Methods and compositions for detecting esophageal neoplasias and/or metaplasias in the esophagus
AssigneeCase Western Reserve University
InventorsSanford D. Markowitz, Helen Moinova, Amitabh Chak, Joseph Willis, Thomas LaFramboise
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Abstract
The disclosure provides methods for identifying genomic loci (e.g., vimentin and/or SqBE18) that are differentially methylated in metaplasias (e.g., Barrett's esophagus) and/or neoplastic cancers (e.g., esophageal cancers). Identification of methylated genomic loci has numerous uses, including for example, to characterize disease risk, to predict responsiveness to therapy, to non-invasively diagnose subjects and to treat subjects determined to have gastrointestinal metaplasias and/or neoplasias.
Claims18
1-64. (canceled)
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 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;
- 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;
- and,
- calculating percent of total reads are methylated reads from the amplifying and measuring steps, whereby the esophageal sample obtained from the subject is classified as a methylated sample when at least 0.1% of the total reads are methylated reads.
Dependencies are inferred from the claim text.