genomic medicine


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.

Open Source or Commercial? Lasse Goerlitz, CLC Bio, Talks Bioinformatics

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

Guests:

Lasse Goerlitz, VP of Communications, CLC Bio
Bio and Contact Info

Listen (5:16) Highest demand coming from agro

Listen (3:06) What is holding back the adoption of genomic medicine?

Listen (4:03) A commercial platform with plug-ins

Listen (3:37) Open source vs commercial software

Listen (4:40) The all-in-one guys

Listen (5:56) Genomics in Europe

The repeating trend from industry to industry is for software to go from fragmented, custom applications toward larger dominant platforms. It's still the early days for bioinformatics, and just who the dominant platforms of the future will be remain unknown. Will they be open source, public platforms or commercial platforms?

CLC Bio, a bioinformatics company has been working on the solution for eight years now and hopes that their platform which works with many different plug-ins will become number one for biologists around the world. In today's show, CLC's VP of Communications, Lasse Goerlitz, talks about their platform and trends in genomics. Currently their heaviest users are in ag bio, but the demand from the clinic is rising. We conclude with a discussion of differences between Europe and the US in the genomics space.

The Roller Coaster of Clinical Genomics with Tim McDaniel

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

Guests:

Tim McDaniels, PhD, Director of Scientific Research at Illumina
Bio and Contact Info

Listen (5:07) Mom diagnosed with rare T-cell cancer

Listen (7:50) Path to genome sequencing

Listen (5:56) Finding two key genes leads to unusual treatment

Listen (5:30) Regression, then reoccurence

Listen (4:54) How has this changed your view of health?

Today's story is a roller coaster of a ride. So far genomic medicine continues to be about those patients who by chance come across someone with knowledge of the latest in genomics.

Tim McDaniel is a Director of Scientific Research at Illumina, and so was in a unique position when his mother was diagnosed with a rare T-cell cancer. In the beginning of her illness, which first manifested as a nasty skin rash, Tim's mother, Beth, was in that "wilderness of rare illnesses." Her chance upon a doctor who had some experience with her cancer was just the beginning of this up and down tale. Tim attended the AGBT conference in Marcos Island, FL as part of his job at Illumina. There a new world opened up to him as he sat in on the presentation of an exciting story of genomic medicine. He encouraged his mother to have her genome sequenced which led to some helpful findings.

The plot of today's show, along with Tim's natural talent for storytelling will keep you on the edge of your seat.

A Great Time to Be in Biology: Steve Quake, Stanford

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

Guests:

Steve Quake, PhD, Professor, Bioengineering, Stanford
Bio and Contact Info

Listen (4:45) Bringing physics to biology

Listen (6:28) New technology driving the study of single cells

Listen (4:30) A great time to be in biology

Listen (4:32) Thoughts on privacy and incidental findings

Listen (4:05) What is holding back the adoption of genomic medicine?

Asked about how he comes up with so many inventions, today's guest, Steve Quake, replies that he is "impatient." It's a quick answer that leaves a lasting sting. Last year when Steve won the Lemelsen-MIT award for being such a mad-inventor, Jim Plummer, dean of the Stanford School of Engineering, wrote of Steve: “It is important to remember that, at just 43 years old, Steve Quake has introduced a number of inventions, any one of which most people would consider a lifetime achievement — and there’s more to come. The true measure of the man, however, is less in his remarkable productivity, but in the profound reach of his inventions".

Beginning with a discussion about the technology Steve developed and commercialized to drive the study of single cell genomics, our interview continues on into the realm of genomic medicine and and the future of biology. Is Steve a believer that we'll be living to 200 yrs old anytime soon? And what are his thoughts on the issue of incidental findings? Listen to Steve's latest ideas in today's program.

NOTE: Since this interview was taped, Steve was elected to the National Academy of Sciences. http://engineering.stanford.edu/research-profile/quake-elected-national-...

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.

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.

Have We Been Missing the Big Picture in NGS? Erik Holmlin, CEO, BioNano Genomics

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

Guest:

Erik Holmlin, PhD, CEO, BioNano Genomics Bio and Contact Info

Listen (4:46) There is a lot of information lost with short read technology

Listen (5:06) What is an example of the practical impact of structural perspective?

Listen (8:49) Is it possible to have one platform that is good at short read and structural view?

Listen (11:28) From the clinic back to the tools space to persue the bottleneck

Listen (1:40) Thoughts on Moleculo

With all the advancement in next gen sequencing, have we actually been missing something important? Erik Holmlin thinks so. He's the CEO of BioNano Genomics, and he's left a career delivering diagnostics to the clinic to go back into the tools space and develop a new sequencing technology that would give a better structural view of the human genome. "I believe, broadly speaking, that the bottleneck in genomic medicine is unique and clinically significant genomic content. And the reason we don't have that is we don't have all the tools that scientists need. So I'm trying to develop those tools." That is a bold statement. In today's interview, I ask Holmlin if there is a new NGS Gospel to be spread?



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