| CPC C12Q 1/6886 (2013.01) [C12Q 1/6827 (2013.01); C12Q 1/6853 (2013.01); G01N 33/574 (2013.01); C12Q 2600/154 (2013.01); C12Q 2600/156 (2013.01)] | 14 Claims |
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1. A method of identifying a human subject for treatment of esophageal neoplasia or metaplasia and treating, comprising:
providing an esophageal sample obtained from the subject and treating with bisulfite to generate a plurality of bisulfite converted SqBE18 nucleic acid sequences;
amplifying the plurality of bisulfite converted SqBE18 nucleic acid sequences to generate amplicons for each bisulfite converted SqBE18 nucleic acid, wherein each amplicon is a read and wherein the amplicon comprises a nucleotide sequence that is at least 90% identical to the nucleotide sequence of SEQ ID NOs: 8318, 8360, 8332, and/or 8374, or a fragment thereof, said fragment comprising at least 50 nucleotides in length;
identifying methylated reads by measuring the number of methylated cytosines of the CpG dinucleotides in each amplicon of the bisulfite converted SqBE18 nucleic acid sequence, wherein a read is classified as a methylated read when at least 70% of the cytosines in the CpG dinucleotides of the individual amplicon of the bisulfite converted SqBE18 nucleic acid sequence is methylated;
calculating a percentage of total reads that are methylated reads from the amplifying and measuring steps, wherein the esophageal sample obtained from the subject has at least 0.1% of the total reads that are methylated reads; and,
administering to the human subject having an esophageal sample with at least 0.1% of the total reads that are methylated reads, cryotherapy, photodynamic therapy (PDT); radiofrequency ablation (RFA); laser ablation; argon plasma coagulation (APC); electrocoagulation (electrofulguration); esophageal stent, endoscopic mucosal resection (EMR), esophagectomy, anti-reflux surgery, and/or a therapeutic agent selected from a proton pump inhibitor, a Histamine H2 receptor blocking agents, an anti-reflux medication, a drug that moves food thru the gastrointestinal tract more quickly, carboplatin and paclitaxel; cisplatin and 5-fluorouracil (5-FU); ECF: epirubicine, cisplatin, and 5-FU; DCF: docetaxel, cisplatin, and 5-FU; Cisplatin with capecitabine; oxaliplatin and either 5-FU or capecitabine; doxorubicin, bleomycin, mitomycin, methotrexate, vinorelbine, topotecan, and irinotecan, trastuzumab, and/or ramucirumab.
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