Systems and methods for detecting hematopoietic neoplasms using deoxyribonucleic acid (DNA) mutations

Abstract

A system may receive DNA sequencing data for a subject, the DNA sequencing data comprising a plurality of variants, wherein the plurality of variants comprise a plurality of copy number variants (CNVs). A system may identify a cytoband variant or a chromosomal variant among the plurality of CNVs. A system may detect a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant.

Description

Docket Number: 20230802-03 / 027644.8492 SYSTEMS AND METHODS FOR DETECTING HEMATOPOIETIC NEOPLASMS USING DEOXYRIBONUCLEIC ACID (DNA) MUTATIONS CROSS-REFERENCE TO RELATED APPLICATIONS

[0001] This application claims the benefit of U.S. Provisional Application No.63 / 452,570, filed on March 16, 2023, and U.S. Provisional Application No.63 / 506,473, filed on June 6, 2023, the entire disclosures of which are hereby incorporated by reference. BACKGROUND

[0002] High-throughput sequencing technology is an advanced detection method compared to conventional one generation sequencing methods. With high-throughput sequencing, such as next- generation sequencing (NGS) or deep sequencing, there is capacity to detect and sequence hundreds of thousands or millions of nucleic acid molecules at one time allowing for thorough analyses of transcriptomes and genomes in one subject. NGS has revolutionized the field of genomics. For example, NGS assays have enabled various applications in genomics research, including whole-genome sequencing, exome sequencing, transcriptome profiling, epigenetics analysis, metagenomics, and many more. NGS assays offer high throughput, speed, and cost-effectiveness compared to conventional sequencing methods, making them widely used in research, clinical diagnostics, and personalized medicine.

[0003] NGS detection methods can detect numerous genes to meet the high demands of clinical detection, and can not only detect known mutation sites, but also unknown mutation sites. NGS can also detect various types of mutations and gene variants in various types of clinical samples, including, but not limited to full blood, bone marrow, tissue, serum, or isolated DNA or RNA. Further, NGS can also identify and profile various forms of cancer, including hematologic neoplasms and other blood related cancers. Hematologic neoplasms are cancers that begin in blood-forming tissue, such as the bone marrow or immune system cells, and impact the normal production and function of blood cells. Genomic and transcriptomic characterization is essential for the diagnosis, risk assessment, therapeutic strategies, disease monitoring, disease progression, and treatment resistance of hematologic neoplasms. However, using genomic and transcriptomic characterization to detect hematologic neoplasms remains challenging. The systems and methods described herein address challenges faced by conventional technologies.Docket Number: 20230802-03 / 027644.8492 SUMMARY

[0004] In some aspects, the techniques described herein relate to a computer-implemented method for detecting hematopoietic neoplasms using deoxyribonucleic acid (DNA) mutations including: receiving DNA sequencing data for a subject, the DNA sequencing data including a plurality of variants, wherein the plurality of variants include a plurality of copy number variants (CNVs); identifying a cytoband variant or a chromosomal variant among the plurality of CNVs; and detecting a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant.

[0005] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the cytoband variant is a cytoband copy number loss.

[0006] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the chromosomal variant is a chromosomal arm loss, a monosomy, or a trisomy.

[0007] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the plurality of variants further include at least one of a single nucleotide variant (SNV), an insertion deletion (indel), an FLT3 internal tandem duplication (FLT3-ITD), and a gene fusion.

[0008] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), myelodysplasia (MDS), chronic lymphocytic leukemia (CLL), non-Hodgkin lymphoma (NHL), or multiple myeloma (MM).

[0009] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), and the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, deletion of chromosome segment 13q, monosomy 17, deletion of chromosome segment 17p, deletion of chromosome segment 20q, and trisomy 22.

[0010] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the hematopoietic neoplasm is myeloproliferative neoplasm (MPN), and the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, trisomy 9, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, deletion of chromosome segment 13q, deletion of chromosome segment 20q, and trisomy 21.Docket Number: 20230802-03 / 027644.8492

[0011] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the hematopoietic neoplasm is myelodysplasia (MDS), and the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, deletion of chromosome segment 9q, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, and deletion of chromosome segment 13q.

[0012] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the hematopoietic neoplasm is chronic lymphocytic leukemia (CLL), and the plurality of CNVs include one or more of monosomy 11, deletion of chromosome segment 11q, deletion of chromosome segment 11q22-23, trisomy 12, monosomy 13, deletion of chromosome segment 13q, deletion of chromosome segment 13q14, monosomy 17, deletion of chromosome segment 17p, and deletion of chromosome segment 17p12-13.

[0013] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the hematopoietic neoplasm is multiple myeloma (MM), and the plurality of CNVs include one or more of hyperdiploid karyotype characterized by trisomy 3, trisomy 5, trisomy 7, trisomy 9, trisomy 11, trisomy 15, and trisomy 19, or deletion of chromosome segment 17p, deletion of chromosome segment 1p, and addition of chromosome segment 1q.

[0014] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the hematopoietic neoplasm is non-Hodgkin lymphoma (NHL), and the plurality of CNVs include deletion of chromosome segment 17p, or fusions of BCL6, BCL2, CCND1, MALT1, and MYC.

[0015] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the DNA sequencing data encodes a plurality of heme-related genes.

[0016] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the DNA sequencing data encodes a genome wide single nucleotide polymorphism (SNP) backbone.

[0017] In some aspects, the techniques described herein relate to a computer-implemented method, wherein the DNA sequencing data encodes a plurality of heme-related genes and a genome wide single nucleotide polymorphism (SNP) backbone.

[0018] In some aspects, the techniques described herein relate to a computer-implemented method, further including generating a report including the DNA sequencing data and the detected hematopoietic neoplasm in the subject.

[0019] In some aspects, the techniques described herein relate to a computer-implemented method, further including generating display data for the report.Docket Number: 20230802-03 / 027644.8492

[0020] In some aspects, the techniques described herein relate to a computer-implemented method, further including transmitting the report over a network.

[0021] In some aspects, the techniques described herein relate to a computer-implemented method, further including, in response to detecting the hematopoietic neoplasm in the subject, providing a diagnosis for the subject.

[0022] In some aspects, the techniques described herein relate to a computer-implemented method, further including, in response to detecting the hematopoietic neoplasm in the subject, providing a prognosis for the subject.

[0023] In some aspects, the techniques described herein relate to a computer-implemented method, further including recommending a treatment for the subject.

[0024] In some aspects, the techniques described herein relate to a method for treating a subject including: detecting, using a computing device, a hematopoietic neoplasm in the subject as described herein; and in response to detecting the hematopoietic neoplasm in the subject, providing a treatment to the subject.

[0025] In some aspects, the techniques described herein relate to a method, further including: obtaining a sample from the subject; extracting DNA from the sample; and sequencing the DNA to obtain the DNA sequencing data.

[0026] In some aspects, the techniques described herein relate to a method, wherein the DNA is sequenced using a next generation sequencing device (NGS).

[0027] In some aspects, the techniques described herein relate to a system for detecting hematopoietic neoplasms including: at least one processor; and a memory operably coupled to the at least one processor, wherein the memory has computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to: receive DNA sequencing data for a subject, the DNA sequencing data including a plurality of variants, wherein the plurality of variants include a plurality of copy number variants (CNVs); identify a cytoband variant or a chromosomal variant among the plurality of CNVs; and detect a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant.

[0028] In some aspects, the techniques described herein relate to a system, wherein the cytoband variant is a cytoband copy number loss.

[0029] In some aspects, the techniques described herein relate to a system, wherein the chromosomal variant is a chromosomal arm loss, a monosomy, or a trisomy.Docket Number: 20230802-03 / 027644.8492

[0030] In some aspects, the techniques described herein relate to a system, wherein the plurality of variants further include at least one of a single nucleotide variant (SNV), an insertion deletion (indel), an FLT3 internal tandem duplication (FLT3-ITD), and a gene fusion.

[0031] In some aspects, the techniques described herein relate to a system, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), myelodysplasia (MDS), chronic lymphocytic leukemia (CLL), non-Hodgkin lymphoma (NHL), or multiple myeloma (MM).

[0032] In some aspects, the techniques described herein relate to a system, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), and the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, deletion of chromosome segment 13q, monosomy 17, deletion of chromosome segment 17p, deletion of chromosome segment 20q, and trisomy 22.

[0033] In some aspects, the techniques described herein relate to a system, wherein the hematopoietic neoplasm is myeloproliferative neoplasm (MPN), and the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, trisomy 9, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, deletion of chromosome segment 13q, deletion of chromosome segment 20q, and trisomy 21.

[0034] In some aspects, the techniques described herein relate to a system, wherein the hematopoietic neoplasm is myelodysplasia (MDS), and the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, deletion of chromosome segment 9q, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, and deletion of chromosome segment 13q.

[0035] In some aspects, the techniques described herein relate to a system, wherein the hematopoietic neoplasm is chronic lymphocytic leukemia (CLL), and the plurality of CNVs include one or more of monosomy 11, deletion of chromosome segment 11q, deletion of chromosome segment 11q22-23, trisomy 12, monosomy 13, deletion of chromosome segment 13q, deletion of chromosome segment 13q14, monosomy 17, deletion of chromosome segment 17p, and deletion of chromosome segment 17p12-13.Docket Number: 20230802-03 / 027644.8492

[0036] In some aspects, the techniques described herein relate to a system, wherein the hematopoietic neoplasm is multiple myeloma (MM), and the plurality of CNVs include one or more of hyperdiploid karyotype characterized by trisomy 3, trisomy 5, trisomy 7, trisomy 9, trisomy 11, trisomy 15, and trisomy 19, or deletion of chromosome segment 17p, deletion of chromosome segment 1p, and addition of chromosome segment 1q.

[0037] In some aspects, the techniques described herein relate to a system, wherein the hematopoietic neoplasm is non-Hodgkin lymphoma (NHL), and the plurality of CNVs include deletion of chromosome segment 17p, or fusions of BCL6, BCL2, CCND1, MALT1, and MYC.

[0038] In some aspects, the techniques described herein relate to a system, wherein the DNA sequencing data encodes a plurality of heme-related genes.

[0039] In some aspects, the techniques described herein relate to a system, wherein the DNA sequencing data encodes a genome wide single nucleotide polymorphism (SNP) backbone.

[0040] In some aspects, the techniques described herein relate to a system, wherein the DNA sequencing data encodes a plurality of heme-related genes and a genome wide single nucleotide polymorphism (SNP) backbone.

[0041] In some aspects, the techniques described herein relate to a system, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to generate a report including the DNA sequencing data and the detected hematopoietic neoplasm in the subject.

[0042] In some aspects, the techniques described herein relate to a system, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to generate display data for the report.

[0043] In some aspects, the techniques described herein relate to a system, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to transmit the report over a network.

[0044] In some aspects, the techniques described herein relate to a system, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to, in response to detecting the hematopoietic neoplasm in the subject, provide a diagnosis for the subject.

[0045] In some aspects, the techniques described herein relate to a system, wherein the memory has further computer-executable instructions stored thereon that, when executed by the atDocket Number: 20230802-03 / 027644.8492 least one processor, cause the at least one processor to, in response to detect the hematopoietic neoplasm in the subject, providing a prognosis for the subject.

[0046] In some aspects, the techniques described herein relate to a system, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to recommend a treatment for the subject.

[0047] It should be understood that the above-described subject matter may also be implemented as a computer-controlled apparatus, a computer process, a computing system, or an article of manufacture, such as a computer-readable storage medium.

[0048] Other systems, methods, features and / or advantages will be or may become apparent to one with skill in the art upon examination of the following drawings and detailed description. It is intended that all such additional systems, methods, features and / or advantages be included within this description and be protected by the accompanying claims. BRIEF DESCRIPTION OF THE DRAWINGS

[0049] The components in the drawings are not necessarily to scale relative to each other. Like reference numerals designate corresponding parts throughout the several views.

