Feasibility of whole genome association study to find SNPs predictive of colorectal cancer outcome

B29 Purpose
 Genome wide association studies (GWAS) have successfully identified low-penetrance loci associated with colorectal (CRC), breast, lung, and prostate cancer. Here we describe the use of high-density SNP arrays to perform a GWAS aimed at identifying candidate germline loci which can predict outcome and might influence success of chemotherapy in stage 2 and 3 CRC.
 Methods
 We typed 318,237 tagSNPs on Illumina HumanHap300duo arrays (Illumina Inc, San Diego, CA) in 933 patients enrolled in the Victor trial of AJCC stage 2 or 3 CRC treated with surgery and chemo- or radiotherapy as appropriate and randomized to rofecoxib or placebo. Two patients were excluded from the analysis due to call rates 99.97% concordance between repeats) and reliable (median call rate 99.95%). Testing each model with a q-q plot did not reveal any substructure in the population tested, with good alignment of observed and expected p-value distribution.
 Of the 309200 autosomal SNPs, 180 failed and 56 were non-informative (monomorphic). 565 SNPs had p