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Inferring parental genomic ancestries using pooled semi-Markov processes

Motivation: A basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent’s genome that comes from specific ancestries (e.g. European, African, Native Am...

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Autores principales: Zou, James Y., Halperin, Eran, Burchard, Esteban, Sankararaman, Sriram
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765873/
https://www.ncbi.nlm.nih.gov/pubmed/26072482
http://dx.doi.org/10.1093/bioinformatics/btv239
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author Zou, James Y.
Halperin, Eran
Burchard, Esteban
Sankararaman, Sriram
author_facet Zou, James Y.
Halperin, Eran
Burchard, Esteban
Sankararaman, Sriram
author_sort Zou, James Y.
collection PubMed
description Motivation: A basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent’s genome that comes from specific ancestries (e.g. European, African, Native American, etc). This has many applications ranging from understanding the inheritance of ancestry-related risks and traits to quantifying human assortative mating patterns. Results: We model the problem of parental genomic ancestry inference as a pooled semi-Markov process. We develop a general mathematical framework for pooled semi-Markov processes and construct efficient inference algorithms for these models. Applying our inference algorithm to genotype data from 231 Mexican trios and 258 Puerto Rican trios where we have the true genomic ancestry of each parent, we demonstrate that our method accurately infers parameters of the semi-Markov processes and parents’ genomic ancestries. We additionally validated the method on simulations. Our model of pooled semi-Markov process and inference algorithms may be of independent interest in other settings in genomics and machine learning. Contact: jazo@microsoft.com
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spelling pubmed-47658732016-03-04 Inferring parental genomic ancestries using pooled semi-Markov processes Zou, James Y. Halperin, Eran Burchard, Esteban Sankararaman, Sriram Bioinformatics Ismb/Eccb 2015 Proceedings Papers Committee July 10 to July 14, 2015, Dublin, Ireland Motivation: A basic problem of broad public and scientific interest is to use the DNA of an individual to infer the genomic ancestries of the parents. In particular, we are often interested in the fraction of each parent’s genome that comes from specific ancestries (e.g. European, African, Native American, etc). This has many applications ranging from understanding the inheritance of ancestry-related risks and traits to quantifying human assortative mating patterns. Results: We model the problem of parental genomic ancestry inference as a pooled semi-Markov process. We develop a general mathematical framework for pooled semi-Markov processes and construct efficient inference algorithms for these models. Applying our inference algorithm to genotype data from 231 Mexican trios and 258 Puerto Rican trios where we have the true genomic ancestry of each parent, we demonstrate that our method accurately infers parameters of the semi-Markov processes and parents’ genomic ancestries. We additionally validated the method on simulations. Our model of pooled semi-Markov process and inference algorithms may be of independent interest in other settings in genomics and machine learning. Contact: jazo@microsoft.com Oxford University Press 2015-06-15 2015-06-10 /pmc/articles/PMC4765873/ /pubmed/26072482 http://dx.doi.org/10.1093/bioinformatics/btv239 Text en © The Author 2015. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Ismb/Eccb 2015 Proceedings Papers Committee July 10 to July 14, 2015, Dublin, Ireland
Zou, James Y.
Halperin, Eran
Burchard, Esteban
Sankararaman, Sriram
Inferring parental genomic ancestries using pooled semi-Markov processes
title Inferring parental genomic ancestries using pooled semi-Markov processes
title_full Inferring parental genomic ancestries using pooled semi-Markov processes
title_fullStr Inferring parental genomic ancestries using pooled semi-Markov processes
title_full_unstemmed Inferring parental genomic ancestries using pooled semi-Markov processes
title_short Inferring parental genomic ancestries using pooled semi-Markov processes
title_sort inferring parental genomic ancestries using pooled semi-markov processes
topic Ismb/Eccb 2015 Proceedings Papers Committee July 10 to July 14, 2015, Dublin, Ireland
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765873/
https://www.ncbi.nlm.nih.gov/pubmed/26072482
http://dx.doi.org/10.1093/bioinformatics/btv239
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