ArticleJournal of medical genetics2019
Impact of DNA source on genetic variant detection from human whole-genome sequencing data.
Article in Journal of medical genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Review
- Comparative genetic analysis of blood and semen samples in sperm donors from Hunan, China.Annals of medicine · 2025Article
- Metagenome-assembled genomes enhance bacterial read decontamination and variant calling in oral samples.iScience · 2025Article
- Individuals with intellectual disability have an increased burden ofmedRxiv : the preprint server for health sciences · 2025Article
- Analytical validation of germline small variant detection using long-read HiFi genome sequencing.Genome research · 2025Article
- Genetic Investigation of Inherited Variants in a Multiplex Autism Spectrum Disorder (ASD) Family Using Whole-Genome Sequencing (WGS).Iranian journal of public health · 2025Article
- Development of a Multifaceted Program for Pharmacogenetics Adoption at an Academic Medical Center: Practical Considerations and Lessons Learned.Clinical pharmacology and therapeutics · 2024Article
- Novel splicing variant and gonadal mosaicism in DYRK1A gene identified by whole-genome sequencing in multiplex autism spectrum disorder families.Neurogenetics · 2024Article
- Comprehensive whole-genome sequence analyses provide insights into the genomic architecture of cerebral palsy.Nature genetics · 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
- A cost-effective sequencing method for genetic studies combining high-depth whole exome and low-depth whole genome.NPJ genomic medicine · 2024Article
- Applications of genome sequencing as a single platform for clinical constitutional genetic testing.Genetics in medicine open · 2024Review
- Gene copy number variation and pediatric mental health/neurodevelopment in a general population.Human molecular genetics · 2023Article
- Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces.International journal of legal medicine · 2023Article
- Isolation of salivary cell-free DNA for cancer detection.PloS one · 2023Article
- Validation of targeted next-generation sequencing panels in a cohort of Polish patients with epilepsy: assessing variable performance across clinical endophenotypes and uncovering novel genetic variants.Frontiers in neurology · 2023Article
- Assessment of the Feasibility of a Future Integrated Larger-Scale Epidemiological Study to Evaluate Health Risks of Air Pollution Episodes in Children.International journal of environmental research and public health · 2022Article
- Preanalytical DNA assessment for downstream applications: How to optimize the management of human biospecimens to support molecular diagnosis-An experimental study.Journal of clinical laboratory analysis · 2022Article
- Parental mosaicism for apparent de novo genetic variants: Scope, detection, and counseling challenges.Prenatal diagnosis · 2022Review
- Direct RNA Nanopore Sequencing of SARS-CoV-2 Extracted from Critical Material from Swabs.Life (Basel, Switzerland) · 2022Article
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhole blood is currently the most common DNA source for whole-genome sequencing (WGS), but for studies requiring non-invasive collection, self-collection, greater sample stability or additional tissue references, saliva or buccal samples may be preferred. However, the relative quality of sequencing data and accuracy of genetic variant detection from blood-derived, saliva-derived and buccal-derived DNA need to be thoroughly investigated.
methodsMatched blood, saliva and buccal samples from four unrelated individuals were used to compare sequencing metrics and variant-detection accuracy among these DNA sources.
resultsWe observed significant differences among DNA sources for sequencing quality metrics such as percentage of reads aligned and mean read depth (p<0.05). Differences were negligible in the accuracy of detecting short insertions and deletions; however, the false positive rate for single nucleotide variation detection was slightly higher in some saliva and buccal samples. The sensitivity of copy number variant (CNV) detection was up to 25% higher in blood samples, depending on CNV size and type, and appeared to be worse in saliva and buccal samples with high bacterial concentration. We also show that methylation-based enrichment for eukaryotic DNA in saliva and buccal samples increased alignment rates but also reduced read-depth uniformity, hampering CNV detection.
conclusionFor WGS, we recommend using DNA extracted from blood rather than saliva or buccal swabs; if saliva or buccal samples are used, we recommend against using methylation-based eukaryotic DNA enrichment. All data used in this study are available for further open-science investigation.
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