False-Negative-Rate Based Approach for Selecting Top Single-Nucleotide Polymorphisms in the First Stage of a Two-Stage Genome-Wide Association Study.

ABSTRACT: Genome-wide association (GWA) studies, where hundreds of thousands of single-nucleotide polymorphisms (SNPs) are tested simultaneously, are becoming popular for identifying disease loci for common diseases. Most commonly, a GWA study involves two stages: the first stage includes testing the association between all SNPs and the disease and the second stage includes replication of SNPs selected from the first stage to validate associations in an independent sample. The first stage is considered to be more fundamental since the second stage is contingent on the results of the first stage. Selection of SNPs from stage one for genotyping in stage two is typically based on an arbitrary threshold or controlling type I errors. These strategies can be inefficient and have potential to exclude genot

SUBMITTER: Huang Z 

PROVIDER: S-EPMC3467022 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature