With the beginning of the influential JP Morgan Healthcare investor conference this week in San Francisco, you can expect an avalanche of news from companies large and small regarding all things therapuetic and diagnostic. With an official count of about 9,000 attendees, there are many more in San Francisco who are there to have other … Read more
The annual AACR (American Association for Cancer Research) meeting was held in Philadelphia PA from April 18-22, and being able to attend several sessions is a privilege. (Yes I’m writing this the morning of the last half-day, knowing that there’s still a full morning of sessions including the last poster session.) Over the years there … Read more
Theral Timpson produces a weekly podcast at Mendelspod.com, and in his latest edition he interviews me about Google X Life Sciences (I wrote about them before here), long-read sequencing (in particular Pacific Biosciences) which then I’m able to discuss the value of complete human diploid sequencing, and my involvement with the Behind the Bench blog. … Read more
Yesterday’s Ion Torrent Proton PII™ and Illumina NextSeq 500™ post certainly got a reaction from several quarters, including detailed pricing information about the 1x75bp format for the high-throughput configuration on the consumables. Instead of making edits to the original here are some clarifying points, as it is clear that Illumina is making a break from … Read more
There has been a lot of publicity around the NextSeq 500 from Illumina, and it appears to have been designed to compete directly against Ion Torrent’s upcoming PII chip. Thanks to a visit to upstate New York last week, I met Dr. Sridar Chittur who told me how important it was to put current information out on this blog, and if I can put out the disclaimers up-front it would be very helpful for those thinking about what benchtop system to purchase over the next several months.
There are several commercial methods for looking at 10’s or 100’s of gene expression levels via a high throughput TaqMan™ assay from Life Technologies / Thermo Fisher Scientific, a competitive offering from Roche, Douglas Scientific, or also Fluidigm. The limitation of these technologies however is the amount of multiplexing a single assay in a given volume, which regardless of the amount of miniaturization does limit the samples by genes evaluated throughput.
To perform RNA-Seq, one looks at all the particular RNA species present, dependent upon the up-front sample preparation. (To clarify, a miRNA experiment would purify small RNAs then go into cDNA synthesis and sequencing; mature polyA+ RNA can be purified and then cDNA made and sequenced etc.) But what about a targeted set of expressed genes to evaluate via NGS?
One of the most interesting liquid handling technologies I’ve seen in a while was from a Limerick (Ireland) company called Gen Cell Biosystems. As a person who used to hear all about Laboratory Automation from the BioRobot™ folks in my days at QIAGEN, as well as the Society for Biomolecular Screening (SBS) also from my prior work in the protein purification and detection business (read: everything and anything about His-tagged proteins), it should not have come as a surprise that several years ago both associations merged to form the Society for Laboratory Automation and Screening (SLAS).
Over the two days right before the annual ASHG (American Society of Human Genetics) meeting in Boston, Life Technologies held a two-day event where several hundred Ion Torrent customers and other interested parties attended.
Updates for three upcoming products (the Ion Chef automated template prep, the PII chip, and a product formerly called Avalanche but is now generically named ‘Isothermal Template Prep’) were shared which were expected. A new more highly accurate sequencing polymerase was announced.
Today Ion Torrent launches a neat product based upon a highly multiplexed technology called AmpliSeq, called the Ion AmpliSeq Exome, covering >97% of the CCDS regions. But before getting into the details, a little context is in order.
Product launches are exciting things, and the Ion Torrent Proton has officially launched (as of the recent Ion World conference September 13-14, 2012). For those who were not able to make it to San Francisco for that two-day event, we now have the videos of four presentations up on the Ion Torrent YouTube channel, and for those who have complained about the ‘lack of data from the Ion Proton’ there’s quite a lot of ground to cover, and there’s a fair amount of interesting items about the PGM too. The Ion World-specific list of videos are linked here on an Ion Torrent Community page for ease of reference.
A Life Technologies-sponsored 2-day conference called Ion World 2012 kicked off yesterday afternoon, with Jonathan Rothberg founder of Ion Torrent, Tim Triche of the Childrens Hospital of Los Angeles, Joe Boland of the Division of Cancer Epidemiology and Genetics at the National Cancer Institute, Shawn Levy of Hudson-Alpha Biotechnology Institute, and Craig Venter from Synthetic Genomics and the J. Craig Venter Institute all speaking.
There is a lot of interest in what is the Next Big Thing in next-generation sequencing. The case can be made that the clinical application of NGS (either targeted sequencing or WES or WGS for cancer genomics) will be that growth driver, but I suspect it will be the next generation of next-generation sequencing.