[0050] FIGURE 1 is a flowchart illustrating example operations for detecting hematopoietic neoplasms using DNA mutations according to an implementation described herein.

[0051] FIGURE 2 is Table 1, which shows copy number variant (CNV) regions.

[0052] FIGURE 3 is Table 2, which shows reportable CNV(s) per specific type of hematopoietic neoplasm.

[0053] FIGURE 4 is an example computing device.

[0054] FIGURE 5 is Table 3, which shows a CNV bioinformatics pipeline for sample of interest and somatic chromosomes according to an example described herein.

[0055] FIGURE 6 is Table 4, which shows a CNV reporting pipeline for sample of interest and somatic chromosomes according to an example described herein. DETAILED DESCRIPTION

[0056] Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art. Methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present disclosure.Docket Number: 20230802-03 / 027644.8492

[0057] The following description of the disclosure is provided as an enabling teaching of the disclosure in its best, currently known embodiment(s). To this end, those skilled in the relevant art will recognize and appreciate that many changes can be made to the various embodiments of the present disclosure, while still obtaining the beneficial results of the present disclosure. It will also be apparent that some of the desired benefits of the present disclosure can be obtained by selecting some of the features of the present disclosure without utilizing other features. Accordingly, those who work in the art will recognize that many modifications and adaptations to the present disclosure are possible and can even be desirable in certain circumstances and are a part of the present disclosure. Thus, the following description is provided as illustrative of the principles of the present disclosure and not in limitation thereof.

[0058] Reference will now be made in detail to the embodiments of the present disclosure, examples of which are illustrated in the drawings and the examples. The present disclosure may, however, be embodied in many different forms and should not be construed as limited to the embodiments set forth herein.

[0059] Terminology

[0060] The term “comprising” and variations thereof as used herein is used synonymously with the term “including” and variations thereof and are open, non-limiting terms. Although the terms “comprising” and “including” have been used herein to describe various embodiments, the terms “consisting essentially of” and “consisting of” can be used in place of “comprising” and “including” to provide for more specific embodiments and are also disclosed. As used in this disclosure and in the appended claims, the singular forms “a”, “an”, “the”, include plural referents unless the context clearly dictates otherwise.

[0061] The following definitions are provided for the full understanding of terms used in this specification.

[0062] The terms "about" and "approximately" are defined as being “close to” as understood by one of ordinary skill in the art. In one non-limiting embodiment the terms are defined to be within 10%. In another non-limiting embodiment, the terms are defined to be within 5%. In still another non-limiting embodiment, the terms are defined to be within 1%.

[0063] As used herein, the terms "may," "optionally," and "may optionally" are used interchangeably and are meant to include cases in which the condition occurs as well as cases in which the condition does not occur. Thus, for example, the statement that a formulation "may include anDocket Number: 20230802-03 / 027644.8492 excipient" is meant to include cases in which the formulation includes an excipient as well as cases in which the formulation does not include an excipient.

[0064] “Composition” refers to any agent that has a beneficial biological effect. Beneficial biological effects include both therapeutic effects, e.g., treatment of a disorder or other undesirable physiological condition, and prophylactic effects, e.g., prevention of a disorder or other undesirable physiological condition. The terms also encompass pharmaceutically acceptable, pharmacologically active derivatives of beneficial agents specifically mentioned herein, including, but not limited to, a vector, polynucleotide, cells, salts, esters, amides, proagents, active metabolites, isomers, fragments, analogs, and the like. When the term “composition” is used, then, or when a particular composition is specifically identified, it is to be understood that the term includes the composition per se as well as pharmaceutically acceptable, pharmacologically active vector, polynucleotide, salts, esters, amides, proagents, conjugates, active metabolites, isomers, fragments, analogs, etc.

[0065] The term “subject” refers to any individual who is the target of administration or treatment. The subject can be a vertebrate, for example, a mammal. In one aspect, the subject can be human, non-human primate, bovine, equine, porcine, canine, or feline. The subject can also be a guinea pig, rat, hamster, rabbit, mouse, or mole. Thus, the subject can be a human or veterinary patient. The term “patient” refers to a subject under the treatment of a clinician, e.g., physician.

[0066] A “control” is an alternative subject or sample used in an experiment for comparison purposes. A control can be "positive" or "negative."

[0067] The term “detect” or “detecting” refers to an output signal released for the purpose of sensing of physical phenomenon. An event or change in environment is sensed and signal output released in the form of light, heat, or a color change (i.e.: color change from red to blue, white to black, or vice versa).

[0068] The term “cancer” is used to address any neoplastic disease. Specifically, it is used here to describe hematological malignancies, including lymphomas, leukemias and myelomas.

[0069] The term “hematopoietic neoplasm” or “hematologic neoplasm” or “hematological malignancy” refers to a group of diseases characterized by the abnormal proliferation or differentiation of cells in the blood-forming tissues, such as the bone marrow, lymph nodes, and spleen. These neoplasms primarily affect the cells involved in hematopoiesis, including red blood cells, white blood cells, and platelets. Hematopoietic neoplasms can be broadly classified into categories, e.g., leukemias, lymphomas, and myelomas.Docket Number: 20230802-03 / 027644.8492

[0070] The term “kit” describes a wide variety of bags, containers, carrying cases, and other portable enclosures which may be used to carry and store solid substances, liquid substances, and other accessories necessary to perform a next generation sequencing, deep sequencing, or high-throughput sequencing / screening assays. Such kits and their contents along with any applicable procedures may be used to provide access to variations detected in the hematologic neoplasms in accordance with the teachings of the present disclosure.

[0071] A "probe" when used in the context of polynucleotide manipulation refers to an oligonucleotide that is provided as a reagent to detect a target potentially present in a sample of interest by hybridizing with the target. Usually, a probe will comprise a label or a means by which a label can be attached, either before or subsequent to the hybridization reaction. Suitable labels include, but are not limited to radioisotopes, fluorochromes, chemiluminescent compounds, dyes, and proteins, including enzymes.

[0072] A "gene" refers to a polynucleotide containing at least one open reading frame that is capable of encoding a particular polypeptide or protein after being transcribed and translated. Any of the polynucleotides sequences described herein may be used to identify larger fragments or full-length coding sequences of the gene with which they are associated. A “gene panel” refers to a compilation, list, or grouping of genes for testing of variations, mutations, and changes in one or more genes.

[0073] “Profiling” refers to a collection of information relating to a specific gene, protein, disease, or disorder. Profiles can describe the risk of disease, preventive care assessments and utilization, and disease prevalence.

[0074] An oligonucleotide refers to a synthetic, short, single-stranded nucleic acid sequence (typically 10-30 nucleotides in length) used to target specified DNA or RNA sequences of interest in a wide range of applications, including, but not limited to biotechnology and genetics testing. The length of an oligonucleotide is usually denoted by “-mer”. For example, an oligonucleotide comprising six nucleotides is a hexamer and an oligonucleotide comprising 25 nucleotides is a “25-mer”. Oligonucleotides can be chemically modified to comprise a detection probe including, but not limited to a fluorophore, an enzyme, a protein, or compound. An oligonucleotide can also be a primer often used in a "polymerase chain reaction". PCR is a reaction in which replicate copies are made of a target polynucleotide using a "pair of primers" or a "set of primers" consisting of an "upstream" and a "downstream" primer, and a catalyst of polymerization, such as a DNA polymerase, and typically a thermally stable polymerase enzyme. Methods for PCR are well known in the art, and taught, forDocket Number: 20230802-03 / 027644.8492 example in "PCR: A PRACTICAL APPROACH" (M. MacPherson et al., IRL Press at Oxford University Press (1991)).

[0075] A “nucleic acid” is a chemical compound that serves as the primary information- carrying molecules in cells and make up the cellular genetic material. Nucleic acids comprise nucleotides, which are the monomers made of a 5-carbon sugar (usually ribose or deoxyribose), a phosphate group, and a nitrogenous base. A nucleic acid can also be a deoxyribonucleic acid (DNA) or a ribonucleic acid (RNA). A chimeric nucleic acid comprises two or more of the same kind of nucleic acid fused together to form one compound comprising genetic material.

[0076] A “variant,” “mutant,” or “derivative” of a particular nucleic acid sequence may be defined as a nucleic acid sequence having at least 50% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the “BLAST 2 Sequences” tool available at the National Center for Biotechnology Information's website. (See Tatiana A. Tatusova, Thomas L. Madden (1999), “Blast 2 sequences—a new tool for comparing protein and nucleotide sequences”, FEMS Microbiol Lett.174:247-250). In some embodiments a variant polynucleotide may show, for example, at least 60%, at least 70%, at least 80%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length relative to a reference polynucleotide.

[0077] As used herein, a “mutation” refers to changing the structure of a gene, resulting in a variant form that may be transmitted to later generations. A mutation is caused by the alteration of single nucleotides in DNA, or the deletion, insertion, or rearrangement of larger sections of genes. A mutation can lead to the expression of a protein that has been changed physically or functionally leading to lethality, non-lethal dysfunction effects, or no effects.

[0078] An “assay standard”, “standard”, or a “verification sample” refers to any molecule, compound, or composition of known quantity (concentration, volume, mass, etc.) used to determine the quantity of an unknown molecule, compound, or composition. A standard is usually used in an assay to quantify a final product of the assay.

[0079] “Hybridizing” refers to the process in which two complementary nucleic acid molecules bind together to form a new double stranded molecule. Binding between the two nucleic acid molecules depends on the appropriate base pairing across the two single stranded molecules.Docket Number: 20230802-03 / 027644.8492

[0080] “Fusing” refers to the process in which two different (usually non-complementary) nucleic acid molecules are joined together to form a new double stranded molecule. Fusing is also an induced process, not dependent on sequence base pairing to force generation of new genes.

[0081] Ranges can be expressed herein as from “about” one particular value, and / or to “about” another particular value. When such a range is expressed, another embodiment includes from the one particular value and / or to the other particular value. Similarly, when values are expressed as approximations, by use of the antecedent “about,” it will be understood that the particular value forms another embodiment. It will be further understood that the endpoints of each of the ranges are significant both in relation to the other endpoint, and independently of the other endpoint. It is also understood that there are a number of values disclosed herein, and that each value is also herein disclosed as “about” that particular value in addition to the value itself. For example, if the value “10” is disclosed, then “about 10” is also disclosed. It is also understood that when a value is disclosed that “less than or equal to” the value, “greater than or equal to the value” and possible ranges between values are also disclosed, as appropriately understood by the skilled artisan. For example, if the value “10” is disclosed the “less than or equal to 10”as well as “greater than or equal to 10” is also disclosed. It is also understood that the throughout the application, data is provided in a number of different formats, and that this data, represents endpoints and starting points, and ranges for any combination of the data points. For example, if a particular data point “10” and a particular data point “15” are disclosed, it is understood that greater than, greater than or equal to, less than, less than or equal to, and equal to 10 and 15 are considered disclosed as well as between 10 and 15. It is also understood that each unit between two particular units are also disclosed. For example, if 10 and 15 are disclosed, then 11, 12, 13, and 14 are also disclosed.

[0082] An "increase" can refer to any change that results in a larger amount of a symptom, disease, composition, condition, or activity. A substance is also understood to increase the genetic output of a gene when the genetic output of the gene product with the substance is greater relative to the output of the gene product without the substance. Also for example, an increase can be a change in the symptoms of a disorder such that the symptoms are more than previously observed. An increase can be any individual, median, or average increase in a condition, symptom, activity, composition in a statistically significant amount. Thus, the increase can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% increase so long as the decrease is statistically significant.Docket Number: 20230802-03 / 027644.8492

[0083] A "decrease" can refer to any change that results in a smaller amount of a symptom, disease, composition, condition, or activity. A substance is also understood to decrease the genetic output of a gene when the genetic output of the gene product with the substance is less relative to the output of the gene product without the substance. Also for example, a decrease can be a change in the symptoms of a disorder such that the symptoms are less than previously observed. A decrease can be any individual, median, or average decrease in a condition, symptom, activity, composition in a statistically significant amount. Thus, the decrease can be a 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, 95, or 100% decrease so long as the decrease is statistically significant.

