Abstract
While genetic relatedness, usually manifested as segments identical by descent (IBD), is ubiquitous in modern large biobanks, current IBD detection methods are not efficient at such a scale. Here, we describe an efficient method, RaPID, for detecting IBD segments in a panel with phased haplotypes. RaPID achieves a time and space complexity linear to the input size and the number of reported IBDs. With simulation, we showed that RaPID is orders of magnitude faster than existing methods while offering competitive power and accuracy. In UK Biobank, RaPID identified 3,335,807 IBDs with a length ≥ 10 cM among 223,507 male X chromosomes in 11 min.
Highlights
In the era of precision medicine, very large genotyped cohorts (VLGCs) with rich phenotype information are becoming available
positional Burrows-Wheeler transform (PBWT) [16] very efficiently finds all exact matches of subsequences at the same locations in different haplotypes with a length greater than L, where L is the length of the match in terms of the number of variant sites
The random projection with PBWT is a general scheme of translating the high-resolution sequences into multiple low-resolution ones, and the approximate highresolution match can be translated into high probability low-resolution exact matches
Summary
In the era of precision medicine, very large genotyped cohorts (VLGCs) with rich phenotype information are becoming available. Unlike traditional cohorts, these cohorts contain up to 0.1–1% of an entire large modern population. These cohorts contain up to 0.1–1% of an entire large modern population At this scale, genetic relatedness among samples is ubiquitous. This is well observed in real cohort data [1, 2], recently supported by a theoretical analysis [3] and by a recent high-profile paper on long-range genealogical search [4]. A unique strength of IBD compared to other population genetics measures is its efficiency for tracking distant relatives.
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