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Rank-invariant estimation of inbreeding coefficients

The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigre...

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Autores principales: Zhang, Qian S., Goudet, Jérôme, Weir, Bruce S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Springer International Publishing 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8733021/
https://www.ncbi.nlm.nih.gov/pubmed/34824382
http://dx.doi.org/10.1038/s41437-021-00471-4
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author Zhang, Qian S.
Goudet, Jérôme
Weir, Bruce S.
author_facet Zhang, Qian S.
Goudet, Jérôme
Weir, Bruce S.
author_sort Zhang, Qian S.
collection PubMed
description The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications.
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spelling pubmed-87330212022-01-18 Rank-invariant estimation of inbreeding coefficients Zhang, Qian S. Goudet, Jérôme Weir, Bruce S. Heredity (Edinb) Article The two alleles an individual carries at a locus are identical by descent (ibd) if they have descended from a single ancestral allele in a reference population, and the probability of such identity is the inbreeding coefficient of the individual. Inbreeding coefficients can be predicted from pedigrees with founders constituting the reference population, but estimation from genetic data is not possible without data from the reference population. Most inbreeding estimators that make explicit use of sample allele frequencies as estimates of allele probabilities in the reference population are confounded by average kinships with other individuals. This means that the ranking of those estimates depends on the scope of the study sample and we show the variation in rankings for common estimators applied to different subdivisions of 1000 Genomes data. Allele-sharing estimators of within-population inbreeding relative to average kinship in a study sample, however, do have invariant rankings across all studies including those individuals. They are unbiased with a large number of SNPs. We discuss how allele sharing estimates are the relevant quantities for a range of empirical applications. Springer International Publishing 2021-11-25 2022-01 /pmc/articles/PMC8733021/ /pubmed/34824382 http://dx.doi.org/10.1038/s41437-021-00471-4 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Zhang, Qian S.
Goudet, Jérôme
Weir, Bruce S.
Rank-invariant estimation of inbreeding coefficients
title Rank-invariant estimation of inbreeding coefficients
title_full Rank-invariant estimation of inbreeding coefficients
title_fullStr Rank-invariant estimation of inbreeding coefficients
title_full_unstemmed Rank-invariant estimation of inbreeding coefficients
title_short Rank-invariant estimation of inbreeding coefficients
title_sort rank-invariant estimation of inbreeding coefficients
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8733021/
https://www.ncbi.nlm.nih.gov/pubmed/34824382
http://dx.doi.org/10.1038/s41437-021-00471-4
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