[0084] "Inhibit," "inhibiting," and "inhibition" mean to decrease an activity, response, condition, disease, or other biological parameter. This can include but is not limited to the complete ablation of the activity, response, condition, or disease. This may also include, for example, a 10% reduction in the activity, response, condition, or disease as compared to the native or control level. Thus, the reduction can be a 10, 20, 30, 40, 50, 60, 70, 80, 90, 100%, or any amount of reduction in between as compared to native or control levels.

[0085] By “reduce” or other forms of the word, such as “reducing” or “reduction,” is meant lowering of an event or characteristic (e.g., tumor growth). It is understood that this is typically in relation to some standard or expected value, in other words it is relative, but that it is not always necessary for the standard or relative value to be referred to. For example, “reduces tumor growth” means reducing the rate of growth of a tumor relative to a standard or a control.

[0086] By “prevent” or other forms of the word, such as “preventing” or “prevention,” is meant to stop a particular event or characteristic, to stabilize or delay the development or progression of a particular event or characteristic, or to minimize the chances that a particular event or characteristic will occur. Prevent does not require comparison to a control as it is typically more absolute than, for example, reduce. As used herein, something could be reduced but not prevented, but something that is reduced could also be prevented. Likewise, something could be prevented but not reduced, but something that is prevented could also be reduced. It is understood that where reduce or prevent are used, unless specifically indicated otherwise, the use of the other word is also expressly disclosed.

[0087] "Biocompatible" generally refers to a material and any metabolites or degradation products thereof that are generally non-toxic to the recipient and do not cause significant adverse effects to the subject.Docket Number: 20230802-03 / 027644.8492

[0088] "Comprising" is intended to mean that the compositions, methods, etc. include the recited elements, but do not exclude others. "Consisting essentially of'' when used to define compositions and methods, shall mean including the recited elements, but excluding other elements of any essential significance to the combination. Thus, a composition consisting essentially of the elements as defined herein would not exclude trace contaminants from the isolation and purification method and pharmaceutically acceptable carriers, such as phosphate buffered saline, preservatives, and the like. "Consisting of'' shall mean excluding more than trace elements of other ingredients and substantial method steps for administering the compositions provided and / or claimed in this disclosure. Embodiments defined by each of these transition terms are within the scope of this disclosure.

[0089] “Effective amount” of an agent refers to a sufficient amount of an agent to provide a desired effect. The amount of agent that is “effective” will vary from subject to subject, depending on many factors such as the age and general condition of the subject, the particular agent or agents, and the like. Thus, it is not always possible to specify a quantified “effective amount.” However, an appropriate “effective amount” in any subject case may be determined by one of ordinary skill in the art using routine experimentation. Also, as used herein, and unless specifically stated otherwise, an “effective amount” of an agent can also refer to an amount covering both therapeutically effective amounts and prophylactically effective amounts. An “effective amount” of an agent necessary to achieve a therapeutic effect may vary according to factors such as the age, sex, and weight of the subject. Dosage regimens can be adjusted to provide the optimum therapeutic response. For example, several divided doses may be administered daily or the dose may be proportionally reduced as indicated by the exigencies of the therapeutic situation.

[0090] A "pharmaceutically acceptable" component can refer to a component that is not biologically or otherwise undesirable, i.e., the component may be incorporated into a pharmaceutical formulation provided by the disclosure and administered to a subject as described herein without causing significant undesirable biological effects or interacting in a deleterious manner with any of the other components of the formulation in which it is contained. When used in reference to administration to a human, the term generally implies the component has met the required standards of toxicological and manufacturing testing or that it is included on the Inactive Ingredient Guide prepared by the U.S. Food and Drug Administration.

[0091] "Pharmaceutically acceptable carrier" (sometimes referred to as a “carrier”) means a carrier or excipient that is useful in preparing a pharmaceutical or therapeutic composition that is generally safe and non-toxic and includes a carrier that is acceptable for veterinary and / or humanDocket Number: 20230802-03 / 027644.8492 pharmaceutical or therapeutic use. The terms "carrier" or "pharmaceutically acceptable carrier" can include, but are not limited to, phosphate buffered saline solution, water, emulsions (such as an oil / water or water / oil emulsion) and / or various types of wetting agents. As used herein, the term "carrier" encompasses, but is not limited to, any excipient, diluent, filler, salt, buffer, stabilizer, solubilizer, lipid, stabilizer, or other material well known in the art for use in pharmaceutical formulations and as described further herein.

[0092] “Pharmacologically active” (or simply “active”), as in a “pharmacologically active” derivative or analog, can refer to a derivative or analog (e.g., a salt, ester, amide, conjugate, metabolite, isomer, fragment, etc.) having the same type of pharmacological activity as the parent compound and approximately equivalent in degree.

[0093] “Therapeutic agent” refers to any composition that has a beneficial biological effect. Beneficial biological effects include both therapeutic effects, e.g., treatment of a disorder or other undesirable physiological condition, and prophylactic effects, e.g., prevention of a disorder or other undesirable physiological condition (e.g., a non-immunogenic cancer). The terms also encompass pharmaceutically acceptable, pharmacologically active derivatives of beneficial agents specifically mentioned herein, including, but not limited to, salts, esters, amides, proagents, active metabolites, isomers, fragments, analogs, and the like. When the terms “therapeutic agent” is used, then, or when a particular agent is specifically identified, it is to be understood that the term includes the agent per se as well as pharmaceutically acceptable, pharmacologically active salts, esters, amides, proagents, conjugates, active metabolites, isomers, fragments, analogs, etc.

[0094] “Therapeutically effective amount” or “therapeutically effective dose” of a composition (e.g. a composition comprising an agent) refers to an amount that is effective to achieve a desired therapeutic result. Therapeutically effective amounts of a given therapeutic agent will typically vary with respect to factors such as the type and severity of the disorder or disease being treated and the age, gender, and weight of the subject. The term can also refer to an amount of a therapeutic agent, or a rate of delivery of a therapeutic agent (e.g., amount over time), effective to facilitate a desired therapeutic effect. The precise desired therapeutic effect will vary according to the condition to be treated, the tolerance of the subject, the agent and / or agent formulation to be administered (e.g., the potency of the therapeutic agent, the concentration of agent in the formulation, and the like), and a variety of other factors that are appreciated by those of ordinary skill in the art. In some instances, a desired biological or medical response is achieved following administration of multiple dosages of the composition to the subject over a period of days, weeks, or years.Docket Number: 20230802-03 / 027644.8492

[0095] The term “treatment” refers to the medical management of a patient with the intent to cure, ameliorate, stabilize, or prevent a disease, pathological condition, or disorder. This term includes active treatment, that is, treatment directed specifically toward the improvement of a disease, pathological condition, or disorder, and also includes causal treatment, that is, treatment directed toward removal of the cause of the associated disease, pathological condition, or disorder. In addition, this term includes palliative treatment, that is, treatment designed for the relief of symptoms rather than the curing of the disease, pathological condition, or disorder; preventative treatment, that is, treatment directed to minimizing or partially or completely inhibiting the development of the associated disease, pathological condition, or disorder; and supportive treatment, that is, treatment employed to supplement another specific therapy directed toward the improvement of the associated disease, pathological condition, or disorder. Treatments according to the present disclosure may be applied preventively, prophylactically, palliatively or remedially. Prophylactic treatments are administered to a subject prior to onset (e.g., before obvious signs of cancer), during early onset (e.g., upon initial signs and symptoms of cancer), or after an established development of cancer. Prophylactic administration can occur for day(s) to years prior to the manifestation of symptoms of an infection.

[0096] Next generation Sequencing (NGS) Assays

[0097] Next-generation sequencing is a massive parallel sequencing technique wherein isolated DNA or RNA samples are amplified, sequenced, and analyzed for complete genomic or transcriptomic overview. This method of sequencing requires smaller sample sizes, less reagents and time, and lower reagent costs while providing whole genome data from a single subject. NGS is described in detail in PCT / US2023 / 011770, filed January 27, 2023, the disclosure of which is expressly incorporated herein by reference in its entirety.

[0098] PCT / US2023 / 011770 describes next generation sequencing assays and methods for profiling hematologic neoplasms. In particular, PCT / US2023 / 011770 discloses DNA-based and RNA- based NGS assay detecting, identifying, and / or profiling neoplasms in particular neoplasms that are characterized into one of six classifications of neoplasms: acute myeloid leukemia (AML), myelodysplasia (MDS), myeloproliferative neoplasm (MPN), non-Hodgkin lymphoma (NHL), chronic lymphocytic leukemia (CLL), and multiple myeloma (MM). It is understood and herein contemplated that wherein the neoplasms is an AML, the AML includes, but is not limited to acute lymphoblastic leukemia (ALL), Lymphoblastic (diffuse) lymphoma, acute myeloblastic leukemia, chronic lymphoblastic leukemia of B cell type, myeloid leukemia, atypical chronic myeloid leukemia BCR / ABL – negative, myeloid sarcoma, acute promyelocytic leukemia, acute myelomonocytic leukemia, acute myeloid leukemia with 11q23-Docket Number: 20230802-03 / 027644.8492 abnormality, chronic myeloid leukemia (CML), B-acute lymphocytic leukemia (B-ALL), and acute myeloid leukemia with multidimensional dysplasia. Similarly, wherein the neoplasm is classified as an MDS, the MDS includes, but is not limited to refractory anemia, refractory cytopenia with multilineage dysplasia, refractory anemia with ringed sideroblasts, refractory cytopenia with multilineage dysplasia and ringed sideroblasts, and refractory anemia with excess blasts. Likewise, wherein the neoplasm is classified as a MPN, the MPN includes, but is not limited to polycythemia vera, chronic myeloproliferative disease, and essential (hemorrhagic) thrombocythemia. It is further understood that wherein the neoplasm classifies as a NHL, the NHL includes, but is not limited to small cell B cell lymphoma (splenic marginal zone lymphoma), mantle cell lymphoma, multiple myeloma, diffuse large B cell lymphoma, peripheral T cell lymphoma (not classified), Waldenstrom macroglobulinemia (WM), follicular lymphoma, Burkitt lymphoma, mucosal-associated lymphoma, and post-transplant lymphoproliferative disorder (PTLD). Additionally, wherein the neoplasm classifies as a CLL, the CLL includes, but is not limited to chronic lymphocytic leukemia of B cell type, small lymphocytic lymphoma (SLL), prolymphocytic leukemia (PLL), large granular lymphocyte (LGL) leukemia, and hairy cell leukemia (HCL). Lastly, when the neoplasm classifies as a MM, the MM includes, but is not limited to smoldering multiple myeloma (SMM), light chain amyloidosis, and Waldenstrom macroglobulinemia (WM).

[0099] It should be understood that the NGS assay can detect multiple changes in a nucleic acid sequence including, but not limited to deletions, additions, insertions, or a variant or derivative thereof. Further NGS can detect known or unknown deletions, insertions / addition, or a variant or derivative thereof. A deletion of a gene comprises removing a part of a gene or an entire / complete gene. A deletion also comprises removal of large segments of a chromosome. In some embodiments, a deletion comprises removal of at least one or more nucleotides from a gene. In some embodiments, a deletion comprises removal of 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231,Docket Number: 20230802-03 / 027644.8492 , 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252,, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273,, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294,, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315,, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336,, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357,, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378,, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399,, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420,, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441,, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456, 457, 458, 459, 460, 461, 462,, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483,, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504,, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525,, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546,, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567,, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588,, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609,, 611, 612, 613, 614, 615, 616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630,, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651,, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671, 672,, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693,, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714,, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735,, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756,, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777,, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798,, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819,, 821, 822, 823, 824, 825, 826, 827, 828, 829, 830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 840,, 842, 843, 844, 845, 846, 847, 848, 849, 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 860, 861,, 863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882,, 884, 885, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 900, 901, 902, 903,Docket Number: 20230802-03 / 027644.8492 904, 905, 906, 907, 908, 909, 910, 911, 912, 913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995, 996, 997, 998, 999, 1000, or more nucleotides. In some embodiments, deletion comprises deletion of segments of a chromosome. In some embodiments, deletion comprises deletion of an entire chromosome.

