ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium
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Abstract
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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The study filtered out putatively contaminated paleogenomes using the contamination warning estimated through linkage disequilibrium and by excluding genomes with contamination indicators in their GroupID name.
“We filtered out putatively contaminated paleogenomes by using the contamination warning estimated through linkage disequilibrium (59) (values of “contamLD_warning” being either “Model_Misspecified” or “Very_High_Contamination” were removed) as well as by excluding genomes that contained “contam” or “possible.contam” in their GroupID name.”
From Past human expansions shaped the spatial pattern of Neanderthal ancestry (2023) · cites this paper as [59]
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- [42]Nakatsuka, Nathan; Harney, Eadaoin; Mallick, Swapan; Mah, Matthew; Patterson, Nick; Reich, David. Estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium. Zenodo. 10.5281/zenodo.3736774. (2020). PMC7418405 32778142 · DOI
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- Authors
- Nakatsuka, N., Harney, É., Mallick, S., Mah, M., Patterson, N., & Reich, D.
- Affiliations
- Harvard University (US)
- Broad Institute (US)
- Corresponding author
- Nakatsuka, Nathan
- Harney, Éadaoin
- Reich, David
- Venue
- Genome Biology
- Published
- 2020-08-10
- Volume
- 21
- Issue
- 1
- Pages
- 199-199
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC7418405
- OpenAlex
- W3047734251
- Cited by
- 45
- References
- 44
- Citations by year
- 2026: 9 · 2025: 4 · 2024: 4 · 2023: 11 · 2022: 4 · 2021: 8 · 2020: 5
- FWCI
- 4.10
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- National Institute of General Medical Sciences (GM007753)
- Max Planck – Harvard Research Center for the Archaeoscience of the Ancient Mediterranean
- National Institutes of Health (HG006399, GM100233)
- Howard Hughes Medical Institute
- John Templeton Foundation (61220)
- Allen Foundation (Allen Discovery Center grant)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- contamination estimation, linkage disequilibrium, autosomal DNA
- MeSH terms
- DNA, Ancient, Haplotypes, Software, Linkage Disequilibrium, DNA Contamination
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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