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Parent-offspring inference in inbred populations

View ORCID ProfileJan-Niklas Runge, View ORCID ProfileBarbara König, View ORCID ProfileAnna K. Lindholm, View ORCID ProfileAndres Bendesky
doi: https://doi.org/10.1101/2021.11.23.469656
Jan-Niklas Runge
1Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
3Université de Strasbourg, CNRS, GMGM UMR 7156, Strasbourg, France
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  • For correspondence: jn.runge@protonmail.com a.bendesky@columbia.edu
Barbara König
2Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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Anna K. Lindholm
2Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
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Andres Bendesky
1Zuckerman Mind Brain Behavior Institute and Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, USA
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  • For correspondence: jn.runge@protonmail.com a.bendesky@columbia.edu
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Abstract

Genealogical relationships are fundamental components of genetic studies. However, it is often challenging to infer correct and complete pedigrees even when genome-wide information is available. For example, inbreeding can obfuscate genetic differences between individuals, making it difficult to even distinguish first-degree relatives such as parent-offspring from full siblings. Similarly, genotyping errors can interfere with the detection of genetic similarity between parents and their offspring. Inbreeding is common in natural, domesticated, and experimental populations and genotyping of these populations often has more errors than in human datasets, so efficient methods for building pedigrees under these conditions are necessary. Here, we present a new method for parent-offspring inference in inbred pedigrees called SPORE (Specific Parent-Offspring Relationship Estimation). SPORE is vastly superior to existing pedigree-inference methods at detecting parent-offspring relationships, in particular when inbreeding is high or in the presence of genotyping errors, or both. SPORE therefore fills an important void in the arsenal of pedigree inference tools.

Author Summary Knowing the genealogical relationships among individuals is critical for genetic analyses, such as for identifying the mutations that cause diseases or that contribute to valuable agricultural traits such as milk production. Although many tools exist for establishing pedigrees using genetic information, these tools fail when individuals are highly inbred, such as in domesticated animals, or in groups of people in which consanguineous matings are common. Furthermore, existing tools do not work well when genetic information has errors at levels observed in modern datasets. Here, we present a novel approach to solve these problems. Our method is significantly more accurate than existing tools and more tolerant of errors in the genetic data. We expect that our method, which is simple to use and computationally efficient, will be a useful tool in a diversity of settings, from the studies of human and natural populations, to agricultural and experimental settings.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Supplemental files added and issues with figure presentation on some PDF readers resolved.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted November 24, 2021.
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Parent-offspring inference in inbred populations
Jan-Niklas Runge, Barbara König, Anna K. Lindholm, Andres Bendesky
bioRxiv 2021.11.23.469656; doi: https://doi.org/10.1101/2021.11.23.469656
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Parent-offspring inference in inbred populations
Jan-Niklas Runge, Barbara König, Anna K. Lindholm, Andres Bendesky
bioRxiv 2021.11.23.469656; doi: https://doi.org/10.1101/2021.11.23.469656

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