Elana Simon at the American Association for Cancer Research

The reason I enjoy coming to large meetings like the American Association for Cancer Research (April 5-9 in San Diego) is the surprising things I learn. And the story of Elana Simon is one of them. She did not appear on the program, but a new award was initiated this […]

Notes from the NCI’s Third Symposium on Translational Genomics

Living in the Washington DC area is a privilege. As a native Californian who has been on the East Coast for about 7 years now, living in the Mid-Atlantic has been so enjoyable for many professional and personal reasons. A case in point is proximity to the National Institutes of […]

WaferGen SmartChip TE™ – a PCR-based approach to target enrichment 2

WaferGen is a California Bay-Area company that originally developed an idea similar to BioTrove, which was to create a solid substrate with nanoliter-sized wells for high throughput real-time PCR. WaferGen’s SmartChip™ has 5,184 wells (that’s a 54 multiple of 96), while BioTrove’s OpenArray™ has 3,072 (that’s a 32 multiple of […]

Ion Chef™ System ships to first customers 2

Way back when I was pouring 35S-labeled dNTP Sanger sequencing polyacrylamide gels (and fond memories of using reagents like degassed acrylamide, TEMED and Silane), robotic automation was at that time only in an industrial or manufacturing context. Now there are many automated liquid handling companies (for example Beckman is a […]

Some clarifications about Ion Torrent PII and NextSeq 500 2

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 […]

The upcoming Proton PII and the NextSeq 500 11

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 […]

Nabsys single molecule mapping technology

Another interesting single-molecule technology is a company out of Providence (RI) called Nabsys. For several years I had heard the name involved in developing single-molecule sequencing technology, and this technology will start its initial product around genomic mapping, rather than sequencing. For background on genomic mapping and CNV analysis along […]

Targeted RNA Sequencing Approaches 1

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 […]

Gen Cell Biosystems’ CLiC NGS Library liquid handler at AGBT 2014 1

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 […]

A favorite talk at AGBT 2014 – Gene Myers (Max Planck Dresden) 3

A thoroughly enjoyable surprise at the Advances in Genome Biology conference last week was hearing Gene Myers of Max Planck Institute of Molecular and Cell Biology in Dresden, Germany. It wasn’t because it was about assembling a de-novo human genome at 54x coverage from a Pacific Biosciences RSII dataset in […]

Oxford Nanopore at AGBT 2014 2

A few attending the Advances in Genome Biology and Technology meeting in Marco Island Florida (February 12 – 15 2014) have blogged about a presentation from David Jaffe (Broad Institute), presenting the first data the next-generation sequencing community has publicly seen from Oxford Nanopore Technologies. For those not familiar with […]

Post-AGBT 2014 Thoughts & Jeffrey Schloss’ Plenary Talk (NHGRI)

Today (February 17, 2014) marks the end of the 2014 Advances in Genome Biology and Technology, an annual gathering whose principals include Dr. Eric Green (Director of the National Human Genome Research Institute) and Dr. Elaine Mardis (co-director, with Rick Wilson, of the Washington University Genome Institute). Every year they […]