commercializing diagnostics

Proteins Are Where It's At: Chip Petricoin, George Mason University


Emanuel "Chip" Petricoin, Co-Director, CAPMM, George Mason University 

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Listen (4:00) Beyond the genome

Listen (5:30) Challenges to mapping the proteome

Listen (10:35) A new level of resolution for studying protein activity

Listen (6:05) 95% of cancer patients treated at the community level

Listen (8:12) Taking the latest in tumor profiling to patients everywhere

Today we continue our series on the democratization of tumor profiling with Chip Petricoin, Co-Director for Applied Proteomics and Molecular Medicine at George Mason University.

Chip says we must now go beyond the genome to the proteome and metabolome to really understand the biology of disease. Chip is particularly interested in hard to treat cancers such as pancreatic cancer.

The proteins are where the action is, insists Chip. Proteins are the drug targets for approved therapies. They comprise most of the biomarkers looked at in routine therapy. And proteins form the pathways and networks that everyone has been talking about.

“There’s no such thing as a gene pathway,” Chip says in today's interview. "Genes don’t form pathways. Genes don’t move. Genes aren’t the software of the cell. Genes are the blueprint. Proteins form the pathways. They do the work."

What are the challenges in characterizing the human proteome, and what new strategies are researchers like Chip using to get at a new level of awareness of protein activity?

Chip's work is being commercialized at two companies. The first, Theranostics Health, is developing a diagnostic that will measure protein activation. Perthera, the second company, uses not only genomics, but also proteomics to profile tumors. Chip explains how Perthera is taking the latest research that, until now, has been accessible only at major research hospitals and makes it available to community oncologists everywhere.

Pioneering Use of the Microbiome: Colleen Cutcliffe, Whole Biome


Colleen Cutcliffe, CEO, Whole Biome
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Listen (2:32) Do we know enough about the microbiome yet to commercialize it?

Listen (5:58) The Complete Biome Test

Listen (6:50) A higher resolution platform for developing new diagnostics and therapeutics

Listen (3:12) What are the low hanging fruit?

Listen (2:25) Going forward what is the biggest unknown for you?

There is an intense research effort underway to find out more about the human microbiome. But do we know enough yet to commercialize it?

Whole Biome is one of a handful of new startups in the microbiome space. It was founded by three former employees of PacBio who decided, yes, they knew enough to begin offering a product, the Complete Biome Test.

One of those founders, and the CEO of Whole Biome, Colleen Cutcliffe, joins us to tell their story.

As entrepreneur trainer Steve Blank said here in a recent interview, startup phase is that time period where a company searches for a successful business model. That certainly applies to Whole Biome. Colleen says that early on, the team saw that there was a gap in bacterial strain resolution that they could fill with a tool, meaning they could offer a much clearer picture of a person’s microbial community than what has been available to researchers.

“Before we even began developing that tool,” Colleen says, "we went out and we talked to people who were key opinion leaders in the field and had been thinking about the microbiome and different diseases for a long time. And we said, hey we feel this is a gap. Do you think this is a tool that would be useful? And they all said, that would be a great tool. And if you start a company around that, we’d love to work with you. And we started the company and went back to them and asked would you like to work with us now. And every single one of them is partnered with us.”

Just what will be their business model? And what are the low hanging fruit Colleen and her team are pursuing? She answers these questions and more in today’s interview.

The FDA on LDT Draft Guidance Notice to Congress


Liz Mansfield, Deputy Office Director of Personalized Medicine, OIR, FDA
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Katie Serrano, Deputy Director of the Division of Chemistry and Toxicology, OIR, FDA
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Listen (4:08) What was submitted to Congress?

Listen (5:09) Why is CLIA not enough?

Listen (4:07) Does the FDA have the resources for this?

Listen (5:54) How will risk be determined?

Listen (2:13) How will you approach panels and whole genome tests?

Listen (2:33) Is NIPT on your radar?

Listen (1:32) What about laboratory developed processes or LDPs?

Listen (1:19) What should labs be doing now?

On July 31, the FDA notified Congress that they will be publishing draft guidance for laboratory developed tests or LDTs.

This means the potential regulation of lots and lots more lab tests. Thousands of diagnostics for diseases like cancer or heart disease or a rare disease.

As with most actions of the FDA, this news has its fans and critics. There are those who feel that a hands off policy of the FDA has fostered innovation and better testing. And there are those who say that some of these tests carry such high risk that they should be regulated as a device or a therapeutic. In any case, others argue, the playing field should be level among test providers.

Here to walk us through what is happening and what will happen is Liz Mansfield and Katie Serrano, both from the Office of Invitro Diagnostics and Radiological health at the FDA.

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

NIH Goes Lean with Steve Blank

Guest: Steve Blank, Author, Entrepreneur, Educator

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Chapters: (Advance the marker)


0:59 What are you up to with the NIH?

4:39 The scientific method for entrepreneurship

8:14 Do scientists resist learning about business?

10:50 "I’m from the U.S. Government, and we need your help!"

17:55 Have you had to adapt your approach for the life sciences?

23:33 What is good for investor returns is not necessarily good for the country

27:33 You were supposed to be retired. What happened?

Steve Blank is a serial entrepreneur who has been teaching his trade at Stanford for some years now. We’ve had some of his student entrepreneurs as guests at Mendelspod.

Steve comes from the world of high tech and always told his students that his approach, dubbed the Lean LaunchPad, doesn’t apply to the life sciences. Until last year.

In a course at UCSF that began in October of 2013, Steve began adapting his ideas for startups in the areas of therapeutics, devices, and diagnostics.

After the class was over, Steve says in today’s interview, he got a call that went, “Hi, you don’t know me. I’m from the US Government, and we need your help.”

Steve is an avid blogger, and customarily puts out summaries of his teaching experiences. It turns out some folks at the National Science Foundation were reading all of his blogs about the UCSF class. They persuaded Steve to bring the class to government and see if he couldn’t help grant recipients have better results in business.

Steve laments that we’ve had no formal mechanism for teaching scientists how to turn research into commercial products.

"Essentially, in giving out these SBIR and STTR grants, we were giving out cars without requiring drivers’ ed. And we are surprised that the cars keep crashing!” he says.

Now, the NIH wants in on the training. This fall Steve will begin a pilot program called I-Corps, or Innovation Corps Team Training Program, to aid in the commercialization of new products and services from SBIR and STTR award projects.

How has Steve adapted his training program for the life sciences? And what resistance is he encountering from scientists? And hey, wait a minute, isn’t Steve supposed to be retired after selling off his eighth and last company for $329M—what happened?

Filmed at his ranch in Pescadero, California, today’s interview catches Steve relaxed and eager to share what he’s learned over the years.

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."

Rethinking Biomarker Development with Anna Barker


Anna Barker, Co-Director, Complex Adaptive Systems Center, ASU

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Listen (7:54) Have we been overly reductionist in the study of disease?

Listen (6:32) Applying new knowledge about complex adaptive systems to biomarker development

Listen (7:09) The National Biomarker Development Alliance

Listen (3:05) What do you think of the 'Snyderome' model?

Listen (5:44) Confident that FDA will regulate LDTs

Southern Arizona is emerging as a hotspot in the world of diagnostics. And one of the leading lights there is Anna Barker, who has been bringing folks together to think about biomarkers for a long time. As the former deputy director of the NCI, she assembled many different groups including the Nanotechnology Alliance for Cancer and The Cancer Genome Atlas (TCGC). She's now at Arizona State University where she co-directs the Complex Adaptive Systems Center and seeks to establish a new paradigm in the way we look at the biology of disease.

Beginning with some philosophy of biology, Anna takes us into her latest thinking on complex systems.

"We have to start thinking of a disease like cancer as a system," she says. "As you perturb one part of it, you perturb all of it. . . . We have to think more 3D."

Anna is someone who likes to go back to the basics, not only in the study of biology, but also in the business side of diagnostics.

In the interview she announces a new National Biomarker Development Alliance (NBDA) that is bringing a higher level of standardization to every phase of biomarker development. She argues that there are several decision points in the process, whether it's to validate an assay, or take it into commercial development. Right now, she says, the diagnostics community does not agree on the current standards for these decision points, or modules, and this is a problem. The aim of the Alliance is to bring the community together to agree on higher standards. The NBDA has just launched their website and is publishing their standards in an effort to better educate those developing diagnostics.

"We believe this approach will really enable us to develop biomarkers more predictably all the way through regulatory approval."

And what are Anna's thoughts on regulation? She says outright that the FDA is going to regulate LDTs.

Ms. Barker's vast experience and deep commitment to better science and better industry standards shine a light for anyone involved in translating biomarkers to the clinic.

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

And by: DxInsights: Presenting a Diagnostics Summit at the Miraval Institute May 4-6.

Dietrich Hauffe of QIAGEN on Clinical NGS


Dietrich Hauffe, Sr. VP, Life Sciences, QIAGEN

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Listen (3:26) What is the big vision for QIAGEN?

Listen (2:26) Business already 50 percent clinical

Listen (3:15) Will NGS replace PCR in clinic?

Listen (6:01) What can you tell us about the GeneReader?

Listen (4:38) Where are we at with genome interpretation?

Listen (5:11) How is QIAGEN's relationship with clinical labs evolving?

QIAGEN is a company on the move. Last year they picked up two bioinformatics platforms, CLC Bio and Ingenuity Systems. They bought Intelligent Biosystems the year before. That purchase was for a new next generation sequencing device. Called the GeneReader, this instrument has been designed specifically for clinical application.

Joining us today is Dietrich Hauffe, the Sr. Vice President of Life Sciences at QIAGEN. Dietrich discusses the GeneReader, which is currently being tested by select customers, and how it fits into QIAGEN's big vision for genomic medicine. The GeneReader offers clinical technicians the ability to do parallel sequencing and to have "random access" to many samples at the same time. The GeneReader will not be able to do whole genome or exome sequencing, however.

Dietrich says that the GeneReader, along with QIAGEN's broad existing product line of sample prep, PCR tests, companion diagnostics, bioinformatics offerings, puts QIAGEN in a unique position in the clinical market. By owning the entire workflow, QIAGEN is in a position to raise the quality and standards in clinical testing.

"We're very much liked for our universal approach," Dietrich says in the interview.

Today's Podcast is sponsored by Biotix - Makers of a Better Tip for Next Gen Sequencing. Find out how Biotix is setting a new standard in sample delivery here.

Is this the Omics-to-Clinic Site We've All Been Waiting for?

Guest: Jonathan Hirsch, Founder, President, Syapse

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Chapters: (Advance the marker)

0:50 Why is Syapse the right solution?

6:12 What are you providing that hasn't already been there?

12:50 "Versioning" and preparing for FDA approval

15:44 How are you driving adoption of your service?

20:30 Scaling with a configurable platform

22:00 When will we see clinical sequencers?

26:14 What does genomic medicine look like in five years?

28:02 A PCORI grant

There are roughly two types of bioinformatics site offerings, "infrastructure" and "analytical" solutions. In our first interview of the year we focus on a new company offering an infrastructure solution, one that covers the end-to-end flow of omics into the clinic. Jonathan Hirsch is the President and Founder of Syapse and says his company is providing some services that have not been available before, particularly in the area of clinical reporting.

Recipient of a recent PCORI (Patient Centered Outcomes Research Initiative) Grant that is funded by the new ACA, Syapse is already offering their services to diagnostics labs who need a solution for reporting to physicians.

"We're in a very interesting place," says Hirsch in today's interview, "where the physicians are actually driving the adoption of IT solutions. And that's the trend that we're playing off."

How will the site scale, and how does Hirsch see genomic medicine in five years? Join us as we begin the year looking deeply into the adoption of personalized medicine.

Note: Hirsch will join Mendelspod Host, Theral Timpson, on two panel discussions on bioinformatics infrastructure later this month:

Jan 28th: PMWC 2014, Mountain View, California at 10:45 am (see details)

Jan 30th: Evening Event at Tres Lounge in San Francisco at 5:00 pm (see details)

Inside the World of Prenatal Diagnostics: Charles Cantor, Sequenom


Charles Cantor, PhD, Chief Scientific Officer, Sequenom

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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.

Yale Genetic Counselor Weighs in on Myriad Case and More: Ellen Matloff


Ellen Matloff, C.G.C., Director, Yale Cancer Genetic Counseling

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Listen (5:05) Genetic counseling before the book was written

Listen (6:10) Myriad actions unprecedented

Listen (4:32) 30-40 % of all genetic tests ordered in error

Listen (5:12) Patents needed for business incentive?

Listen (3:09) Too few genetic counselors? Just Myriad propaganda

Listen (4:02) What is the Myriad database?

Listen (5:26) Why is the gene patent decision so personal for you?

Listen (2:32) DTC genomics not accurate, protected or helpful

When Ellen Matloff heard news of the recent Supreme Court decision invalidating some of Myriad's BRCA patents, she was overcome with tears. Tears of relief.

The first genetic counselor at Yale's School of Medicine, Ellen has had a front row seat to the long saga of gene patents, particularly the BRCA patents of Myriad Genetics. In today's interview Ellen recalls the days when the BRCA genes were first made known and explains the huge benefits the gene tests provided to her patients.

Then Myriad cracked down on their patents in a way Ellen calls "unprecedented" and "surreal."

Getting snubbed at every turn by Myriad--and then by her own peers for taking a position against gene patents has made this journey very personal for Ellen. Today she tells her view of gene patent history and gives her take on the burgeoning world of clinical genomics.

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."

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.

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