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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Bibliographic Details
Published in:PLoS computational biology 2020-08, Vol.16 (8), p.e1008065-e1008065
Main Authors: Pei, Jingwen, Zhang, Yiming, Nielsen, Rasmus, Wu, Yufeng
Format: Article
Language:English
Subjects:
Algorithms
Biology and Life Sciences
Computer and Information Sciences
Computer science
Computer simulation
Computers
Engineering and Technology
Families & family life
Family relations
Genealogy
Genetic aspects
Genetics
Genomes
Genotype & phenotype
Grandparents
Haplotypes
Markov analysis
Markov chains
Markov processes
Methods
Parents & parenting
Physical sciences
Population
Population genetics
Probabilistic inference
Research and Analysis Methods
Software
Statistical analysis
Statistical inference
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Summary: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.
ISSN:1553-7358
1553-734X
1553-7358
DOI:10.1371/journal.pcbi.1008065