A hybrid bayesian approach for genome-wide association studies on related individuals

Bioinformatics
A Yazdani, D B Dunson

Abstract

Both single marker and simultaneous analysis face challenges in GWAS due to the large number of markers genotyped for a small number of subjects. This large p small n problem is particularly challenging when the trait under investigation has low heritability. In this article, we propose a two-stage approach that is a hybrid method of single and simultaneous analysis designed to improve genomic prediction of complex traits. In the first stage, we use a Bayesian independent screening method to select the most promising SNPs. In the second stage, we rely on a hierarchical model to analyze the joint impact of the selected markers. The model is designed to take into account familial dependence in the different subjects, while using local-global shrinkage priors on the marker effects. We evaluate the performance in simulation studies, and consider an application to animal breeding data. The illustrative data analysis reveals an encouraging result in terms of prediction performance and computational cost. Akram.Yazdani@uth.tmc.edu Supplementary data are available at Bioinformatics online.

References

Apr 28, 2007·Science·UNKNOWN Diabetes Genetics Initiative of Broad Institute of Harvard and MIT, Lund University, and Novartis Institutes of BioMedical RShaun Purcell
Jun 8, 2007·Nature·UNKNOWN Wellcome Trust Case Control Consortium
Apr 9, 2008·Nature Genetics·Michael N WeedonTimothy M Frayling
Apr 18, 2008·Bioinformatics·Bo Peng, Christopher I Amos
Jul 26, 2008·PLoS Genetics·Clive J HoggartDavid J Balding
Jan 1, 2008·Journal of the Royal Statistical Society. Series B, Statistical Methodology·Hao Helen Zhang
Jul 22, 2009·Genetics·Daniel GianolaRohan Fernando
Aug 8, 2009·Science·Edward S BucklerMichael D McMullen
Sep 19, 2009·Nature Reviews. Genetics·Matthew Stephens, David J Balding
Sep 29, 2009·Annals of Statistics·Larry Wasserman, Kathryn Roeder
Apr 3, 2010·Proceedings of the National Academy of Sciences of the United States of America·Haiyan HuangXianghong Jasmine Zhou
Dec 16, 2010·Bioinformatics·Jiahan LiRongling Wu
May 28, 2011·BMC Bioinformatics·Xiaodong CaiShizhong Xu
May 30, 2012·BMC Proceedings·Mohammad M ShariatiLuc Janss
Jan 31, 2014·Statistica Sinica·Artin ArmaganJaeyong Lee
Feb 7, 2014·Bioinformatics·David C KesslerDavid B Dunson

❮ Previous
Next ❯

Citations

Feb 2, 2016·Journal of Biomedical Informatics·Azam YazdaniEric Boerwinkle
Jun 23, 2016·Metabolomics : Official Journal of the Metabolomic Society·Azam YazdaniEric Boerwinkle
Nov 16, 2017·Statistical Applications in Genetics and Molecular Biology·Christopher McMahanBens Pardamean

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.