DNA sequencing


Traveling in Time One Minute Per Minute: David Orban

This interview originally aired January 8, 2013.

Guest:

David Orban, CEO of Dotsub Bio and Contact Info

Listen (2:35) What is Dotsub?

Listen (9:30) Why should we think about the future?

Listen (3:08) Do we have more control of the future in this age of science and technology?

Listen (6:07) Why is it so hard to agree on the future?

Listen (6:55) We are part of a biological experiment run amok that we are now running

Listen (5:31) Will scientists be the new world rulers?

Why should we think about the future, I ask David Orban, the CEO of Dotsub in today's interview. David is an "unabashed" futurist. At Dotsub, a video sharing site with translation services, David is taking part in what he calls the move to a "network society." I'm not asking David why we should have goals or plan say an interview on Tuesday of next week, or a doctor visit in three weeks. I'm talking about far into the future. How much control do we have over the future? Actually, what is the future? David has thought and talked a lot about these questions and shares his observations on future trends, particularly those of biotech. "We're part of a biological experiment run amok," he says in the interview. "And now we are running it."

Podcast brought to you by: Assay Depot - the world's largest cloud-based marketplace for research services. With Assay Depot, you can easily find the perfect research service provider and manage your project from anywhere in the world.

Inside the World of Prenatal Diagnostics: Charles Cantor, Sequenom

Guests:

Charles Cantor, PhD, Chief Scientific Officer, Sequenom

Bio and Contact Info

Listen (6:39) What led you to Sequenom?

Listen (3:08) What has been the biggest challenge in commercializing NIPT?

Listen (6:12) Sequenom view on patent controversy

Listen (6:33) How good is the quality of the tests?

Listen (2:48) Do you plan to submit tests to FDA?

Listen (5:25) Diagnosing cancer during pregnancy and the issue of incidental findings

Listen (2:44) Three improvements needed from sequencing tools

Listen (3:07) The possibilities of in-utero therapy

On October 17 of 2011, Sequenom announced a clinical study had been published in the journal of Genetics in Medicine on their new sequencing based prenatal test for Down Syndrome. On the same day, the company launched their MaterniT21test. The rapid clinical adoption of this test--and those from three competing companies -- is without a doubt the biggest success story for the use of DNA sequencing in the clinic. According to the Wall Street Journal, in 2012, Sequenom alone sold 61.000 tests.

Today Fortune ran a piece on non-invasive prenatal testing (NIPT) predicting "the adoption of NIPT across the board as a standard test for all pregnant mothers, something as routine as ultrasound."

What has been the biggest challenge in commercializing a test using DNA sequencing? Does Sequenom have plans to submit the test to the FDA for approval? Dr. Cantor is not shy about answering tough questions. In today's show he walks us through the challenges the company faces, including emerging ethical quandaries such as the question of reporting incidental findings and the new possibilities for in-utero therapy.

Podcast brought to you by: Myraqa Clinical Research: The CRO for Point of Care and PMA Diagnostics.

and by: Roche Molecular Systems: A proud sponsor of today's podcast.

Genus envy

In 1997, a breakthrough was made in rare/orphan disease research. An evolutionarily conserved gene called NPC1 was shown to be responsible for Niemann-Pick disease type C, a degenerative lysosomal storage disorder that affects 1 in 150,000 people on Earth, half of whom manifest symptoms as children. The discovery of NPC1 should have unleashed a torrent of follow up studies in simple model organisms like yeast, worms and flies, all of which have an ancestral version of NPC1. Instead, what followed was a trickle, with clunky rodent models getting all the basic research attention.

Joel Dudley Discusses New Book, "Exploring Personal Genomics"

Guests:

Joel Dudley, Co-Author, Director of Biomedical Informatics, Mt. Sinai School of Medicine Bio and Contact Info

Listen (1:46) The bet on computation and genomics at Mt. Sinai Hospital

Listen (2:32) A new handbook, Exploring Personal Genomics

Listen (6:34) Who is the audience for the book?

Listen (4:05) What did you learn from the project?

Listen (3:25) How can the book help clinicians?

Listen (6:58) NuMedii and drug repurposing

One of the major obstacles to personalized medicine is that today's generation of clinicians are not up on the latest in genomics. Today's guest is a rising star in the world of genomic medicine who has written a book to address this issue. Coming from Atul Butte's lab at Stanford, then co-founding a company to commercialize algorithms for repurposing drugs, Joel Dudley is now working with Eric Schadt at Mt. Sinai Medical Center in New York. Joel was an author on one of the first papers to interpret a genome which put him on the front lines of genomic medicine. He's now taken this journey as a genomics hacker and put it into a handbook with co-author Konrad Karczewski, "Exploring Personal Genomics."

The book reviews the various sequencing technologies as well as the emerging bioinformatics platforms for analyzing the sequence data. Though full of technical detail and many images, some of which have never been seen in print, the two authors aimed for an audience such as clinicians who don't know that much about informatics or "Google and Facebook hackers" with little knowledge of biology. "We wanted to make it as accessible as possible," says Dudley in the interview, "but what we did not want it to be was a stuffy textbook . . . that would only be given out at universities."

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

Dietrich Stephan Hits the Refresh Button with SV Bio

Guests:

Dietrich Stephan, Founder, CEO, SV Bio Bio and Contact Info

Listen (5:24) What makes this the right time for SV Bio?

Listen (6:03) What does the SV Bio product look like?

Listen (2:38) Healthcare IT behind by several decades

Listen (6:52) How are you selling your product?

Listen (6:11) Whole genome pricing level still uncertain

Listen (5:02) The big ambition

On January 15th of this year a new company, Silicon Valley Biosystems, or SV Bio, was launched in the clinical genome interpretation space. And just this past week the company's lab gained CLIA certification. Founder and CEO, Dietrich Stephan was the creator several years back of Navigenics, a direct-to-consumer approach to personalized medicine. Navigenics was acquired by Life Technologies in the summer of last year. Stephan is quoted in Bio-It World as saying he “wanted to hit the refresh button and do the necessary inventing around rare variants now that the time is right.” Today he joins us to share his ambition for what he considers THE scalable platform and tell us why the time is right for SV Bio and genomic medicine.

Podcast brought to you by: Myraqa Clinical Research: The CRO for Point of Care and PMA Diagnostics.

and by: Roche Molecular Systems: A proud sponsor of today's podcast.

After Buyout, Cliff Reid, Complete Genomics Stay on Track

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

Guests:

Cliff Reid, PhD, CEO, Complete Genomics Bio and Contact Info

Listen (3:32) Audience questions about Long Fragment Read technology

Listen (3:53) From 200 to 5000 people

Listen (4:11) How do you respond to national security questions?

Listen (4:39) Genomic tests will be commodotized like computers

Listen (7:38) Thoughts on bioinformatics

Listen (2:44) Conversation of bioethics being changed by Facebook generation

Listen (2:51) Future role at the company

In March of 2006, Cliff Reid teamed up with Rade Drmanac and John Curson and founded a company to commercialize a new DNA sequencing platform. But rather than make another sequencing tool and sell it, the company, known as Complete Genomics, would use a different model. They would be devoted entirely to sequencing human genomes as a service. In February of 2009 the company announced its first human genome. By the end of '09, Complete had sequenced 50 human genomes. And in the 3rd quarter of 2010, they sequenced and analyzed 300 human genomes. In 2012, BGI, or Beijing Genomics Institute, offered to purchase Complete for $117 million, and after clearing regulatory hurdles in the US and China, on March 18th the acquisition of Complete was complete.

CEO, Cliff Reid, joins us today in one of his first interviews after the buyout sounding as enthusiastic and on track as he did in our earlier interview. He admits there's a joke in his family that "the fourth time is the charm," because he was involved with two other startups that were ahead of their time. Cliff will be staying on as CEO with the same vision of advancing clinical genome sequencing. He says the company will be commercializing their LFR or Long Fragment Read technology, and he answers questions from our audience about when and how. Acknowledging that the company didn't have the staying power to get to the clinical market and were squeezed out of the research market by an unforeseen preference for exome sequencing, Cliff is still bullish that the price of genome tests must continue to come down further to make a difference in healthcare around the world.

Eric Topol and His "Creative Destruction"

Podcast brought to you by: The Burrill and Buck Aging Conference Explore how innovative approaches from regenerative medicine to digital health stand to change our notion of what it means to grow old.

Guests:

Eric Topol, MD, Cardiologist, Genetic Researcher, and Technologist Bio and Contact Info

Listen (6:22) Patient stories heard at Future of Genomic Medicine Conference

Listen (4:34) Medical community's response to book

Listen (6:02) "I just wish I could go back and start medical school again"

Listen (4:30) Eradicate fee for service

Listen (3:05) Craig Venter: Quality of sequencing has gone down

Listen (4:29) "De"personalized medicine?

Listen (0:58) Excited about rollout of sensors

Eric Topol joins us to discuss what was perhaps the most talked about book in the life sciences in 2012, his "The Creative Destruction of Medicine." In his book, Topol tells of the now arriving era of individualized medicine and the rise of "homo digitus," or digital man. In today's show, Topol dives into some key topics from the book such as how to deal with misaligned incentives in healthcare. "I just wish I could go back and start medical school again because this is truly an era . . a renaissance, an enlightenment in the medical space," says Topol when asked about what he advises young people.

