Rapid detection of identity-by-descent tracts for mega-scale datasets

Ruhollah Shemirani, Gillian M. Belbin, Christy L. Avery, Eimear E. Kenny, Christopher R. Gignoux () and José Luis Ambite ()
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Ruhollah Shemirani: University of Southern California
Gillian M. Belbin: Icahn School of Medicine at Mount Sinai
Christy L. Avery: University of North Carolina at Chapel Hill
Eimear E. Kenny: Icahn School of Medicine at Mount Sinai
Christopher R. Gignoux: University of Colorado Anschutz Medical Campus
José Luis Ambite: University of Southern California

Nature Communications, 2021, vol. 12, issue 1, 1-13

Abstract: Abstract The ability to identify segments of genomes identical-by-descent (IBD) is a part of standard workflows in both statistical and population genetics. However, traditional methods for finding local IBD across all pairs of individuals scale poorly leading to a lack of adoption in very large-scale datasets. Here, we present iLASH, an algorithm based on similarity detection techniques that shows equal or improved accuracy in simulations compared to current leading methods and speeds up analysis by several orders of magnitude on genomic datasets, making IBD estimation tractable for millions of individuals. We apply iLASH to the PAGE dataset of ~52,000 multi-ethnic participants, including several founder populations with elevated IBD sharing, identifying IBD segments in ~3 minutes per chromosome compared to over 6 days for a state-of-the-art algorithm. iLASH enables efficient analysis of very large-scale datasets, as we demonstrate by computing IBD across the UK Biobank (~500,000 individuals), detecting 12.9 billion pairwise connections.

Date: 2021
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DOI: 10.1038/s41467-021-22910-w

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