Spatial Localization of Recent Ancestors for Admixed Individuals

Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over nonmodel-bas...

Full description

Bibliographic Details
Main Authors:	Yang, Wen-Yun, Platt, Alexander, Chiang, Charleston Wen-Kai, Eskin, Eleazar, Novembre, John, Pasaniuc, Bogdan
Format:	Online
Language:	English
Published:	Genetics Society of America 2014
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267945/

id	pubmed-4267945
recordtype	oai_dc
spelling	pubmed-42679452014-12-23 Spatial Localization of Recent Ancestors for Admixed Individuals Yang, Wen-Yun Platt, Alexander Chiang, Charleston Wen-Kai Eskin, Eleazar Novembre, John Pasaniuc, Bogdan Investigations Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over nonmodel-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum. We devise efficient algorithms based on hidden Markov models to localize on a map the recent ancestors (e.g., grandparents) of admixed individuals, joint with assigning ancestry at each locus in the genome. We validate our methods by using empirical data from individuals with mixed European ancestry from the Population Reference Sample study and show that our approach is able to localize their recent ancestors within an average of 470 km of the reported locations of their grandparents. Furthermore, simulations from real Population Reference Sample genotype data show that our method attains high accuracy in localizing recent ancestors of admixed individuals in Europe (an average of 550 km from their true location for localization of two ancestries in Europe, four generations ago). We explore the limits of ancestry localization under our approach and find that performance decreases as the number of distinct ancestries and generations since admixture increases. Finally, we build a map of expected localization accuracy across admixed individuals according to the location of origin within Europe of their ancestors. Genetics Society of America 2014-11-03 /pmc/articles/PMC4267945/ /pubmed/25371484 http://dx.doi.org/10.1534/g3.114.014274 Text en Copyright © 2014 Yang et al. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution Unported License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Yang, Wen-Yun Platt, Alexander Chiang, Charleston Wen-Kai Eskin, Eleazar Novembre, John Pasaniuc, Bogdan
spellingShingle	Yang, Wen-Yun Platt, Alexander Chiang, Charleston Wen-Kai Eskin, Eleazar Novembre, John Pasaniuc, Bogdan Spatial Localization of Recent Ancestors for Admixed Individuals
author_facet	Yang, Wen-Yun Platt, Alexander Chiang, Charleston Wen-Kai Eskin, Eleazar Novembre, John Pasaniuc, Bogdan
author_sort	Yang, Wen-Yun
title	Spatial Localization of Recent Ancestors for Admixed Individuals
title_short	Spatial Localization of Recent Ancestors for Admixed Individuals
title_full	Spatial Localization of Recent Ancestors for Admixed Individuals
title_fullStr	Spatial Localization of Recent Ancestors for Admixed Individuals
title_full_unstemmed	Spatial Localization of Recent Ancestors for Admixed Individuals
title_sort	spatial localization of recent ancestors for admixed individuals
description	Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over nonmodel-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum. We devise efficient algorithms based on hidden Markov models to localize on a map the recent ancestors (e.g., grandparents) of admixed individuals, joint with assigning ancestry at each locus in the genome. We validate our methods by using empirical data from individuals with mixed European ancestry from the Population Reference Sample study and show that our approach is able to localize their recent ancestors within an average of 470 km of the reported locations of their grandparents. Furthermore, simulations from real Population Reference Sample genotype data show that our method attains high accuracy in localizing recent ancestors of admixed individuals in Europe (an average of 550 km from their true location for localization of two ancestries in Europe, four generations ago). We explore the limits of ancestry localization under our approach and find that performance decreases as the number of distinct ancestries and generations since admixture increases. Finally, we build a map of expected localization accuracy across admixed individuals according to the location of origin within Europe of their ancestors.
publisher	Genetics Society of America
publishDate	2014
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267945/
_version_	1613168119463804928

Spatial Localization of Recent Ancestors for Admixed Individuals

Similar Items