Found in Translation

by Melissa Kamkar on June 19, 2013 in Genomics
Tokyo | Genomics Renaissance | Clarity LIMS

The Genomics Renaissance – 10th International Workshop on Advanced Genomics, Tokyo Japan, May 21-23, 2013

While my colleagues in Europe attended the Illumina EMEA Scientific Summit, I traveled in the opposite direction. As the Field Application Scientist for Asia Pacific, I attended the 10th Annual International Workshop on Advanced Genomics with our new distributor, World Fusion Co., LTD, in Tokyo, Japan.

Attending this conference was a first for GenoLogics, and we were happy to see other major players in genomics in Japan:  Illumina, Life Technologies, Roche, Qiagen, PacBio, Sequenom, Agilent, Fluidigm, Perkin Elmer, and many more.

World Fusion will be helping us get BaseSpace Clarity LIMS into the hands of people who need it in Japan. They are also responsible for distributing other NGS software favorites such as CLC Bio and Life Science Knowledge Bank (LSKB).

While there, I was able to slip out of the booth to attend several presentations, which included a range of different genomic technologies and applications. While many of the talks were in Japanese, I’ve included a few interesting highlights for customers considering the Ion Proton or Ion Torrent systems.

Thinking about implementing an Ion Proton sequencing system?

Joseph Boland, Director of Research and Development at the Cancer Genomics Research Laboratory at the National Cancer Institute can provide some insight.  In his talk “Exome, Transcriptome, and Whole Genome Sequencing on Life’s Proton Sequencer: Cost Effective, Rapid Turnaround and High Impact Discoveries at the Cancer Genomics Research Laboratory,”  Joseph discussed his organization’s experience with Life Technologies’ Ion Torrent™ Personal Genome Machine (PGM) and Ion Proton™ sequencing systems.

While six PGMs serve as the lab’s workhorse for amplicon sequencing, the lab’s four Ion Proton instruments have each been producing 4-8 exomes per day. On average, Mr. Boland reported that it takes only 3.5 sequencing hours, plus the analysis, which takes an additional 8-11 hours. To date, the team has surpassed 315 runs on the Proton machine and completed more than 200 exomes. They are using LifeTech’s TargetSeq Exome v2 kit. Throughput currently sits at 12.6GB per machine.

For more information, I recommend reviewing Joseph’s publication, which you can find here.

Are you a Torrent user?

Andrew Felton, in his talk titled “High Throughput Genome Scale Bench-top Semiconductor Sequencing Roadmap – Ion Torrent™,” provided a thorough update.  Version 3.6 of the Torrent Suite Software enables tunable variant calling. I should note that this software interfaces with BaseSpace Clarity LIMS to automate data capture to and from the Ion Torrent and the LIMS. Andrew also mentioned  Ion Reporter software, which provides automated informatics and interpretation.

Switching gears from informatics solutions to hardware, Andrew recommends Proton. P I chip for whole exome and transcriptome sequencing while the PII chip is recommended for whole genomes. Additionally Andrew reported that the throughput of PI chip as of Feb 2013 is at 15.2 GB.

Just as interesting as hardware and software updates was the mention of the progress of PGM FDA approval. Andrew mentioned that this processes is expected to be done by end of 2013.

Happy sequencing!  For more information, contact us with any questions.

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