[0100] An addition / insertion comprises adding or inserting nucleotides, oligonucleotides, or polynucleotides into a gene. An addition / insertion can also be a duplication, wherein a segment of a gene or an entire / complete gene is repeated contiguously. In some embodiments, an addition / insertion comprises adding at least one or more nucleotides to a gene. In some embodiments, an addition / insertion comprises adding 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409, 410, 411, 412, 413, 414, 415, 416, 417, 418, 419, 420, 421, 422, 423, 424, 425, 426, 427, 428, 429, 430, 431, 432, 433, 434, 435, 436, 437, 438, 439, 440, 441, 442, 443, 444, 445, 446, 447, 448, 449, 450, 451, 452, 453, 454, 455, 456,Docket Number: 20230802-03 / 027644.8492 457, 458, 459, 460, 461, 462, 463, 464, 465, 466, 467, 468, 469, 470, 471, 472, 473, 474, 475, 476, 477, 478, 479, 480, 481, 482, 483, 484, 485, 486, 487, 488, 489, 490, 491, 492, 493, 494, 495, 496, 497, 498, 499, 500, 501, 502, 503, 504, 505, 506, 507, 508, 509, 510, 511, 512, 513, 514, 515, 516, 517, 518, 519, 520, 521, 522, 523, 524, 525, 526, 527, 528, 529, 530, 531, 532, 533, 534, 535, 536, 537, 538, 539, 540, 541, 542, 543, 544, 545, 546, 547, 548, 549, 550, 551, 552, 553, 554, 555, 556, 557, 558, 559, 560, 561, 562, 563, 564, 565, 566, 567, 568, 569, 570, 571, 572, 573, 574, 575, 576, 577, 578, 579, 580, 581, 582, 583, 584, 585, 586, 587, 588, 589, 590, 591, 592, 593, 594, 595, 596, 597, 598, 599, 600, 601, 602, 603, 604, 605, 606, 607, 608, 609, 610, 611, 612, 613, 614, 615, 616, 617, 618, 619, 620, 621, 622, 623, 624, 625, 626, 627, 628, 629, 630, 631, 632, 633, 634, 635, 636, 637, 638, 639, 640, 641, 642, 643, 644, 645, 646, 647, 648, 649, 650, 651, 652, 653, 654, 655, 656, 657, 658, 659, 660, 661, 662, 663, 664, 665, 666, 667, 668, 669, 670, 671, 672, 673, 674, 675, 676, 677, 678, 679, 680, 681, 682, 683, 684, 685, 686, 687, 688, 689, 690, 691, 692, 693, 694, 695, 696, 697, 698, 699, 700, 701, 702, 703, 704, 705, 706, 707, 708, 709, 710, 711, 712, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722, 723, 724, 725, 726, 727, 728, 729, 730, 731, 732, 733, 734, 735, 736, 737, 738, 739, 740, 741, 742, 743, 744, 745, 746, 747, 748, 749, 750, 751, 752, 753, 754, 755, 756, 757, 758, 759, 760, 761, 762, 763, 764, 765, 766, 767, 768, 769, 770, 771, 772, 773, 774, 775, 776, 777, 778, 779, 780, 781, 782, 783, 784, 785, 786, 787, 788, 789, 790, 791, 792, 793, 794, 795, 796, 797, 798, 799, 800, 801, 802, 803, 804, 805, 806, 807, 808, 809, 810, 811, 812, 813, 814, 815, 816, 817, 818, 819, 820, 821, 822, 823, 824, 825, 826, 827, 828, 829, 830, 831, 832, 833, 834, 835, 836, 837, 838, 839, 840, 841, 842, 843, 844, 845, 846, 847, 848, 849, 850, 851, 852, 853, 854, 855, 856, 857, 858, 859, 860, 861, 862, 863, 864, 865, 866, 867, 868, 869, 870, 871, 872, 873, 874, 875, 876, 877, 878, 879, 880, 881, 882, 883, 884, 885, 886, 887, 888, 889, 890, 891, 892, 893, 894, 895, 896, 897, 898, 899, 900, 901, 902, 903, 904, 905, 906, 907, 908, 909, 910, 911, 912, 913, 914, 915, 916, 917, 918, 919, 920, 921, 922, 923, 924, 925, 926, 927, 928, 929, 930, 931, 932, 933, 934, 935, 936, 937, 938, 939, 940, 941, 942, 943, 944, 945, 946, 947, 948, 949, 950, 951, 952, 953, 954, 955, 956, 957, 958, 959, 960, 961, 962, 963, 964, 965, 966, 967, 968, 969, 970, 971, 972, 973, 974, 975, 976, 977, 978, 979, 980, 981, 982, 983, 984, 985, 986, 987, 988, 989, 990, 991, 992, 993, 994, 995, 996, 997, 998, 999, 1000, or more nucleotides.

[0101] In some embodiments, a duplication comprises repeating a gene at least one time. In some embodiments, a duplication comprises repeating a gene 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more.

[0102] A “single nucleotide variant”, “SNV”, or “single nucleotide polymorphism” refers to a nucleic acid sequence variation wherein a single nucleotide (adenine, thymine, cytosine, or guanine)Docket Number: 20230802-03 / 027644.8492 in the genome sequence is altered into another nucleotide. In some embodiments, the nucleic acid sequence comprises a single nucleotide variant.

[0103] An “insertion-deletion” or “indel” refers to nucleic acid variant wherein a deletion and an insertion occur at the same time at the same genomic location, possibly resulting in a protein not folding or functioning properly. Therefore, an “insertion-deletion” variant requires at least nucleotide to be removed and at least one nucleotide to be added. In some embodiments, the nucleic acid sequence comprises an insertion-deletion variant.

[0104] A ”chimeric fusion” or “gene fusion” variant refers to a nucleic acid formed when two or more genes (usually from two distinct genomic locations) combine into one new gene, and express proteins with functions differing from that of the parent proteins. In some embodiments, the nucleic acid sequence comprises a gene fusion variant.

[0105] A “structural variant” refers to a nucleic acid, usually 1000 base pairs, or 1 kilobases (kb), in size, wherein the overall chromosomal structure is altered. “Structural variations” can further comprise other variations, including, but not limited to deletions, insertions, indels, copy number variations, duplications, inversion, substitutions, and derivatives thereof. In some embodiments, the nucleic acid comprises a structural variant.

[0106] A ”copy number variant” or “CNV” refers to nucleic acid sequence wherein the number of copies of a specific DNA segment within a genome is different from the expected two copies (i.e., one from each parent), and the number of copies of the specific DNA segment within the genome varies between species and individuals with a species. A “copy number variant” can involve the deletion (loss) of genetic material or the duplication (gain) of additional copies. A “copy number variant” is a specific type of “structural variant”. In some embodiments, the nucleic acid sequence comprises a copy number variant.

[0107] In some embodiments, the CNV is a cytoband variant such as copy number loss. Copy number loss refers to a genetic alteration in which a specific region of DNA within a genome is deleted or lost, resulting in a decrease in the number of copies of that DNA segment. It involves the loss of one or more copies of a particular gene or genomic region. Copy number loss can occur in both somatic cells (non-germline cells) and germline cells (cells that give rise to eggs or sperm). Somatic copy number losses are often associated with cancer and other genetic disorders, while germline copy number losses can be inherited and passed down through generations. Copy number losses can vary in size, ranging from small deletions affecting a single gene or a few base pairs to larger deletions encompassing entire chromosomes or chromosomal regions. The consequences of copy number lossDocket Number: 20230802-03 / 027644.8492 depend on the specific genes or genomic regions involved and their functional importance. Copy number loss can disrupt gene dosage and result in haploinsufficiency, where the remaining copy of the gene cannot produce enough protein to maintain normal cellular function. This can lead to various genetic disorders and diseases, depending on the affected genes. In cancer, copy number losses are commonly observed as a result of genomic instability and can contribute to tumor development and progression. Loss of tumor suppressor genes, which normally control cell growth and prevent the formation of tumors, can occur through copy number loss events.

[0108] In some embodiments, the CNV is a chromosomal variant such as chromosomal arm loss, chromosomal loss, or chromosomal gain. Chromosomal arm loss refers to the loss of an entire chromosomal arm or a significant portion of it. Each chromosome has two arms, referred to as the "p" arm (short arm) and the "q" arm (long arm), separated by the centromere. Chromosomal arm loss can occur in both somatic cells (non-germline cells) and germline cells (cells that give rise to eggs or sperm). The loss of a chromosomal arm is typically caused by genetic events such as chromosomal deletions, translocations, or large-scale structural rearrangements. These events can lead to the loss of genetic material and disrupt the normal balance of gene dosage, potentially affecting the function and regulation of genes located on the affected arm. Chromosomal arm loss can have significant consequences on an individual's health and development, depending on the specific chromosome involved and the genes located on the affected arm. The loss of essential genes or regulatory elements can result in developmental abnormalities, intellectual disabilities, and an increased risk of certain genetic disorders or diseases.

[0109] A “chromosomal loss” or “monosomy” refers to a genetic condition characterized by the presence of only one copy of a particular chromosome in an individual's cells, instead of the usual two copies. Monosomy is relatively rare and often has significant health consequences, as the absence of a chromosome can disrupt normal development and lead to various physical and intellectual disabilities. The most well-known example of monosomy is Turner syndrome, also known as 45,X or 45,X0. In Turner syndrome, one of the sex chromosomes, typically one of the X chromosomes, is missing or partially missing in females. The majority of individuals with Turner syndrome have a single X chromosome (45,X), although other variations with partial deletions or mosaicism (presence of cells with different chromosomal makeup) can occur. Monosomy can occur with other chromosomes as well. It should be understood that monosomy 45 is provided only as an example. As noted above, monosomy can occur with other chromosomes.Docket Number: 20230802-03 / 027644.8492

[0110] A “chromosomal gain” or “trisomy” refers to a genetic condition where there is an extra copy of a specific chromosome in an individual’s cells. In humans, the usual number of chromosomes is 46, with 23 pairs, where one chromosome in each pair is inherited from each parent. Trisomy occurs when there is a presence of three copies of a particular chromosome instead of the usual two copies. The most well-known example of trisomy is Down syndrome, also known as trisomy 21. In Down syndrome, there is an extra copy of chromosome 21, resulting in a total of three copies instead of the usual two. Trisomy 21 is typically caused by an error in cell division called nondisjunction, which leads to an extra chromosome being present in the resulting gamete (egg or sperm) that combines with another gamete during fertilization. Trisomy can occur with other chromosomes as well, although they are generally less common and often associated with more severe health effects. Examples include trisomy 18 (Edwards syndrome) and trisomy 13 (Patau syndrome), where there is an extra copy of chromosomes 18 and 13, respectively. It should be understood that trisomy 21, trisomy 18 and trisomy 13 are provided only as examples. As noted above, trisomy can occur with other chromosomes.

