RNA was available from 175 tumor and nontumor tissue pairs who were part of the Diet, Activity, and Lifestyle study, which is an incident, population-based, case-control study of colon cancer conducted in Utah, the Kaiser Permanente Medical Research Program (KPMRP), and the Twin Cities Metropolitan area. Tumor tissue for RNA extraction was available from the Utah and KPMRP sites. Cases had to have tumor registry verification of a first primary adenocarcinoma of the colon and diagnosed between October 1991 and September 1994 to be eligible for the study. Tumor tissue was obtained for 97% of all Utah cases and for 85% of all KPMRP cases (Slattery et al., 2000 (link)) and included those who signed informed consent and those retrieved by local tumor registries and sent to study investigators without personal identifiers. Individuals with known adenomatous polyposis coli (APC), Crohn’s disease, or inflammatory bowel disease were not eligible for the study. Individuals with MSI high tumors were sequenced for inherited mutations in mismatch repair genes and excluded from the study if such mutations existed (Samowitz et al., 2001 (link)). The study was approved by the Institutional Review Board of the University of Utah and at KPMRP.
We have previously assessed these tumor samples for TP53 and KRAS mutations, the CpG island methylator phenotype (CIMP) using the classic panel (Samowitz et al., 2005 (link)), and MSI and MSS based on the mononucleotides BAT26 and TGFbRII and a panel of 10 tetranucleotide repeats that were correlated highly with the Bethesda Panel (Slattery et al., 2000 (link)); our study was done prior to the Bethesda Panel development. The classic CIMP panel consisted of five markers, hMLH1, p16, and MINT1, MINT2, and MINT31. Tumors were scored as CIMP high if two or more of the CpG islands were methylated otherwise they were classified as CIMP low.