Document Type

Conference Proceeding

Publication Date

1-2017

Department

Mathematics, Statistics, and Computer Science

Keywords

Hardy-Weinberg formula, probabilities, multiple imputation, statistical hypothesis testing

Abstract

The use of posterior probabilities to summarize genotype uncertainty is pervasive across genotype, sequencing and imputation platforms. Prior work in many contexts has shown the utility of incorporating genotype uncertainty (posterior probabilities) in downstream statistical tests. Typical approaches to incorporating genotype uncertainty when testing Hardy-Weinberg equilibrium tend to lack calibration in the type I error rate, especially as genotype uncertainty increases. We propose a new approach in the spirit of genomic control that properly calibrates the type I error rate, while yielding improved power to detect deviations from Hardy-Weinberg Equilibrium. We demonstrate the improved performance of our method on both simulated and real genotypes.

Comments

Presented at the 2017 Pacific Symposium on Biocomputing, held on the Big Island of Hawaii, January 3-7, 2017.

Source Publication Title

Proceedings of the Pacific Symposium on Biocomputing

Publisher

World Scientific Publishing Company

Volume

22

First Page

368

DOI

10.1142/9789813207813_0035

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