[0111] An “FLT3 internal tandem duplication” or “FLT3-ITD” refers to a specific mutation found in the FLT3 gene, which encodes a receptor tyrosine kinase called FMS-like tyrosine kinase 3. FLT3-ITD is commonly associated with acute myeloid leukemia (AML). The FLT3-ITD mutation involves the insertion of a tandem repeat of a portion of the FLT3 gene within the DNA sequence. This duplication results in an abnormal form of the FLT3 protein with altered structure and function. The FLT3 protein normally plays a role in regulating the growth and survival of hematopoietic stem cells, which give rise to various blood cell types. The FLT3-ITD mutation involves the insertion of a tandem repeat of a portion of the FLT3 gene within the DNA sequence. This duplication results in an abnormal form of the FLT3 protein with altered structure and function. The FLT3 protein normally plays a role in regulating the growth and survival of hematopoietic stem cells, which give rise to various blood cell types. FLT3-ITD mutations are observed in approximately 25-30% of AML cases, making it one of the most common genetic alterations in this disease. Patients with FLT3-ITD-positive AML often have a poorer prognosis, as the mutation is associated with a higher risk of relapse and reduced overall survival compared to those without the mutation.

[0112] In some implementations, the nucleic acid sequence can include one or more variants including a copy number variant, a single nucleotide variant, an insertion deletion (indel), an FLT3-ITD, a gene fusion, or combinations thereof. For example, in one implementation, the nucleic acid sequence includes a copy number variant. Optionally, the copy number variant is a copy number loss. Alternatively or additionally, the copy number variant is a chromosomal arm loss, monosomy, orDocket Number: 20230802-03 / 027644.8492 trisomy. The nucleic acid sequence optionally further includes (i.e., in addition to a CNV) one or more of an SNV, indel, FLT3-ITD, gene fusion, or combinations thereof.

[0113] Example Methods for Detecting Hematopoietic Neoplasms using DNA Mutations

[0114] Detecting hematologic neoplasms using a genomic analysis is challenging using existing technologies. Challenges include, but are not limited to:

[0115] Genetic Heterogeneity: Hematologic neoplasms exhibit significant genetic heterogeneity. Different subtypes can have distinct genomic alterations, making it challenging to identify common diagnostic or prognostic markers or therapeutic targets. Comprehensive genomic profiling and classification of these neoplasms require extensive analysis and interpretation of complex datasets.

[0116] Clonal Evolution: Hematologic neoplasms are often characterized by clonal evolution, where the genetic landscape of the cancer cells changes over time. This evolution can result in the emergence of subclones with different genetic alterations and varying response to treatment. Characterizing the complete clonal architecture and identifying key driver mutations can be challenging due to the presence of minor subclones or low-frequency mutations.

[0117] Transcriptomic Complexity: Hematologic neoplasms display a wide range of gene expression patterns, reflecting the diverse cell types involved and their dynamic interactions within the tumor microenvironment. Analyzing transcriptomic data requires advanced bioinformatics tools to decipher complex gene expression profiles, identify differentially expressed genes, and understand the functional implications of these changes.

[0118] Limited Biomarker Availability: Although genomic and transcriptomic analysis can provide valuable insights into hematologic neoplasms, the identification and validation of reliable biomarkers for diagnosis, prognosis, and treatment response prediction remain challenging. It can be difficult to distinguish driver mutations or gene expression changes from passenger alterations that do not contribute to the pathogenesis of the disease.

[0119] The systems and systems described herein address the challenges above. In particular, the systems and methods analyze DNA sequencing data for a subject. The DNA sequencing data encodes a plurality of heme-related genes, a genome wide single nucleotide polymorphism (SNP) backbone, or both a plurality of heme-related genes and SNP backbone. The techniques described herein include identifying a plurality of CNVs, particularly one or more cytoband and / or chromosomal variants (see e.g., Fig.2, Table 1), in the DNA sequencing data. It should be understood thatDocket Number: 20230802-03 / 027644.8492 conventional technologies have yet to use CNVs at the cytoband and / or chromosomal level to detect hematopoietic neoplasms. The techniques described herein further include detecting a hematopoietic neoplasm in the subject based on the identified CNVs (see e.g., Fig.3, Table 2). Optionally, the techniques described herein further include providing a diagnosis, prognosis, and / or treatment based on the detection.

[0120] Referring now to Fig.1, a flowchart illustrating example operations for detecting hematopoietic neoplasms using DNA mutations is shown. This disclosure contemplates that the example operations can be performed using one or more computing devices (e.g., at least the basic configuration illustrated in Fig.4 by box 402). The method for detecting hematopoietic neoplasms according to the method of Fig.1 includes using alterations (e.g., cytoband and / or chromosomal level variants) not considered by conventional technologies to detect hematopoietic neoplasms. Additionally, detection of hematopoietic neoplasms using the method shown in Fig.1 can be completed more quickly (e.g., 1-3 days) than conventional technologies, which typically have a turn-around-time of weeks for genomic and / or transcriptomic analysis.

[0121] At step 110, the method includes receiving DNA sequencing data for a subject. As described herein, the DNA sequencing data includes a plurality of variants, where the plurality of variants include a plurality of copy number variants (CNVs). Optionally, in some implementations, the plurality of variants further include (i.e., in addition to CNVs) at least one of a single nucleotide variant (SNV), an insertion deletion (indel), an FLT3 internal tandem duplication (FLT3-ITD), and a gene fusion.

[0122] In some implementations, the DNA sequencing data encodes a plurality of heme-related genes. Example heme-related genes are described in PCT / US2023 / 011770, filed January 27, 2023, the disclosure of which is expressly incorporated herein by reference in its entirety. Alternatively, in some implementations, the DNA sequencing data encodes a genome wide single nucleotide polymorphism (SNP) backbone. The term “single nucleotide polymorphism backbone” or “SNP backbone” refers to a core set of SNPs used as a reference or framework for genotyping or genetic analysis. SNPs are the most common type of genetic variation in the human genome, where a single nucleotide (A, T, C, or G) is altered at a specific position in the DNA sequence. SNPs can occur throughout the genome and are typically used as genetic markers to study genetic diversity, population genetics, and the association of specific variations with traits or diseases. The SNP backbone typically includes a representative set of SNPs that are informative for the population or specific research objectives. These SNPs are genotyped or analyzed to identify and compare genetic variations among individuals or populations. The selection of SNPs for the backbone often takes into consideration factorsDocket Number: 20230802-03 / 027644.8492 such as their frequency in the population, functional relevance, coverage of different genomic regions, and linkage disequilibrium patterns (correlation of variations at nearby positions). The chosen SNPs serve as representative markers to capture the genetic variation present in the studied population. As used herein, a genome wide SNP backbone includes a plurality (e.g., hundreds of thousands or millions) of SNPs that identify genetic variants associated with hematologic neoplasms. Alternatively, in some implementations, the DNA sequencing data encodes both a plurality of heme-related genes and a genome wide SNP backbone.

[0123] The DNA sequencing data can be obtained using a DNA sequencing device such as an NGS instrument that reads DNA strands and outputs an electrical waveform. A basecalling module (e.g., hardware, software, or combination thereof) of the NGS instrument transforms the electrical waveform into nucleobase sequences. In other words, the basecalling module receives the electrical waveform output by the sequencing device and outputs sequencing reads (A, T, C, G). The sequencing reads are optionally in text-based format such as FASTQ format. NGS systems are known in the art. For example, the iSEQ 100 NGS sequencing system from Illumina, Inc. of San Diego, California is a sequencing platform that can be used with the systems and methods described herein. It should be understood that NGS systems are provided only as an example. This disclosure contemplates using other high-throughput sequencing systems including, but not limited to, third-generation sequencing systems.

[0124] DNA sequencing is a laboratory technique used to determine the precise order of nucleotides (A, T, C, and G) in a DNA molecule. To sequence the DNA in a tissue sample, one or more of the following steps are performed:

[0125] Sample collection: Collect a tissue sample from the subject. In the implementations described herein, the tissue sample is a blood, bone marrow, serum, or fluid sample. Additionally, the subject is a mammal. In some embodiments, the subject is a human.

[0126] DNA extraction: Isolate the DNA from the tissue sample. DNA extraction kits and protocols for isolating DNA are known in the art.

[0127] DNA purification: Once the DNA is extracted, purify the DNA to remove impurities and contaminants that may interfere with the sequencing process. Purification kits and protocols are known in the art.

[0128] Library preparation: Prepare a DNA library for sequencing. This includes fragmenting the DNA into smaller pieces, adding adapters to the fragments, and amplifying them using polymerase chain reaction (PCR). The adapters allow the DNA fragments to be attached to a solid surface (e.g., a sequencing flow cell or microarray) and enable the sequencing reaction to occur.Docket Number: 20230802-03 / 027644.8492

[0129] Sequencing: Perform the DNA sequencing using a suitable sequencing platform or technology. As described herein, a high-throughput DNA sequencing system such as NGS device can be used.

[0130] Data analysis: Once the sequencing is complete, process and analyze the resulting raw data. This may include converting the raw sequencing data into a readable format, aligning the sequences to a reference genome (if available), identifying variants, and interpreting the genetic information obtained.

[0131] At step 120, the method includes identifying a cytoband variant or a chromosomal variant among the plurality of CNVs. In some implementations, one or more cytoband variants are identified. For example, the cytoband variant can be a cytoband copy number loss. Alternatively or additionally, in some implementations, one or more chromosomal variants are identified. For example, the chromosomal variant can be a chromosomal arm loss, a monosomy, or a trisomy. Optionally, in some implementations, both cytoband and chromosomal variants are identified. Example CNVs including cytoband and chromosomal level variants are shown in Table 1 (Fig.2).

[0132] At step 130, the method includes detecting a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant. The hematopoietic neoplasm can be acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), myelodysplasia (MDS), chronic lymphocytic leukemia (CLL), non- Hodgkin lymphoma (NHL), or multiple myeloma (MM). In other words, the plurality of variants including the cytoband variant or the chromosomal variant serve as a biomarker for the type of hematopoietic neoplasm. Each type of hematopoietic neoplasm is associated with a respective plurality of variants. Example reportable CNVs per specific type of hematopoietic neoplasm are shown in Table 2 (Fig.3).

[0133] In some implementations, the hematopoietic neoplasm is acute myeloid leukemia (AML). For this type of neoplasm, the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, deletion of chromosome segment 13q, monosomy 17, deletion of chromosome segment 17p, deletion of chromosome segment 20q, and trisomy 22. This is shown in Table 2 (Fig.3). In some aspects, the biomarker or signature for AML includes all of the CNVs listed here (and shown in Table 2). In some aspects, the biomarker or signature for AML includes only some of the CNVs listed here (and shown in Table 2).Docket Number: 20230802-03 / 027644.8492

[0134] In some implementations, the hematopoietic neoplasm is myeloproliferative neoplasm (MPN). For this type of neoplasm, the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, trisomy 9, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, deletion of chromosome segment 13q, deletion of chromosome segment 20q, and trisomy 21. This is shown in Table 2 (Fig.3). In some aspects, the biomarker or signature for MPN includes all of the CNVs listed here (and shown in Table 2). In some aspects, the biomarker or signature for MPN includes only some of the CNVs listed here (and shown in Table 2).

[0135] In some implementations, the hematopoietic neoplasm is myelodysplasia (MDS). For this type of neoplasm, the plurality of CNVs include one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, deletion of chromosome segment 9q, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, and deletion of chromosome segment 13q. This is shown in Table 2 (Fig.3). In some aspects, the biomarker or signature for MDS includes all of the CNVs listed here (and shown in Table 2). In some aspects, the biomarker or signature for MDS includes only some of the CNVs listed here (and shown in Table 2).

[0136] In some implementations, the hematopoietic neoplasm is chronic lymphocytic leukemia (CLL). For this type of neoplasm, the plurality of CNVs include one or more of monosomy 11, deletion of chromosome segment 11q, deletion of chromosome segment 11q22-23, trisomy 12, monosomy 13, deletion of chromosome segment 13q, deletion of chromosome segment 13q14, monosomy 17, deletion of chromosome segment 17p, and deletion of chromosome segment 17p12-13. This is shown in Table 2 (Fig.3). In some aspects, the biomarker or signature for CLL includes all of the CNVs listed here (and shown in Table 2). In some aspects, the biomarker or signature for CLL includes only some of the CNVs listed here (and shown in Table 2).

