correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes

Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulatio...

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Autores principales: Nyerki, Emil, Kalmár, Tibor, Schütz, Oszkár, Lima, Rui M., Neparáczki, Endre, Török, Tibor, Maróti, Zoltán
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9972692/
https://www.ncbi.nlm.nih.gov/pubmed/36855115
http://dx.doi.org/10.1186/s13059-023-02882-4
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author Nyerki, Emil
Kalmár, Tibor
Schütz, Oszkár
Lima, Rui M.
Neparáczki, Endre
Török, Tibor
Maróti, Zoltán
author_facet Nyerki, Emil
Kalmár, Tibor
Schütz, Oszkár
Lima, Rui M.
Neparáczki, Endre
Török, Tibor
Maróti, Zoltán
author_sort Nyerki, Emil
collection PubMed
description Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×–11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02882-4.
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spelling pubmed-99726922023-03-01 correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes Nyerki, Emil Kalmár, Tibor Schütz, Oszkár Lima, Rui M. Neparáczki, Endre Török, Tibor Maróti, Zoltán Genome Biol Method Kinship analysis from very low-coverage ancient sequences has been possible up to the second degree with large uncertainties. We propose a new, accurate, and fast method, correctKin, to estimate the kinship coefficient and the confidence interval using low-coverage ancient data. We perform simulations and also validate correctKin on experimental modern and ancient data with widely different genome coverages (0.12×–11.9×) using samples with known family relations and known/unknown population structure. Based on our results, correctKin allows for the reliable identification of relatedness up to the 4th degree from variable/low-coverage ancient or badly degraded forensic whole genome sequencing data. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02882-4. BioMed Central 2023-02-28 /pmc/articles/PMC9972692/ /pubmed/36855115 http://dx.doi.org/10.1186/s13059-023-02882-4 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Nyerki, Emil
Kalmár, Tibor
Schütz, Oszkár
Lima, Rui M.
Neparáczki, Endre
Török, Tibor
Maróti, Zoltán
correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
title correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
title_full correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
title_fullStr correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
title_full_unstemmed correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
title_short correctKin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
title_sort correctkin: an optimized method to infer relatedness up to the 4th degree from low-coverage ancient human genomes
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9972692/
https://www.ncbi.nlm.nih.gov/pubmed/36855115
http://dx.doi.org/10.1186/s13059-023-02882-4
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