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A quick guide to application compatibility for Oragene – PCR to NGS

Posted by Shauna White on Wed, Sep 03, 2014 @ 13:09 PM

Oragene DNA saliva validationsIn a recent article on The Genetic Link, we talked about going global and how our regulatory strategy helps support our customers who are conducting genetic research. Today, I am focusing on the work we do to ensure our products' compatibility with the technologies our genetic research and testing customers use in the field and in their labs.

DNA Genotek is committed to demonstrating compatibility[1] and suitability of DNA from Oragene/saliva samples on the most common genetic testing platforms.  We’ve worked very hard to make sure our products integrate with the tools being used today as well as with new innovations as they come online. We know that our customers expect our products to perform well on downstream applications. We also know that no two customers are alike and we therefore want to provide optimal flexibility and confidence when you choose Oragene* for your saliva-based DNA collection.

Here is a quick guide to some of the most popular application compatibility for Oragene**. In each case, we provide a link to the study that has full details on the compatibility testing. This is not a complete list and many more are available in the support section of our web site

Next generation sequencing (NGS)

Agilent SureSelect Exome capture sequenced on GAIIx - Using the Agilent SureSelect Human All Exon Kit to capture regions totaling 38Mb = 1.22% of human genomic regions, this study demonstrates saliva performs equivalently to blood and is suitable for investigating  genetic variations using next generation sequencing technologies. More information is available here

Whole genome sequencing of DNA from Oragene/saliva samples by Complete Genomics - Whole genome sequencing data generated from saliva samples of both high and low bacterial load were found to yield high quality data with low error rates, and the results were comparable to data from DNA derived from blood or cell lines

Impact of sample type on whole genome sequencing - In this study, we investigate the performance of DNA extracted from saliva collected using Oragene in whole genome sequencing and the effect of sample type on variant calling.  

Analysis of the effect of sample type on variant calling confidence for whole genome sequencing - Using paired blood and saliva WGS data from two family trios, we investigate the effects of sample type on the detected variants (SNPs and INDELs) and systematically investigate the causes of any differences. 

Exome array validation of DNA from Oragene/saliva samples - In this study we extracted DNA from Oragene/saliva samples stored at room temperature (~23°C) for over 7 years and evaluated the performance on both the Illumina® HumanExome v1.1 array and Whole Exome Sequencing on the Illumina HiSeq 2000 after enrichment using the Agilent SureSelect Human All Exon v4+UTRs 71Mb Kit. 

Raindance HLA capture and next generation sequencing on HiSeq2000 - This study illustrates that DNA from Oragene/saliva samples is a dependable alternative to blood for HLA typing, including typing by Next Generation Sequencing applications. 

Microarray

SNP discovery on Illumina microarray technologies - This study investigates the use of genomic DNA extracted from saliva collected using Oragene for SNP and CNV analysis on Illumina BeadChip technologies

CNV analysis on the Agilent CGH array – This current study evaluates the performance of gDNA from saliva on the Agilent Human Genome CGH Array 244K. 

SNP and CNV analysis on the Affymetrix SNP 6.0 array – This study investigates using saliva as s source of gDNA for the evaluation of genotyping and CNV analysis and demonstrates the intra-donor reproducibility of the results. 

PCR

DNA Sequencing on the ABI PRISM - DNA from Oragene/saliva samples is reliably sequenced using the ABI PRISM® 377 DNA sequencer. 

Taqman SNP genotyping - DNA collected with the Oragene self-collection kit works well with TaqMan® SNP genotyping assays. SNPs in the thymidylate synthetase and apolipoprotein E genes were reliably detected. 

Long-range PCR - For long-range PCR, DNA from Oragene®/saliva samples is equal in performance to DNA isolated from blood. (link to: http://www.dnagenotek.com/ROW/pdf/MK-AN-013.pdf)

And there’s always more coming

The application compatibility work doesn’t end here. We are continually conducting new studies to make sure our validations are the most current possible. If you are interested in any of our ongoing validation studies, contact your DNA Genotek Account Manager or send an email to info@dnagenotek.com

[1] All DNA Genotek protocols, white papers and application notes are available in the support section of our website at www.dnagenotek.com.

* Oragene•DNA is not available for sale in the United States. Oragene•DISCOVER is for research use only, not for use in diagnostic procedures. 
** DNA Genotek reported data is for research use only and not for use in the treatment or diagnosis of any human subject. 

Tags: DNA saliva, next generation sequencing, NGS, microarray, exome sequencing

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This blog is intended to provide information to educate readers about molecular testing and genetic sample collection and DNA Genotek products.  Some of the information on this blog represents emerging scientific research or data developed for research purposes only. More information here.

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Welcome to The Genetic Link, a blog providing new insights into DNA and RNA sample collection by DNA Genotek. DNA Genotek is a subsidiary of OraSure Technologies, Inc.

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