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.

Details

Title
RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
Author
Ardalan Naseri; Liu, Xiaoming; Tang, Kecong; Zhang, Shaojie; Degui Zhi
Pages
1-15
Section
Method
Publication year
2019
Publication date
2019
Publisher
BioMed Central
ISSN
14747596
e-ISSN
1474760X
Source type
Scholarly Journal
Language of publication
English
DOI
https://doi.org/10.1186/s13059-019-1754-8
ProQuest document ID
3200616313
Copyright
© 2019. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.