title: A POWERFUL METHOD FOR INCLUDING GENOTYPE UNCERTAINTY IN TESTS OF HARDY-WEINBERG EQUILIBRIUM.
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.
authors.affiliation: Department of Biostatistics, University of Michigan, Ann Arbor, MI, 48109, USA, beckandy@umich.edu.
authors.forename: Andrew
authors.initials: A
authors.lastname: Beck
authors.forename: Alexander
authors.initials: A
authors.lastname: Luedtke
authors.forename: Keli
authors.initials: K
authors.lastname: Liu
authors.forename: Nathan
authors.initials: N
authors.lastname: Tintle
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D005787:Gene Frequency; D015894:Genome, Human; D005838:Genotype; D006801:Humans; D016013:Likelihood Functions; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide; D011336:Probability; D035501:Uncertainty