Detecting gastrointestinal neoplasms

Abstract

Provided herein is technology for gastrointestinal neoplasia screening and particularly, but not exclusively, to methods, compositions, and related uses for detecting the presence of gastrointestinal neoplasm, and classifying the site location of such a gastrointestinal neoplasm (e.g., a colorectal region, a pancreaticobiliary region, a gastroesophageal region).

1 . (canceled) 
     
     
         2 . A method of characterizing a biological sample, the method comprising:
 determining a methylation profile in at least one differentially methylated region (DMR) of a DNA sample obtained from a subject having or suspected of having a gastrointestinal neoplasm by treating the sample with a reagent that modifies DNA in a methylation-specific manner;   wherein the at least one DMR is comprised in at least one gene selected from QKI, PDGFD, and ELOVL2.   
     
     
         3 . The method of  claim 2 , wherein determining the methylation profile of the at least one DMR comprises determining the presence or absence of methylation at one or more CpG sites. 
     
     
         4 . The method of  claim 3 , wherein the one or more CpG sites are present in a coding region, a non-coding region, and/or a regulatory region of a gene. 
     
     
         5 . The method of  claim 2 , wherein determining the methylation profile of the at least one DMR comprises determining a methylation frequency. 
     
     
         6 . The method of  claim 2 , wherein determining the methylation profile of the at least one DMR comprises determining a methylation pattern. 
     
     
         7 . The method of  claim 2 , wherein the at least one DMR comprises an increased methylation percentage as compared to a control DNA sample, wherein the control DNA sample is from a subject that does not have a gastrointestinal neoplasm. 
     
     
         8 . The method of  claim 2 , wherein the at least one DMR comprises an increased hypermethylation ratio as compared to a control DNA sample, wherein the control DNA sample is from a subject that does not have a gastrointestinal neoplasm. 
     
     
         9 . The method of  claim 2 , wherein the at least one DMR is associated with an area under a ROC curve (AUC) greater than or equal to 0.5, and wherein the ROC curve discriminates between a subject having or suspected of having a gastrointestinal neoplasm and a control DNA sample. 
     
     
         10 . The method of  claim 2 , wherein determining the methylation profile of the at least one DMR comprises performing at least one of methylation-specific PCR, quantitative methylation-specific PCR, methylation-specific DNA restriction enzyme analysis, quantitative bisulfite pyrosequencing, flap endonuclease assay, PCR-flap assay, and bisulfite genomic sequencing PCR. 
     
     
         11 . The method of  claim 2 , wherein the at least one DMR is comprised in at least two genes selected from QKI, PDGFD, and ELOVL2. 
     
     
         12 . The method of  claim 11 , wherein the at least two genes are selected from:
 (i) QKI and PDGFD;   (ii) QKI and ELOVL2; and   (iii) PDGFD and ELOVL2.   
     
     
         13 . The method of  claim 2 , wherein the at least one DMR is comprised in at least three genes selected from QKI, PDGFD, and ELOVL2. 
     
     
         14 . The method of  claim 2 , wherein the biological sample is a stool sample, a urine sample, a tissue sample, a plasma sample, a blood sample, or an excretion sample. 
     
     
         15 . The method of  claim 14 , wherein the tissue sample is an upper gastrointestinal tissue sample. 
     
     
         16 . The method of  claim 14 , wherein the tissue sample is a lower gastrointestinal tissue sample. 
     
     
         17 . The method of  claim 2 , wherein the reagent that modifies DNA in a methylation-specific manner comprises one or more of a methylation-sensitive restriction enzyme, a methylation-dependent restriction enzyme, and a bisulfite reagent. 
     
     
         18 . The method of  claim 2 , wherein determining the methylation profile of at least one DMR comprises amplifying a region of the at least one DMR using a set of primers. 
     
     
         19 . The method of  claim 18 , wherein the at least one DMR is comprised in at least one gene selected from QKI, PDGFD, and ELOVL2, and wherein the set of primers are selected from:
 (i) SEQ ID NOs 1 and 2 corresponding to a region of QKI;   (ii) SEQ ID NOs 3 and 4 corresponding to a region of PDGFD; and   (iii) SEQ ID NOs 5 and 6 corresponding to a region of ELOVL2.   
     
     
         20 . The method of  claim 2 , wherein the at least one DMR is comprised in at least one gene selected from QKI, PDGFD, and ELOVL2, and at least one additional DMR is comprised in at least one gene selected from BMP3, PCBP3, MAX.chr12.133484978-133485739, MAX.chr11.123301058-123301255, and MAXchr7.25896389-25896501.