Ion GeneStudio S5: The latest iteration of Thermo Fisher Scientific NGS

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

SeraCare Precision Oncology

Seracare precision medicine ngs control reference material seraseq mutation mix
The Seraseq Solid Tumor Mutation Mix-I (AF20), the first product from SeraCare’s Precision Medicine Group

This post is about Seracare’s new direction for Precision Medicine (in particular Precision Oncology), and the launch of a new product the Seraseq Solid Tumor Mutation Mix-I (AF20). But I’ll start first with a story from my days at Illumina.

It was ten years ago this week that I last launched a product. It was the Illumina Infinium Human-1 Genotyping BeadChip, and it took months of hard work, many core-team meetings, plenty of long days and many hallway discussions about the finest details of the product. Long days and many meetings go together: how can you get the things you commit to in a meeting ever done if you go to many meetings?

And in case anyone is wondering, yes that is the job of a Product Manager – you get to work hard and work closely with a team from across different areas of the company (research, manufacturing, quality, support, and engineering) and you get to experience many ups-and-downs, and learn things about yourself and others through this experience that you carry with you. These may be hard days, but they are good ones.

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Targeted RNA Sequencing Approaches

Happiness is getting more of what you want, in RNA-Seq as in other things...
Happiness is getting more of what you want, in RNA-Seq as in other things…

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?

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Gen Cell Biosystems’ CLiC NGS Library liquid handler at AGBT 2014

Standing in front of the CLiC LP at AGBT
Standing in front of the CLiC LP at AGBT

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).

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Ion Chef, PII Chip, Isothermal Template Prep and a new Hi-Q Enzyme at Ion World 2013

Ion World announcements
Ion World announcements

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.

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Readlengths do matter in Next Generation Sequencing

Notebook cover from AGBT 2009 (c) Dale Yuzuki

Recently I was asked about how important readlengths are, in the context of where MiSeq and Ion Torrent PGM currently stand in the marketplace. As the 454 advertisement used to say until recently, ‘Length Matters’. Given a number of recent announcements from Ion Torrent and the other folks in San Diego, let’s assess where we are.

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