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本文引用的文献

1
Genome-wide comparisons of variation in linkage disequilibrium.连锁不平衡中变异的全基因组比较。
Genome Res. 2009 Oct;19(10):1849-60. doi: 10.1101/gr.092189.109. Epub 2009 Jun 18.
2
Genome-wide and fine-resolution association analysis of malaria in West Africa.全基因组关联分析和西非疟疾的精细分辨率分析。
Nat Genet. 2009 Jun;41(6):657-65. doi: 10.1038/ng.388. Epub 2009 May 24.
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Power consequences of linkage disequilibrium variation between populations.群体间连锁不平衡变异的幂次后果。
Genet Epidemiol. 2009 Feb;33(2):128-35. doi: 10.1002/gepi.20366.
4
Genome-wide detection and characterization of positive selection in human populations.人类群体中正选择的全基因组检测与特征分析。
Nature. 2007 Oct 18;449(7164):913-8. doi: 10.1038/nature06250.
5
A second generation human haplotype map of over 3.1 million SNPs.一张包含超过310万个单核苷酸多态性的第二代人类单倍型图谱。
Nature. 2007 Oct 18;449(7164):851-61. doi: 10.1038/nature06258.
6
Contrasting linkage-disequilibrium patterns between cases and controls as a novel association-mapping method.将病例组与对照组之间的连锁不平衡模式进行对比，作为一种新型关联定位方法。
Am J Hum Genet. 2006 May;78(5):737-746. doi: 10.1086/503710. Epub 2006 Mar 13.
7
Bayesian logistic regression using a perfect phylogeny.使用完美系统发育的贝叶斯逻辑回归。
Biostatistics. 2007 Jan;8(1):32-52. doi: 10.1093/biostatistics/kxj030. Epub 2006 Mar 23.
8
A fine-scale linkage-disequilibrium measure based on length of haplotype sharing.一种基于单倍型共享长度的精细尺度连锁不平衡度量。
Am J Hum Genet. 2006 Apr;78(4):615-28. doi: 10.1086/502632. Epub 2006 Feb 13.
9
Bayesian spatial modeling of haplotype associations.单倍型关联的贝叶斯空间建模。
Hum Hered. 2003;56(1-3):32-40. doi: 10.1159/000073730.
10
On the identification of disease mutations by the analysis of haplotype similarity and goodness of fit.通过单倍型相似性和拟合优度分析来鉴定疾病突变。
Am J Hum Genet. 2003 Apr;72(4):891-902. doi: 10.1086/373881. Epub 2003 Feb 27.

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.

DOI:10.1093/bioinformatics/btq327
PMID:20554688
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2916719/
Abstract

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.

摘要

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。