[0137] In some implementations, the hematopoietic neoplasm is multiple myeloma (MM). For this type of neoplasm, the plurality of CNVs comprise one or more of hyperdiploid karyotype characterized by trisomy 3, trisomy 5, trisomy 7, trisomy 9, trisomy 11, trisomy 15, and trisomy 19, or deletion of chromosome segment 17p, deletion of chromosome segment 1p, and addition of chromosome segment 1q. In some aspects, the biomarker or signature for MM includes all of the CNVs listed here. In some aspects, the biomarker or signature for MM includes only some of the CNVs listed here.Docket Number: 20230802-03 / 027644.8492

[0138] In some implementations, the hematopoietic neoplasm is non-Hodgkin lymphoma (NHL). For this type of neoplasm, the plurality of CNVs include deletion of chromosome segment 17p, or fusions of BCL6, BCL2, CCND1, MALT1, and MYC. In some aspects, the biomarker or signature for NHL includes all of the variants listed here. In some aspects, the biomarker or signature for NHL includes only some of the variants listed here.

[0139] Optionally, in some implementations, the method further includes generating a report including the DNA sequencing data and the detected hematopoietic neoplasm in the subject. Optionally, the report is integrated into the subject’s electronic health record (EHR). Alternatively or additionally, the method optionally further includes generating display data for the report. Alternatively or additionally, the method optionally further includes transmitting the report over a network. This disclosure contemplates that operations related to generation of the report can be performed using one or more computing devices (e.g., at least the basic configuration illustrated in Fig.4 by box 402).

[0140] In some implementations, the method optionally further includes, in response to detecting the hematopoietic neoplasm in the subject, providing a diagnosis for the subject. The diagnosis can be the type of hematopoietic neoplasm. As described herein, the CNVs described above and / or shown in Table 2 can be used to diagnosis the type of hematopoietic neoplasm. In some aspects, this disclosure contemplates that the CNVs described above and / or shown in Table 2 are the only information used to make the diagnosis. Optionally, in other aspects, the CNVs described above and / or shown in Table 2 are used in combination with other test results (e.g., clinical evaluation, blood tests, bone marrow biopsy, imaging studies, etc.) to make the diagnosis. Additionally, the method optionally further includes, in response to detecting the hematopoietic neoplasm in the subject, providing a prognosis for the subject. Alternatively or additionally, the method optionally further includes recommending a treatment for the subject. Treatment approaches can vary depending on the specific subtype, stage, and patient factors but may include, but are not limited to, chemotherapy, radiation therapy, immunotherapy, targeted therapies, and stem cell transplantation. This disclosure contemplates that the operations related to providing diagnosis, prognosis, and / or treatment options can be performed using one or more computing devices (e.g., at least the basic configuration illustrated in Fig.4 by box 402).

[0141] Optionally, in some implementations, the method further includes administering the recommended treatment to the subject.

[0142] Example Computing DeviceDocket Number: 20230802-03 / 027644.8492

[0143] It should be appreciated that the logical operations described herein with respect to the various figures may be implemented (1) as a sequence of computer implemented acts or program modules (i.e., software) running on a computing device (e.g., the computing device described in Fig.4), (2) as interconnected machine logic circuits or circuit modules (i.e., hardware) within the computing device and / or (3) a combination of software and hardware of the computing device. Thus, the logical operations discussed herein are not limited to any specific combination of hardware and software. The implementation is a matter of choice dependent on the performance and other requirements of the computing device. Accordingly, the logical operations described herein are referred to variously as operations, structural devices, acts, or modules. These operations, structural devices, acts and modules may be implemented in software, in firmware, in special purpose digital logic, and any combination thereof. It should also be appreciated that more or fewer operations may be performed than shown in the figures and described herein. These operations may also be performed in a different order than those described herein.

[0144] Referring to Fig.4, an example computing device 400 upon which the methods described herein may be implemented is illustrated. It should be understood that the example computing device 400 is only one example of a suitable computing environment upon which the methods described herein may be implemented. Optionally, the computing device 400 can be a well- known computing system including, but not limited to, personal computers, servers, handheld or laptop devices, multiprocessor systems, microprocessor-based systems, network personal computers (PCs), minicomputers, mainframe computers, embedded systems, and / or distributed computing environments including a plurality of any of the above systems or devices. Distributed computing environments enable remote computing devices, which are connected to a communication network or other data transmission medium, to perform various tasks. In the distributed computing environment, the program modules, applications, and other data may be stored on local and / or remote computer storage media.

[0145] In its most basic configuration, computing device 400 typically includes at least one processing unit 406 and system memory 404. Depending on the exact configuration and type of computing device, system memory 404 may be volatile (such as random access memory (RAM)), non- volatile (such as read-only memory (ROM), flash memory, etc.), or some combination of the two. This most basic configuration is illustrated in Fig.4 by box 402. The processing unit 406 may be a standard programmable processor that performs arithmetic and logic operations necessary for operation of the computing device 400. The computing device 400 may also include a bus or other communication mechanism for communicating information among various components of the computing device 400.Docket Number: 20230802-03 / 027644.8492

[0146] Computing device 400 may have additional features / functionality. For example, computing device 400 may include additional storage such as removable storage 408 and non- removable storage 410 including, but not limited to, magnetic or optical disks or tapes. Computing device 400 may also contain network connection(s) 416 that allow the device to communicate with other devices. Computing device 400 may also have input device(s) 414 such as a keyboard, mouse, touch screen, etc. Output device(s) 412 such as a display, speakers, printer, etc. may also be included. The additional devices may be connected to the bus in order to facilitate communication of data among the components of the computing device 400. All these devices are well known in the art and need not be discussed at length here.

[0147] The processing unit 406 may be configured to execute program code encoded in tangible, computer-readable media. Tangible, computer-readable media refers to any media that is capable of providing data that causes the computing device 400 (i.e., a machine) to operate in a particular fashion. Various computer-readable media may be utilized to provide instructions to the processing unit 406 for execution. Example tangible, computer-readable media may include, but is not limited to, volatile media, non-volatile media, removable media and non-removable media implemented in any method or technology for storage of information such as computer readable instructions, data structures, program modules or other data. System memory 404, removable storage 408, and non- removable storage 410 are all examples of tangible, computer storage media. Example tangible, computer-readable recording media include, but are not limited to, an integrated circuit (e.g., field- programmable gate array or application-specific IC), a hard disk, an optical disk, a magneto-optical disk, a floppy disk, a magnetic tape, a holographic storage medium, a solid-state device, RAM, ROM, electrically erasable program read-only memory (EEPROM), flash memory or other memory technology, CD-ROM, digital versatile disks (DVD) or other optical storage, magnetic cassettes, magnetic tape, magnetic disk storage or other magnetic storage devices.

[0148] In an example implementation, the processing unit 406 may execute program code stored in the system memory 404. For example, the bus may carry data to the system memory 404, from which the processing unit 406 receives and executes instructions. The data received by the system memory 404 may optionally be stored on the removable storage 408 or the non-removable storage 410 before or after execution by the processing unit 406.

[0149] It should be understood that the various techniques described herein may be implemented in connection with hardware or software or, where appropriate, with a combination thereof. Thus, the methods and apparatuses of the presently disclosed subject matter, or certainDocket Number: 20230802-03 / 027644.8492 aspects or portions thereof, may take the form of program code (i.e., instructions) embodied in tangible media, such as floppy diskettes, CD-ROMs, hard drives, or any other machine-readable storage medium wherein, when the program code is loaded into and executed by a machine, such as a computing device, the machine becomes an apparatus for practicing the presently disclosed subject matter. In the case of program code execution on programmable computers, the computing device generally includes a processor, a storage medium readable by the processor (including volatile and non-volatile memory and / or storage elements), at least one input device, and at least one output device. One or more programs may implement or utilize the processes described in connection with the presently disclosed subject matter, e.g., through the use of an application programming interface (API), reusable controls, or the like. Such programs may be implemented in a high level procedural or object-oriented programming language to communicate with a computer system. However, the program(s) can be implemented in assembly or machine language, if desired. In any case, the language may be a compiled or interpreted language and it may be combined with hardware implementations.

[0150] Exemplary Embodiments

[0151] Embodiment 1. A computer-implemented method for detecting hematopoietic neoplasms using deoxyribonucleic acid (DNA) mutations comprising: receiving DNA sequencing data for a subject, the DNA sequencing data comprising a plurality of variants, wherein the plurality of variants comprise a plurality of copy number variants (CNVs); identifying a cytoband variant or a chromosomal variant among the plurality of CNVs; and detecting a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant.

[0152] Embodiment 2. The computer-implemented method of embodiment 1, wherein the cytoband variant is a cytoband copy number loss.

[0153] Embodiment 3. The computer-implemented method of embodiment 1 or 2, wherein the chromosomal variant is a chromosomal arm loss, a monosomy, or a trisomy.

[0154] Embodiment 4. The computer-implemented method of any one of embodiments 1-3, wherein the plurality of variants further comprise at least one of a single nucleotide variant (SNV), an insertion deletion (indel), an FLT3 internal tandem duplication (FLT3-ITD), and a gene fusion.

[0155] Embodiment 5. The computer-implemented method of any one of embodiments 1-4, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), myelodysplasia (MDS), chronic lymphocytic leukemia (CLL), non- Hodgkin lymphoma (NHL), or multiple myeloma (MM).Docket Number: 20230802-03 / 027644.8492

[0156] Embodiment 6. The computer-implemented method of any one of embodiments 1-4, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, deletion of chromosome segment 13q, monosomy 17, deletion of chromosome segment 17p, deletion of chromosome segment 20q, and trisomy 22.

[0157] Embodiment 7. The computer-implemented method of any one of embodiments 1-4, wherein the hematopoietic neoplasm is myeloproliferative neoplasm (MPN), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, trisomy 9, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, deletion of chromosome segment 13q, deletion of chromosome segment 20q, and trisomy 21.

[0158] Embodiment 8. The computer-implemented method of any one of embodiments 1-4, wherein the hematopoietic neoplasm is myelodysplasia (MDS), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, deletion of chromosome segment 9q, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, and deletion of chromosome segment 13q.

[0159] Embodiment 9. The computer-implemented method of any one of embodiments 1-4, wherein the hematopoietic neoplasm is chronic lymphocytic leukemia (CLL), and the plurality of CNVs comprise one or more of monosomy 11, deletion of chromosome segment 11q, deletion of chromosome segment 11q22-23, trisomy 12, monosomy 13, deletion of chromosome segment 13q, deletion of chromosome segment 13q14, monosomy 17, deletion of chromosome segment 17p, and deletion of chromosome segment 17p12-13.

[0160] Embodiment 10. The computer-implemented method of any one of embodiments 1-4, wherein the hematopoietic neoplasm is multiple myeloma (MM), and the plurality of CNVs comprise one or more of hyperdiploid karyotype characterized by trisomy 3, trisomy 5, trisomy 7, trisomy 9, trisomy 11, trisomy 15, and trisomy 19, or deletion of chromosome segment 17p, deletion of chromosome segment 1p, and addition of chromosome segment 1q.

[0161] Embodiment 11. The computer-implemented method of any one of embodiments 1-4, wherein the hematopoietic neoplasm is non-Hodgkin lymphoma (NHL), and theDocket Number: 20230802-03 / 027644.8492 plurality of CNVs comprise deletion of chromosome segment 17p, or fusions of BCL6, BCL2, CCND1, MALT1, and MYC.

[0162] Embodiment 12. The computer-implemented method of any one of embodiments 1-11, wherein the DNA sequencing data encodes a plurality of heme-related genes.

[0163] Embodiment 13. The computer-implemented method of any one of embodiments 1-11, wherein the DNA sequencing data encodes a genome wide single nucleotide polymorphism (SNP) backbone.

