ArticleGenome biology2020
ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
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- Genetic formation and regional disparities of Kra-Dai and Hmong-Mien speakers inferred from ancient genomes of cave burial populations in southwest China.Molecular biology and evolution · 2026Article
- Exploration of hanging coffin customs and the bo people in China through comparative genomics.Nature communications · 2025Article
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- Multidisciplinary study of human remains from the 3rd century mass grave in the Roman city of Mursa, Croatia.PloS one · 2025Article
- Life history and ancestry of the late Upper Palaeolithic infant from Grotta delle Mura, Italy.Nature communications · 2024Article
- Assessing the impact of post-mortem damage and contamination on imputation performance in ancient DNA.Scientific reports · 2024Article
- Article
- Review: Computational analysis of human skeletal remains in ancient DNA and forensic genetics.iScience · 2023Review
- Biological and substitute parents in Beaker period adult-child graves.Scientific reports · 2023Article
- Past human expansions shaped the spatial pattern of Neanderthal ancestry.Science advances · 2023Article
- Descent, marriage, and residence practices of a 3,800-year-old pastoral community in Central Eurasia.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Density separation of petrous bone powders for optimized ancient DNA yields.Genome research · 2023Article
- Article
- Community-engaged ancient DNA project reveals diverse origins of 18th-century African descendants in Charleston, South Carolina.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- hapCon: estimating contamination of ancient genomes by copying from reference haplotypes.Bioinformatics (Oxford, England) · 2022Article
- Mitochondrial DNA Consensus Calling and Quality Filtering for Constructing Ancient Human Mitogenomes: Comparison of Two Widely Applied Methods.International journal of molecular sciences · 2022Article
- South-to-north migration preceded the advent of intensive farming in the Maya region.Nature communications · 2022Article
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Authors and funding
6 authors.
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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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