Abstract:
: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.
journal_name
Nat Communjournal_title
Nature communicationsauthors
Nait Saada J,Kalantzis G,Shyr D,Cooper F,Robinson M,Gusev A,Palamara PFdoi
10.1038/s41467-020-19588-xsubject
Has Abstractpub_date
2020-11-30 00:00:00pages
6130issue
1issn
2041-1723pii
10.1038/s41467-020-19588-xjournal_volume
11pub_type
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