ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to...

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Autores principales: Nakatsuka, Nathan, Harney, Éadaoin, Mallick, Swapan, Mah, Matthew, Patterson, Nick, Reich, David
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2020
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418405/
https://www.ncbi.nlm.nih.gov/pubmed/32778142
http://dx.doi.org/10.1186/s13059-020-02111-2
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author Nakatsuka, Nathan
Harney, Éadaoin
Mallick, Swapan
Mah, Matthew
Patterson, Nick
Reich, David
author_facet Nakatsuka, Nathan
Harney, Éadaoin
Mallick, Swapan
Mah, Matthew
Patterson, Nick
Reich, David
author_sort Nakatsuka, Nathan
collection PubMed
description We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD.
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spelling pubmed-74184052020-08-12 ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium Nakatsuka, Nathan Harney, Éadaoin Mallick, Swapan Mah, Matthew Patterson, Nick Reich, David Genome Biol Software We report a method called ContamLD for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA. ContamLD leverages the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors: for example, less than 1.5% standard error in cases with less than 10% contamination and 500,000 sequences covering SNPs. This method is optimized for application to aDNA, taking advantage of characteristic aDNA damage patterns to provide calibrated contamination estimates, and is available at https://github.com/nathan-nakatsuka/ContamLD. BioMed Central 2020-08-10 /pmc/articles/PMC7418405/ /pubmed/32778142 http://dx.doi.org/10.1186/s13059-020-02111-2 Text en © The Author(s) 2020 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/. The Creative Commons Public Domain Dedication waiver (http://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 Software
Nakatsuka, Nathan
Harney, Éadaoin
Mallick, Swapan
Mah, Matthew
Patterson, Nick
Reich, David
ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
title ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
title_full ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
title_fullStr ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
title_full_unstemmed ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
title_short ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
title_sort contamld: estimation of ancient nuclear dna contamination using breakdown of linkage disequilibrium
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7418405/
https://www.ncbi.nlm.nih.gov/pubmed/32778142
http://dx.doi.org/10.1186/s13059-020-02111-2
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