Department of Genetics, New Research Building, Harvard Medical School, 77 Ave. Louis Pasteur, Boston, MA, 02115, USA.
Harvard-MIT Division of Health Sciences and Technology, Harvard Medical School, Boston, MA, 02115, USA.
Genome Biol. 2020 Aug 10;21(1):199. doi: 10.1186/s13059-020-02111-2.
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 .
我们报告了一种称为 ContamLD 的方法，通过测量由于污染物 DNA 的引入而导致个体测序中连锁不平衡的破坏来估计常染色体古 DNA（aDNA）污染。ContamLD 利用了这样一个观点，即污染物应该具有与所研究个体无关的单倍型。使用模拟数据，我们证实 ContamLD 可以准确地推断出低标准误差的污染率：例如，在污染率低于 10%且覆盖 SNP 的序列少于 50 万的情况下，标准误差小于 1.5%。该方法经过优化，可应用于 aDNA，利用特征性的 aDNA 损伤模式提供校准的污染估计值，并可在 https://github.com/nathan-nakatsuka/ContamLD 上获得。
