Association analysis using next-generation sequence data from publicly available control groups: the robust variance score statistic.

ABSTRACT:

Motivation

Sufficiently powered case-control studies with next-generation sequence (NGS) data remain prohibitively expensive for many investigators. If feasible, a more efficient strategy would be to include publicly available sequenced controls. However, these studies can be confounded by differences in sequencing platform; alignment, single nucleotide polymorphism and variant calling algorithms; read depth; and selection thresholds. Assuming one can match cases and controls on the basis of ethnicity and other potential confounding factors, and one has access to the aligned reads in both groups, we investigate the effect of systematic differences in read depth and selection threshold when comparing allele frequencies between cases and controls. We propose a novel likelihood-based

SUBMITTER: Derkach A 

PROVIDER: S-EPMC4103600 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature