genomic medicine

FDA Crackdown on 23andMe Delays a Revolution in Medicine, Says Medical Geneticist, Gholson Lyon


Gholson Lyon, Assist. Professor, Coldspring Harbor

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Listen (3:39) Why are you a fan of 23andMe?

Listen (4:58) What about the quality?

Listen (1:13) PGP limited in participation compared to 23andMe

Listen (11:45) Are you against regulation of CoDx or Rx?

Listen (4:29) Delaying the revolution

Listen (2:25) How do you envision the revolution?

About a week ago we featured a regulatory expert on the program explaining why the FDA's letter telling 23andMe to stop selling their PGS test is a good thing. Today we feature an outspoken fan of the DTC company, Gholson Lyon, medical geneticist at Cold Spring Harbor Laboratory.

Gholson is himself a happy customer of 23andMe, and says he's found the service invaluable. In 2011, Gholson led a team in the identification of a new rare genetic disease, Ogden Syndrome, which caused the death of a four month old Utah boy. At the time, Gholson did genetic tests on the boy's family, but was unable to return their results because the tests were not done in a CLIA laboratory. This led Gholson to become an advocate for doing genetic tests for research in a CLIA facility so that results might be returned to patients. Since the 23andMe service is done in a CLIA approved lab, Gholson found the company an excellent place to do genome wide testing.

But is CLIA regulation--which guarantees analytic validity--good enough for the kind of disease risk reports put out by 23andMe to their more than 500,000 customers? Gholson says yes. And regulating the tests further will cut out an important part of a new revolution in medicine.

Gholson acknowledges the diagnostics industry is attempting to bring up the quality of genetic tests, but says that industry companies are producing one-off tests done without the broader context of the genome. This is why he likes the 23andMe service.

"If you don't sequence or genotype the rest of there person's genome, then you have no knowledge about their ancestry and what population they come from. And so you really cannot predict the expression of a particular mutation in that person," he says in the interview.

Gholson also points out that by being a DTC company, 23andMe has been able to recruit many many more participants and data sets than a non-profit, such as the Personal Genome Project, of which he's also a member.

Just how far does Gholson go in his stance against regulation? And how does he envision this revolution in medicine?

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

An Industrial Revolution of Digital Healthcare: Interview with Sultan Meghji


Sultan Meghji, Founder, Reformation Medicine

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Listen (4:20) The end of technology as a specialty

Listen (4:12) Sequencing devices still a bottleneck for clinical genomics

Listen (4:39) How to become a bioinformatician in six months

Listen (4:39) Basic scientists vs. technicians

Listen (8:19) Going through the Industrial Revolution of digital health

Listen (5:05) Do you think about bioethics?

Listen (4:49) Yes to regulation, and yes to access for everyone

Data scientists like Sultan Meghji are a highly valued species in today's world. Beginning his career at the National Center for Supercomputing Applications (NCSA) where he worked on original internet technologies, Sultan has used his expertise in several industries, including finance, air transportation, and now biotechnology.

We've had Sultan on for a couple shows already, and his broad experience and far reaching vision made him an obvious choice for our series, The Bioinformatician Bottleneck.

"We could graduate ten times what we're graduating every year for a decade, and I still wouldn't be convinced that we have enough [bioinformaticians]," he says in today's interview.

What to do about it? Sultan has suggestions, one of which is to have a "Khan Academy style program for How to Become a Bioinformatician in 6 Months." What about the years it takes to train great basic scientists in an age when biologists are already being called "mere technicians?" Sultan says technicians can handle much of the work of commercializing research.

Sultan goes on to suggest there are other important bottlenecks, including the sequencing tools space. Does he stop to think about bioethics? And is he for or against FDA regulation of personal genomic information? Today's show is far reaching and centered around Sultan's goal of bringing genomics to the masses.

"It's almost like the Industrial Revolution of digital healthcare," he says. "We're going to call it something else, but . . .at some point my blood, or some part of me, is going to go into a diagnostic black box, and out is going to come some recommendation that a doctor didn't actually look at. And I'm going to take it to the bank."

Podcast brought to you by: Roswell Park Cancer Insititute, dedicated to understanding, preventing and curing cancer for over 115 years.

5 Myths of Genomic Medicine

No topic has been more popular at Mendelspod than that of genomic medicine.  This is partly an editorial decision.  But it also comes to us from every direction.  And it is very exciting to hear stories of new knowledge about human biology being translated into precision healthcare.  We have featured the major players in the NGS tools industry and some of the newcomers working on “next next gen”.  We’ve featured data analytics companies and some of the new genomic interpretation and reporting groups who are setting up shop.  We have interviewed professors talking about their latest discover

The Fun Problems: Hank Greely Talks Bioethics

Guest: Hank Greely, Professor of Law, Stanford

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Chapters: (Advance the marker)

0:39 What led you to bioethics?

3:51 Problems that can't have clean answers

7:27 How do you know when you're successful?

11:17 Informed consent, privacy

20:18 What is your definition for ethics?

25:35 Intentional selection/eugenics

30:02 Carefully drawn regulation will help the industry

The advance of biotechnology presents society with some thorny issues. And it's just these problems which Hank Greely, a law professor at Stanford, seeks out. In today's interview, Greely asserts that, as if it wasn't already tough enough pursuing the scientific problems, there are others which are hard in different ways.

"Some of these problems can't have clean answers where principles that we really care about generally are in conflict," he says. "The best you can do is look for less bad compromises."

What are Greely's ideas on incidental or secondary findings? On informed consent and privacy? On eugenics? What is his definition for ethics in general? What for many in the industry is a briar patch, Greely nimbly dances through with aplomb.

Podcast brought to you by: Chempetitive Group - "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."

Toward a New Paradigm in Regulating Diagnostics: Liz Mansfield, FDA


Liz Mansfield, Director of Personalized Medicine, OIVD, FDA

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Listen (5:04) New report on personalized medicine

Listen (1:54) How is the FDA handling CoDx associated with breakthrough therapies?

Listen (1:52) Is the FDA open to seeing the use of POC tests as CoDx?

Listen (5:11) How much authority do you actually have?

Listen (3:10) Regulating whole genome tests

Listen (2:00) Are we headed to a world of CoRx?

Listen (5:35) Moving toward a new paradigm of diagnostics regulation

We're happy to have Liz Mansfield from the FDA to the program as part of our series on CoDx. Liz is Director of Personalized Medicine in the Office of In Vitro Diagnostics.

The symbiotic relationship between business and regulation has been part of our American history from the days of the railroads to the present age of genomic medicine. New technology is constantly presenting difficult questions to the public, opportunities for business, and challenges for regulators. For example, there are a slew of new point-of-care tests coming on the market. How open is the FDA to seeing these tests used as CoDx? And how is the regulatory body preparing to evaluate a test on 3 billion base pairs, a whole human genome. Some wonder if the FDA will lose its relevance in the genomic age when there are vast amounts of data floating around and a whole genome test is easily available.

In today's interview, Mansfield chips away at these questions with confidence and a certain amount of humility in the face of the coming technologies. Unable to say whether any company has yet sought approval on a whole genome test, she does say that the team at FDA is preparing for such time.

"We've seen this coming," she says. "Huge amounts of data can be drawn out of a single sample. And we've had to come up with a new paradigm for regulation where we're not to look at each individual measurement so closely. We're going to have to ask for representative measurements and trust those more than we have in the past."

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

Editor's Note: Our apologies for the static in the interview. Liz was on an internet phone at her office and there is slight interference. Also, since this show was published, the FDA cleared a Dx Assay on Illumina's MiSeq platform (Nov 20, 2013).

Pioneer in the Virtual World Announces Three New Life Science Conferences

My first LinkedIn invite was sent by a young businessman named Greg Cruikshank.  He was listed as the founder of Labroots.

Not knowing a thing at the time about social media, I wanted to understand more about this site that expected me to type in my resume and share it with the whole world.  And who was Greg Cruikshank and Labroots?

Joel Dudley Discusses New Book, "Exploring Personal Genomics"


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


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.


Lasse Goerlitz, VP of Communications, CLC Bio
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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.