Compositions for characterizing development of esophageal adenocarcinoma in patients and methods of use thereof

A method, comprising:

• (a) obtaining a sample of an esophageal tissue from a subject,
• wherein the sample of the esophageal tissue comprises or is suspected of comprising a break of chromosome 2 (chr2), a break of chromosome 10 (chr10), a break of chromosome 16 (chr16), or any combination thereof, and
• (b) detecting in the sample of esophageal tissue whether the break of chr2 is present, whether the break of chr10 is present, whether the break of chr16 is present, or any combination thereof, by contacting the sample of esophageal tissue with a first detectably labeled probe, a second detectably labeled probe, a third detectably labeled probe, or any combination thereof, and detecting binding between:
• (i) the first detectably labeled probe and the break of chr2,
• (ii) the second detectably labeled probe and the break of chr10,
• (iii) the third detectably labeled probe and the break of chr16, or
• (iv) any combination thereof.

A kit, comprising:

• (i) SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or any combination thereof, and
• (ii) instructions for performing an assay for detecting:
• (a) a first translocation, a second translocation, a third translocation, or any combination thereof,
• wherein
• (i) the first translocation comprises a break of chromosome 2 (chr2) with a fusion of the break of chr2 with chromosome 10 (chr10),
• (ii) the second translocation comprises a break of chr10 with A fusion of the break of chr10 with chromosome 16 (chr16), and
• (iii) the third translocation comprises a break of chr16 with a fusion of the break of chr16 with chr2;
• or
• (b) a break at chr2, a break at chr10, a break at chr 16, or any combination thereof.

A method, comprising:

• (a) obtaining a sample of an esophageal tissue from a subject,
• wherein the sample of the esophageal tissue comprises or is suspected of comprising a first translocation, a second translocation, a third translocation, or any combination thereof,
• wherein
• (i) the first translocation comprises a break of chromosome 2 (chr2) without a fusion of the break of chr2 with chromosome 10 (chr10),
• (ii) the second translocation comprises a break of chr10 without a fusion of the break of chr10 with chromosome 16 (chr16), and
• (iii) the third translocation comprises a break of chr16 without a fusion of the break of chr16 with chr2;
• and
• (b) detecting in the sample of esophageal tissue whether the first translocation is present, whether the second translocation is present, whether the third translocation is present, or any combination thereof, by contacting the sample of esophageal tissue with a first detectably labeled probe, a second detectably labeled probe, a third detectably labeled probe, or any combination thereof, and detecting binding between:
• (i) the first detectably labeled probe and the first translocation,
• (ii) the second detectably labeled probe and the second translocation,
• (iii) the third detectably labeled probe and the third translocation, or
• (iv) any combination thereof.

A kit, comprising:

• (i) SEQ ID NO:1, SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:7, SEQ ID NO:8, or any combination thereof, and
• (ii) instructions for performing an assay for detecting:
• (a) a first translocation, a second translocation, a third translocation, or any combination thereof,
• wherein
• (i) the first translocation comprises a break of chromosome 2 (chr2) without a fusion of the break of chr2 with chromosome 10 (chr10),
• (ii) the second translocation comprises a break of chr10 without fusion of the break of chr10 with chromosome 16 (chr16), and
• (iii) the third translocation comprises a break of chr16 without a fusion of the break of chr16 with chr2;
• or
• a break at chr2, a break at chr10, a break at chr 16, or any combination thereof.