ArticleScientific reports2022
The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families.
Article in Scientific reports, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers, 1 of them a synthesis that pooled it.
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Who cites it
43 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Increased expression of human endogenous retrovirus K in endomyocardial biopsies from patients with cardiomyopathy - a transcriptomics meta-analysis.BMC genomics · 2024Pooled it
- De novo assembly and authentication of ancient DNA metagenomes with nf-core/mag.PLoS computational biology · 2026Article
- Systematic detection of Oxford Nanopore adapter and barcode contamination in GenBank.BMC genomics · 2026Article
- SwarmGenomics: A Unified Pipeline for Individual-Based Whole-Genome Analyses.Molecular ecology resources · 2026Article
- Predicting bloodstream infection by plasma cell-free metagenomic sequencing: a prospective cohort study.The Lancet. Microbe · 2026Observational
- DNA sequence contamination analyzer (DNASCAN): a supervised analysis toolkit for detecting and removing DNA contaminants.BMC bioinformatics · 2026Article
- NGSTroubleFinder: a tool for detection and quantification of contamination and kinship across human NGS data.NAR genomics and bioinformatics · 2026Article
- Clinical metagenomics for diagnosis and surveillance of viral pathogens.Nature reviews. Microbiology · 2026Review
- Development of a multiplex ddPCR assay for simultaneous absolute quantification of bacterial, fungal, and human DNA.PloS one · 2026Article
- A framework of Microbial Genomic Database for clinical metagenomic pathogen diagnosis: development and multi-cohort evaluation.Frontiers in cellular and infection microbiology · 2026Article
- The presence of persistent synovial inflammation after "Eradication" unmasks the "Unseen" dormant state of infection allowing the prediction of infection free survival in total joint replacements.Journal of translational medicine · 2025Article
- Contamination of fungal genomes of Onygenaceae (Phylum Ascomycota) in public databases: incidence, detection, and impact.BMC genomics · 2025Article
- Use of the CHM13-T2T genome improves metagenomic analysis by minimizing host DNA contamination.mSystems · 2025Article
- The multi-kingdom cancer microbiome.Nature microbiology · 2025Review
- Targeted decontamination of sequencing data with CLEAN.NAR genomics and bioinformatics · 2025Article
- NextVir: Enabling classification of tumor-causing viruses with genomic foundation models.PLoS computational biology · 2025Article
- Flexible, production-scale, human whole genome sequencing on a benchtop sequencer.BMC genomics · 2025Article
- Gut and Joint Microbiomes: Implications in Osteoarthritis.Rheumatic diseases clinics of North America · 2025Review
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
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7 authors.
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Abstract
The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.
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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.