Fluidigm Europe has announced a new technical poster describing how its Access Array™ chip technology has been used by the Core Genotyping facility at the National Cancer Institute (Bethesda, MD) to capture and sequence the entire Epstein Barr Virus (EBV) genome from 4 individual patient DNA samples in a single sequence capture run.
Furthermore the authors describe how, by addition of short DNA barcodes (MIDs) to each sample during processing, they were able to pool all of their samples into a single Roche 454 sequencing run, then bioinformatically separate each sample and genomic variant during data analysis.
The ubiquitous nature of the Epstein Barr Virus (EBV) makes it a very attractive focus for genetic sequence analysis; moreover, identification of tumor-associated strains of EBV have major public impact especially in populations where EBV Malignancies are endemic. The ability to easily and cost-effectively capture and sequence the entire EBV virus from human DNA will enable researchers to vastly increase the breadth of knowledge of the virus's numerous variants.
The Fluidigm Access Array™ integrated fluidic circuit is a microfluidics chip which houses thousands of nanoscale reaction chambers. The Access Array is configured to run 48 samples and 48 primer pairs simultaneously for a total of 2304 reactions.
The authors describe how they evaluated and validated two protocols using the Access Array™ system to conduct, short and long-range capture. The short range protocol captures target lengths up to 700bp, while the long-range protocol currently captures up to 5Kb.
Overall, the NCI scientists concluded that the EBV genome sequencing project demonstrated quality sequencing results on a small scale. The implementation of a long range protocol on Fluidigm's Access Array™ system provided consistent and reliable target sequence capture as evidenced by consistent yields and high quality sequence reads on their Roche 454 sequencing platform, and can be used for other next generation sequencing platforms as well. Performing long range capture on the Access Array™ system considerably reduced the required reagents while streamlining the capture process resulting in reduced turnaround times, requiring less gDNA and reagents, and fewer manual manipulations.