[0164] Embodiment 14. The computer-implemented method of any one of embodiments 1-11, wherein the DNA sequencing data encodes a plurality of heme-related genes and a genome wide single nucleotide polymorphism (SNP) backbone.

[0165] Embodiment 15. The computer-implemented method of any one of embodiments 1-14, further comprising generating a report comprising the DNA sequencing data and the detected hematopoietic neoplasm in the subject.

[0166] Embodiment 16. The computer-implemented method of embodiment 15, further comprising generating display data for the report.

[0167] Embodiment 17. The computer-implemented method of embodiment 15 or 16, further comprising transmitting the report over a network.

[0168] Embodiment 18. The computer-implemented method of any one of embodiments 1-17, further comprising, in response to detecting the hematopoietic neoplasm in the subject, providing a diagnosis for the subject.

[0169] Embodiment 19. The computer-implemented method of any one of embodiments 1-17, further comprising, in response to detecting the hematopoietic neoplasm in the subject, providing a prognosis for the subject.

[0170] Embodiment 20. The computer-implemented method of embodiment 18 or 19, further comprising recommending a treatment for the subject.

[0171] Embodiment 21. A method for treating a subject comprising: detecting, using a computing device, a hematopoietic neoplasm in the subject according to any one of embodiments 1-20; and in response to detecting the hematopoietic neoplasm in the subject, providing a treatment to the subject.

[0172] Embodiment 22. The method of embodiment 21, further comprising: obtaining a sample from the subject; extracting DNA from the sample; and sequencing the DNA to obtain the DNA sequencing data.Docket Number: 20230802-03 / 027644.8492

[0173] Embodiment 23. The method of embodiment 22, wherein the DNA is sequenced using a next generation sequencing device (NGS).

[0174] Embodiment 24. A system for detecting hematopoietic neoplasms comprising: at least one processor; and a memory operably coupled to the at least one processor, wherein the memory has computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to: receive DNA sequencing data for a subject, the DNA sequencing data comprising a plurality of variants, wherein the plurality of variants comprise a plurality of copy number variants (CNVs); identify a cytoband variant or a chromosomal variant among the plurality of CNVs; and detect a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant.

[0175] Embodiment 25. The system of embodiment 24, wherein the cytoband variant is a cytoband copy number loss.

[0176] Embodiment 26. The system of embodiment 24 or 25, wherein the chromosomal variant is a chromosomal arm loss, a monosomy, or a trisomy.

[0177] Embodiment 27. The system of any one of embodiments 24-26, wherein the plurality of variants further comprise at least one of a single nucleotide variant (SNV), an insertion deletion (indel), an FLT3 internal tandem duplication (FLT3-ITD), and a gene fusion.

[0178] Embodiment 28. The system of any one of embodiments 24-27, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), myelodysplasia (MDS), chronic lymphocytic leukemia (CLL), non-Hodgkin lymphoma (NHL), or multiple myeloma (MM).

[0179] Embodiment 29. The system of any one of embodiments 24-27, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, deletion of chromosome segment 13q, monosomy 17, deletion of chromosome segment 17p, deletion of chromosome segment 20q, and trisomy 22.

[0180] Embodiment 30. The system of any one of embodiments 24-27, wherein the hematopoietic neoplasm is myeloproliferative neoplasm (MPN), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, trisomy 9, deletion of chromosome segment 9p, deletion of chromosomeDocket Number: 20230802-03 / 027644.8492 segment 11q, deletion of chromosome segment 12p, deletion of chromosome segment 13q, deletion of chromosome segment 20q, and trisomy 21.

[0181] Embodiment 31. The system of any one of embodiments 24-27, wherein the hematopoietic neoplasm is myelodysplasia (MDS), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, deletion of chromosome segment 9q, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, and deletion of chromosome segment 13q.

[0182] Embodiment 32. The system of any one of embodiments 24-27, wherein the hematopoietic neoplasm is chronic lymphocytic leukemia (CLL), and the plurality of CNVs comprise one or more of monosomy 11, deletion of chromosome segment 11q, deletion of chromosome segment 11q22-23, trisomy 12, monosomy 13, deletion of chromosome segment 13q, deletion of chromosome segment 13q14, monosomy 17, deletion of chromosome segment 17p, and deletion of chromosome segment 17p12-13.

[0183] Embodiment 33. The system of any one of embodiments 24-27, wherein the hematopoietic neoplasm is multiple myeloma (MM), and the plurality of CNVs comprise one or more of hyperdiploid karyotype characterized by trisomy 3, trisomy 5, trisomy 7, trisomy 9, trisomy 11, trisomy 15, and trisomy 19, or deletion of chromosome segment 17p, deletion of chromosome segment 1p, and addition of chromosome segment 1q.

[0184] Embodiment 34. The system of any one of embodiments 24-27, wherein the hematopoietic neoplasm is non-Hodgkin lymphoma (NHL), and the plurality of CNVs comprise deletion of chromosome segment 17p, or fusions of BCL6, BCL2, CCND1, MALT1, and MYC.

[0185] Embodiment 35. The system of any one of embodiments 24-34, wherein the DNA sequencing data encodes a plurality of heme-related genes.

[0186] Embodiment 36. The system of any one of embodiments 24-34, wherein the DNA sequencing data encodes a genome wide single nucleotide polymorphism (SNP) backbone.

[0187] Embodiment 37. The system of any one of embodiments 24-34, wherein the DNA sequencing data encodes a plurality of heme-related genes and a genome wide single nucleotide polymorphism (SNP) backbone.

[0188] Embodiment 38. The system of any one of embodiments 24-37, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to generate a report comprising the DNA sequencing data and the detected hematopoietic neoplasm in the subject.Docket Number: 20230802-03 / 027644.8492

[0189] Embodiment 39. The system of embodiment 38, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to generate display data for the report.

[0190] Embodiment 40. The system of embodiment 38 or 39, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to transmit the report over a network.

[0191] Embodiment 41. The system of any one of embodiments 24-40, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to, in response to detecting the hematopoietic neoplasm in the subject, provide a diagnosis for the subject.

[0192] Embodiment 42. The system of any one of embodiments 24-40, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to, in response to detect the hematopoietic neoplasm in the subject, providing a prognosis for the subject.

[0193] Embodiment 43. The system of embodiment 41 or 42, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to recommend a treatment for the subject.

[0194] Examples

[0195] The following examples are put forth so as to provide those of ordinary skill in the art with a complete disclosure and description of how the compounds, compositions, articles, devices and / or methods claimed herein are made and evaluated, and are intended to be purely exemplary and are not intended to limit the disclosure. Efforts have been made to ensure accuracy with respect to numbers (e.g., amounts, temperature, etc.), but some errors and deviations should be accounted for. Unless indicated otherwise, parts are parts by weight, temperature is in ^C or is at ambient temperature, and pressure is at or near atmospheric.

[0196] Pan-Heme Server

[0197] The Pan-Heme server finds genomic alterations in tumor DNA. It combines several types of analysis for the discovery of these alterations: DNA SNVs and small indels, large deletions / insertions / LOH, FLT3-ITD discovery, and fusion genes. The Pan-Heme server starts with fastQ data generated by an Illumina sequencer, and generates structured results for each type of variation, as well as generating the body of a PDF document containing this information. The Pan-Heme server doesDocket Number: 20230802-03 / 027644.8492 not require any PHI information, only an “alias” which it used to match fastQ data with a particular “order”, thus making it suitable for “cloud” deployment, outside of the institutions firewall.

[0198] The system is deployed using Docker Compose on a commodity Linux server. The code is written in Python version 3.9. Multi-tasking is achieved by running eleven separate docker components within the Docker Compose bundle, all of which (except the REST listener) go through infinite loops of run, sleep, wake, run, sleep etc., and all of which communicate through a shared database. Each component is single-threaded, but Docker Compose enables multi-tasking. Each component queries the database for an order that has the correct state for it to operate on, it then completes its operation and updates the database entry for the order to the new state.

[0199] As an example, the Illumina sequencer generates eight fastQ files for each sample (i.e. order or alias). A service monitors the fastQ directory until these files are generated. Once they are, a flag (dna_fastq_complete) is set to True for the order. A concatenation service queries the database for orders that have this flag set, and for each of these orders, concatenate these files down to two, and sets another flag (dna_fastq_concat_complete ) to True. Both the aligner service and the Alissa A&C uploader service continuously sleep, wake up, and query for orders with that status, and when they find them, start the bam file generation process and the Alissa upload process in parallel, each only working on one order at a time, and then setting the appropriate completion flag (bam_complete and uploaded2Alissa, respectively) on that order before sleeping, waking and running the query again. As soon as an order is marked bam_complete it can be found by the FLT3-ITD and CNV services for further processing.

[0200] When all steps are complete, results can be returned to the calling application. Because DNA sequencing and RNA sequencing are separate workflows, the application can send partial results when one or the other of these completes, and then final results when both are complete.

[0201] Overview

[0202] The DNA-based copy number variant (CNV) component of the pan-heme assay detects genome wide CNV(s) and is divided into four groups based upon the relative size of each that include gene specific, cytoband, chromosomal arm, and chromosome (Table 1, Fig.2). This approach is unique by extending CNV(s) beyond the gene level to include cytoband and chromosomal variants. All CNV groups include copy number loss with copy number gain restricted to the chromosomal level for use in this specific test. This uniqueness is extended even further by applying known knowledge of clinical utility per specific type of hematopoietic neoplasm (Table 2, Fig.3).Docket Number: 20230802-03 / 027644.8492

[0203] Bioinformatics CNV Analysis

[0204] From a bioinformatics perspective, CNV detection, is performed using a custom read depth software specifically developed for this assay. Prior to the development of the sample of interest CNV bioinformatics pipeline reference control sample population was created for comparison of read depth. The reference control sample group consists of 30 bone marrow samples that had been previously tested for chimerism and negative or less than 2% for recipient alleles ensuring that the reference group was as close as possible in comparison to sample collection and source as the samples to be tested. The mean depth and standard deviation (s.d.) of each probe for the reference control sample group was calculated to serve as the means for calling loss or gain. Given the relatively small number of Y chromosomes in the reference control sample group and the lack of clinically relevant information for sex chromosome gain or loss a decision was made to restrict CNV analysis to somatic chromosomes.

[0205] For all CNV calls, except for gene specific evaluations, analysis is based upon cytoband analysis (Appendix Supplementary Table 1) using the OneSeq capture probe design, which was designed for a mean capture depth of 50-100x. CNV analysis is divided into six main steps as detailed in Table 3, Fig.5.

[0206] Once individual probes and cytobands are classified as potential gain or loss an additional algorithm is applied for reporting. Reporting is done at the level of whole chromosome, chromosomal arm, cytoband, and gene for ATM, RB1, and TP53 for the clinically relevant list of CNV(s) (Table 4, Fig.6) that are specific for a given hematopoietic neoplasm classification. Additionally, the intent of this algorithm is to avoid redundant reporting of CNV(s) on a given chromosome such that chromosomal loss or gain would not be reported when there is whole chromosome loss or gain, respectively, and with the same application for cytoband and chromosomal arm loss or gain.

