Patent ID: 11874277
Assignee: PROPHASE LABS, INC.
Field: Measurement (Instruments)
Classification: CPC C  G | IPC G

Claim 0:
1. A method of assessing risk of developing esophageal adenocarcinoma in a subject, comprising:
(a) determining the expression level of a set of marker genes comprising ISG15, DAD1, UBE2N, S100P, and at least one of LTF, CNDP2, SET and GPI in a test esophageal tissue sample from the subject by:
(i) processing a formalin fixed paraffin embedded (FFPE) test esophageal tissue sample obtained from the subject to reverse formalin cross-links by heating the FFPE sample in a detergent-free buffer to generate a processed FFPE sample,
(ii) digesting the processed FFPE sample with trypsin to generate a trypsin digested FFPE sample, and
(iii) analyzing the trypsin-digested FFPE sample with a targeted mass spectrometry assay to detect and quantify target trypsin-digest peptides corresponding to each of the marker genes wherein the target trypsin-digest peptide corresponding to ISG15 comprises an amino acid sequence of SEQ ID NO: 11 or SEQ ID NO: 12; the target trypsin-digest peptide corresponding to LTF comprises an amino acid sequence of SEQ ID NO: 54 or SEQ ID NO: 58; the target trypsin-digest peptide corresponding to CNDP2 comprises an amino acid sequence of SEQ ID NO: 20 or SEQ ID NO: 31; the target trypsin-digest peptide corresponding to DAD1 comprises an amino acid sequence of SEQ ID NO: 7 or SEQ ID NO: 9; the target trypsin-digest peptide corresponding to SET comprises an amino acid sequence of SEQ ID NO: 50; the target trypsin-digest peptide corresponding to UBE2N comprises an amino acid sequence of SEQ ID NO: 1 or SEQ ID NO: 5; the target trypsin-digest peptide corresponding to S100P comprises an amino acid sequence of SEQ ID NO: 67 or SEQ ID NO: 68; wherein levels of each trypsin-digest peptide correlate with expression levels of each corresponding marker gene in the test esophageal tissue sample; and

(b) comparing the expression level of each marker gene in the test esophageal tissue sample to the expression level of each marker gene in a control formalin fixed paraffin embedded (FFPE) esophageal tissue sample, wherein increased expression of: ISG15, DAD1, UBE2N, S100P, and at least one of LTF, CNDP2, SET and GPI in the test tissue sample relative to the control esophageal tissue sample indicates an increased risk of developing esophageal adenocarcinoma.