How to Estimate Measurement Error Variance Associated with Ancestry Proportion Estimates

• Activity Number: 252
• Type: Contributed
• Date/Time: Monday, August 2, 2010 : 2:00 PM to 3:50 PM
• Sponsor: Section on Statistics in Epidemiology
• Author(s): Jasmin Divers*+ and David T. Redden and Raymond J. Carrol and David B. Allison
• Companies: Wake Forest University Health Sciences and The University of Alabama at Birmingham and Texas A&M University and The University of Alabama at Birmingham
• Keywords: population stratification ; admixture ; type I error inflation ; power ; measurement error variance ; reliability

Abstract

We show how the measurement error variance (MEV) associated with individual ancestry proportion estimates (IAPEs) can be estimated when the number of ancestral populations is greater than 2. We extend existing internal consistency measures (ICMs) to provide an estimate of the MEV, and compare it with the MEV estimated using the repeated measurements approach (RMA). Both approaches work by dividing the genotyped markers into subsets. We also examine the effect of subset's cardinal and informativeness content on performance. All comparisons are with simulated data. Compared to the RMA, the ICMs provide less biased and more precise estimates. Both methods tend to perform better when a large number of subsets with similar cardinals are used. Our results will facilitate the application of measurement error correction methods in association tests and other genomic research involving IAPEs.