sequencing


It’s Pretty Bad: Andy Brooks of RUCDR on Sample Quality

The future of diagnostics is in the hands of those taking care of the biospecimen samples says, Andy Brooks our final guest in the series, Improving Biospecimen Standards. Andy is the Chief Operating Officer at Rutgers University Cell and DNA Repository, or RUCDR.

While acknowledging that the current state of tissue sample collection, handling and storage is “pretty bad,”  Andy points to areas where progress has been made. And he would know. RUCDR serves as the biorepository for 4 NIH institutes. A biobank such as RUCDR is a unique place where various segments of biomedical research—academia, industry, regulation-- come together.

Andy was at the convergence summit put together last December by Carolyn Compton and the National Biomarker Development Alliance (see our interview with Carolyn here) to develop some standards in this area. While he’s excited to see Carolyn rally the community and bring CAP and the FDA on board, he sounds a warning.

“There’s only so much you can do to standardize samples at the time of collection and control for variables, some of which are uncontrollable," he says.

So what can be done?

Andy and his colleagues at RUCDR have made important strides toward developing what one of our former guests called a "tissue quality index,” a score that will tell you whether a sample in storage is what you think it is. While they don’t have an overall score yet, Andy and his team have worked with companies like Fluidigm and Wafergen to develop a panel that measures the quality of some analytes and can predict the performance of a sample.

We end the interview with Andy’s thoughts on the future of genomic consent.

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Faces of Leadership in Diagnostics: Mara Aspinall

Guest:

Mara Aspinall, Founder, DxInsights

Bio and Contact Info

Listen (2:43) DxInsights and EPEMED

Listen (3:53) Diagnostics 5.0

Listen (2:43) International School of Biomedical Diagnostics

Listen (3:43) FDA Guidance on LDTs: the right time? the right move?

Listen (3:53) Angelina Jolie: a teaching moment

Listen (4:17) What translational gap?

Listen (1:56) Educating payers

You could call her Ms. Dx Education. Mara Aspinall has served as CEO of diagnostics companies big and small, but she’s also spent a great deal of time building a diagnostics community. Some of the early meetings of the Personalized Medicine Coalition took place in her home.

Recently Mara has stepped up her efforts in diagnostics education: that of the industry players, of physicians, and also of the next generation. She’s a co-founder of DxInsights, a new non-profit focused on better education that has already put on their first conference. DxInsights recently announced a partnership with EPEMED, or the European version of the Personalized Medicine Coalition, to create a new Knowledge Center. She is perhaps most proud of helping to create a new International School of Biomedical Diagnostics which has enrolled their first graduate students this year. This school is a first of its kind, pulling faculty expertise from various organizations in Southern Arizona as well as Dublin City University.

“We have medical school students requesting that sequencing--and what I call “Diagnostics 5.0”-- be a part of their curriculum, and it has not been,” she says in today’s interview.

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Mara is a supporter of the FDA’s recent move on LDTs, saying that the current system for diagnostics has not been working. She thinks new regulation that levels the playing field among the various players will help to spur business and innovation because it offers a more predictable path to market.

We end with her thoughts on physician and payer education.

Podcast brought to you by: Slone Partners - Premier talent. Delivered.

George Church at 60

Guest:

George Church, Professor of Genetics, Harvard Medical School 

Bio and Contact Info

Listen (6:11) Church's Law

Listen (6:45) Colbert, Der Spiegel and Regenesis

Listen (2:49) Do you have a hobby?

Listen (8:22) The promise of 3D sequencing

Listen (4:42) Is long reads the NGS story of the year?

Listen (6:02) Have you heard any good arguments against GMOs?

Listen (5:46) How much wet lab vs. coding for the new biologist?

Listen (2:57) 60th Birthday Bash

If we have celebrities in the life science industry, George Church of Harvard is one of them. Author, professor, entrepreneur, advisor—the list goes on and on. One of the special things about George is his commitment to advocate for science to the larger community. With everything else he has going on, he makes time to talk on programs like ours.

We launched Mendelspod with a George Church interview. Three years later, it’s a treat to have him on again to talk about his work, career, philosophy, and take a few questions from the audience.

Thanks to IDT for underwriting this show.

Podcast Sponsor: Integrated DNA Technologies - providing custom double-stranded gBlocks Gene Fragments of up to 2 kb, for easy gene construction.

Short Read Sequencing Not Up to the Task of Characterizing Transcriptome Says Mike Snyder of Stanford

Guest:

Mike Snyder, Director, Center for Genomics & Personalized Medicine, Stanford Bio and Contact Info

Listen (5:44) Current method for figuring out transcriptomes is crazy

Listen (4:18) Long reads necessary to find paternal or maternal alleles

Listen (4:31) Practical applications of the transcriptome

Listen (4:41) Has the race to the $1,000 Genome been at the expense of quality?

Listen (6:33) If price drops for long reads is there a future for short reads?

Today we launch the much anticipated series on The Rise of Long Read Sequencing with Mike Snyder, Chair of Genetics at Stanford. Mike has been working four years on what has become known as the “Snyderome” (or "Narcissome" as his colleagues call affectionately call it), looking at hundreds of thousands of his own molecular biomarkers regularly over time. Lately Mike has been focused particularly on his transcriptome, or RNA molecules.

The transcriptome is studied by looking at individual isoforms. On average, every gene has five or six isoforms or transcripts. Recently Mike has co-authored a couple papers showing that it is difficult to identify full-length transcript isoforms using the current short read sequencing technology.

“The way we figure out transcriptomes now is kind of crazy if you think about it," he says. "We take RNA. We blow it up into little fragments, and then we try to assemble them back together to understand what the transcription looked like in the first place. That’s a horrible way to do this.”

Mike explains how PacBio's long read technology is opening up new possibilities for characterizing the transcriptome and identifies some of the practical applications that might come from his research.

So what does this mean about the future of NGS? If PacBio or one of the emerging nanopore sequencing companies can offer long reads at high throughput, is there any reason why a researcher would use short read technology?

"If the long reads are high quality and cheap, you wouldn't need the short reads. . . [long reads] would take over the market." Mike says.

Reflecting on the rapid changes we've seen in the NGS space from year to year, he says, "next year we'll probably have a whole different conversation."

Roche Sequencing Preparing a Full Workflow Liquid Biopsy Platform

Today's interview is with John Palma, Senior Director of Medical Affairs with Roche SequencingSolutions. John says that Roche is going for a best-in-class, full workflow liquid biopsy solution, from sample prep to final data reporting.

So what will be the competitive advantage to Roche's liquid biopsy platform? Which analytes are they focused on: circulating tumor cells, cell free DNA, exosomes? And will they go RUO or IVD?

The incredible growth of prenatal diagnostics has rapidly advanced liquid biopsy technology, says John. And Roche is already a major player in the prenatal space with their Harmony test.



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