Journal
GENOME BIOLOGY
Volume 21, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-020-02111-2
Keywords
Ancient DNA; Linkage disequilibrium; Contamination; Autosomal DNA; Nuclear DNA
Funding
- NIGMS [GM007753]
- MHAAM fellowship
- National Institutes of Health [HG006399, GM100233]
- Allen Discovery Center grant from the Paul Allen Foundation
- John Templeton Foundation [61220]
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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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