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Abstract Details

Activity Number: 183
Type: Contributed
Date/Time: Monday, July 30, 2012 : 10:30 AM to 12:20 PM
Sponsor: Section on Statistics in Epidemiology
Abstract - #306591
Title: Two-Stage Extreme Phenotype Sequencing Design for Discovering and Testing Common and Rare Genetic Variants: Efficiency and Power
Author(s): Guolian Kang*+ and Jinbo Chen
Companies: St. Jude Children's Research Hospital and University of Pennsylvania
Address: Department of Biostatistics, Memphis, TN, 38105, United States
Keywords: Two-stage design ; Next-generation sequencing ; SNP discovery ; Rare variants
Abstract:

Next-generation sequencing technology provides an unprecedented opportunity to identify rare susceptibility variants. A two-stage design has been advocated to be a practical option. In stage I, variants are discovered by sequencing the whole genomes of a small number of carefully selected individuals. In stage II, the discovered variants of a large number of individuals are genotyped to assess association. Individuals with extreme phenotypes are typically selected in stage I. Using simulated data for unrelated individuals, we explore two important aspects of this two-stage design: the efficiency of discovering common and rare single-nucleotide polymorphisms (SNPs) in stage I and the impact of incomplete SNP discovery in stage I on the power of testing associations in stage II. We apply a sum test and a sum of squared score test for gene-based association analyses evaluating the power of the two-stage design. We obtained that when individuals with trait values more extreme than the 99.7 to 99th quantile are included in stage I, the two-stage design could achieve the same as or even higher power than one-stage design if the rare causal variants have large effect sizes.


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