about 25 nucleotides. In some embodiments, the isolated nucleic acid molecule comprises or consists of at least about 18 nucleotides. In some embodiments, the isolated nucleic acid molecule comprises or consists of at least about 15 nucleotides. In some embodiments, the isolated nucleic acid molecule comprises or consists of about 10 to about 35, about 10 to about 30, about 10 to about 25, about 12 to about 30, about 12 to about 28, about 12 to about 24, about 15 to about 30, about 15 to about 25, about 18 to about 30, about 18 to about 25, about 18 to about 24, or about 18 to about 22 nucleotides. In some embodiments, the isolated nucleic acid molecule comprises or consists of about 18 to about 30 nucleotides.In some embodiments, the isolated nucleic acid molecule comprises or consists of at least about 15 nucleotides to at least about 35 nucleotides.

[0231] In some embodiments, such isolated nucleic acid molecules hybridize under stringent conditions to an LY75 variant nucleic acid molecule (such as a genomic nucleic acid molecule, an mRNA molecule, and / or a cDNA molecule). Such nucleic acid molecules can be used, for example, as probes, primers, mutation-specific probes, or mutation-specific primers as described or exemplified herein, including, but not limited to, primers, probes, antisense RNA, shRNA, and siRNA, each of which is described in more detail elsewhere herein and can be used in any of the methods described herein.

[0232] In some embodiments, such isolated nucleic acid molecules hybridize under stringent conditions to CD164 variant nucleic acid molecules (such as genomic nucleic acid molecules, mRNA molecules, and / or cDNA molecules). Such nucleic acid molecules can be used, for example, as probes, primers, mutation-specific probes, or mutation-specific primers as described or exemplified herein, including, but not limited to, primers, probes, antisense RNA, shRNA, and siRNA, each of which is described in more detail elsewhere herein and can be used in any of the methods described herein.

[0233] In some embodiments, such isolated nucleic acid molecules hybridize under stringent conditions to PARP1 variant nucleic acid molecules (such as genomic nucleic acid molecules, mRNA molecules, and / or cDNA molecules). Such nucleic acid molecules can be used, for example, as probes, primers, mutation-specific probes, or mutation-specific primers as described or exemplified herein, including, but not limited to, primers, probes, antisense RNA, shRNA, and siRNA, each of which is described in more detail elsewhere herein and can be used in any of the methods described herein.

[0234] In some embodiments, the isolated nucleic acid molecule hybridizes to at least about 15 contiguous nucleotides of a nucleic acid molecule that is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to an LY75 variant genomic nucleic acid molecule, an LY75 variant mRNA molecule, and / or an LY75 variant cDNA molecule. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 100 nucleotides, or about 15 to about 35 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 100 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 35 nucleotides.

[0235] In some embodiments, the isolated nucleic acid molecule hybridizes to at least about 15 contiguous nucleotides of a nucleic acid molecule that is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to a CD164 variant genomic nucleic acid molecule, a CD164 variant mRNA molecule, and / or a CD164 variant cDNA molecule. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 100 nucleotides, or about 15 to about 35 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 100 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 35 nucleotides.

[0236] In some embodiments, the isolated nucleic acid molecule hybridizes to at least about 15 contiguous nucleotides of a nucleic acid molecule that is at least about 70%, at least about 75%, at least about 80%, at least about 85%, at least about 90%, at least about 95%, at least about 96%, at least about 97%, at least about 98%, at least about 99%, or 100% identical to a PARP1 variant genomic nucleic acid molecule, a PARP1 variant mRNA molecule, and / or a PARP1 variant cDNA molecule. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 100 nucleotides, or about 15 to about 35 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 100 nucleotides. In some embodiments, the isolated nucleic acid molecule consists of or comprises about 15 to about 35 nucleotides.

[0237] In some embodiments, the mutation-specific probe and the mutation-specific primer comprise DNA. In some embodiments, the mutation-specific probe and the mutation-specific primer comprise RNA.

[0238] In some embodiments, the probes and primers described herein (including mutation-specific probes and mutation-specific primers) have nucleotide sequences that specifically hybridize to any of the nucleic acid molecules disclosed herein, or a complementary strand thereof. In some embodiments, the probes and primers specifically hybridize to any of the nucleic acid molecules disclosed herein under stringent conditions.

[0239] In some embodiments, primers, including mutation-specific primers, can be used in second generation or high throughput sequencing. In some examples, primers, including mutation-specific primers, can be modified. In particular, primers can include various modifications used in various steps of, for example, Massive Parallel Signature Sequencing (MPSS), Polony sequencing, and 454 pyrosequencing. Modified primers can be used in several steps of the process, including biotinylated primers in the cloning step, and fluorescently labeled primers used in the bead loading and detection steps. Polony sequencing is typically performed using paired-end tag libraries, where each molecule of DNA template is about 135 bp in length. Biotinylated primers are used in the bead loading and emulsion PCR. Fluorescently labeled degenerate nonamer oligonucleotides are used in the detection step. Adapters can contain 5'-biotin tags for immobilizing DNA libraries on streptavidin-coated beads.

[0240] The probes and primers described herein can be used to detect nucleotide variations within any of the LY75 variant genomic nucleic acid molecules, LY75 variant mRNA molecules, and / or LY75 variant cDNA molecules disclosed herein.The primers described herein can be used to amplify LY75 variant genomic nucleic acid molecules, LY75 variant mRNA molecules, or LY75 variant cDNA molecules, or fragments thereof.

[0241] The probes and primers described herein can also be used to detect nucleotide variations in any of the CD164 variant genomic nucleic acid molecules, CD164 variant mRNA molecules, and / or CD164 variant cDNA molecules disclosed herein.The primers described herein can be used to amplify CD164 variant genomic nucleic acid molecules, CD164 variant mRNA molecules, or CD164 variant cDNA molecules, or fragments thereof.

[0242] The probes and primers described herein can also be used to detect nucleotide variations in any of the PARP1 variant genomic nucleic acid molecules, PARP1 variant mRNA molecules, and / or PARP1 variant cDNA molecules disclosed herein. The primers described herein can be used to amplify CD164 variant genomic nucleic acid molecules, PARP1 variant mRNA molecules, or PARP1 variant cDNA molecules, or fragments thereof.

[0243] In the context of this disclosure, "specifically hybridizes" means that a probe or primer (e.g., a variant-specific probe or variant-specific primer) does not hybridize to a nucleic acid sequence encoding an LY75 reference-type genomic nucleic acid molecule, a CD164 reference-type genomic nucleic acid molecule, a PARP1 reference-type genomic nucleic acid molecule, an LY75 reference-type mRNA molecule, or a CD164 reference-type mRNA molecule, a PARP1 reference-type mRNA molecule, an LY75 reference-type cDNA molecule, a CD164 reference-type cDNA molecule, and / or a PARP reference-type cDNA molecule.

[0244] In some embodiments, the probe (such as, for example, a mutation-specific probe) comprises a label. In some embodiments, the label is a fluorescent label, a radioactive label, or biotin.

[0245] The present disclosure also provides a support comprising a substrate to which any one or more of the probes disclosed herein are attached. A solid support is a solid-state substrate or support to which molecules such as any of the probes disclosed herein can associate. One form of solid support is an array. Another form of solid support is an array detector. An array detector is a solid support to which multiple different probes are attached in an array, grid, or other organized pattern. The form of the solid-state substrate is a microtiter dish, such as a standard 96-well format. In some embodiments, a multi-well glass slide can be used, which typically contains one array per well.

[0246] The nucleotide sequence of the LY75 reference genomic nucleic acid molecule is set forth in SEQ ID NO:1 (ENSG00000054219.11 encompassing chr2:159,803,355-159,904,756 within the GRCh38 / hg38 human genome assembly). The nucleotide sequence of the LY75 variant genomic nucleic acid molecule is set forth in SEQ ID NO:2 (rs78446341; C70,612T; codons 70,611-70,613 CCG-CTG; 101,402 bp). In some embodiments, the LY75 variant genomic nucleic acid molecule is rs147820690 comprising a C>T variation at position chr2:159878663 (GRCh38.p13;NC_000002.12:g.159878663C>T).

[0247] The nucleotide sequence of the LY75 reference type mRNA molecule is set forth in SEQ ID NO: 3 (NM_002349.4; isoform 1; 6,932 nt; LY75 segment). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 4 (ENST00000504764.5; isoform 2; 5,650 nt; LY75-CD302). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 5 (ENST00000505052.1; isoform 3; 5,482 nt; LY75-CD302). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 6 (NM_001198759.1; isoform 4; 8,919 nt; LY75-CD302). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 7 (NM_001198760.1; isoform 5; 8,751 nt; LY75-CD302). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 8 (AY184222.1; isoform 6; 5,622 nt; LY75-CD302). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 9 (AY314006.1; isoform 7; 5,454 nt; LY75-CD302). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 10 (AB208915.1; isoform 8; 5,713 nt; LY75-segment). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 11 (AF011333.1; isoform 9; 6,928 nt; LY75-segment). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 12 (AF064827.1; isoform 10; 5,169 nt; LY75-segment). The nucleotide sequence of another LY75 reference type mRNA molecule is set forth in SEQ ID NO: 13 (ENST00000263636.4; isoform 11; 6,886 nt; LY75-segment).

[0248] The nucleotide sequence of an LY75 variant mRNA molecule is set forth in SEQ ID NO: 14 (NM_002349.4; isoform 1; rs78446341; C3,814T; codons 3,813-3,815 CCG-CUG; 6,932 nt; LY75 segment). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 15 (ENST00000504764.5; isoform 2; rs78446341; C3,768T; codons 3,767-3,769 CCG-CUG; 5,650 nt; LY75-CD302). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 16 (ENST00000505052.1; isoform 3; rs78446341; C3,768T; codons 3,767-3,769 CCG-CUG; 5,482 nt; LY75-CD302). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 17 (NM_001198759.1; isoform 4; rs78446341; C3,814T; codons 3,813-3,815 CCG-CUG; 8,919 nt; LY75-CD302). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 18 (NM_001198760.1; isoform 5; rs78446341; C3,814T; codons 3,813-3,815 CCG-CUG; 8,751 nt; LY75-CD302). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 19 (AY184222.1; isoform 6; rs78446341; C3,740T; codons 3,739-3,741 CCG-CUG; 5,622 nt; LY75-CD302). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 20 (AY314006.1; isoform 7; rs78446341; C3,740T; codons 3,739 to 3,741 CCG to CUG; 5,454 nt; LY75-CD302).The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 21 (AB208915.1; isoform 8; C2,594T; codons 2,593-2,595 CCG-CUG; 5,713 nt; LY75-segment). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 22 (AF011333.1; isoform 9; C3,793T; codons 3,792-3,794 CCG-CUG; 6,928 nt; LY75-segment). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 23 (AF064827.1; isoform 10; C3,740T; codons 3,739-3,741 CCG-CUG; 5,169 nt; LY75-segment). The nucleotide sequence of another LY75 variant mRNA molecule is set forth in SEQ ID NO: 24 (ENST00000263636.4; isoform 11; C3,768T; codons 3,767-3,769 CCG-CUG; 6,886 nt; LY75-segment). In some embodiments, the LY75 variant mRNA molecule is any of the above-mentioned mRNA molecule isoforms generated from the LY75 variant genomic nucleic acid molecule rs147820690, which contains a C>T variation at position chr2:159878663 (GRCh38.p13;NC_000002.12:g.159878663C>T).

[0249] The nucleotide sequence of the LY75 reference type cDNA molecule is set forth in SEQ ID NO:25. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:26. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:27. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:28. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:29. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:30. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:31. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:32. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:33. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:34. The nucleotide sequence of another LY75 reference type cDNA molecule is set forth in SEQ ID NO:35.

[0250] The nucleotide sequence of an LY75 variant cDNA molecule is set forth in SEQ ID NO: 36. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 37. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 38. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 39. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 40. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 41. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 42. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 43. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 44. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 45. The nucleotide sequence of another LY75 variant cDNA molecule is set forth in SEQ ID NO: 46. In some embodiments, the LY75 variant cDNA molecule is any cDNA molecule generated from any mRNA isoform molecule generated from the LY75 variant genomic nucleic acid molecule rs147820690, which contains a C>T variation at position chr2:159878663 (GRCh38.p13;NC_000002.12:g.159878663C>T).

[0251] The amino acid sequence of the LY75 reference polypeptide is set forth in SEQ ID NO: 47 (isoform 1; AAC17636.1) and is 1,722 amino acids in length. The amino acid sequence of another LY75 reference polypeptide is set forth in SEQ ID NO: 48 (isoform 2; NP_001185688.1) and is 1,873 amino acids in length. The amino acid sequence of another LY75 reference polypeptide is set forth in SEQ ID NO: 49 (isoform 3; NP_001185689.1) and is 1,817 amino acids in length. The amino acid sequence of another LY75 reference polypeptide is set forth in SEQ ID NO: 50 (isoform 4; BAD92152.1) and is 1,340 amino acids in length.

[0252] The amino acid sequence of the LY75 variant polypeptide is set forth in SEQ ID NO:51 (isoform 1; AAC17636.1; Pro1,247Leu) and is 1,722 amino acids in length. The amino acid sequence of another LY75 variant polypeptide is set forth in SEQ ID NO:52 (isoform 2; NP_001185688.1; Pro1,247Leu) and is 1,873 amino acids in length. The amino acid sequence of another LY75 variant polypeptide is set forth in SEQ ID NO:53 (isoform 3; NP_001185689.1; Pro1,247Leu) and is 1,817 amino acids in length. The amino acid sequence of another LY75 variant polypeptide is set forth in SEQ ID NO:54 (isoform 4; BAD92152.1; Pro865Leu) and is 1,340 amino acids in length. In some embodiments, the LY75 variant polypeptide is G525E generated from the LY75 variant genomic nucleic acid molecule rs147820690, which contains a C>T variation at position chr2:159878663 (GRCh38.p13;NC_000002.12:g.159878663C>T).

[0253] The nucleotide sequence of the CD164 reference genomic nucleic acid molecule is set forth in SEQ ID NO: 55 (ENSG00000135535.1 encompassing chr6:109,366,514 to 109,381,739 in the GRCh38 / hg38 human genome assembly). The nucleotide sequence of the CD164 variant genomic nucleic acid molecule is set forth in SEQ ID NO: 56 (rs3799840; T297A; 15,226 bp).

[0254] The nucleotide sequence of the CD164 reference type mRNA molecule is set forth in SEQ ID NO: 57 (NM_001346500; isoform 1; 2,992 nt). The nucleotide sequence of another CD164 reference type mRNA molecule is set forth in SEQ ID NO: 58 (ENST00000413644.6; isoform 2; 2,414 nt). The nucleotide sequence of another CD164 reference type mRNA molecule is set forth in SEQ ID NO: 59 (NM_006016.6; isoform; 3 3,020 nt). The nucleotide sequence of another CD164 reference type mRNA molecule is set forth in SEQ ID NO: 60 (ENST00000275080.11; isoform 4; 2,954 nt). The nucleotide sequence of another CD164 reference type mRNA molecule is set forth in SEQ ID NO: 61 (ENST00000324953.9; isoform 5; 2,936 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 62 (ENST00000512821.5; isoform 6; 964 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 63 (NM_001142403.3; isoform 7; 2,424 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 64 (NM_001142402.3; isoform 8; 2,963 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 65 (NM_001142401.3; isoform 9; 2,981 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 66 (D14043.1; isoform 10; 2,427 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 67 (AF299341.1; isoform 11; 2,929 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 68 (AF299342.1; isoform 12; 2,950 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 69 (AF299343.1; isoform 13; 2,968 nt).The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 70 (BC011522.3; isoform 14; 3,010 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 71 (AK301692.1; isoform 15; 1,294 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 72 (AK303525.1; isoform 16; 1,386 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 73 (AK315908.1; isoform 17; 1,386 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 74 (AF106518.1; isoform; 18 537 nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 75 (AF263279.1; isoform 19; 594nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 76 (FJ200494.1; isoform 20; 590nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 77 (AK312357.1; isoform 21; 683nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 78 (ENST00000368961.6; isoform 22; 3,106nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 79 (ENST00000310786.5; isoform 23; 2,993nt). The nucleotide sequence of another CD164 reference-type mRNA molecule is set forth in SEQ ID NO: 80 (ENST00000504373.1; isoform 24; 1,402 nt).

[0255] The nucleotide sequence of the CD164 reference type cDNA molecule is set forth in SEQ ID NO: 81. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 82. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 83. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 84. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 85. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 86. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 87. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 88. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 89. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 90. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 91. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 92. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 93. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 94. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 95. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 96. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 97. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 98. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 99. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 100. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 101. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 102. The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO: 103.The nucleotide sequence of another CD164 reference type cDNA molecule is set forth in SEQ ID NO:104.

[0256] The amino acid sequence of the CD164 reference type polypeptide is set forth in SEQ ID NO: 105 (isoform 1) and is 163 amino acids in length. The amino acid sequence of another CD164 reference type polypeptide is set forth in SEQ ID NO: 106 (NP_001135875.1; isoform 2) and is 189 amino acids in length. The amino acid sequence of another CD164 reference type polypeptide is set forth in SEQ ID NO: 107 (AAG53906.1; isoform 3) and is 197 amino acids in length. The amino acid sequence of another CD164 reference type polypeptide is set forth in SEQ ID NO: 108 (NP_001135873.1; isoform 4) and is 184 amino acids in length. The amino acid sequence of another CD164 reference type polypeptide is set forth in SEQ ID NO: 109 (NP_001135874.1; isoform 5) and is 178 amino acids in length. The amino acid sequence of another CD164 reference type polypeptide is set forth in SEQ ID NO: 110 (isoform 6) and is 157 amino acids in length. The amino acid sequence of another CD164 reference type polypeptide is set forth in SEQ ID NO: 111 (BAG63164.1; isoform 7) and is 156 amino acids in length. The amino acid sequence of another CD164 reference type polypeptide is set forth in SEQ ID NO: 112 (ACO54891.1; isoform 8) and is 147 amino acids in length.

[0257] The nucleotide sequence of the PARP1 reference genomic nucleic acid molecule is set forth in SEQ ID NO:113 (ENSG00000143799.14 encompassing chr1:226,360,691 to 226,408,093 in the GRCh38 / hg38 human genome assembly).

[0258] The nucleotide sequence of the PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 114 (ENST00000366794.10; isoform 1; 3,978 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 115 (ENST00000677203.1; isoform 2; 3,850 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 116 (J03473.1; isoform 3; 3,795 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 117 (BC037545; isoform 4; 3,677 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 118 (M18112.1; isoform 5; 3,640 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 119 (M32721.1; isoform 6; 3,660 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 120 (AK303340.1; isoform 7; 3,371 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 121 (M17081.1; isoform 8; 1,771 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 122 (AK312339.1; isoform 9; 3,132 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 123 (BC018620.1; isoform 10; 827 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 124 (BC014206; isoform 11; 902 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 125 (ENST00000366792.3; isoform 12; 553nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 126 (ENST00000629232.1; isoform 13; 477nt).The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 127 (ENST00000366790.3; isoform 14; 570 nt). The nucleotide sequence of another PARP1 reference-type mRNA molecule is set forth in SEQ ID NO: 128 (ENST00000366794.6; isoform 15; 3,958 nt).

[0259] The nucleotide sequence of the PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 129. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 130. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 131. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 132. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 133. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 134. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 135. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 136. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 137. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 138. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 139. The nucleotide sequence of another PARP1 reference type cDNA molecule is set forth in SEQ ID NO: 140. The nucleotide sequence of another PARP1 reference-type cDNA molecule is set forth in SEQ ID NO: 141. The nucleotide sequence of another PARP1 reference-type cDNA molecule is set forth in SEQ ID NO: 142. The nucleotide sequence of another PARP1 reference-type cDNA molecule is set forth in SEQ ID NO: 143.

[0260] The amino acid sequence of the PARP1 reference type polypeptide is set forth in SEQ ID NO: 144 (AAB59447.1; isoform 1) and has a length of 1,014 amino acids. The amino acid sequence of another PARP1 reference type polypeptide is set forth in SEQ ID NO: 145 (isoform 2) and has a length of 971 amino acids. The amino acid sequence of another PARP1 reference type polypeptide is set forth in SEQ ID NO: 146 (BAG64403.1; isoform 3) and has a length of 993 amino acids. The amino acid sequence of another PARP1 reference type polypeptide is set forth in SEQ ID NO: 147 (AAA51599.1; isoform 4) and has a length of 574 amino acids. The amino acid sequence of another PARP1 reference type polypeptide is set forth in SEQ ID NO: 148 (AAH18620.1; isoform 5) and has a length of 232 amino acids. The amino acid sequence of another PARP1 reference type polypeptide is set forth in SEQ ID NO: 149 (AAH14206.1; isoform 6) and has a length of 250 amino acids. The amino acid sequence of another PARP1 reference polypeptide is set forth in SEQ ID NO: 150 (isoform 7) and is 108 amino acids in length. The amino acid sequence of another PARP1 reference polypeptide is set forth in SEQ ID NO: 151 (isoform 8) and is 155 amino acids in length.

[0261] The nucleotide sequence of the DNMT3A reference genomic nucleic acid molecule is set forth in SEQ ID NO: 212 (ENSG00000119772.17 encompassing chr2:25,227,855 to 25,342,590 in the GRCh38 / hg38 human genome assembly).

[0262] The nucleotide sequence of the DNMT3A reference type mRNA molecule is set forth in SEQ ID NO: 213 (ENST00000264709.7; isoform 1; 9,501 nt). The nucleotide sequence of another DNMT3A reference type mRNA molecule is set forth in SEQ ID NO: 214 (ENST00000321117.10; isoform 2; 9,421 nt). The nucleotide sequence of another DNMT3A reference type mRNA molecule is set forth in SEQ ID NO: 215 (ENST00000406659.3; isoform 3; 1,775 nt). The nucleotide sequence of another DNMT3A reference type mRNA molecule is set forth in SEQ ID NO: 216 (ENST00000380746.8; isoform 4; 3,589 nt). The nucleotide sequence of another DNMT3A reference type mRNA molecule is set forth in SEQ ID NO: 217 (ENST00000402667.1; isoform 5; 2,300 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 218 (NM_175629.2; isoform 6; 4,395 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 219 (NM_001320892.2; isoform 7; 1,714 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 220 (NM_175630.1; isoform 8; 1,808 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 221 (NM_001320893.1; isoform 9; 3,638 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 222 (NM_153759.3; isoform 10; 3,608 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 223 (NM_001375819.1; isoform 11; 3,473 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 224 (BC043617.1; isoform 12; 4,294 nt).The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 225 (AF331856.1; isoform 13; 4,258 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 226 (AB208833.1; isoform 14; 4,476 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 227 (BC018214.1; isoform 15; 1,758 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 228 (AF480163.1; isoform 16; 2,371 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 229 (BC023612.2; isoform 17; 1,113 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 230 (AF067972.2; isoform 18; 3,005 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 231 (BC051864.1; isoform 19; 943 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 232 (ENST00000321117.9; isoform 20; 4,279 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 233 (ENST00000380756.4; isoform 21; 4,477 nt). The nucleotide sequence of another DNMT3A reference-type mRNA molecule is set forth in SEQ ID NO: 234 (ENST00000683760.1; isoform 22; 3,585 nt).

[0263] The nucleotide sequence of the DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 235. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 236. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 237. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 238. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 239. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 240. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 241. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 242. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 243. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 244. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 245. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 246. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 247. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 248. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 249. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 250. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 251. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 252. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 253. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 254. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 255. The nucleotide sequence of another DNMT3A reference type cDNA molecule is set forth in SEQ ID NO: 256.

[0264] The amino acid sequence of the DNMT3A reference type polypeptide is set forth in SEQ ID NO: 257 (NP_783328.1; isoform 1) and is 912 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 258 (NP_001307821.1; isoform 2) and is 166 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 259 (NP_715640.2; isoform 3) and is 723 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 260 (NP_001362748.1; isoform 4) and is 689 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 261 (NP_001307822.1; isoform 5) and is 760 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 262 (AAL57039.1; isoform 6) and is 909 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 263 (BAD92070.1; isoform 7) and is 811 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 264 (AAH18214.1; isoform 8) and is 285 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 265 (AAH23612.1; isoform 9) and is 351 amino acids in length. The amino acid sequence of another DNMT3A reference type polypeptide is set forth in SEQ ID NO: 266 (AAH23612.1; isoform 10) and is 781 amino acids in length.

[0265] The nucleotide sequence of the ASXL1 reference genomic nucleic acid molecule is set forth in SEQ ID NO: 267 (ENSG00000171456.20 encompassing chr20:32,358,330 to 32,439,260 in the GRCh38 / hg38 human genome assembly).

[0266] The nucleotide sequence of the ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 268 (ENST00000651418.1; isoform 1; 3,146 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 269 (ENST00000375687.10; isoform 2; 7,052 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 270 (ENST00000542461.5; isoform 3; 1,068 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 271 (ENST00000613218.4; isoform 4; 7,038 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 272 (ENST00000646367.1; isoform 5; 1,065 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 273 (ENST00000620121.4; isoform 6; 5,374 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 274 (ENST00000646985.1; isoform 7; 6,666 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 275 (ENST00000497249.6; isoform 8; 495 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 276 (ENST00000375689.5; isoform 9; 812 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 277 (ENST00000306058.9; isoform 10; 6,591 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 278 (NM_001164603.1; isoform 11; 1,084 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 279 (BC100280.1; isoform 12; 1,078 nt).The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 280 (BC064984.1; isoform 13; 1,009 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 281 (AJ438952.2; isoform 14; 6,864 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 282 (AK122923.1; isoform 15; 4,685 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 283 (AB023195.2; isoform 16; 6,088 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 284 (AL117518.1; isoform 17; 4,055 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 285 (ENST00000375687.5; isoform 18; 7,031 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 286 (ENST00000497249.2; isoform 19; 296 nt). The nucleotide sequence of another ASXL1 reference-type mRNA molecule is set forth in SEQ ID NO: 287 (ENST00000555343.2; isoform 20; 1,034 nt).

[0267] The nucleotide sequence of an ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 288. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 289. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 290. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 291. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 292. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 293. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 294. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 295. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 296. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 297. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 298. The nucleotide sequence of another ASXL1 reference-type cDNA molecule is set forth in SEQ ID NO: 299. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 300. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 301. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 302. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 303. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 304. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 305. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 306. The nucleotide sequence of another ASXL1 reference type cDNA molecule is set forth in SEQ ID NO: 307.

[0268] The amino acid sequence of the ASXL1 reference type polypeptide is set forth in SEQ ID NO: 308 (isoform 1) and is 625 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 309 (CAD27708.1; isoform 2) and is 1,541 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 310 (NP_001158075.1; isoform 3) and is 85 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 311 (isoform 4) and is 1,480 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 312 (isoform 5) and is 75 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 313 (isoform 6) and is 81 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 314 (isoform 7) and is 1,536 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 315 (AAH64984.1; isoform 8) and is 84 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 316 (BAG53800.1; isoform 9) and is 1,462 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 317 (BAA76822.2; isoform 10) and is 1,368 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 318 (isoform 11) and is 1,341 amino acids in length. The amino acid sequence of another ASXL1 reference type polypeptide is set forth in SEQ ID NO: 319 (isoform 12) and is 60 amino acids in length. Another ASXL1 reference type polypeptide amino acid sequence is set forth in SEQ ID NO:320 (isoform 13) and is 57 amino acids in length.

[0269] Genomic nucleic acid molecules, mRNA molecules, and cDNA molecules can be from any organism.For example, genomic nucleic acid molecules, mRNA molecules, and cDNA molecules can be from humans, or from another organism, such as non-human mammals, rodents, mice, or rats, orthologs.It is understood that gene sequences within a population can differ due to polymorphisms, such as single nucleotide polymorphisms.The examples provided herein are merely exemplary sequences.Other sequences are also possible.

[0270] Also provided herein are functional polynucleotides that can interact with the disclosed nucleic acid molecules. Examples of functional polynucleotides include, but are not limited to, antisense molecules, aptamers, ribozymes, triplex-forming molecules, and external guide sequences. Functional polynucleotides can act as effectors, inhibitors, modulators, and stimulators of the specific activity of target molecules, or functional polynucleotides can have de novo activity independent of any other molecules.

[0271] The isolated nucleic acid molecules disclosed herein can include RNA, DNA, or both RNA and DNA. The isolated nucleic acid molecules can also be linked or fused to heterologous nucleic acid sequences, for example in a vector, or heterologous labels. For example, the isolated nucleic acid molecules disclosed herein can be present as exogenous donor sequences in or containing a vector that includes the isolated nucleic acid molecule and a heterologous nucleic acid sequence. The isolated nucleic acid molecules can also be linked or fused to heterologous labels. The labels can be directly detectable (e.g., fluorophores) or indirectly detectable (e.g., haptens, enzymes, or fluorophore quenchers). Such labels can be detectable by spectroscopic, photochemical, biochemical, immunochemical, or chemical means. Such labels include, for example, radioactive labels, pigments, dyes, chromogens, spin labels, and fluorescent labels. The labels can also be, for example, chemiluminescent, metal-containing, or enzymes, where enzyme-dependent secondary generation of a signal occurs. The term "label" may also refer to a "tag" or hapten that can be selectively attached to a binding molecule such that the binding molecule is subsequently added with a substrate and used to generate a detectable signal. For example, biotin can be used as a tag with an avidin or streptavidin conjugate of horseradish peroxidase (HRP) to bind to the tag and tested using a colorimetric (e.g., tetramethylbenzidine (TMB)) or fluorogenic substrate to detect the presence of HRP. Exemplary labels that can be used as tags to facilitate purification include, but are not limited to, myc, HA, FLAG or 3xFLAG, 6xHis or polyhistidine, glutathione-S-transferase (GST), maltose binding protein, epitope tags, or the Fc portion of an immunoglobulin. Numerous labels include, for example, particles, fluorophores, haptens, enzymes, and their colorimetric, fluorogenic, and chemiluminescent substrates, as well as other labels.

[0272] Percent identity (or percent complementarity) between specific stretches of nucleotide sequences in nucleic acid molecules or amino acid sequences in polypeptides can be routinely determined using the BLAST program (basic local alignment search tool) and PowerBLAST program (Altschul et al., J. Mol. Biol., 1990, 215, 403-410; Zhang and Madden, Genome Res., 1997, 7, 649-656), or the Gap program (Wisconsin Sequence Analysis Package, Version 8 for UNIX, Genetics Computer Group, University Research Park, Madison Wis.) using default settings that utilize the Smith and Waterman algorithm (Adv. Appl. Math., 1981, 2, 482-489). When referring to percent sequence identity in this specification, a higher percentage of sequence identity is preferred over a lower one.

[0273] As used herein, the phrase "corresponding to" or grammatical variations thereof, when used in the context of numbering a particular nucleotide or sequence of nucleotides or positions, refers to the numbering of the designated reference sequence when that particular nucleotide or nucleotide sequence is compared to a reference sequence (e.g., SEQ ID NO:1, SEQ ID NO:55, or SEQ ID NO:113, etc.). In other words, the residue (e.g., nucleotide or amino acid) number or residue (e.g., nucleotide or amino acid) position of a particular polymer is specified with reference to the reference sequence, not by the actual position number of that residue within that particular nucleotide or nucleotide sequence. For example, a particular nucleotide sequence can be aligned to a reference sequence by introducing gaps to optimize residue matching between the two sequences. In these cases, although gaps exist, the numbering of the residues in a particular nucleotide or nucleotide sequence is done with respect to the reference sequence to which it is aligned.

[0274] The nucleotide and amino acid sequences listed in the accompanying sequence listing are shown using standard letter abbreviations for nucleotide bases and three letter codes for amino acids. The nucleotide sequences follow the standard convention of beginning at the 5'-terminus of the sequence and proceeding toward the 3'-terminus (i.e., from left to right in each sequence). Only one strand of each nucleotide sequence is shown, but the complementary strand is understood to be included by reference to the shown strand. The amino acid sequences follow the standard convention of beginning at the amino-terminus of the sequence and proceeding in a forward direction toward the carboxy-terminus (i.e., from left to right in each sequence).

[0275] The present disclosure also provides a method for stratifying lung cancer patients suitable for treatment with PARP1 inhibitors.The method includes determining whether the patient has DNMT3A R882H somatic mutation or TET2 somatic mutation deficiency.The patient with DNMT3A R882H somatic mutation or TET2 somatic mutation deficiency can be excluded from PARP1 inhibitor treatment regimen.

[0276] The disclosure also provides CHIP-preventing or reducing therapeutic agents for use in preventing and / or reducing CHIP in a subject having an LY75 variant genomic nucleic acid molecule, a CD164 variant genomic nucleic acid molecule, and / or a PARP1 variant genomic nucleic acid molecule, an LY75 variant mRNA molecule, a CD164 variant mRNA molecule, and / or a PARP1 variant mRNA molecule, or an LY75 variant cDNA molecule, a CD164 variant cDNA molecule, and / or a PARP1 variant cDNA molecule. Any of the CHIP-preventing or reducing therapeutic agents described herein can be used in these methods.

[0277] The disclosure also provides the use of a therapeutic agent that prevents or reduces CHIP for use in the preparation of a medicament for preventing or reducing CHIP in a subject having an LY75 variant genomic nucleic acid molecule, a CD164 variant genomic nucleic acid molecule, and / or a PARP1 variant genomic nucleic acid molecule, an LY75 variant mRNA molecule, a CD164 variant mRNA molecule, and / or a PARP1 variant mRNA molecule, or an LY75 variant cDNA molecule, a CD164 variant cDNA molecule, and / or a PARP1 variant cDNA molecule. Any of the therapeutic agents that prevent or reduce CHIP described herein can be used in these methods.

[0278] The present disclosure also provides an LY75 inhibitor for use in preventing or reducing CHIP in a subject having an LY75 variant genomic nucleic acid, an LY75 variant mRNA molecule, or an LY75 variant cDNA molecule.Any of the LY75 inhibitors described herein can be used in these methods.

[0279] The present disclosure also provides CD164 inhibitor for use in preventing or reducing CHIP CHIP in subjects with CD164 variant genomic nucleic acid molecule, CD164 variant mRNA molecule, or CD164 variant cDNA molecule.Any of the CD164 inhibitors described herein can be used in these methods.

[0280] The present disclosure also provides the PARP1 inhibitor for use in preventing or reducing CHIP in the subject having PARP1 variant genomic nucleic acid molecule, PARP1 variant mRNA molecule, or PARP1 variant cDNA molecule.Any of the PARP1 inhibitors described herein can be used in these methods.

[0281] The present disclosure also provides an LY75 inhibitor for use in the preparation of a medicament for preventing or reducing CHIP in a subject having an LY75 variant genomic nucleic acid molecule, an LY75 variant mRNA molecule, or an LY75 variant cDNA molecule.Any of the LY75 inhibitors described herein can be used in these methods.

[0282] The present disclosure also provides CD164 inhibitors for use in preparing the medicament for preventing or reducing CHIP in subjects with CD164 variant genomic nucleic acid molecule, CD164 variant mRNA molecule, or CD164 variant cDNA molecule.Any of the CD164 inhibitors described herein can be used in these methods.

[0283] The present disclosure also provides PARP1 inhibitors for use in preparing the medicament for preventing or reducing CHIP in subjects with PARP1 variant genomic nucleic acid molecules, PARP1 variant mRNA molecules, or PARP1 variant cDNA molecules.Any of the PARP1 inhibitors described herein can be used in these methods.

[0284] All patent documents, websites, other publications, accession numbers, etc. cited above or below are incorporated by reference in their entirety for all purposes to the same extent as if each individual document was specifically and individually indicated to be incorporated by reference as such. Where various versions of a sequence are associated with accession numbers at different times, the version associated with the accession number at the effective filing date of this application is meant. Effective filing date means the earlier of the actual filing date or the filing date of the priority application to which the accession number refers, if applicable. Similarly, where different versions of publications, websites, etc. have been published at different times, the version last published at the effective filing date of the application is meant unless otherwise indicated. Any feature, step, element, embodiment, or aspect of the present disclosure may be used in combination with any other feature, step, element, embodiment, or aspect, unless otherwise indicated. Although the present disclosure has been described in some detail by way of illustration and example for purposes of clarity and understanding, it will be apparent that certain changes and modifications may be practiced within the scope of the appended claims.

