Next Gen Sequencing – Page 5 – Next Generation Technologist

Dana Pe’er, Garry Noland and single-cell proteomics at AACR

April 10, 2014 by Dale Yuzuki

Standing-room only crowd at the 2014 AACR Symposium "Single Cell Analysis of the Tumor" — Standing-room only crowd at the 2014 AACR Symposium “Single Cell Analysis of the Tumor”

During AACR a number of great sessions were presented at ‘meet the expert’ sessions at 7am in the morning. One benefit of coming out West from the East Coast is not being able to stay up past 10:30pm or so local time, and waking up on my own at 4:30am local time every day. (A friend from the NCI told me he doesn’t like to ‘ping-pong between time zones’, and I whole-heartedly agree!)

At one of the these 7am sessions was one by Dana Pe’er of Columbia University, entitled “Understanding tumor heterogeneity using 40 markers at single cell resolution”. I thought: intriguing title, this should be interesting.

Steven Rosenberg and T-Cell Immunotherapy for Cancer

April 8, 2014 by Dale Yuzuki

Steven Rosenberg, NCI at a 2014 AACR Plenary Session

As a person who worked at a melanoma research institute once upon a time (the John Wayne Cancer Institute in Santa Monica California, by the way), it was a pleasure to hear Steven Rosenberg’s plenary talk at the AACR meeting in San Diego. A lot has happened since 1997.

It was in the mid-1990’s that I was working in the laboratory of Dr. David Hoon, and the Institute was one of the few groups at that time that had several groups working on tumor immunology. One of our main ‘competitors’ in the tumor immunology field (for metastatic melanoma) was Steven Rosenberg of the National Cancer Institute, which had the history of being the longest NCI Research Program Project grantees at that time (JWCI had the second-longest one).

Elana Simon at the American Association for Cancer Research

April 7, 2014 by Dale Yuzuki

Elana Simon receiving the Junior Champion Cancer Research Award, AACR 2014

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 year by the AACR organization called the ‘Junior Champion Cancer Research Award’, and she was the recipient. Her story began when she was 12 years old, diagnosed with a rare Fibrolamellar Hepatocellular Carcinoma, a form of liver cancer. Surgery was their only treatment option.

Notes from the NCI’s Third Symposium on Translational Genomics

March 28, 2014 by Dale Yuzuki

Edison Liu, director of Jackson Laboratories Center for Personalized Medicine, at the NCI Third Symposium on Translational Genomics — Edison Liu, director of Jackson Laboratories Center for Personalized Medicine, at 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 Health, and last week I had the opportunity to attend the NCI’s Third Symposium on Translational Genomics. With speakers like Edison Liu (the leader of the new Jackson Laboratory personalized medicine center in CT founded in 2011 with $1.1B in public and private funding), George Church (who I haven’t heard in-person since the 2012 AGBT meeting), and others who I have personally interacted with at the NCI in the past (Snorri Thorgeirsson, Louis Staudt and Jean Claude Zenklusen), I knew that this meeting was going to be worth attending.

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

March 24, 2014March 19, 2014 by Dale Yuzuki

A WaferGen chip, finger and photo courtesy Dale Yuzuki — A WaferGen chip, photo courtesy Dale Yuzuki

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 96). The concept is that each well contains a real-time assay master mix and the sample of interest, and a flexible format of sample number / real-time targets (either gene expression or end-point genotyping) can be performed in a single run.

Ion Chef™ System ships to first customers

March 14, 2014March 13, 2014 by Dale Yuzuki

Ion Chef Shipments going out (photo credit to Michael Aken of Life Technologies)

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 popular choice, but Tecan and Hamilton and others share the market), and many options when it comes to setting up reactions in a 96-well format.

But when it comes to taking a single next-generation sequencing library molecule, affixing that molecule to a bead or particle (or in the case of a 5500xl Wildfire or Illumina flowcell) and then amplifying that molecule 1000’s or 100’s of thousands of times is not a trivial task. This is typically termed ‘template preparation’ – alternatively Illumina calls it ‘cluster generation’.

Some clarifications about Ion Torrent PII and NextSeq 500

March 11, 2014 by Dale Yuzuki

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

The upcoming Proton PII and the NextSeq 500

March 10, 2014March 10, 2014 by Dale Yuzuki

Record PI runs with a 20.5GB at the top, from the Ion Community site

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.

Nabsys single molecule mapping technology

March 3, 2014 by Dale Yuzuki

Close-up of Nabsys Chip 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 with the competitive landscape, here are prior pieces written previously called BioNano Genomics, Opgen and Copy Number Variation, and an update on BioNano from last Fall’s ASHG meeting. So while BioNano Genomics and OpGen both use optical mapping of single molecules, Nabsys uses electrical detection. (Cue the optical vs. digital detection methodology of Ion Torrent here).

Targeted RNA Sequencing Approaches

February 24, 2014 by Dale Yuzuki

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?

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

February 20, 2014 by Dale Yuzuki

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).

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

February 20, 2014February 19, 2014 by Dale Yuzuki

The LifeTech Variant Detective Showcase at AGBT 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 a fraction (some 1/36th) of the time, it wasn’t because of the elegance of the presentation – it was because it was for the first time in 10 years that Gene Myers attended AGBT, and for a simple reason – he did not consider short-read sequencing ‘intellectually satisfying’.

You know you are hearing from an unusually talented person when they talk about things that are intellectually satisfying.