Detection of Identical-By-Descent (IBD) segments provides a fundamental measure of genetic relatedness and plays a key role in a wide range of analyses. We develop FastSMC, an IBD detection algorithm that combines a fast heuristic search with accurate coalescent-based likelihood calculations. FastSMC enables biobank-scale detection and dating of IBD segments within several thousands of years in the past. We apply FastSMC to 487,409 UK Biobank samples and detect ~214 billion IBD segments transmitted by shared ancestors within the past 1500 years, obtaining a fine-grained picture of genetic relatedness in the UK. Sharing of common ancestors strongly correlates with geographic distance, enabling the use of genomic data to localize a sample’s birth coordinates with a median error of 45 km. We seek evidence of recent positive selection by identifying loci with unusually strong shared ancestry and detect 12 genome-wide significant signals. We devise an IBD-based test for association between phenotype and ultra-rare loss-of-function variation, identifying 29 association signals in 7 blood-related traits.

血统相同 (IBD) 片段的检测提供了遗传相关性的基本测量，并在广泛的分析中发挥着关键作用。我们开发了 FastSMC，这是一种 IBD 检测算法，它将快速启发式搜索与精确的基于合并的似然计算相结合。 FastSMC 能够对过去几千年的 IBD 片段进行生物样本库规模的检测和年代测定。我们将 FastSMC 应用到 487,409 个英国生物库样本中，检测到过去 1500 年间由共同祖先传播的约 2140 亿个 IBD 片段，从而获得了英国遗传相关性的精细图景。共同祖先的共享与地理距离密切相关，因此可以使用基因组数据来定位样本的出生坐标，中位误差为 45 公里。我们通过识别具有异常强烈的共同祖先的基因座来寻找最近正选择的证据，并检测 12 个全基因组显着信号。我们设计了一种基于 IBD 的测试，用于检测表型与极其罕见的功能丧失变异之间的关联，识别出 7 个血液相关性状中的 29 个关联信号。