[0285] The following examples are provided to further illustrate the embodiments. They are intended to illustrate, not limit, the claimed embodiments. The following examples provide those skilled in the art with a disclosure and explanation of how the compounds, compositions, articles, devices and / or methods described herein are made and evaluated, and are intended to be merely illustrative and are not intended to limit the scope of any claims. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperatures, etc.), but some error and deviation can be accounted for. Unless otherwise indicated, parts are parts by weight, temperature is °C or is ambient temperature, and pressure is at or near atmospheric pressure. EXAMPLES

[0286] Example 1: Common variants at the LY75-CD302 / LY75-CD302 locus are associated with CHIP Several common variants at the LY75 / CD302 / LY75-CD302 locus are associated with CHIP, including the LY75 missense rs78446341 (see Table 4). [Table 6] [Table 7]

[0287] Common LY75-CD302 locus variants present within eQTLs of neighboring genes are shown in Table 5. [Table 8] [Table 9]

[0288] Fine mapping of the LY75-CD302 locus identified rs78446341 as likely (approximately 80%) to drive the association signal at this locus (data not shown). Furthermore, all LY75 burden masks suggest a reduced CHIP risk (see Figure 1). Furthermore, the effect of the ly75 locus varies among CHIP mutation carriers (see Figure 2).

[0289] The LY75 missense p.Pro1247Leu was significantly associated with platelets, neutrophils, and lymphocytes in the UKB 500K (see Table 6; variant=2:159834145:G:A; HGVS=p.Pro1247Leu). [Table 10]

[0290] An additional rare pLoF and a rare missense variant in LY75 were also associated with decreased odds of CHIP (Table 7, phenotype=CHIP; and see Figure 3). [Table 11]

[0291] Example 2: Common variants within the CD164 locus are associated with CHIP Although multiple common variant signals within the CD164 locus are associated with CHIP, fine mapping does not point to a causative gene (data not shown). Furthermore, eQTL data support the effect of variants on CD164 expression (see Table 8). [Table 12] [Table 13]

[0292] Example 3: Common variants within the PARP1 locus are associated with CHIP The PARP1 1:226367601:A:C missense variant was in complete LD with the index SNP and showed protective association (see Figure 4). Other CHIP-associated variants were significant eQTL for PARP1 (see Figure 5).

[0293] Example 4: Somatic mutations in DNMT3A and / or ASXL1 are associated with an increased risk of developing lung cancer Using exome sequencing data from the UKB Exome Sequencing Consortium, we identified somatic CHIP mutation carriers across 454,787 UKB participants. This was complemented by generating an additional CHIP call set across 133,370 individuals in the DiscoverEHR cohort. These represent the largest CHIP call sets to date and were used to perform genetic association studies for CHIP across 29,669 CHIP mutation carriers in the UKB and replication was performed in 14,766 CHIP mutation carriers in the DiscoverEHR cohort. 27 loci associated with CHIP in UKB with genome-wide significance were identified and replicated in DiscoverEHR. Furthermore, phenotypic associations were examined for both CHIP somatic mutation carriers and germline CHIP risk loci across 35,000 traits in the UK Biobank.

[0294] The analysis described herein includes only CHIP carriers with the greatest proliferation of blood cells carrying the CHIP mutation (estimated to have approximately 20% or more of blood cells carrying the CHIP mutation). We determined whether CHIP carriers were at higher risk of developing solid tumors (see FIG. 6), and found that high variant allele fraction (VAF) carriers had a significantly higher risk of developing lung cancer (HR=1.62 (1.41-1.87), p=1.36*10-11), and a moderately higher risk of developing prostate cancer (HR=1.17 (1.04-1.31), p=7.1*10-3), and breast cancer (HR=1.15 (1.002-1.322), p=0.047). No increased risk of developing colon cancer was found (HR=0.96 (0.79-1.16), p=0.66). Models that estimate event risk based on CHIP mutation subtype (e.g., carriers must have a DNMT3A mutation) suggest that these associations with prostate and breast cancer are primarily driven by DNMT3A mutations.

[0295] Given the strong association of CHIP with hematological and lung cancers, and the association of smoking with CHIP and lung cancer, we performed additional analyses stratified by smoking status to test whether these associations were driven by smoking and simply marked by CHIP mutations. High VAF CHIP carriers were significantly more likely to be smokers (2.37 (1.86-3.03), p=5.24). * 10-12) and non-smokers (2.05 (1.68-2.49), P = 7.47 * 10-13) had an increased risk of developing hematologic cancers, and this pattern was similar across all CHIP carriers and across associations with the CHIP mutation subtype ASXL1-CHIP. The risk of lung cancer in all CHIP carriers was significantly higher than in smokers (HR = 1.45 (1.28-1.63), p = 1.10 * 10-9) and non-smokers (HR = 1.45 (1.18-1.80), P = 5.46 * 10-4), and in fact, in CHIP holders with VAF ≥ 10%, the risk was higher in non-smokers (HR non-smokers = 1.93 (1.47-2.54), P = 2.86 * Compared with 10-6, HR smokers = 1.56 (1.33-1.84), p = 7.32 * 10-8). For subsetting into DNMT3A-CHIP and ASXL1-CHIP, the patterns were similar. Overall, the model suggests that CHIP mutation carriers are at elevated risk for hematologic and lung cancers independent of smoking, but that CHIP likely also marks additional hematologic cancer risk attributable to smoking.

[0296] In summary, in longitudinal analyses, individuals with CHIP somatic mutations in either DNMT3A or ASXL1 were found to have an increased risk of lung cancer in both smokers and non-smokers, indicating that CHIP is an independent risk factor for malignancies outside the hematopoietic system.

[0297] Example 5: Effect of PARPi on cells with CHIP gene mutation To determine if PARP1 inhibitors have an effect on in vitro cells harboring CHIP gene mutations, variants / mutations were incorporated into cell lines using CRISPR-Cas9 and specifically optimized sgRNA target sequences, as well as donor sequences for DNMT3A knock-in. Functional modeling of identified CHIP-GWAS loci was performed. Selected PARP1 loci from CHIP-GWAS analysis showed significant association to protective PARP1 germline variants in DNMT3A (data not shown). Panels A and B of Figure 7 show systematic tracking of the percentage of HDR and indels in PARPi-treated cells. Cells were treated with PARPi for 8 days and then subjected to Sanger sequencing across each locus to determine population dynamics. Panel A of Figure 7 shows RPE-1 hTERT cells with CRISPR-mediated knock-in of the DNMT3A-R882H allele. This indicates that there is no effect of PARP1 inhibitor treatment on cells with DNMT3A variant alleles, which remain unchanged in the population compared to DMSO (control / vehicle) alone. Thus, PARP1 inhibitors had no effect on cells with DNMT3A-R882H variants. As shown in panel A of FIG. 7, percentages (%) represent the percent of sequences derived from that indicated allele in the legend, and all three legend items add up to approximately 100% for each of the samples. Thus, the wild-type allele in the DMSO group (blue group) has an average of about 16% (16% of sequences in the cell population are wild-type). The R882H allele in DMSO (black group) has about 24% (24% of sequences derived from the cell population have the R882H mutation). The indel in DMSO (red group) has about 60% (60% of sequences in the population have the indel (nucleotide insertion / deletion) allele). The sum of wild type, R882H, and indels in the DMSO group is approximately 100% of the analyzed sequences.

