Many Phenotypes Without Many False Discoveries: Error Controlling Strategies for Multitrait Association Studies
ABSTRACT
The genetic basis of multiple phenotypes such as gene expression, metabolite levels, or imaging features is often investigated by testing a large collection of hypotheses, probing the existence of association between each of the traits and hundreds of thousands of genotyped variants. Appropriate multiplicity adjustment is crucial to guarantee replicability of findings, and the false discovery rate (FDR) is frequently adopted as a measure of global error. In the interest of interpretability, results are often summarized so that reporting focuses on variants discovered to be associated to some phenotypes. We show th...
Source: Genetic Epidemiology - December 1, 2015 Category: Epidemiology Authors: Christine B. Peterson, Marina Bogomolov, Yoav Benjamini, Chiara Sabatti Tags: Research Article Source Type: research
Issue Information
(Source: Genetic Epidemiology)
Source: Genetic Epidemiology - November 16, 2015 Category: Epidemiology Tags: Issue Information Source Type: research
Multiple SNP Set Analysis for Genome‐Wide Association Studies Through Bayesian Latent Variable Selection
ABSTRACT
The power of genome‐wide association studies (GWAS) for mapping complex traits with single‐SNP analysis (where SNP is single‐nucleotide polymorphism) may be undermined by modest SNP effect sizes, unobserved causal SNPs, correlation among adjacent SNPs, and SNP‐SNP interactions. Alternative approaches for testing the association between a single SNP set and individual phenotypes have been shown to be promising for improving the power of GWAS. We propose a Bayesian latent variable selection (BLVS) method to simultaneously model the joint association mapping between a large number of SNP sets and complex trai...
Source: Genetic Epidemiology - October 30, 2015 Category: Epidemiology Authors: Zhao‐Hua Lu, Hongtu Zhu, Rebecca C. Knickmeyer, Patrick F. Sullivan, Stephanie N. Williams, Fei Zou, Tags: Research Article Source Type: research
Successful Replication of GWAS Hits for Multiple Sclerosis in 10,000 Germans Using the Exome Array
ABSTRACT
Genome‐wide association studies (GWAS) successfully identified various chromosomal regions to be associated with multiple sclerosis (MS). The primary aim of this study was to replicate reported associations from GWAS using an exome array in a large German study. German MS cases (n = 4,476) and German controls (n = 5,714) were genotyped using the Illumina HumanExome v1‐Chip. Genotype calling was performed with the Illumina Genome StudioTM Genotyping Module, followed by zCall. Single‐nucleotide polymorphisms (SNPs) in seven regions outside the human leukocyte antigen (HLA) region showed genome‐wide significa...
Source: Genetic Epidemiology - October 27, 2015 Category: Epidemiology Authors: Theresa Dankowski, Dorothea Buck, Till F. M. Andlauer, Gisela Antony, Antonios Bayas, Lukas Bechmann, Achim Berthele, Thomas Bettecken, Andrew Chan, Andre Franke, Ralf Gold, Christiane Graetz, Jürgen Haas, Michael Hecker, Stefan Herms, Carmen Infante‐D Tags: Research Article Source Type: research
Genetic Variants Influencing Joint Damage in Mexican Americans and European Americans With Rheumatoid Arthritis
ABSTRACT
Joint destruction in rheumatoid arthritis (RA) is heritable, but knowledge on specific genetic determinants of joint damage in RA is limited. We have used the Immunochip array to examine whether genetic variants influence variation in joint damage in a cohort of Mexican Americans (MA) and European Americans (EA) with RA. We studied 720 MA and 424 EA patients with RA. Joint damage was quantified using a radiograph of both hands and wrists, scored using Sharp's technique. We conducted association analyses with the transformed Sharp score and the Immunochip single nucleotide polymorphism (SNP) data using PLINK. In MA...
Source: Genetic Epidemiology - October 26, 2015 Category: Epidemiology Authors: Rector Arya, Inmaculada del Rincon, Vidya S. Farook, Jose F Restrepo, Diedre A Winnier, Marcel J Fourcaudot, Daniel F Battafarano, Marcio Almeida, Satish Kumar, Joanne E Curran, Christopher P. Jenkinson, John Blangero, Ravindranath Duggirala, Agustin Esca Tags: Research Article Source Type: research
