Detection of colorectal cancer

Abstract

The present disclosure provides, among other things, methods for colorectal cancer screening and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer screening that include analysis of methylation status of one or more methylation biomarkers, and compositions related thereto. In various embodiments, the present disclosure provides methods for colorectal cancer screening that include screening methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA. In various embodiments, the present disclosure provides methods for colorectal cancer screening that include screening methylation status of one or more methylation biomarkers in cfDNA, e.g., in ctDNA, using MSRE-qPCR.

1 . A method of screening for colorectal cancer, the method comprising determining the methylation status of at least one DMR of LONRF2, at least one DMR of PDGFD, and at least one DMR of FGF14
 in DNA of a human subject, wherein the DNA is cell-free DNA of the human subject, and diagnosing colorectal cancer in the subject.   
     
     
         2 .- 3 . (canceled) 
     
     
         4 . The method of  claim 1 , the method comprising determining whether the one or more methylation loci are hypermethylated as compared to a reference, wherein hypermethylation is indicative of colorectal cancer. 
     
     
         5 .- 9 . (canceled) 
     
     
         10 . The method of  claim 1 , wherein the method comprises determining the methylation status of DMR FGF14 '577. 
     
     
         11 . The method of  claim 1 , wherein the method comprises determining the methylation status of DMR PDGFD '388. 
     
     
         12 .- 14 . (canceled) 
     
     
         15 . The method of  claim 1 , wherein one or more of the DMRs are amplified by oligonucleotide primer pairs provided in Table 13. 
     
     
         16 . The method of  claim 1 , wherein the DNA is isolated from blood, plasma, urine, saliva, or stool of the human subject. 
     
     
         17 .- 29 . (canceled) 
     
     
         30 . The method of  claim 1 , wherein methylation status is determined using one or more members selected from the group consisting of methylation sensitive restriction enzyme quantitative polymerase chain reaction (MSRE-qPCR), Methylation-Specific PCR, Methylation Specific Nuclease-assisted Minor-allele Enrichment PCR, and next-generation sequencing. 
     
     
         31 .- 41 . (canceled) 
     
     
         42 . The method of  claim 1 , wherein the method comprises determining the methylation status of DMR PDGFD '921. 
     
     
         43 . The method of  claim 1 , wherein the method comprises determining the methylation status of DMR LONRF2 '387. 
     
     
         44 . The method of  claim 1 , wherein the method comprises determining the methylation status of at least one DMR of CNRIP1. 
     
     
         45 . The method of  claim 44 , wherein the method comprises determining the methylation status of at least one of the following DMRs: CNRIP1 '272 and CNRIP1 '232. 
     
     
         46 . The method of  claim 1 , wherein methylation status is determined using massively parallel sequencing.