Scientific Posters
Oragene•DNA
Saliva collected using the Oragene® self-collection kit is a non- invasive alternative to blood as a source of large amounts of high quality genomic DNA. Oragene enables large-scale population studies by improving donor access and compliance, and its utility has been well-documented in over one thousand peer-reviewed publications. However, data on the performance of DNA from saliva in Whole Genome Sequencing is scarce in the existing literature.
In this study, we present a systematic, multi-sample analysis of the effect of sample type (blood vs. saliva) on variant calling confidence and the effect of bacterial DNA in saliva on sequence alignment.
The Oragene®•DNA collection kit facilitates access to donor and enables large-scale population studies. While the general quality and utility of DNA collected from saliva with Oragene is supported by over one thousand peer-reviewed publications, data on Whole Genome Sequencing (WGS) is more limited.
In this study, we investigate the source of unaligned reads in both the blood and saliva sample data. Additionally, we examine the effects of sample type on the detected variants (SNPs and INDELs) using paired blood and saliva WGS data from two family trios.
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.
The Oragene®•DNA collection kit enables scalable donor access and large-scale population studies. While the general quality and utility of DNA collected from saliva with Oragene is supported by over 1000 peer-reviewed publications, data on Whole Genome Sequencing (WGS) is more limited in previous studies.
The use of saliva as a source of genomic DNA for research and clinical studies has grown in popularity due to the ease of collection and participant compliance. The Coriell Personalized Medicine Collaborative (CPMC) has been using Oragene collection kits for the past six years as the source of genomic DNA, initially for genotyping on the Affymetrix Genome-Wide Human SNP Nsp/Sty 6.0 array, and for the past four years, also for genotyping on the Affymetrix DMET Plus array.
MK-00288: Impact of sample source on variant discovery: a saliva vs blood comparison (pdf)
Recent advances in Next Generation Sequencing technologies, coupled with cost reductions, have made NGS a more practical tool for studies requiring larger cohorts. Saliva collected using Oragene® self-collection kits is a non-invasive alternative to blood for obtaining high quality genomic DNA.
Non-invasive sample collection has been demonstrated to dramatically increase donor compliance. Saliva collected with Oragene® provides a non-invasive alternative to blood samples for collecting large amounts of high quality genomic DNA that is suitable for array based GWAS and Next Generation Sequencing studies.
MK-00229: Whole Genome Sequencing of a family trio using DNA extracted from saliva (pdf)
In recent years there have been significant advancements in Next Generation Sequencing (NGS) technology and reduced cost. This combination has made NGS a more practical and economical tool for studies requiring larger numbers of samples.
Non-invasive sample collection can greatly improve the success of a research study by ensuring donor compliance. Use of saliva collection for gDNA has been demonstrated to increase compliance rates.
Non-invasive and easy-to-use DNA sample collection technologies can greatly improve the success of a research study by ensuring donor compliance and acceptance into a study.
Transplant centres and marrow donor registries continue to evolve their processes and technology with the goal of reducing time required to find a match for a patient in need of a hematopoietic stem cell transplant.
With the rapid technological advancement and decreasing cost of next generation sequencing that has occurred over the last few years, it has become more practical to sequence larger numbers of samples.
Saliva is a reliable source of DNA for use with the Agilent SureSelect Human All Exon Kit and sequencing using paired-end methodology on the Illumina Genome Analyzer II as demonstrated by the coverage (98.7%), depth (74x), and genome alignment (97.3%).
This poster presents the results of a study that evaluates the performance of gDNA from saliva on the Agilent Human Genome CGH Array 244K.
The use of genomic DNA extracted from saliva collected using Oragene•DNA self-collection kits for SNP and CNV analysis is evaluated on Illumina BeadChip technologies. The performance of paired blood and saliva samples are compared and the intra-donor reproducibility of the results is demonstrated.
Anthony Nolan Trust investigated the move from blood to self collection specimens for molecular HLA typing of volunteers wishing to join the registry. Scientific publications and personal recommendations led to a belief that an Oragene system would be amenable to high throughput automated DNA extraction with yield and quality acceptable for molecular typing requirements.
For any type of genetic analysis (e.g. population studies, clinical genetic testing, paternity testing, pharmacogenomic testing), non-invasive and easy-to-use sample collection techniques are preferred because they increase compliance rates and reduce costs.
Saliva DNA that is extracted with Oragene•DNA performs equivalent to or better than blood extracted DNA when used in the Affymetrix Targeted Genotyping assay.
SNP Genotyping of Saliva and DNA using Affymetrix® GeneChip® Targeted Genotyping System (pdf)
Saliva DNA that is extracted with Oragene•DNA performs equivalent to or better than blood extracted DNA when used in the Affymetrix Targeted Genotyping assay.
Comprehensive Gene Sequence Analysis from Bloodspot and Saliva DNA (pdf)
DNA yield from 250 µl of saliva is similar to yield from 1 ml of whole blood, and resulted in similar performance with the Ambry Genetics TTGE and sequencing protocols.
Diagnostic Assessment of ORAGENE DNA Self-collection kit (pdf)
DNA self-collection kit is a reliable and safe alternative to peripheral blood collection.
The use of Oragene kit coupled with manual/automated DNA extraction provide high quality DNA for genetic analyses, and sufficient quantities to be archived for future studies.
Scientific Posters
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