Methods and compositions for detecting esophageal neoplasias and/or metaplasias in the esophagus

A method for classifying an esophageal sample from a human subject as a methylated sample, comprising:

• providing an esophageal sample obtained from the subject and treating with a compound(s) that converts unmethylated cytosine bases to a different nucleotide base to generate a plurality of converted SqBE18 nucleic acid sequences;
• amplifying the plurality of converted SqBE18 nucleic acid sequences to generate amplicons for each converted SqBE18 nucleic acid, wherein each amplicon is a read and wherein the amplicon comprises a nucleotide sequence that is at least 50 nucleotides in length;
• wherein primers used to amplify the portion of the converted SqBE18 nucleic acid sequence comprise SEQ ID NOs:
• 8388 and/or 8402,
• measuring the number of methylated cytosines of the CpG dinucleotides in each amplicon of the 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 converted SqBE18 nucleic acid sequence are methylated;
• and,
• calculating a percentage of total reads that are methylated reads from the amplifying and measuring steps wherein the sample has at least 0.1% of the total reads that are methylated reads, whereby the esophageal sample obtained from the subject is classified as a methylated sample.

A method for detecting methylation status of an esophageal sample from a human subject suspected of having esophageal neoplasia or metaplasia, comprising:

• providing an esophageal sample obtained from the subject and treating with a compound(s) that converts unmethylated cytosine bases to a different nucleotide base to generate a plurality of converted SqBE18 nucleic acid sequences;
• amplifying the plurality of converted SqBE18 nucleic acid sequences to generate amplicons for each 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;
• measuring the number of methylated cytosines of the CpG dinucleotides in each amplicon of the 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 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 human subject has at least 0.1% of the total reads that are methylated reads, whereby the esophageal sample obtained from the subject is classified as a methylated sample;
• and
• administering an endoscopy to the human subject with a methylated sample.

A method of diagnosing a subject that has an esophageal neoplasia or metaplasia, comprising:

• providing an esophageal sample obtained from the subject and treating with a compound(s) that converts unmethylated cytosine bases to a different nucleotide base to generate a plurality of converted SqBE18 nucleic acid sequences;
• amplifying the plurality of converted SqBE18 nucleic acid sequences to generate amplicons for each converted SqBE18 nucleic acid, wherein each amplicon is a read and wherein the amplicon comprises a nucleotide sequence that is at least 50 nucleotides in length;
• wherein primers used to amplify the portion of the converted SqBE18 nucleic acid sequence comprise SEQ ID NOs:
• 8388 and/or 8402;
• measuring the number of methylated cytosines of the CpG dinucleotides in each amplicon of the 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 converted SqBE18 nucleic acid sequence are methylated;
• and,
• calculating a percentage of total reads that are methylated reads from the amplifying and measuring steps wherein the sample has at least 0.1% of the total reads that are methylated reads, whereby the subject is diagnosed with esophageal neoplasia or metaplasia.