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Pedigree reconstruction from poor quality genotype data

Wang, J; (2019) Pedigree reconstruction from poor quality genotype data. Heredity , 122 pp. 719-728. 10.1038/s41437-018-0178-7. Green open access

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Abstract

Marker genotype data could suffer from a high rate of errors such as false alleles and allelic dropouts (null alleles) in situations such as SNPs from low-coverage next-generation sequencing and microsatellites from noninvasive samples. Use of such data without accounting for mistyping properly could lead to inaccurate or incorrect inferences of family relationships such as parentage and sibship. This study shows that markers with a high error rate are still informative. Simply discarding them could cause a substantial loss of precious information, and is impractical in situations where virtually all markers (e.g. SNPs from low-coverage next-generation sequencing, microsatellites from noninvasive samples) suffer from a similarly high error rate. This study also shows that some previous error models are valid for markers of low error rates, but fail for markers of high error rates. It proposes an improved error model and demonstrates, using simulated and empirical data of a high error rate (say, >0.5), that it leads to more accurate sibship and parentage inferences than previous models. It suggests that, in reality, markers of high error rates should be used rather than discarded in pedigree reconstruction, so long as the error rates can be estimated and used properly in the analyses.

Type: Article
Title: Pedigree reconstruction from poor quality genotype data
Open access status: An open access version is available from UCL Discovery
DOI: 10.1038/s41437-018-0178-7
Publisher version: https://doi.org/10.1038/s41437-018-0178-7
Language: English
Additional information: 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/.
Keywords: Molecular ecology, Population genetics
UCL classification: UCL
UCL > Provost and Vice Provost Offices
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Genetics, Evolution and Environment
URI: https://discovery.ucl.ac.uk/id/eprint/10065234
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