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There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control…

We consider applying Bayesian Variable Selection Regression, or BVSR, to genome-wide association studies and similar large-scale regression problems. Currently, typical genome-wide association studies measure hundreds of thousands, or…

Polygenic risk score (PRS) analysis is a powerful method been used to estimate an individual's genetic risk towards targeted traits. PRS analysis could be used to obtain evidence of a genetic effect beyond Genome-Wide Association Studies…

In this paper we have proposed a model for the distribution of allelic probabilities for generating populations as reliably as possible. Our objective was to develop such a model which would allow simulating allelic probabilities with…

We present an alternative method for genome-wide association studies (GWAS) that is more powerful than the regular GWAS method for locus detection. The regular GWAS method suffers from a substantial multiple-testing burden because of the…

Code-switching (CSW) is a common phenomenon among multilingual speakers where multiple languages are used in a single discourse or utterance. Mixed language utterances may still contain grammatical errors however, yet most existing Grammar…

Replication helps ensure that a genotype-phenotype association observed in a genome-wide association (GWA) study represents a credible association and is not a chance finding or an artifact due to uncontrolled biases. We discuss…

The Population Stability Index (PSI) is a widely used measure in credit risk modeling and monitoring within the banking industry. Its purpose is to monitor for changes in the population underlying a model, such as a scorecard, to ensure…

The paramount importance of replicating associations is well recognized in the genome-wide associaton (GWA) research community, yet methods for assessing replicability of associations are scarce. Published GWA studies often combine…

PLINK 1 is a widely used open-source C/C++ toolset for genome-wide association studies (GWAS) and research in population genetics. However, the steady accumulation of data from imputation and whole-genome sequencing studies has exposed a…

Recent advances and reflections on reproducible human neuroscience, especially brain-wide association studies (BWAS) leveraging large datasets, have led to divergent and sometimes opposing views on research practices and priorities. The…

Assessing the statistical power to detect susceptibility variants plays a critical role in GWA studies both from the prospective and retrospective points of view. Power is empirically estimated by simulating phenotypes under a disease model…

In this paper, we investigate the impact of high-dimensional Principal Component (PC) adjustments on inferring the effects of variables on outcomes, with a focus on applications in genetic association studies where PC adjustment is commonly…

Motivated by the inquiries of weak signals in underpowered genome-wide association studies (GWASs), we consider the problem of retaining true signals that are not strong enough to be individually separable from a large amount of noise. We…

Joint analysis of multiple phenotypes can increase statistical power in genetic association studies. Principal component analysis, as a popular dimension reduction method, especially when the number of phenotypes is high-dimensional, has…

Bayesian modeling helps applied researchers articulate assumptions about their data and develop models tailored for specific applications. Thanks to good methods for approximate posterior inference, researchers can now easily build, use,…

Under complete linkage disequilibrium (LD), robust tests often have greater power than Pearson's chi-square test and trend tests for the analysis of case-control genetic association studies. Robust statistics have been used in…

Inference of population structure from genetic data plays an important role in population and medical genetics studies. With the advancement and decreasing cost of sequencing technology, the increasingly available whole genome sequencing…

Collection of genotype data in case-control genetic association studies may often be incomplete for reasons related to genes themselves. This non-ignorable missingness structure, if not appropriately accounted for, can result in…

Testing the association between a phenotype and many genetic variants from case-control data is essential in genome-wide association study (GWAS). This is a challenging task as many such variants are correlated or non-informative.…