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Inferring the ancestry of parents and grandparents from genetic data

Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction. However, this is rarely the case in real data. In this paper we show that the distribution of admixtur...

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Autores principales: Pei, Jingwen, Zhang, Yiming, Nielsen, Rasmus, Wu, Yufeng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449501/
https://www.ncbi.nlm.nih.gov/pubmed/32797037
http://dx.doi.org/10.1371/journal.pcbi.1008065
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author Pei, Jingwen
Zhang, Yiming
Nielsen, Rasmus
Wu, Yufeng
author_facet Pei, Jingwen
Zhang, Yiming
Nielsen, Rasmus
Wu, Yufeng
author_sort Pei, Jingwen
collection PubMed
description Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction. However, this is rarely the case in real data. In this paper we show that the distribution of admixture tract lengths in a genome contains information about the admixture proportions of the ancestors of an individual. We develop a Hidden Markov Model (HMM) framework for estimating the admixture proportions of the immediate ancestors of an individual, i.e. a type of decomposition of an individual’s admixture proportions into further subsets of ancestral proportions in the ancestors. Based on a genealogical model for admixture tracts, we develop an efficient algorithm for computing the sampling probability of the genome from a single individual, as a function of the admixture proportions of the ancestors of this individual. This allows us to perform probabilistic inference of admixture proportions of ancestors only using the genome of an extant individual. We perform extensive simulations to quantify the error in the estimation of ancestral admixture proportions under various conditions. To illustrate the utility of the method, we apply it to real genetic data.
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spelling pubmed-74495012020-09-02 Inferring the ancestry of parents and grandparents from genetic data Pei, Jingwen Zhang, Yiming Nielsen, Rasmus Wu, Yufeng PLoS Comput Biol Research Article Inference of admixture proportions is a classical statistical problem in population genetics. Standard methods implicitly assume that both parents of an individual have the same admixture fraction. However, this is rarely the case in real data. In this paper we show that the distribution of admixture tract lengths in a genome contains information about the admixture proportions of the ancestors of an individual. We develop a Hidden Markov Model (HMM) framework for estimating the admixture proportions of the immediate ancestors of an individual, i.e. a type of decomposition of an individual’s admixture proportions into further subsets of ancestral proportions in the ancestors. Based on a genealogical model for admixture tracts, we develop an efficient algorithm for computing the sampling probability of the genome from a single individual, as a function of the admixture proportions of the ancestors of this individual. This allows us to perform probabilistic inference of admixture proportions of ancestors only using the genome of an extant individual. We perform extensive simulations to quantify the error in the estimation of ancestral admixture proportions under various conditions. To illustrate the utility of the method, we apply it to real genetic data. Public Library of Science 2020-08-14 /pmc/articles/PMC7449501/ /pubmed/32797037 http://dx.doi.org/10.1371/journal.pcbi.1008065 Text en © 2020 Pei et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Pei, Jingwen
Zhang, Yiming
Nielsen, Rasmus
Wu, Yufeng
Inferring the ancestry of parents and grandparents from genetic data
title Inferring the ancestry of parents and grandparents from genetic data
title_full Inferring the ancestry of parents and grandparents from genetic data
title_fullStr Inferring the ancestry of parents and grandparents from genetic data
title_full_unstemmed Inferring the ancestry of parents and grandparents from genetic data
title_short Inferring the ancestry of parents and grandparents from genetic data
title_sort inferring the ancestry of parents and grandparents from genetic data
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449501/
https://www.ncbi.nlm.nih.gov/pubmed/32797037
http://dx.doi.org/10.1371/journal.pcbi.1008065
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