ArticleScientific reports2020
Contaminating DNA in human saliva alters the detection of variants from whole genome sequencing.
Article in Scientific reports, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 27 citations in OpenAlex.
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- Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples.iScience · 2025Article
- Flexible, production-scale, human whole genome sequencing on a benchtop sequencer.BMC genomics · 2025Article
- Genomic and transcriptomic sequencing in prostate cancer.Current opinion in oncology · 2025Review
- Nanotechnology-Based Modern Biosensors for the Detection of SARS-CoV-2 Virus.Indian journal of microbiology · 2025Review
- The Black and African American Connections to Parkinson's Disease (BLAAC PD) study protocol.BMC neurology · 2024Article
- A novel approach of kinship determination based on the physical length of genetically shared regions of chromosomes.Genes & genomics · 2024Article
- Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses.BMC genomics · 2024Article
- Maternal Periconceptional Folic Acid Supplementation and DNA Methylation Patterns in Adolescent Offspring.The Journal of nutrition · 2023Article
- Isolation of salivary cell-free DNA for cancer detection.PloS one · 2023Article
- Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces.International journal of legal medicine · 2023Article
- Visual inspection reveals a novel pathogenic mutation inMolecular medicine reports · 2022Article
- The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families.Scientific reports · 2022Article
- Proof of concept for multiplex amplicon sequencing for mutation identification using the MinION nanopore sequencer.Scientific reports · 2022Article
- Cancer Neoantigens: Challenges and Future Directions for Prediction, Prioritization, and Validation.Frontiers in oncology · 2022Review
- DNA Methylation Variation Is Identified in Monozygotic Twins Discordant for Non-syndromic Cleft Lip and Palate.Frontiers in cell and developmental biology · 2021Article
- Quantification of DNA, in dried blood, saliva tinged with blood in comparision with fresh blood for forensic identification- A pilot study.Journal of oral and maxillofacial pathology : JOMFPArticle
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Cells obtained from human saliva are commonly used as an alternative DNA source when blood is difficult or less convenient to collect. Although DNA extracted from saliva is considered to be of comparable quality to that derived from blood, recent studies have shown that non-human contaminating DNA derived from saliva can confound whole genome sequencing results. The most concerning complication is that non-human reads align to the human reference genome using standard methodology, which can critically affect the resulting variant genotypes identified in a genome. We identified clusters of anomalous variants in saliva DNA derived reads which aligned in an atypical manner. These reads had only short regions of identity to the human reference sequence, flanked by soft clipped sequence. Sequence comparisons of atypically aligning reads from eight human saliva-derived samples to RefSeq genomes revealed the majority to be of bacterial origin (63.46%). To partition the non-human reads during the alignment step, a decoy of the most prevalent bacterial genome sequences was designed and utilised. This reduced the number of atypically aligning reads when trialled on the eight saliva-derived samples by 44% and most importantly prevented the associated anomalous genotype calls. Saliva derived DNA is often contaminated by DNA from other species. This can lead to non-human reads aligning to the human reference genome using current alignment best-practices, impacting variant identification. This problem can be diminished by using a bacterial decoy in the alignment process.
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