ArticleGenome research2020
Ancestry-agnostic estimation of DNA sample contamination from sequence reads.
Article in Genome research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 59 papers, 1 of them a synthesis that pooled it.
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Who cites it
59 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.The EMBO journal · 2026Article
- Tissue-specific gene dosage disruption is a key feature and pathogenic mechanism of structural variants in the human genome.Genome medicine · 2026Article
- Population-scale genomic screening reveals high frequency of actionable secondary findings in Chinese newborns.NPJ genomic medicine · 2026Article
- NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.NAR genomics and bioinformatics · 2026Article
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- Genetic contribution to severe COVID-19 in adults under 60 years without major comorbidities in the German National Pandemic Cohort Network (NAPKON).Human genomics · 2026Article
- Ancient genomes reveal early-stage admixture and genetic diversity in the Northwestern Kyushu Yayoi.Scientific reports · 2026Article
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- Microbiome analysis of 940 lung cancers in never-smokers reveals lack of clinically relevant associations.Nature communications · 2025Article
- Targeted adaptive sampling enables clinical pharmacogenomics testing and genome-wide genotyping.Scientific reports · 2025Article
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- Mitochondrial Genome Variants and Nuclear Mitochondrial DNA Segments in 7331 Individuals from NyuWa and 1KGP.Genomics, proteomics & bioinformatics · 2025Article
Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
Detecting and estimating DNA sample contamination are important steps to ensure high-quality genotype calls and reliable downstream analysis. Existing methods rely on population allele frequency information for accurate estimation of contamination rates. Correctly specifying population allele frequencies for each individual in early stage of sequence analysis is impractical or even impossible for large-scale sequencing centers that simultaneously process samples from multiple studies across diverse populations. On the other hand, incorrectly specified allele frequencies may result in substantial bias in estimated contamination rates. For example, we observed that existing methods often fail to identify 10% contaminated samples at a typical 3% contamination exclusion threshold when genetic ancestry is misspecified. Such an incomplete screening of contaminated samples substantially inflates the estimated rate of genotyping errors even in deeply sequenced genomes and exomes. We propose a robust statistical method that accurately estimates DNA contamination and is agnostic to genetic ancestry of the intended or contaminating sample. Our method integrates the estimation of genetic ancestry and DNA contamination in a unified likelihood framework by leveraging individual-specific allele frequencies projected from reference genotypes onto principal component coordinates. Our method can also be used for estimating genetic ancestries, similar to LASER or
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.