Dr. Topol recently hosted the Future of Genomic Medicine Conference at The Scripps in San Diego, and he begins the interview giving some highlights of patient stories.

Bioinformatics 3.0: an App Economy with Matt Landry, Biomatters

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

Guest: Matt Landry, CTO, Biomatters
Bio and Contact Info

Chapters: (Advance the marker)

0:37 What is the focus of Biomatters?

4:32 Hack or bioinformatician?

8:52 Are you seeing the commoditization of bioinformatics?

10:38 Bioinformatics 3.0: an app economy

16:49 The state of genomic medicine in New Zealand

21:59 Have you started thinking beyond the cloud?

Matt Landry calls himself a hack rather than a bioinformatician. He's the Chief Technology Officer at Biomatters, a bioinformatics company based in New Zealand that provides an easy-to-use desktop application for biologists. In today's show, Landry explains that coming up with a user friendly platform called Geneious has been the main driver for the company. If you're looking to write your own command line, Geneious is probably not for you, says Matt. He believes that the next phase for bioinformatics will go the user friendly direction and be based on an app model similar to the Apple platform. This makes him very interested in the two cloud based platforms offered by Illumina and now the new one released in beta by DNAnexus.

New Zealand is a country with a small population and a national health service, and Matt comments on the opportunities for genomic medicine in such a country. How do we change the culture of the medical ecosystem, and what comes after the cloud? Matt works out on the front lines and tackles these questions head on.

Looking at the Big Picture in Bioinformatics with Christophe Lambert, Golden Helix

Podcast brought to you by: Ingenuity Variant Analysis - Identify causal variants from human sequencing data in just hours.

. . . and by Biotix - makers of A BETTER TIP(TM) for Next Gen Sequencing

Guest:

Christophe Lambert, PhD , CEO, Golden Helix, Inc Bio and Contact Info

Listen (6:56) Beware the lure of solving tough problems for a small market

Listen (8:32) Is Illumina competing with their customers?

Listen (9:37) If the end user isn't buying, no one is selling

Listen (6:36) Learning from our GWAS mistakes

Listen (4:14) Where has Golden Helix found success?

Today we transition from our series on sequencing to one on bioinformatics. Christophe Lambert is the CEO of Golden Helix, a bioinformatics company based in Bozeman, Montana. With some degrees in computer science, Lambert saw early on the potential for IT in bio and began Golden Helix back in 1998, the same year Ingenuity Systems was founded. A research internship led to some funding from Glaxo Welcome and Lambert says he "started writing code in his bedroom" with no one to talk to but his wife.

Lambert's fourteen years in the business combined with his ability to think systematically has given him an insightful perspective on the industry. He's one of the few in this exploding field who acknowledges that the industry is quite small, not yet really making it to the clinic. "When the end user is not buying, no one is selling," he says in today's show. Lambert's impulse is to always look at the macro picture, probing why the science isn't there yet and what societal issues are holding back genomic medicine. I tried to pull him back a bit and get more information on Golden Helix, but half way through the interview, I just went with him. I highly recommend his blog at http://blog.goldenhelix.com/?author=5. This Montana Canadian has something to say.

Debating ENCODE Part II: Ross Hardison, Penn St.

Podcast brought to you by: See your company name here. - Promote your organization by aligning it with today's latest trends.

Guests:

Ross Hardison, PhD, Professor of Biochemistry and Molecular Biology, Penn State University Bio and Contact Info

Listen (3:39) ENCODE has provided valuable data

Listen (3:36) Lineage specific selection

Listen (6:50) Looking for specific biochemical activities that are important

Listen (9:28) It's not so simple as big science vs small science

Listen (4:08) Have the critisicms changed your mind at all?

Listen (4:11) The debate itself a great outcome

In an earlier show, we interviewed Dan Graur and Michael Eisen about the ENCODE project, a massive research undertaking to further characterize the human genome. It’s been done by over 400 researchers at a cost of over $400 million. Both of the guests were quite critical of the published findings of the project and of big projects like this in general.

To represent the ENCODE project we're joined by Ross Hardison, a professor of Biochemistry and Molecular Biology at Penn State University and a collaborator on the ENCODE project from the beginning. Ross says he is delighted with the debate about how much of the genome is functional that the Graur paper has excited. And he makes a strong argument that the ENCODE team was focused on specific biochemical activities, and that these are important. He says Graur's charge on our previous show that the project might have called 100% of the genome functional because all DNA replicates, "just silly." He also says that Graur's and Eisen's rants about Big Science don't mean much to him. He considers himself a researcher funded by RO1's just as they are. It's not as simple as Big Science vs. Small Science. What was the goal of ENCODE and are they reaching that goal, we ask Hardison in Part II of Debating Encode.




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