基于单核苷酸多态性数据协方差的贝叶斯方法，用于检测个体群体间连锁不平衡模式的差异。
A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.
机构信息
Department of Epidemiology and Public Health, London School of Hygiene and Tropical Medicine, London, UK.
出版信息
Bioinformatics. 2010 Aug 15;26(16):1999-2003. doi: 10.1093/bioinformatics/btq327. Epub 2010 Jun 16.
MOTIVATION
Quantifying differences in linkage disequilibrium (LD) between sub-groups can highlight genetic regions or sites under selection and/or associated with disease, and may have utility in trans-ethnic mapping studies.
RESULTS
We present a novel pseudo Bayes factor (PBF) approach that assess differences in covariance of genotype frequencies from single nucleotide polymorphism (SNP) data from a genome-wide study. The magnitude of the PBF reflects the strength of evidence for a difference, while accounting for the sample size and number of SNPs, without the requirement for permutation testing to establish statistical significance. Application of the PBF to HapMap and Gambian malaria SNP data reveals regional LD differences, some known to be under selection.
AVAILABILITY AND IMPLEMENTATION
The PBF approach has been implemented in the BALD (Bayesian analysis of LD differences) C++ software, and is available from http://homepages.lshtm.ac.uk/tgclark/downloads.
动机
量化亚组间连锁不平衡（LD）的差异可以突出受选择和/或与疾病相关的遗传区域或位点，并且在跨种族映射研究中可能具有实用性。
结果
我们提出了一种新的伪贝叶斯因子（PBF）方法，该方法可评估来自全基因组研究中单核苷酸多态性（SNP）数据的基因型频率协方差的差异。PBF 的幅度反映了对差异的证据强度，同时考虑了样本量和 SNP 数量，而无需进行置换检验来确定统计显著性。将 PBF 应用于 HapMap 和冈比亚疟疾 SNP 数据揭示了区域 LD 差异，其中一些已知受到选择。
可及性和实现
PBF 方法已在 BALD（LD 差异的贝叶斯分析）C++软件中实现，并可从 http://homepages.lshtm.ac.uk/tgclark/downloads 获得。
Zotero 插件