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Genome-wide association studies(GWAS) have proven to be highly useful in revealing the genetic basis of complex diseases. At present, most GWAS are studies of a particular single disease diagnosis against controls. However, in practice, an…
Genome-wide association studies have become increasingly common due to advances in technology and have permitted the identification of differences in single nucleotide polymorphism (SNP) alleles that are associated with diseases. However,…
Self-supervised pre-training methods have brought remarkable breakthroughs in the understanding of text, image, and speech. Recent developments in genomics has also adopted these pre-training methods for genome understanding. However, they…
The objective of a genome-wide association study (GWAS) is to associate subsequences of individuals' genomes to the observable characteristics called phenotypes (e.g., high blood pressure). Motivated by the GWAS problem, in this paper we…
Genome-wide association study (GWAS) tests single nucleotide polymorphism (SNP) markers across the genome to localize the underlying causal variant of a trait. Because causal variants are seldom observed directly, a surrogate model based on…
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…
Adaptation in response to selection on polygenic phenotypes may occur via subtle allele frequencies shifts at many loci. Current population genomic techniques are not well posed to identify such signals. In the past decade, detailed…
Investigating the genetic architecture of complex diseases is challenging due to the multifactorial and interactive landscape of genomic and environmental influences. Although genome-wide association studies (GWAS) have identified thousands…
Genome-wide association studies (GWAS) provide a means of examining the common genetic variation underlying a range of traits and disorders. In addition, it is hoped that GWAS may provide a means of differentiating affected from unaffected…
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…
Genome-wide association studies (GWAS) have led to the discovery of numerous single nucleotide polymorphisms (SNPs) associated with various phenotypes and complex diseases. However, the identified genetic variants do not fully explain the…
Learning tasks such as those involving genomic data often poses a serious challenge: the number of input features can be orders of magnitude larger than the number of training examples, making it difficult to avoid overfitting, even when…
Since the emergence of genome-wide association studies (GWASs), estimation of the narrow sense heritability explained by common single-nucleotide polymorphisms (SNPs) via linear mixed model approaches became widely used. As in most GWASs,…
Motivation: In spite of great success of genome-wide association studies (GWAS), multiple challenges still remain. First, complex traits are often associated with many single nucleotide polymorphisms (SNPs), each with small or moderate…
The recent explosion of genetic and high dimensional biobank and 'omic' data has provided researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of hundreds to thousands of related phenotypes. However,…
Following the publication of an attack on genome-wide association studies (GWAS) data proposed by Homer et al., considerable attention has been given to developing methods for releasing GWAS data in a privacy-preserving way. Here, we…
Genome Wide Association Studies (GWAS) and eQTL analyses have produced a large and growing number of genetic associations linked to a wide range of human phenotypes. As of 2013, there were more than 11,000 SNPs associated with a trait as…
Genome-wide association studies (GWAS) have achieved great success in the genetic study of Alzheimer's disease (AD). Collaborative imaging genetics studies across different research institutions show the effectiveness of detecting genetic…
When testing for the association of a single SNP with a phenotypic response, one usually considers an additive genetic model, assuming that the mean of of the response for the heterozygous state is the average of the means for the two…
Large case/control Genome-Wide Association Studies (GWAS) often include groups of related individuals with known relationships. When testing for associations at a given locus, current methods incorporate only the familial relationships…