The Genetic Link

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Article by: Rafal Iwasiow

Oragene is a reliable source of DNA for next generation sequencing

2011-03-28

This week, at Genomics Disorders 2011 in Cambridge, UK, DNA Genotek presented a poster reflecting new research findings. Building on the success of previous Genomic Disorders meetings, this year’s venue presented an exciting blend of genomic science and clinical medicine. The meeting’s goal is to bring together scientists and clinicians interested in genomic variation in humans and the mechanisms by which variations exert phenotypic effects. We used this opportunity to showcase new research findings that demonstrate Oragene•DNA is a reliable source of DNA for next generation sequencing.

In recent years we have observed significant advancements in next generation sequencing, decreasing costs and acceptance of targeted capture technologies. Together these factors are enabling the use of next generation sequencing for clinical applications. It is quickly becoming more realistic and economical to process large numbers of samples for the purpose of genetic analysis. Such analysis requires the collection of reliable, high quality samples. Oragene•DNA provides an alternative method to blood samples for collecting large amounts of high quality genomic DNA that is suitable for next generation sequencing applications. At Genomic Disorders, DNA Genotek presented a study where we investigated DNA extracted from saliva collected using Oragene•DNA for use with the Agilent SureSelect Human All Exon Kit and paired-end sequencing on the Illumina Genome Analyzer II.

To evaluate the performance of saliva samples collected using Oragene•DNA, we compared the data against DNA from blood samples collected from the same individuals. Using the SureSelect Human All Exon Kit to capture regions totaling 38Mb = 1.22% of human genomic regions we observed a mean coverage of 98.48% against the targeted sequences at a mean depth of 77x. No significant difference was observed between blood or saliva samples. Using paired-end sequencing on the Illumina Genome Analyzer II we observed a mean lane yield of 6,352,886 kbases of which 46.1% corresponded to exon sequences. In comparison to samples not enriched using the Agilent SureSelect Human All Exon Kit we observed only 1.2% of bases corresponding to the exon regions with a mean depth of 2.4x. Interestingly, samples that were not enriched had 91.5% of their sequence align to the reference human genome indicating that saliva can also be used for whole genome sequencing.

The high depth of coverage and depth of sequencing achieved by using DNA from saliva with the Agilent SureSelect Human All Exon Kit and sequencing using paired-end sequencing on a single lane of the Illumina Genome Analyzer II allows us to confidently mine the data for SNPs of interest or for novel SNP discovery. As such, here we demonstrate the ability to use either blood or saliva to investigate genetic variations using next generation sequencing technologies. As a proof of concept we report the ability to use either blood or saliva samples to investigate previously reported SNPs rs2075650 (APOE), rs10513025 (SEMA5A), rs2736990 (SNCA), and rs356220 (SNCA).

Want to see the full poster? Click here.

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