RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts

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. R...

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Detalles Bibliográficos
Autores principales: Naseri, Ardalan, Liu, Xiaoming, Tang, Kecong, Zhang, Shaojie, Zhi, Degui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6659282/
https://www.ncbi.nlm.nih.gov/pubmed/31345249
http://dx.doi.org/10.1186/s13059-019-1754-8
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author Naseri, Ardalan
Liu, Xiaoming
Tang, Kecong
Zhang, Shaojie
Zhi, Degui
author_facet Naseri, Ardalan
Liu, Xiaoming
Tang, Kecong
Zhang, Shaojie
Zhi, Degui
author_sort Naseri, Ardalan
collection PubMed
description 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 method while offering competitive power and accuracy. In UK Biobank, RaPID identified 3,335,807 IBDs with a lenght ≥ 10 cM among 223,507 male X chromosomes in 11 min. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1754-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-66592822019-08-01 RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts Naseri, Ardalan Liu, Xiaoming Tang, Kecong Zhang, Shaojie Zhi, Degui Genome Biol Method 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 method while offering competitive power and accuracy. In UK Biobank, RaPID identified 3,335,807 IBDs with a lenght ≥ 10 cM among 223,507 male X chromosomes in 11 min. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s13059-019-1754-8) contains supplementary material, which is available to authorized users. BioMed Central 2019-07-25 /pmc/articles/PMC6659282/ /pubmed/31345249 http://dx.doi.org/10.1186/s13059-019-1754-8 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Naseri, Ardalan
Liu, Xiaoming
Tang, Kecong
Zhang, Shaojie
Zhi, Degui
RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
title RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
title_full RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
title_fullStr RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
title_full_unstemmed RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
title_short RaPID: ultra-fast, powerful, and accurate detection of segments identical by descent (IBD) in biobank-scale cohorts
title_sort rapid: ultra-fast, powerful, and accurate detection of segments identical by descent (ibd) in biobank-scale cohorts
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6659282/
https://www.ncbi.nlm.nih.gov/pubmed/31345249
http://dx.doi.org/10.1186/s13059-019-1754-8
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