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 .

中文翻译：

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ContamLD：利用连锁不平衡的破坏来估计古代核 DNA 污染


我们报告了一种称为 ContamLD 的方法，通过测量测序个体中由于引入污染物 DNA 导致的连锁不平衡破坏来估计常染色体古 DNA (aDNA) 污染。 ContamLD 利用了污染物应具有与研究个体不相关的单倍型这一理念。使用模拟数据，我们确认 ContamLD 能够准确推断污染率，且标准误差较低：例如，在污染率低于 10% 且覆盖 SNP 的 500,000 个序列的情况下，标准误差低于 1.5%。该方法针对 aDNA 的应用进行了优化，利用特征 aDNA 损伤模式来提供校准的污染估计，可在 https://github.com/nathan-nakatsuka/ContamLD 上获取。