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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Bibliographic Details
Published in:Genome Biology 2020-08, Vol.21 (1), p.199-199, Article 199
Main Authors: Nakatsuka, Nathan, Harney, Éadaoin, Mallick, Swapan, Mah, Matthew, Patterson, Nick, Reich, David
Format: Article
Language:English
Subjects:
Ancient DNA
Autosomal DNA
Contaminants
Contamination
Deoxyribonucleic acid
DNA
DNA Contamination
DNA damage
DNA, Ancient - analysis
Estimates
Genomes
Haplotypes
Linkage Disequilibrium
Methods
Mitochondrial DNA
Nuclear DNA
Nucleotide sequence
Population
Single-nucleotide polymorphism
Software
X chromosomes
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Summary: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 .
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-020-02111-2