Granted Patent
B2
US 12,351,876 · App. 16/315,608 · Granted Jul 8, 2025
Colon cancer methylation markers and uses thereof
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Abstract
Disclosed herein are methods and kits for identifying a subject as having colon cancer. Also provided herein are methods and kits for determining the prognosis of a subject having colon cancer and for determining the progression of colon cancer in a subject.
Claims (19)
1. A method of treating a colon cancer in a subject, the method comprising:
(a) obtaining a treated genomic DNA sample derived from a cell-free DNA (cfDNA) sample from the subject, wherein the treated genomic DNA sample is suitable for a methylation analysis;
(b) performing a next-generation sequencing technique on the treated genomic DNA;
(c) mapping sequencing reads from the next-generation sequencing technique to a reference genome using a software tool to determine the methylation status of cg10673833 and cg08088171;
(d) generating a methylation profile comprising data of the methylation status cg10673833 and cg08088171;
(e) identifying the subject as having the colon cancer by comparing the methylation profile with a control; and
(f) administering to the subject having the colon cancer an effective amount of a therapeutic agent selected from the group consisting of capecitabine, cetuximab, doxorubicin, fluorouracil injection, irinotecan hydrochloride, leucovorin calcium, oxaliplatin, panitumumab, ramucirumab, regorafenib, Ziv-aflibercept, and a combination thereof.
2. The method of claim 1 , wherein the methylation profile further comprises data from cg13420112, cg14642259, cg20973720, cg27536151, cg24741563 and cg22979615.
3. The method of claim 1 , wherein the cfDNA sample comprises a blood sample.
4. The method of claim 1 , wherein the methylation status is a methylation rate.
5. The method of claim 4 , wherein the methylation rate is a proportion of sequence reads showing methylation at cg10673833 and cg08088171 divided by the total number of reads covering cg10673833 and cg08088171.
6. The method of claim 1 , wherein the colon cancer is a relapsed or refractory colon cancer.
7. The method of claim 1 , wherein the colon cancer is a metastatic colon cancer.
8. The method of claim 1 , where the colon cancer is adenocarcinoma, gastrointestinal carcinoid tumors, gastrointestinal stromal tumors, primary colorectal lymphoma, leiomyosarcoma, or melanoma and squamous cell carcinoma.
9. The method of claim 1 , further comprising extracting genomic DNA from the cfDNA sample to obtain an extracted genomic DNA.
10. The method of claim 9 , further comprising treating the extracted genomic DNA to generate the treated genomic DNA, wherein the treated genomic DNA is suitable for use in a methylation analysis procedure for detecting the methylation status of cg10673833 and cg08088171.
11. The method of claim 10 , wherein the treating of the extracted genomic DNA comprises processing the extracted genomic DNA with a deaminating agent.
12. The method of claim 1 , wherein the next-generation sequencing technique is a digital PCR sequencing method.
13. The method of claim 1 , wherein the methylation profile further comprises data from cg24583770.
Assignments (4)
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Oct 15, 2024
From: YOUHEALTH ONCOTECH, LIMITED
To: HELIO HEALTH INC.
Reel/Frame 068906/0059 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Dec 9, 2019
From: HOU, RUI; ZHENG, LIANGHONG
To: YOUHEALTH BIOTECH, LIMITED
Reel/Frame 051222/0740 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Dec 9, 2019
From: YOUHEALTH BIOTECH, LIMITED
To: YOUHEALTH ONCOTECH, LIMITED
Reel/Frame 051222/0755 →
ASSIGNMENT OF ASSIGNOR'S INTEREST
Recorded Dec 9, 2019
From: ZHANG, KANG
To: THE REGENTS OF THE UNIVERSITY OF CALIFORNIA
Reel/Frame 051232/0065 →
Continuity (2)
Provisional Application
62358776
· Jul 6, 2016
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