ContamLD

ContamLD estimates autosomal contamination levels in ancient DNA (aDNA) samples by measuring linkage disequilibrium breakdown to distinguish authentic ancient haplotypes from contaminant DNA.

Key Features:

• Linkage Disequilibrium Breakdown Analysis: Measures breakdown of linkage disequilibrium by detecting haplotypes uncorrelated with the ancient individual's haplotypes.
• Accurate Estimation with Low Error Rates: Simulations demonstrate less than a 1.5% standard error when contamination is below 10%, given at least 500,000 sequences covering single nucleotide polymorphisms (SNPs).
• Optimization for Ancient DNA: Leverages characteristic aDNA damage patterns to provide calibrated contamination estimates for ancient specimens.

Scientific Applications:

• Paleogenomics: Assessing and quantifying autosomal contamination to improve reliability of ancient genome analyses.
• Archaeogenetics: Enabling reconstruction of genetic histories from ancient specimens by reducing confounding modern DNA.
• Evolutionary analyses: Supporting interpretation of evolutionary processes by providing precise contamination estimates for downstream analyses.

Methodology:

Analyzes haplotype correlations and deviations from expected linkage disequilibrium patterns in sequenced aDNA and quantifies contamination using statistical modeling and simulation-based calibration.