Shrinkage estimation for robust and efficient screening of single-SNP association from case-control genome-wide association studies.

ABSTRACT: Population-based case-control design has become one of the most popular approaches for conducting genome-wide association scans for rare diseases like cancer. In this article, we propose a novel method for improving the power of the widely used single-single-nucleotide polymorphism (SNP) two-degrees-of-freedom (2 d.f.) association test for case-control studies by exploiting the common assumption of Hardy-Weinberg Equilibrium (HWE) for the underlying population. A key feature of the method is that it can relax the assumed model constraints via a completely data-adaptive shrinkage estimation approach so that the number of false-positive results due to the departure of HWE is controlled. The method is computationally simple and is easily scalable to association tests involving hundreds of tho

SUBMITTER: Luo S 

PROVIDER: S-EPMC3103068 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature