ContamLD: estimation of ancient nuclear DNA contamination using breakdown of linkage disequilibrium

被引：26

作者：

Nakatsuka, Nathan ^{[1
,2
,3
]}

Harney, Eadaoin ^{[1
,3
,4
]}

Mallick, Swapan ^{[1
,3
]}

Mah, Matthew ^{[1
,3
]}

Patterson, Nick ^{[3
]}

Reich, David ^{[1
,3
,5
,6
]}

机构：

[1] Harvard Med Sch, Dept Genet, New Res Bldg,77 Ave Louis Pasteur, Boston, MA 02115 USA

[2] Harvard Med Sch, Harvard Mit Div Hlth Sci & Technol, Boston, MA 02115 USA

[3] Harvard Univ, Dept Human Evolutionary Biol, 16 Divin Ave, Cambridge, MA 02138 USA

[4] Harvard Univ, Dept Organism & Evolutionary Biol, 16 Divin Ave, Cambridge, MA 02138 USA

[5] Broad Inst MIT & Harvard, Cambridge, MA 02141 USA

[6] Harvard Med Sch, Howard Hughes Med Inst, Boston, MA 02115 USA

来源：

GENOME BIOLOGY | 2020年 / 21卷 / 01期

基金：

美国国家卫生研究院;

关键词：

Ancient DNA; Linkage disequilibrium; Contamination; Autosomal DNA; Nuclear DNA; MITOCHONDRIAL GENOME SEQUENCE; NEANDERTHAL; HISTORY; ADMIXTURE; SAMPLES; CAVE;

D O I：

10.1186/s13059-020-02111-2

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页数：22

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