𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Inference from genome-wide association studies using a novel Markov model

✍ Scribed by Fay J. Hosking; Jonathan A. C. Sterne; George Davey Smith; Peter J. Green

Publisher
John Wiley and Sons
Year
2008
Tongue
English
Weight
205 KB
Volume
32
Category
Article
ISSN
0741-0395

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

In this paper we propose a Bayesian modeling approach to the analysis of genome‐wide association studies based on single nucleotide polymorphism (SNP) data. Our latent seed model combines various aspects of k‐means clustering, hidden Markov models (HMMs) and logistic regression into a fully Bayesian model. It is fitted using the Markov chain Monte Carlo stochastic simulation method, with Metropolis‐Hastings update steps. The approach is flexible, both in allowing different types of genetic models, and because it can be easily extended while remaining computationally feasible due to the use of fast algorithms for HMMs. It allows for inference primarily on the location of the causal locus and also on other parameters of interest. The latent seed model is used here to analyze three data sets, using both synthetic and real disease phenotypes with real SNP data, and shows promising results. Our method is able to correctly identify the causal locus in examples where single SNP analysis is both successful and unsuccessful at identifying the causal SNP. Genet. Epidemiol. 2008. © 2008 Wiley‐Liss, Inc.

📜 SIMILAR VOLUMES

Using cases to strengthen inference on t
Using cases to strengthen inference on the association between single nucleotide polymorphisms and a secondary phenotype in genome-wide association studies
✍ Huilin Li; Mitchell H. Gail; Sonja Berndt; Nilanjan Chatterjee 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 142 KB 👁 2 views

## Abstract Case‐control genome‐wide association studies provide a vast amount of genetic information that may be used to investigate secondary phenotypes. We study the situation in which the primary disease is rare and the secondary phenotype and genetic markers are dichotomous. An analysis of the

A novel bayesian graphical model for gen
A novel bayesian graphical model for genome-wide multi-SNP association mapping
✍ Yu Zhang 📂 Article 📅 2011 🏛 John Wiley and Sons 🌐 English ⚖ 344 KB 👁 1 views

## Abstract Most disease association mapping algorithms are based on hypothesis testing procedures that test one variant at a time. Those methods lose power when the disease mutations are jointly tagged by multiple variants, or when gene‐gene interaction exist. Nearby variants are also correlated,

Genome-wide association studies using ha
Genome-wide association studies using haplotype clustering with a new haplotype similarity
✍ Lina Jin; Wensheng Zhu; Jianhua Guo 📂 Article 📅 2010 🏛 John Wiley and Sons 🌐 English ⚖ 302 KB

## Abstract Association analysis, with the aim of investigating genetic variations, is designed to detect genetic associations with observable traits, which has played an increasing part in understanding the genetic basis of diseases. Among these methods, haplotype‐based association studies are bel

A novel haplotype-sharing approach for g
A novel haplotype-sharing approach for genome-wide case-control association studies implicates the calpastatin gene in Parkinson's disease
✍ Andrew S. Allen; Glen A. Satten 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 285 KB 👁 2 views

## Abstract The large number of markers considered in a genome‐wide association study (GWAS) has resulted in a simplification of analyses conducted. Most studies are analyzed one marker at a time using simple tests like the trend test. Methods that account for the special features of genetic associ

Association between a variation in LRCH1
Association between a variation in LRCH1 and knee osteoarthritis: A genome-wide single-nucleotide polymorphism association study using DNA pooling
✍ Tim D. Spector; Richard H. Reneland; Steven Mah; Ana M. Valdes; Deborah J. Hart; 📂 Article 📅 2006 🏛 John Wiley and Sons 🌐 English ⚖ 163 KB 👁 1 views

## Abstract ## Objective To perform a large‐scale association analysis of single‐nucleotide polymorphisms (SNPs) in patients with radiographically defined osteoarthritis (OA) of the knee. ## Methods We examined >25,000 SNPs located within ∼14,000 genes for associations with radiographically defi