Related papers: Fast Genome-Wide QTL Analysis Using Mendel
The widely used genetic pleiotropic analysis of multiple phenotypes are often designed for examining the relationship between common variants and a few phenotypes. They are not suited for both high dimensional phenotypes and high…
Annotations of gene structures and regulatory elements can inform genome-wide association studies (GWAS). However, choosing the relevant annotations for interpreting an association study of a given trait remains challenging. We describe a…
Admixture mapping is a popular tool to identify regions of the genome associated with traits in a recently admixed population. Existing methods have been developed primarily for identification of a single locus influencing a dichotomous…
In many scientific and engineering applications, one has to solve not one but a sequence of instances of the same problem. Often times, the problems in the sequence are linked in a way that allows intermediate results to be reused. A…
Imputation using external reference panels is a widely used approach for increasing power in GWAS and meta-analysis. Existing HMM-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian…
Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms…
Clinical adoption of human genome sequencing requires methods with known accuracy of genotype calls at millions or billions of positions across a genome. Previous work showing discordance amongst sequencing methods and algorithms has made…
The recent development of artificial intelligence (AI) technology, especially the advance of deep neural network (DNN) technology, has revolutionized many fields. While DNN plays a central role in modern AI technology, it has been rarely…
Mendelian randomization uses genetic variants to make causal inferences about the effect of a risk factor on an outcome. With fine-mapped genetic data, there may be hundreds of genetic variants in a single gene region any of which could be…
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation…
Combining data from several case-control genome-wide association (GWA) studies can yield greater efficiency for detecting associations of disease with single nucleotide polymorphisms (SNPs) than separate analyses of the component studies.…
Genome-wide association studies (GWAS) have been widely used to examine the association between single nucleotide polymorphisms (SNPs) and complex traits, where both the sample size n and the number of SNPs p can be very large. Recently,…
Because of the recent advances of genome sequences, a large number of human genome sequences are available for the study of human genetics. Genome-wide association studies typically focus on associations between single-nucleotide…
In genetic association studies, detecting phenotype-genotype association is a primary goal. We assume that the relationship between the data -phenotype, genetic markers and environmental covariates - can be modelled by a generalized linear…
Given the complexity of genetic risk prediction, there is a critical need for the development of novel methodologies that can effectively capture intricate genotype--phenotype relationships (e.g., nonlinear) while remaining statistically…
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…
Motivation: The availability of thousands of invidual genomes of one species should boost rapid progress in personalized medicine or understanding of the interaction between genotype and phenotype, to name a few applications. A key…
The aim of this paper is to propose a novel estimation method of using genetic-predicted observations to estimate trans-ancestry genetic correlations, which describes how genetic architecture of complex traits varies among populations, in…
Next generation sequencing technology rapidly produces massive volume of data and quality control of this sequencing data is essential to any genomic analysis. Here we present MEEPTOOLS, which is a collection of open-source tools based on…
In order to associate complex traits with genetic polymorphisms, genome-wide association studies process huge datasets involving tens of thousands of individuals genotyped for millions of polymorphisms. When handling these datasets, which…