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Activity Number: 218 - Statistical Advances in the Design and Analysis of Sequence-Based Genetic Association Studies
Type: Invited
Date/Time: Monday, July 30, 2018 : 2:00 PM to 3:50 PM
Sponsor: Section on Statistics in Genomics and Genetics
Abstract #326842
Title: On the Design of Sequence-Based Case-Control Studies with External Controls
Author(s): Debashree Ray* and Pranav Yajnik and Michael Lee Boehnke
Companies: Johns Hopkins University and University of Michigan and University of Michigan
Keywords: Case-control study; External controls; Experimental design; Low-frequency variants; Sequence-based GWAS; Trend test

There is a growing evidence of the role of low-frequency and rare genetic variants in complex disease etiology. With improvements in sequencing technologies, genome-wide association studies (GWAS) are now focusing on associations of both common and low-frequency genetic variants with complex traits. However, a case-control GWAS requires a large number of deeply sequenced individuals to detect disease-associated low-frequency/rare variants that still remains prohibitively expensive. Of late, there has been an increased interest in expanding sample size by augmenting a case-control GWAS with deeply sequenced individuals from other studies (at no added sequencing cost) as controls (referred to as 'external controls'). Here, we explore questions of optimal experimental design when external controls (with poor or no information on disease status) are added to an internal case-control sample (with carefully phenotyped disease status). We also discuss benefits of including more internal controls when systematic allele frequency differences exist between internal and external datasets (occurs when internal and external samples are poorly matched or are sequenced/processed separately).

Authors who are presenting talks have a * after their name.

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