[0298] Panel B of Figure 7 shows CRISPR-mediated TET2 deficiency in HEK293T cells. Cells with potential loss-of-function alleles (indel / KO alleles) were resistant to PARP1 inhibitor treatment in olaparib and talazoparib conditions, and the percentage of indels (mutated alleles) was increased compared to DMSO (control / vehicle). This means that cells with TET2 KO / indel alleles survive better than wild-type alleles in response to treatment with PARP1 inhibitors. Therefore, in this case, it may be desirable to avoid PARP1 inhibitor treatment in order not to increase clonal selection of TET2 mutant / variant alleles that cause the deficiency.

[0299] Example 6: Joint fine mapping of common and rare variants at the LY75 locus DNMT3A, the most frequently mutated gene across the CHIP phenotype, had the highest number of significantly associated loci (n = 23), the majority of which overlapped with association signals across CHIP. At the locus on chromosome 2, rs78446341 (P1247L in LY75) was associated with a decreased risk of DNMT3A-CHIP (OR = 0.78 (0.72 to 0.84), P = 3.70 × 10 -10 ), and were prioritized by fine mapping. LY75 is characterized by lymphocyte-specific expression and is thought to be involved in antigen presentation and lymphocyte proliferation. A second rare (AAF=0.002) missense variant (rs147820690-T,G525E) was also identified that was associated with a reduced risk of DNMT3A-CHIP with near genome-wide significance (OR=0.48 (0.36-0.63), P=1.15×10 -7 ). This variant is predicted to be more likely to be damaging (CADD = 23.6) when conditioning for common variant signal at this locus (i.e., this rare variant signal is independent of the common variant signal at this locus) and maintains association (OR = 0.63 (0.51 to 0.77), P = 4.80 × 10 -6). This variant was also prioritized by fine mapping. Finally, these signals in PARP1 and LY75 were replicated in GHS (see FIG. 8).

[0300] The more common LY75 missense variant (rs78446341-A, P1247L) is located in the extracellular domain of lymphocytic antigen 75, also known as DEC-205 / CD205, which plays a role in antigen capture, processing, and presentation. The rarer LY75 missense variant (rs147820690-T, G525E) is located in the C-type lectin domain and has been reported to directly interact with the ligands of this receptor. The protective association with this variant identified herein appears to be most pronounced for DNMT3A-CHIP and mLOY, highlighting LY75 as a therapeutic target for antagonism of CH in general.

[0301] To further evaluate whether the association of rare variants at the LY75 locus (rs147820690-T) is independent of other common and rare variant signals, joint fine mapping (using FINEMAP) was performed on common and rare variants at this locus when rarer variants were included, and then used for genome-wide fine mapping. In contrast to the genome-wide fine mapping described above, this fine mapping sensitivity analysis was performed only at UKB, focusing on the LY75 locus and including all variants in the dataset. That is, fine mapping analysis was performed as described above, with a MAF>0.0000000001. FINEMAP suggests that three credible intervals are the most concise at this locus (posterior probability = 0.8), which is consistent with our reported results when performing genome-wide fine mapping, while the fourth credible interval (posterior probability = 0.11) identifies rs147820690-T as the top signal (PIP = 0.133) among 9,417 variants at the 95% credible interval. This fine mapping approach also prioritizes rs78446341-A (CPIP = 0.92, CS = 2). Furthermore, the median pairwise LD between the SNPs in this fourth credible interval is very low (6.7 × 10 compared to 0.995, 0.962, and 0.831 for the first three credible intervals, respectively). -4 Thus, these fine mapping results provide additional support for both LY75 missense variants, and the fact that the signal of the rs147820690-T rare variant is not driven by tagging of other rare variants.

[0302] In addition to those described herein, various modifications of the described subject matter will become apparent to those skilled in the art from the foregoing description. Such modifications are also intended to fall within the scope of the appended claims. Each reference cited in this application (including, but not limited to, journal articles, U.S. and non-U.S. patents, patent application publications, international patent application publications, gene bank accession numbers, etc.) is incorporated herein by reference in its entirety and for all purposes.

Claims

1. A composition for preventing or reducing the onset of clonal hematopoiesis of undetermined potential (CHIP) in a subject, the composition comprising a lymphocyte antigen 75 (LY75) inhibitor, a surface cluster of antigen 164 (CD164) inhibitor, or a poly(ADP-ribose) polymerase 1 (PARP1) inhibitor, or any combination thereof.

2. 10. The composition of claim 1, wherein the subject is at risk of developing a hematological cancer, a myeloid malignancy, a lymphoid malignancy, atherosclerotic cardiovascular disease, coronary heart disease, myocardial infarction, or severe calcific aortic stenosis.

3. the LY75 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an LY75 nucleic acid molecule; the CD164 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to a CD164 nucleic acid molecule; or The composition of claim 1 or claim 2, wherein the PARP1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to a PARP1 nucleic acid molecule.

4. The composition of claim 3 , wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), or a short hairpin RNA (shRNA).

5. A composition for treating a subject having or at risk of developing CHIP, comprising a lymphocyte antigen 75 (LY75) inhibitor, a surface cluster of antigens 164 (CD164) inhibitor, or a poly(ADP-ribose) polymerase 1 (PARP1) inhibitor, or any combination thereof; wherein the treatment determining whether the subject has an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule; obtaining or having obtained a biological sample from the subject; A sequence analysis is performed or has been performed on the biological sample to determine whether the subject has a genotype that includes the LY75 variant nucleic acid molecule, the CD164 variant nucleic acid molecule, and / or the PARP1 variant nucleic acid molecule. It is determined by administering or continuing to administer a standard dose of a therapeutic agent that prevents or reduces the development of CHIP to a subject who is LY75 reference type, CD164 reference type, and / or PARP1 reference type; and / or administering to said subject an LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof; administering or continuing to administer a therapeutic agent that prevents or reduces the occurrence of CHIP to a subject who is heterozygous for an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule, at a standard dose or less, and / or administering to said subject an LY75 inhibitor, a CD164 inhibitor, or a PARP1 inhibitor, or any combination thereof; or administering or continuing to administer to a subject who is homozygous for said LY75 variant nucleic acid molecule, said CD164 variant nucleic acid molecule, and / or said PARP1 variant nucleic acid molecule, a therapeutic agent that prevents or reduces the occurrence of said CHIP at an amount that is the same as or less than a standard dose; A composition wherein the presence of a genotype having the LY75 variant nucleic acid molecule, the CD164 variant nucleic acid molecule, and / or the PARP1 variant nucleic acid molecule indicates that the subject has a reduced risk for developing CHIP.

6. 6. The composition of claim 5, wherein the subject is at risk of developing a blood cancer, a myeloid malignancy, a lymphoid malignancy, atherosclerotic cardiovascular disease, coronary heart disease, myocardial infarction, or severe calcific aortic stenosis.

7. the subject is an LY75 reference type; 7. The composition of claim 5 or claim 6, wherein the subject is receiving or continues to receive a standard dose of a therapeutic agent that prevents or reduces the development of CHIP and is administered the LY75 inhibitor.

8. the subject is CD164 reference type; The composition of claim 5 or claim 6, wherein the subject is receiving or continues to receive a standard dose of a therapeutic agent that prevents or reduces the onset of CHIP and is administered the CD164 inhibitor.

