CN-122003508-A - Genome and methylation biomarkers for predicting copy number loss/gene deletion

Abstract

Disclosed herein are methods, compositions, and devices for diagnosing and treating cancer. The method includes sequencing a set of regions in a cell-free nucleic acid molecule and detecting one or more biomarkers indicative of cancer.

Inventors

• SEAN GORDON
• Catalin Barbasioru
• Evan Werner
• Andrew M Ge Luosi
• Dennis Torkunov
• Jitika Yaramatchili

Assignees

• 夸登特健康公司

Dates

Publication Date

20260508

Application Date

20241004

Priority Date

20240229

Claims (20)

1. 1. A method, comprising: generating a methylation profile for at least one nucleic acid sequence obtained from a human subject, and Selecting a treatment appropriate for the human subject based on the methylation profile.
2. 2. The method of any preceding claim, wherein the methylation profile comprises at least one Differential Methylation Region (DMR).
3. 3. The method of any preceding claim, wherein the at least one DMR is determined based on a comparison to a threshold determined from one or more healthy subjects.
4. 4. The method of any preceding claim, wherein the methylation profile characterizes functional acquisition of at least one or more genes.
5. 5. The method of any preceding claim, wherein the methylation profile characterizes the loss of function of at least one or more genes.
6. 6. The method of any preceding claim, wherein the methylation profile characterizes a genomic mutation.
7. 7. The method of any preceding claim, wherein the methylation profile characterizes a gene target.
8. 8. The method of any preceding claim, wherein the methylation profile characterizes gene dysfunction.
9. 9. The method of any preceding claim, wherein the characterization is of a gene target capable of conferring synthetic lethality.
10. 10. The method of any preceding claim, wherein the characterization is based on hypermethylation status.
11. 11. The method of any preceding claim, wherein the one or more genes comprise CDKN2A.
12. 12. The method of any preceding claim, wherein the one or more genes comprise a metabolic enzyme.
13. 13. The method of any preceding claim, wherein the metabolic enzyme comprises methylthioadenosine phosphorylase (MTAP).
14. 14. The method of any preceding claim, wherein the methylation profile is detected using a Methyl Binding Domain (MBD) zonal assay.
15. 15. The method of any preceding claim, wherein the MBD partition assay comprises combining more than one nucleic acid molecule from the human subject with a solution comprising an amount of Methyl Binding Domain (MBD) protein to produce a nucleic acid-MBD protein solution, and washing the nucleic acid-MBD protein solution more than once with a salt solution to produce a plurality of nucleic acid fractions, a single nucleic acid fraction having a threshold number of methylated cytosines in a region of more than one nucleic acid having at least a threshold cytosine-guanine content.
16. 16. The method of any one of the preceding claims, wherein the treatment comprises a PRMT5-MTA5 inhibitor and/or immunotherapy.
17. 17. The method of any preceding claim, wherein genomic mutation and/or gene dysfunction modulates PRMT5-MTA complex and/or MTA accumulation.
18. 18. The method of any preceding claim, wherein detecting comprises a method selected from the group consisting of Next Generation Sequencing (NGS), third Generation Sequencing (TGS), sanger sequencing, microarray analysis, PCR, fluorescence In Situ Hybridization (FISH), real-time PCR (RT-PCR), digital PCR (dPCR), drop digital PCR (ddPCR), targeted sequencing, nanopore sequencing, short read sequencing, long read sequencing techniques (e.g., pacbi and nanopore).
19. 19. The method of any one of the preceding claims, wherein the patient is afflicted with a cancer selected from the group consisting of breast cancer, lung cancer, prostate cancer, colorectal cancer, skin cancer, ovarian cancer, pancreatic cancer, leukemia, lymphoma, liver cancer, cervical cancer, brain cancer, gastric cancer, kidney cancer, bladder cancer, thyroid cancer, esophageal cancer, melanoma, testicular cancer, epithelioid sarcoma, recurrent or refractory follicular lymphoma, non-hodgkin lymphoma (NHL), recurrent or refractory adult T-cell leukemia/lymphoma (R/R ATL), follicular lymphoma, castration-resistant prostate cancer (CRPC), small cell lung cancer, and sarcoma.
20. 20. The method of any one of the preceding claims, wherein the sample is selected from the group consisting of blood, plasma, cell-free DNA (cfDNA), cell-free RNA (cfRNA), saliva, urine, cerebrospinal fluid, synovial fluid, amniotic fluid, lymph, semen, vaginal fluid, tear fluid, breast milk, mucus, sweat, pericardial fluid, pleural fluid, peritoneal fluid, bile, and interstitial fluid.

