Lung cancer methylation markers and uses thereof
View Patent ↗Disclosed herein are methods and kits for identifying a subject as having lung cancer. Also provided herein are methods and kits for determining the prognosis of a subject having lung cancer and for determining the progression of lung cancer in a subject.
1. A method of treating a lung 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, the cfDNA sample 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 a methylation status of cg10673833;
(d) generating a methylation profile comprising data of the methylation status of cg10673833;
(e) identifying the subject as having the lung cancer by comparing the methylation profile with a control; and
(f) administering to the subject having the lung cancer an effective amount of a therapeutic agent selected from the group consisting of alectinib, afatinib, bevacizumab, carboplatin, ceritinib, crizotinib, docetaxel, doxorubicin, erlotinib, everolimus, gefitinib, gemcitabine, mechlorethamine hydrochloride, methotrexate, necitumumab, nivolumab, paclitaxel, pembrolizumab, ramucirumab, vinorelbine tartrate, and a combination thereof.
2. The method of claim 1 , wherein the cfDNA sample comprises a blood sample.
3. The method of claim 1 , wherein the methylation status is a methylation rate.
4. The method of claim 3 , wherein the methylation rate of is the proportion of sequence reads showing methylation at cg10673833 divided by the total number of reads covering cg10673833.
5. The method of claim 1 , wherein the lung cancer is a relapsed or refractory lung cancer.
6. The method of claim 1 , wherein the lung cancer is a metastatic lung cancer.
7. The method of claim 1 , where the lung cancer is non-small cell lung cancer (NSCLC), small cell lung cancer (SCLC), bronchial carcinoids or mesothelioma.
8. The method of claim 7 , wherein the non-small cell lung cancer comprises adenocarcinoma, squamous cell carcinoma, large cell carcinoma or large cell neuroendocrine tumors.
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.
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 detecting of the methylation status comprises subjecting the treated genomic DNA to hybridization with a first probe, wherein the first probe hybridizes to the treated genomic derived from a methylated occurrence of cg10673833.
13. The method of claim 12 , wherein the detecting of the methylation status comprises subjecting the treated genomic DNA to hybridization with a second probe, wherein the second probe hybridizes to the treated genomic DNA derived from an unmethylated occurrence of cg10673833.
14. The method of claim 1 , wherein the next-generation sequencing technique is a digital PCR sequencing method.
15. The method of claim 1 , further comprising processing an extracted genomic DNA from the biological sample to convert unmethylated cytosines to uracil.
16. The method of claim 1 , wherein the methylation profile further comprises data of the methylation status of one or more of cg01602690, cg03993087, cg04383154, cg04933208, cg05784951, cg06352912, cg06800849, cg07464206, cg08089301, cg14419975, cg15545942, cg15963326, cg19924352, cg20691722, cg21845794, cg24398479, cg05346286, cg07903001, cg17894293, cg03169557, cg04549287, cg07649862, or cg08682723.
17. The method of claim 16 , wherein the methylation profile further comprises data of the methylation status of cg01602690, cg03993087, cg04383154, cg04933208, cg05784951, cg06352912, cg06800849, cg07464206, cg08089301, cg14419975, cg15545942, cg15963326, cg19924352, cg20691722, cg21845794, cg24398479, cg05346286, cg07903001, cg17894293, cg03169557, cg04549287, cg07649862, and cg08682723.