9. the subject is PARP1 reference type; The composition of claim 5 or claim 6, wherein the subject is receiving or continues to receive a standard dose of a therapeutic agent that prevents or reduces the onset of CHIP and is administered the PARP1 inhibitor.

10. the subject is heterozygous for the LY75 variant nucleic acid molecule; The composition of claim 5 or claim 6, wherein the subject is administered or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at a dose equal to or less than a standard dose, and is administered the LY75 inhibitor.

11. the subject is heterozygous for the CD164 variant nucleic acid molecule; The composition of claim 5 or claim 6, wherein the subject is administered or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at an amount equal to or less than the standard dose and is administered the CD164 inhibitor.

12. the subject is heterozygous for the PARP1 variant nucleic acid molecule; The composition of claim 5 or claim 6, wherein the subject is administered or continues to be administered a therapeutic agent that prevents or reduces the onset of CHIP at an amount equal to or less than the standard dose, and is administered the PARP1 inhibitor.

13. 7. The composition of claim 5 or 6, wherein the LY75, CD164, or PARP1 variant nucleic acid molecule is a missense variant, splice site variant, stop-gain variant, start-loss variant, stop-loss variant, frameshift variant, or in-frame indel variant, or a variant encoding a truncated predicted loss-of-function polypeptide.

14. The composition of claim 13, wherein the LY75 variant nucleic acid molecule encodes a predicted loss-of-function polypeptide of a truncated LY75, the CD164 variant nucleic acid molecule encodes a predicted loss-of-function polypeptide of a truncated CD164, or the PARP1 variant nucleic acid molecule encodes a predicted loss-of-function polypeptide of a truncated PARP1.

15. The composition of claim 5 or 6, wherein the LY75 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an LY75 nucleic acid molecule.

16. 16. The composition of claim 15, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), or a short hairpin RNA (shRNA).

17. 1. An in vitro method for identifying a subject's susceptibility to the development of clonal hematopoiesis of undetermined potential (CHIP), said method comprising: determining or having determined the presence or absence of an LY75 variant nucleic acid molecule, a CD164 variant nucleic acid molecule, and / or a PARP1 variant nucleic acid molecule in a biological sample obtained from said subject; the subject being a LY75 reference type, a CD164 reference type, and / or a PARP1 reference type indicates that the subject has an increased risk for developing CHIP; The method, wherein the subject being heterozygous or homozygous for the LY75 variant nucleic acid molecule, the CD164 variant nucleic acid molecule, and / or the PARP1 variant nucleic acid molecule indicates that the subject has a reduced risk for developing CHIP.

18. 18. The method of claim 17, wherein the LY75, CD164, or PARP1 variant nucleic acid molecule is a missense variant, splice site variant, stop-gain variant, start-loss variant, stop-loss variant, frameshift variant, or in-frame indel variant, or a variant encoding a truncated predicted loss-of-function polypeptide.

19. 19. The method of claim 18, wherein the LY75 variant nucleic acid molecule encodes a predicted loss-of-function polypeptide of a truncated LY75, the CD164 variant nucleic acid molecule encodes a predicted loss-of-function polypeptide of a truncated CD164, or the PARP1 variant nucleic acid molecule encodes a predicted loss-of-function polypeptide of a truncated PARP1.

20. A composition for preventing or reducing clonal hematopoiesis of undetermined potential (CHIP) in a subject, comprising a therapeutic agent that prevents or reduces the onset of CHIP, The object is an LY75 variant genomic nucleic acid molecule, a CD164 variant genomic nucleic acid molecule, and / or a PARP1 variant genomic nucleic acid molecule; an LY75 variant mRNA molecule, a CD164 variant mRNA molecule, and / or a PARP1 variant mRNA molecule, or LY75 variant cDNA molecules, CD164 variant cDNA molecules, and / or PARP1 variant cDNA molecules The composition is identified as having:

21. A composition for preventing or reducing clonal hematopoiesis of undetermined potential (CHIP) in a subject, comprising a lymphocyte antigen 75 (LY75) inhibitor; The object is a) a reference form of an LY75 genomic nucleic acid molecule, an LY75 mRNA molecule, or an LY75 cDNA molecule; or b) i) an LY75 variant genomic nucleic acid molecule; ii) an LY75 variant mRNA molecule, or iii) LY75 variant cDNA molecules The composition, wherein the composition is heterozygous for 22. A composition for preventing or reducing clonal hematopoiesis of undetermined potential (CHIP) in a subject, comprising a cluster of differentiation 164 (CD164) inhibitor; The object is a) a reference form of a CD164 genomic nucleic acid molecule, a CD164 mRNA molecule, or a CD164 cDNA molecule; or b) i) a CD164 variant genomic nucleic acid molecule; ii) a CD164 variant mRNA molecule, or iii) CD164 variant cDNA molecules The composition, wherein the composition is heterozygous for 23. A composition for preventing or reducing clonal hematopoiesis of undetermined potential (CHIP) in a subject, comprising a poly(ADP-ribose) polymerase 1 (PARP1) inhibitor; The object is a) a reference form of a PARP1 genomic nucleic acid molecule, a PARP1 mRNA molecule, or a PARP1 cDNA molecule; or b) i) a PARP1 variant genomic nucleic acid molecule; ii) a PARP1 variant mRNA molecule, or iii) PARP1 variant cDNA molecules The composition, wherein the composition is heterozygous for

24. 22. The composition of claim 21, wherein the LY75 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to an LY75 nucleic acid molecule.

25. 25. The composition of claim 24, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), or a short hairpin RNA (shRNA).

26. The composition of claim 22, wherein the CD164 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to a CD164 nucleic acid molecule.

27. 27. The composition of claim 26, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), or a short hairpin RNA (shRNA).

28. 24. The composition of claim 23, wherein the PARP1 inhibitor comprises an inhibitory nucleic acid molecule that hybridizes to a PARP1 nucleic acid molecule.

29. 29. The composition of claim 28, wherein the inhibitory nucleic acid molecule comprises an antisense nucleic acid molecule, a small interfering RNA (siRNA), or a short hairpin RNA (shRNA).

30. 1. An in vitro method for identifying a subject's susceptibility to developing lung cancer, said method comprising: determining or having determined the presence or absence of one or more somatic clonal hematopoiesis of undetermined potential (CHIP) mutations in DNA methyltransferase 3 alpha (DNMT3A) and / or ASXL transcription factor 1 (ASXL1) in a biological sample obtained from the subject; the subject having a CHIP somatic mutation in DNMT3A and / or ASXL1 indicates that the subject has an increased risk for developing lung cancer; The method, wherein the subject's absence of a CHIP somatic mutation in DNMT3A and / or ASXL1 indicates that the subject does not have an increased risk for developing lung cancer.

31. 31. The method of claim 30, wherein the lung cancer comprises non-small cell lung cancer, small cell lung cancer, mesothelioma, pulmonary carcinoid tumor, or chest wall tumor.

32. 1. An in vitro method for stratifying lung cancer patients suitable for treatment with a PARP1 inhibitor, said method comprising: determining whether the patient has a DNMT3A R882H somatic mutation or a TET2 somatic mutation deficiency; The method wherein said patient having a DNMT3A R882H somatic mutation or a TET2 somatic mutation deficiency is excluded from a PARP1 inhibitor treatment regimen.