ArticleBMC biology2017
Patterns of cross-contamination in a multispecies population genomic project: detection, quantification, impact, and solutions.
Article in BMC biology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
52 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The gut, vaginal, and urine microbiome in overactive bladder: a systematic review.International urogynecology journal · 2022Pooled it
- Low-level contamination confounds population genomic analysis.G3 (Bethesda, Md.) · 2026Article
- Evaluation of the diagnostic value of metagenomic next-generation sequencing for zoonotic cestodeFood and waterborne parasitology · 2026Article
- Molecular Phylogeny of "Chemosensory Proteins" in Bacteria and Arthropods: CSP as an Extremely Ancient Gene.Journal of molecular evolution · 2026Article
- Residual DNA impurities in AAV vectors-nature and transcription.Molecular therapy. Methods & clinical development · 2025Article
- Exon Capture Museomics Deciphers the Nine-Banded Armadillo Species Complex and Identifies a New Species Endemic to the Guiana Shield.Systematic biology · 2025Article
- Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2025Article
- Blood microbiome signatures in systemic diseases: current insights, methodological pitfalls, and future horizons.Frontiers in cellular and infection microbiology · 2025Review
- Contamination Survey of Insect Genomic and Transcriptomic Data.Animals : an open access journal from MDPI · 2024Article
- Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii.BMC genomics · 2024Article
- GTax: improving de novo transcriptome assembly by removing foreign RNA contamination.Genome biology · 2024Article
- Influence of social lifestyles on host-microbe symbioses in the bees.Ecology and evolution · 2023Article
- Article
- BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.Microbiome · 2023Article
- A Large-Scale Study into Protist-Animal Interactions Based on Public Genomic Data Using DNA Barcodes.Animals : an open access journal from MDPI · 2023Article
- Amplicon sequencing allows differential quantification of closely related parasite species: an example from rodent Coccidia (Eimeria).Parasites & vectors · 2023Article
- Killer Knots: Molecular Evolution of Inhibitor Cystine Knot Toxins in Wandering Spiders (Araneae: Ctenidae).Toxins · 2023Article
- Article
- SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data.NAR genomics and bioinformatics · 2022Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundContamination is a well-known but often neglected problem in molecular biology. Here, we investigated the prevalence of cross-contamination among 446 samples from 116 distinct species of animals, which were processed in the same laboratory and subjected to subcontracted transcriptome sequencing.
resultsUsing cytochrome oxidase 1 as a barcode, we identified a minimum of 782 events of between-species contamination, with approximately 80% of our samples being affected. An analysis of laboratory metadata revealed a strong effect of the sequencing center: nearly all the detected events of between-species contamination involved species that were sent the same day to the same company. We introduce new methods to address the amount of within-species, between-individual contamination, and to correct for this problem when calling genotypes from base read counts.
conclusionsWe report evidence for pervasive within-species contamination in this data set, and show that classical population genomic statistics, such as synonymous diversity, the ratio of non-synonymous to synonymous diversity, inbreeding coefficient F
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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.