[0207] As the bioinformatics pipeline calls CNV(s) at the cytoband, or combined cytoband, level an analysis was done for cytobands with poor performance based upon mean depth of all probes in that cytoband across all runs of the SeraCare DNA-PC (positive control). Any cytoband with an average mean depth of all reads less than 2 s.d. of all cytobands across all runs of the cell line positive control are considered as poor performance (Appendix Supplementary Table 2). All censored cytobands are periocentromeric and typically involved both the p and q pericentromeric region for that chromosome and involved 19 of 23 chromosomes.Docket Number: 20230802-03 / 027644.8492

[0208] Appendix Supplementary Table 1: One-seq captureDocket Number: 20230802-03 / 027644.8492 chr1 1.43E+08 147000000 q21.1 chr1 1.47E+08 150300000 q21.2Docket Number: 20230802-03 / 027644.8492 chr10 40200000 42300000 q11.1 chr10 42300000 46100000 q11.21Docket Number: 20230802-03 / 027644.8492 chr11 53700000 55700000 q11 chr11 55700000 59900000 q12.1Docket Number: 20230802-03 / 027644.8492 chr12 56600000 58100000 q13.3 chr12 58100000 63100000 q14.1Docket Number: 20230802-03 / 027644.8492 chr13 55300000 59600000 q21.1 chr13 59600000 62300000 q21.2Docket Number: 20230802-03 / 027644.8492 chr14 83600000 84900000 q31.2 chr14 84900000 89800000 q31.3Docket Number: 20230802-03 / 027644.8492 chr16 0 7900000 p13.3 chr16 7900000 10500000 p13.2Docket Number: 20230802-03 / 027644.8492 chr17 58300000 61100000 q23.2 chr17 61100000 62600000 q23.3Docket Number: 20230802-03 / 027644.8492 chr19 43400000 45200000 q13.31 chr19 45200000 48000000 q13.32Docket Number: 20230802-03 / 027644.8492 chr2 1.35E+08 136800000 q21.3 chr2 1.37E+08 142200000 q22.1Docket Number: 20230802-03 / 027644.8492 chr20 42100000 46400000 q13.12 chr20 46400000 49800000 q13.13Docket Number: 20230802-03 / 027644.8492 chr3 13300000 16400000 p25.1 chr3 16400000 23900000 p24.3Docket Number: 20230802-03 / 027644.8492 chr3 1.43E+08 148900000 q24 chr3 1.49E+08 152100000 q25.1Docket Number: 20230802-03 / 027644.8492 chr4 98800000 101100000 q23 chr4 1.01E+08 107700000 q24Docket Number: 20230802-03 / 027644.8492 chr5 68400000 73300000 q13.2 chr5 73300000 76900000 q13.3Docket Number: 20230802-03 / 027644.8492 chr6 46200000 51800000 p12.3 chr6 51800000 52900000 p12.2Docket Number: 20230802-03 / 027644.8492 chr7 28000000 28800000 p15.1 chr7 28800000 35000000 p14.3Docket Number: 20230802-03 / 027644.8492 chr8 23300000 27400000 p21.2 chr8 27400000 28800000 p21.1Docket Number: 20230802-03 / 027644.8492 chr9 18500000 19900000 p22.1 chr9 19900000 25600000 p21.3Docket Number: 20230802-03 / 027644.8492 Chr Start Stop Cytoband chr1 121500000 1.25E+08 p11.1Docket Number: 20230802-03 / 027644.8492 chr9 50700000 65900000 q12

[0209] Although the subject matter has been described in language specific to structural features and / or methodological acts, it is to be understood that the subject matter defined in the appended claims is not necessarily limited to the specific features or acts described above. Rather, the specific features and acts described above are disclosed as example forms of implementing the claims.

Claims

Docket Number: 20230802-03 / 027644.8492 WHAT IS CLAIMED:

1. A computer-implemented method for detecting hematopoietic neoplasms using deoxyribonucleic acid (DNA) mutations comprising: receiving DNA sequencing data for a subject, the DNA sequencing data comprising a plurality of variants, wherein the plurality of variants comprise a plurality of copy number variants (CNVs); identifying a cytoband variant or a chromosomal variant among the plurality of CNVs; and detecting a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant.

2. The computer-implemented method of claim 1, wherein the cytoband variant is a cytoband copy number loss.

3. The computer-implemented method of claim 1, wherein the chromosomal variant is a chromosomal arm loss, a monosomy, or a trisomy.

4. The computer-implemented method of claim 1, wherein the plurality of variants further comprise at least one of a single nucleotide variant (SNV), an insertion deletion (indel), an FLT3 internal tandem duplication (FLT3-ITD), and a gene fusion.

5. The computer-implemented method of claim 1, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), myelodysplasia (MDS), chronic lymphocytic leukemia (CLL), non-Hodgkin lymphoma (NHL), or multiple myeloma (MM).

6. The computer-implemented method of claim 1, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, deletion of chromosome segment 13q, monosomy 17, deletion of chromosome segment 17p, deletion of chromosome segment 20q, and trisomy 22.

7. The computer-implemented method of claim 1, wherein the hematopoietic neoplasm is myeloproliferative neoplasm (MPN), and the plurality of CNVs comprise one or more of monosomy 5,Docket Number: 20230802-03 / 027644.8492 deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, trisomy 9, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, deletion of chromosome segment 13q, deletion of chromosome segment 20q, and trisomy 21.

8. The computer-implemented method of claim 1, wherein the hematopoietic neoplasm is myelodysplasia (MDS), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, deletion of chromosome segment 9q, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, and deletion of chromosome segment 13q.

9. The computer-implemented method of claim 1, wherein the hematopoietic neoplasm is chronic lymphocytic leukemia (CLL), and the plurality of CNVs comprise one or more of monosomy 11, deletion of chromosome segment 11q, deletion of chromosome segment 11q22-23, trisomy 12, monosomy 13, deletion of chromosome segment 13q, deletion of chromosome segment 13q14, monosomy 17, deletion of chromosome segment 17p, and deletion of chromosome segment 17p12-13.

10. The computer-implemented method of claim 1, wherein the hematopoietic neoplasm is multiple myeloma (MM), and the plurality of CNVs comprise one or more of hyperdiploid karyotype characterized by trisomy 3, trisomy 5, trisomy 7, trisomy 9, trisomy 11, trisomy 15, and trisomy 19, or deletion of chromosome segment 17p, deletion of chromosome segment 1p, and addition of chromosome segment 1q.

11. The computer-implemented method of claim 1, wherein the hematopoietic neoplasm is non-Hodgkin lymphoma (NHL), and the plurality of CNVs comprise deletion of chromosome segment 17p, or fusions of BCL6, BCL2, CCND1, MALT1, and MYC.

12. The computer-implemented method of claim 1, wherein the DNA sequencing data encodes a plurality of heme-related genes.

13. The computer-implemented method of claim 1, wherein the DNA sequencing data encodes a genome wide single nucleotide polymorphism (SNP) backbone.Docket Number: 20230802-03 / 027644.8492 14. The computer-implemented method of claim 1, wherein the DNA sequencing data encodes a plurality of heme-related genes and a genome wide single nucleotide polymorphism (SNP) backbone.

15. The computer-implemented method of claim 1, further comprising generating a report comprising the DNA sequencing data and the detected hematopoietic neoplasm in the subject.

16. The computer-implemented method of claim 15, further comprising generating display data for the report.

17. The computer-implemented method of claim 15 or 16, further comprising transmitting the report over a network.

18. The computer-implemented method of claim 1, further comprising, in response to detecting the hematopoietic neoplasm in the subject, providing a diagnosis for the subject.

19. The computer-implemented method of claim 1, further comprising, in response to detecting the hematopoietic neoplasm in the subject, providing a prognosis for the subject.

20. The computer-implemented method of claim 18 or 19, further comprising recommending a treatment for the subject.

21. A method for treating a subject comprising: detecting, using a computing device, a hematopoietic neoplasm in the subject according to any one of claims 1-20; and in response to detecting the hematopoietic neoplasm in the subject, providing a treatment to the subject.

22. The method of claim 21, further comprising: obtaining a sample from the subject; extracting DNA from the sample; and sequencing the DNA to obtain the DNA sequencing data.Docket Number: 20230802-03 / 027644.8492 23. The method of claim 22, wherein the DNA is sequenced using a next generation sequencing device (NGS).

24. A system for detecting hematopoietic neoplasms comprising: at least one processor; and a memory operably coupled to the at least one processor, wherein the memory has computer- executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to: receive DNA sequencing data for a subject, the DNA sequencing data comprising a plurality of variants, wherein the plurality of variants comprise a plurality of copy number variants (CNVs); identify a cytoband variant or a chromosomal variant among the plurality of CNVs; and detect a hematopoietic neoplasm in the subject based, at least in part, on the plurality of variants including the cytoband variant or the chromosomal variant.

25. The system of claim 24, wherein the cytoband variant is a cytoband copy number loss.

26. The system of claim 24 or 25, wherein the chromosomal variant is a chromosomal arm loss, a monosomy, or a trisomy.

27. The system of claim 24, wherein the plurality of variants further comprise at least one of a single nucleotide variant (SNV), an insertion deletion (indel), an FLT3 internal tandem duplication (FLT3-ITD), and a gene fusion.

28. The system of claim 24, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), myeloproliferative neoplasm (MPN), myelodysplasia (MDS), chronic lymphocytic leukemia (CLL), non-Hodgkin lymphoma (NHL), or multiple myeloma (MM).

29. The system of claim 24, wherein the hematopoietic neoplasm is acute myeloid leukemia (AML), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, deletion of chromosomeDocket Number: 20230802-03 / 027644.8492 segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, deletion of chromosome segment 13q, monosomy 17, deletion of chromosome segment 17p, deletion of chromosome segment 20q, and trisomy 22.

30. The system of claim 24, wherein the hematopoietic neoplasm is myeloproliferative neoplasm (MPN), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, trisomy 8, trisomy 9, deletion of chromosome segment 9p, deletion of chromosome segment 11q, deletion of chromosome segment 12p, deletion of chromosome segment 13q, deletion of chromosome segment 20q, and trisomy 21.

31. The system of claim 24, wherein the hematopoietic neoplasm is myelodysplasia (MDS), and the plurality of CNVs comprise one or more of monosomy 5, deletion of chromosome segment 5q, monosomy 7, deletion of chromosome segment 7q, deletion of chromosome segment 9q, deletion of chromosome segment 11q, deletion of chromosome segment 12p, monosomy 13, and deletion of chromosome segment 13q.

32. The system of claim 24, wherein the hematopoietic neoplasm is chronic lymphocytic leukemia (CLL), and the plurality of CNVs comprise one or more of monosomy 11, deletion of chromosome segment 11q, deletion of chromosome segment 11q22-23, trisomy 12, monosomy 13, deletion of chromosome segment 13q, deletion of chromosome segment 13q14, monosomy 17, deletion of chromosome segment 17p, and deletion of chromosome segment 17p12-13.

33. The system of claim 24, wherein the hematopoietic neoplasm is multiple myeloma (MM), and the plurality of CNVs comprise one or more of hyperdiploid karyotype characterized by trisomy 3, trisomy 5, trisomy 7, trisomy 9, trisomy 11, trisomy 15, and trisomy 19, or deletion of chromosome segment 17p, deletion of chromosome segment 1p, and addition of chromosome segment 1q.

34. The system of claim 24, wherein the hematopoietic neoplasm is non-Hodgkin lymphoma (NHL), and the plurality of CNVs comprise deletion of chromosome segment 17p, or fusions of BCL6, BCL2, CCND1, MALT1, and MYC.Docket Number: 20230802-03 / 027644.8492 35. The system of claim 24, wherein the DNA sequencing data encodes a plurality of heme- related genes.

36. The system of claim 24, wherein the DNA sequencing data encodes a genome wide single nucleotide polymorphism (SNP) backbone.

37. The system of claim 24, wherein the DNA sequencing data encodes a plurality of heme- related genes and a genome wide single nucleotide polymorphism (SNP) backbone.

38. The system of claim 24, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to generate a report comprising the DNA sequencing data and the detected hematopoietic neoplasm in the subject.

39. The system of claim 38, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to generate display data for the report.

40. The system of claim 38 or 39, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to transmit the report over a network.

41. The system of claim 24, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to, in response to detecting the hematopoietic neoplasm in the subject, provide a diagnosis for the subject.

42. The system of claim 24, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to, in response to detect the hematopoietic neoplasm in the subject, providing a prognosis for the subject.Docket Number: 20230802-03 / 027644.8492 43. The system of claim 41 or 42, wherein the memory has further computer-executable instructions stored thereon that, when executed by the at least one processor, cause the at least one processor to recommend a treatment for the subject.

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