Evaluation of allele-specific somatic changes of genome-wide association study susceptibility alleles in human colorectal cancers.

When the imbalances observed in our samples at the SNPs rs6983267 , rs961253 , rs3802842 , rs10411210 , rs4444235 , rs4779584 , and rs9929218 were combined with those published previously [19] , [35] , we observed a highly significant relative loss of the non-risk T allele of rs6983267 (p-value = 2.94×10 −5 ).

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While none of the SNPs reached statistical significance for allele-specific imbalance at α = 0.05, three SNPs ( rs16892766, rs6983267, rs7136702 ) showed a trend for allele-specific imbalance (p-values<0.10) prior to Bonferroni correction for multiple comparison (n = 16).

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Our rigorous requirements for inclusion of data may limit detection of borderline significant allelic imbalance, particularly in tumor samples containing non-tumor cells.

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