2021-08-12
Blood collection for genomic DNA presents several disadvantages: it is invasive and inconvenient for the donor, requires a trained medical professional, must be refrigerated for transportation and storage, and is difficult to transport across borders. All these factors can add significant costs to any genetic study and impact compliance rates.
Overcoming those hurdles is as simple as spitting in a tube! Saliva collection provides a non-invasive alternative source of genomic DNA for use in genetic analysis 1 and is as reliable as blood in many downstream applications, such as:
- Single-nucleotide polymorphisms (SNP)/copy number variation (CNV) microarrays
- Next generation sequencing (NGS)
- HLA (Human Leukocyte Antigen) typing
- Microsatellite analysis
- Whole genome amplification
Don’t take my word for it, the proof is in the pudding (or data as Scientists prefer to call it). The following are examples that demonstrate the compatibility and proven performance of saliva with several downstream applications.
Whole genome sequencing (WGS)
Saliva samples collected in Oragene devices yield human genomes comparable to blood samples with high-quality results and low error rates. A study conducted by Seven Bridges genomics and DNA Genotek, compared blood and saliva samples in whole-genome sequencing using Illumina’s HiSeq 2000 100bp Paired-end 30x coverage. 2
The team found:
- No significant difference in the total number of variants (single-nucleotide polymorphisms (SNPs) and INDELs (insertions and deletions)) are called from blood and saliva.
- Concordance differences in saliva/blood pairs are eliminated when blood data are downsampled to a coverage equal to saliva.
- Bacterial reads do not accumulate enough to affect mutation calling.
In another Seven Bridges and DNA Genotek study, the team investigated the source of unaligned reads in both the blood and saliva sample data.
We show that many of the reads failing to map to the human reference either align directly to species contained in the human microbiome database or bear similarities to other known bacterial and viral species. Overall, our analysis shows that there is no significant difference in variants detected between saliva and blood when samples are sequenced to the same coverage. 2
Related Content: Is whole genome sequencing the new first-line test for children with genetic diseases?; High quality libraries for human WGS with direct saliva Input; The impact of bacterial DNA in saliva on whole genome sequencing
Exome sequencing
Saliva is compatible with the Illumina Genome Analyzer II for whole exome sequencing (WES). A study was conducted using saliva collected in Oragene devices and blood to evaluate if saliva was a reliable source of DNA for next generation sequencing.
Exome enriched saliva and blood samples identified a similar mean number of variants: 28,738 from saliva and 28,067 from blood. 98.5% coverage of the exon regions was targeted by the SureSelect All Exon kit for both exome enriched saliva and blood samples.3
Related Content: Reliability & stability of Oragene samples for WGS & exome sequencing
Single-nucleotide polymorphism (SNP) genotyping
Another study was conducted to investigate the use of genomic DNA extracted from saliva collected with Oragene•DNA self-collection kits for SNP and CNV analysis on Illumina BeadChip technologies. The performance compared paired blood and saliva samples to demonstrate the intra-donor reproducibility of the results.4
- Saliva collected using the Oragene•DNA self-collection kit provides genomic DNA of sufficient quality for genotyping on the Illumina Human610-Quad and both genotyping and CNV analysis on the Human1M-Duo BeadChip arrays.
- Both saliva and blood samples performed better on the Human1M-Duo.
- DNA from saliva does not vary over time, as demonstrated through the intra-donor genotyping concordance and CNV reproducibility of samples taken from the same donor on different days.
- DNA from saliva generates highly concordant data compared with DNA from blood for the same donor, as demonstrated by the genotyping concordance and CNV reproducibility.
Related Content: DNA saliva samples for SNP and CNV analysis on microarrays
HLA typing
Saliva is compatible with Illumina® HiSeqTM 2000 for HLA typing using NGS. Blood and saliva samples were sequenced in an internal study for HLA typing to evaluate the performance of DNA from Oragene/saliva samples compared to DNA the data against DNA from blood samples collected from the same individuals for HLA typing. 5
- Prepared saliva and blood libraries were of equivalent quality (Table 2).
- Samples were successfully barcoded and multiplexed in a single sequencing run.
- Saliva and blood had similar mean quality scores of approximately 34.5.
- Mean coverage for both saliva and blood exceeded 100.
- HLA call concordance between saliva and blood was 100%.
- HLA calls were 100% concordant with previously reported results for these donors using current HLA-typing methodologies.
This study illustrates that DNA from Oragene/saliva samples is a dependable alternative to blood for HLA typing, including Next Generation Sequencing applications. In agreement with previous exome and whole genome sequencing studies we demonstrated that Oragene/saliva samples are a reliable source of DNA for Next Generation Sequencing applications. 5
Related Content: How to ensure the best sequencing results from saliva samples, Saliva as a sample type for genomic applications
Saliva is a reliable source of DNA for all types of genetic testing and research applications.
Want to learn more about what other downstream platforms are compatible with saliva samples?
Send us an email at info@dnagenotek.com for more information or click the picture below to request free samples to try in the lab.
References:
[1] https://www.dnagenotek.com/ROW/pdf/PD-WP-012.pdf
[2] https://www.dnagenotek.com/ROW/pdf/MK-00426.pdf
[3] https://www.dnagenotek.com/ROW/pdf/MK-00014.pdf
[4] https://www.dnagenotek.com/ROW/pdf/MK-008.pdf