Description

Genome and methylation biomarkers for predicting copy number loss/gene deletion Cross Reference to Related Applications The present application claims the benefit of U.S. provisional application No. 63/559,749 filed on 29 nd 2 nd 2024 and U.S. provisional application No. 63/588,630 filed on 6 th 10 rd 2023. Both of which are incorporated by reference in their entirety for all purposes. Background Cancer is a major cause of disease worldwide. Every year, tens of millions of people worldwide are diagnosed with cancer, and more than half of the patients eventually die from it. Cancer is listed in many countries as the second most common cause of death following cardiovascular disease. Early detection is associated with improved outcome for many cancers. The 5' -methylthioadenosine phosphorylase (MTAP) gene is located in the chromosomal region 9p 21. MTAP deficiency is a common event in a variety of human cancers, however, its biological role in tumorigenesis is still unclear. MTAP gene is flanked by CDKN2A and miR-31, and in many different tumors, this gene is often co-deleted with CDKN2A and CDKN2B genes encoding tumor suppressors p15, p16, p19 and interferon alpha and beta located at miR-31 telomeres. Selective MTAP deficiency due to selective deletion of MTAP locus or methylation of MTAP promoter without co-deletion of CDKN2 gene was also reported. Summary of The Invention Described herein is a method comprising detecting methylation of at least one of more than one site, generating more than one or more metrics for each of the more than one site, and processing the one or more metrics to characterize at least one cis-regulatory network element in a regulatory network. In various embodiments, characterizing the at least one cis-regulatory network element includes determining the presence, absence, of the at least one cis-regulatory network element in the regulatory network. In various embodiments, at least one cis-regulatory network element includes, for example, genetic variations, insertions/deletions, homologous deletions (homdel), fusions, and/or other mutations. In various embodiments, the determination characterizes the sample. In other embodiments, at least one cis-regulatory network element is capable of changing the regulatory sub-loop. In other embodiments, the cis-regulatory network element comprises an epigenetic regulator (regulator). In other embodiments, the regulator sub-loop is bi-directional. In other embodiments, the modulator sub-loop increases methylation in more than one target. In other embodiments, the regulatory network comprises additional cis-regulatory network elements. In other embodiments, additional cis-regulatory network elements can alter the regulatory sub-loop. In other embodiments, the additional cis-regulatory network element comprises a regulatory node. In other embodiments, the regulatory node is a blocking point (point of interdiction). In other embodiments, the regulator sub-loop includes additional regulation nodes. In other embodiments, the additional conditioning node is a blocking point. Described herein is a method comprising generating a methylation profile for at least one nucleic acid sequence obtained from a human subject, and selecting a treatment appropriate for the human subject based on the methylation profile. In other embodiments, the methylation profile includes at least one Differential Methylation Region (DMR). In other embodiments, the at least one DMR is determined based on a comparison to a threshold determined from one or more healthy subjects. In other embodiments, methylation signatures characterize functional gain of at least one or more genes. In other embodiments, methylation signatures are indicative of the loss of function of at least one or more genes. In other embodiments, the methylation profile characterizes a genomic mutation. In other embodiments, the methylation profile characterizes a gene target. In other embodiments, the methylation profile characterizes a gene dysfunction. In other embodiments, the characterization is of a gene target capable of conferring synthetic lethality. In other embodiments, the characterization is based on hypermethylation status. In other embodiments, the one or more genes comprise CDKN2A. In other embodiments, the one or more genes include a metabolic enzyme. In other embodiments, the metabolic enzyme comprises a methylthioadenosine phosphorylase (MTAP). In other embodiments, methylation profiles are detected using a Methyl Binding Domain (MBD) zonal assay. In other embodiments, the MBD partitioning assay includes combining more than one nucleic acid molecule from a human subject with a solution comprising an amount of Methyl Binding Domain (MBD) protein to produce a nucleic acid-MBD protein solution, and washing the nucleic acid-MBD protein solution with a salt solution more than once to produce a plurality of nucleic acid fractions, a single nucleic acid fraction having a threshold number of met