High-Resolution Detection of Identity by Descent in Unrelated Individuals
High-Resolution Detection of Identity by Descent in Unrelated Individuals
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DOI：
10.1016/j.ajhg.2010.02.021
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发表时间：
2010-04-09
影响因子：
9.8
通讯作者：
Browning, Brian L.
中科院分区：
文献类型：
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作者：
Browning, Sharon R.;Browning, Brian L.
在群体样本中检测最近的血统同一性（IBD）对于基于群体的连锁作图以及高度准确的基因型插补和单倍型阶段推断是重要的。我们提出了一种检测人群样本中近期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，我们的方法可以检测到的长度为2厘米的片段与中等功率和可以忽略不计的错误发现率在II lumina 550 K数据在西北欧。我们将我们的方法与GERMLINE和PUNK进行比较，我们表明我们的方法具有明显优于这些现有方法的分辨率水平，从而扩展了最近IBD在高密度SNP数据分析中的实用性。我们调查了欧洲血统的英国个体样本中的四个基因组区域，发现平均而言，在给定的位置，我们的方法在II lumina 550K数据中每10，000对个体中检测到2.7个IBD。我们还提出了方法和结果检测纯合性的血统（HBD）和调查的全基因组样本中的1373个英国人的欧洲血统。我们在给定的位置平均每10，000人中检测到4.7个HBD。我们的方法在免费提供的BEAGLE软件包中实现。
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 II lumina 550K data in Northwestern Europeans. We compare our method with GERMLINE and PUNK, 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 II lumina 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.