Validation of the use of DNA pools and primer extension in association studies of sporadic colorectal cancer for selection of candidate SNPs.

Colorectal cancer (CRC) is a multifactorial disease that involves both lifestyle and genetic factors. To identify single nucleotide polymorphisms (SNPs) associated with sporadic CRC, we used pooled DNA samples representing 230 cases with sporadic CRC and 540 controls. The allele frequency of the SNPs was estimated in the two pools using a genotyping method based on primer extension and capillary electrophoresis (CE). The sensitivity of the method was high, which permitted the detection of an odds ratio (OR) of 1.5. Validation of the method showed that it is robust, linear, sensitive, and reproducible. Of the 224 SNPs investigated, 20 potential candidates associated with CRC were identified, including IL6 -174G>C (g.22062318G>C), XRCC1 c.685 C>T (p.Arg194Trp), PPARGC1A g.92945042C>T (3'UTR 96516), GSTP1 c.342A>C (p.Ile105Val), GSTM1 c.573C>G (p.Lys173Asn), and SULT1A1 g.19934792G>A (p.Arg213His). All were borderline significant, and none were significant at the 5% level. A high number of the SNPs (40%) were not polymorphic in our population. We conclude that instead of looking for single risk factors, investigators should examine individual combinations of potential risk factors to clarify the genetic predisposition to CRC. 2006 Wiley-Liss, Inc.