Imputation without doing imputation: a new method for the detection of non-genotyped causal variants.

ABSTRACT: Genome-wide association studies allow detection of non-genotyped disease-causing variants through testing of nearby genotyped SNPs. This approach may fail when there are no genotyped SNPs in strong LD with the causal variant. Several genotyped SNPs in weak LD with the causal variant may, however, considered together, provide equivalent information. This observation motivates popular but computationally intensive approaches based on imputation or haplotyping. Here we present a new method and accompanying software designed for this scenario. Our approach proceeds by selecting, for each genotyped "anchor" SNP, a nearby genotyped "partner" SNP, chosen via a specific algorithm we have developed. These two SNPs are used as predictors in linear or logistic regression analysis to generate a final

SUBMITTER: Howey R 

PROVIDER: S-EPMC4150535 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature