Department of Statistics, University of Auckland, Auckland, New Zealand.
Am J Hum Genet. 2010 Apr 9;86(4):526-39. doi: 10.1016/j.ajhg.2010.02.021. Epub 2010 Mar 18.
Detection of recent identity by descent (IBD) in population samples is important for population-based linkage mapping and for highly accurate genotype imputation and haplotype-phase inference. We present a method for detection of recent IBD in population samples. Our method accounts for linkage disequilibrium between SNPs to enable full use of high-density SNP data. We find that our method can detect segments of a length of 2 cM with moderate power and negligible false discovery rate in Illumina 550K data in Northwestern Europeans. We compare our method with GERMLINE and PLINK, and we show that our method has a level of resolution that is significantly better than these existing methods, thus extending the usefulness of recent IBD in analysis of high-density SNP data. We survey four genomic regions in a sample of UK individuals of European descent and find that on average, at a given location, our method detects IBD in 2.7 per 10,000 pairs of individuals in Illumina 550K data. We also present methodology and results for detection of homozygosity by descent (HBD) and survey the whole genome in a sample of 1373 UK individuals of European descent. We detect HBD in 4.7 individuals per 10,000 on average at a given location. Our methodology is implemented in the freely available BEAGLE software package.
检测群体样本中的近期同源(IBD)对于基于群体的连锁映射以及高度准确的基因型推断和单倍型相位推断非常重要。我们提出了一种用于检测群体样本中近期 IBD 的方法。我们的方法考虑了 SNP 之间的连锁不平衡,以充分利用高密度 SNP 数据。我们发现,我们的方法可以在北欧人群的 Illumina 550K 数据中以中等功率和可忽略的假发现率检测到 2cM 长度的片段。我们将我们的方法与 GERMLINE 和 PLINK 进行了比较,并表明我们的方法具有显著优于这些现有方法的分辨率水平,从而扩展了近期 IBD 在高密度 SNP 数据分析中的用途。我们在一个具有欧洲血统的英国个体样本中调查了四个基因组区域,发现平均而言,在给定位置,我们的方法在 Illumina 550K 数据中检测到每 10000 对个体中有 2.7 对 IBD。我们还提出了用于检测同源性纯合(HBD)的方法,并在 1373 名具有欧洲血统的英国个体样本中调查了整个基因组。我们在给定位置平均检测到每 10000 个人中有 4.7 个人的 HBD。我们的方法已在免费提供的 BEAGLE 软件包中实现。