What Translational Gap? Michael Pishvaian on Advances in Tumor Profiling


Michael Pishvaian, Assistant Professor, Georgetown University; CMO, Perthera 

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Listen (4:08) Untapped potential

Listen (6:24) What is the biggest challenge in the biomarker development process?

Listen (7:54) Taking personalized medicine to hospitals everywhere

Listen (5:30) Must do better in assessing value of personalized medicine

When we talk about personalized medicine, we often hear that doctors are out of touch with the latest research, particularly those not at major medical research universities. Not so, says Michael Pishvaian, researcher and doctor at Medstar Georgetown University Hospital.

Our first guest in a new series, "Democratizing Personalized Medicine: Advances in Tumor Profiling," Michael says that in the last two years the “retailization" of diagnostic tools has made personalized medicine for cancer available to all doctors.

Spending sixty percent of his time in research and forty percent seeing patients, Michael is involved in the entire flow of biomarker development, from discovery to patient care. His specialty is in GI cancers, where there is “an untapped potential for using biomarkers.” When Michael finds biomarkers that are useful to target a therapy, he’s immediately able to enroll his patients in a clinical trial.

But Michael works at a major research hospital. What about those doctors working in community hospitals?

Michael argues that all the new research on tumor biomarkers is being made available at the community hospital level.

“In just the last two to three years there has been a real explosion of retail diagnostic/molecular testing companies that have the capacity to give as much, if not more, genetic and molecular information about a patient’s tumor than can be found at any major institution,” he says.

Michael is the CMO for one such private company, Perthera, which is offering the latest in tumor profiling to doctors everywhere through their "virtual tumor board."

“I don’t think doctors are out of touch. . . . It’s not so much that they don’t have access or the knowledge base for personalized medicine. It really just has to do with time and effort and first hand experience to know how to put it all together,” he says.

Paperwork, Not Algorithms the Biggest Challenge for Large Bioinformatics Projects, Says David Haussler, UCSC


David Haussler, Director, Center for Biomolecular Science and Engineering, UCSC
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Listen (8:08) Paperwork not algorithms the biggest challenge with bioinformatics

Listen (7:01) With Amazon Cloud around are compute and storage still issues?

Listen (3:23) Global Alliance for Genomics and Health

Listen (5:05) What are the technical challenges yet to be tackled?

Listen (7:35) A global bioinformatics utility has to be an NGO

David Haussler and his team at UC Santa Cruz have gone from one large bioinformatics project to another. After creating the original Genome Browser (which still gets over 1 million hits per month), David worked to build a large data set for cancer genomics, The Cancer Genome Atlas.

“With more data comes statistical power,” David says in today’s show. “The only way we can separate out the “driver” mutations from the “passenger” mutations is to have a large sample of different cancers."

This makes sense. One needs millions of samples to see when a mutation is just random, or when it occurs with true statistical frequency. So what have been the challenges to building such a large data set?

David says issues around consent and privacy have actually held up his projects more than any technical difficulties. For example, the NIH has had several meetings for over a year now to determine whether their data can be put on the commercial cloud. In addition there are issues connecting large medical institutions around the country and various countries from around the world. David is a co-founder of the Global Alliance for Genomics and Health, which he says is nearing the tipping point of being THE bioinformatics utility that will be globally adopted.

In the days of commercial offerings such as Amazon Cloud, is compute and storage still a problem? And what, after the privacy issues are seen to, are the technical challenges for bioinformaticians like Haussler?

Podcast brought to you by: National Biomarker Development Alliance - Collaboratively creating standards for end-to-end systems-based biomarker development—to advance precision medicine

Pre-Leukemic Stem Cells with Liran Shlush

Guest: Liran Shlush, Researcher, Princess Margaret Cancer Center

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Listen (4:44) Preleukemic stem cells

Listen (7:42) Implications for AML therapy and diagnosis

Listen (2:21) Implications for other cancers

Listen (6:14) Importance of population genetics tools

One of the common topics on our show these days is how researchers can ask better questions. It takes being master at science, but also being connected with patients and their health problems.

Today's guest, Liran Shlush, a cancer researcher at Princess Margaret Cancer Center in Toronto, solved this by being one of those rare physician-scientists. And it's paying off big time.

In February, Liran and a group from the lab of John Dick at the University of Toronto published a major finding into the biology of acute myeloid leukemia (AML). In today's interview, Liran tells us about the discovery of what he terms "pre-leukemic" stem cells. These mutant stem cells go on to form cancerous cells. When AML patients are treated with chemo, the cancerous cells are killed, but the mutant stem cells are still there and can cause recurrence. The finding holds a lot of promise for both treatment, earlier diagnosis, and new screening for AML and perhaps other cancers as well.

Liran was a post doc at the time of the discovery. He tells of his journey from Israel to John Dick's lab in Canada and the lessons along the way. What led him to ask the right questions?

"The scientific lesson I learned--and I was lucky to learn it early in my career--" he says, "is that nothing in biology makes sense except in the light of evolution."

Podcast Sponsor: Integrated DNA Technologies - Introducing the evolution of NGS capture panels

4 Reasons Clinical Trials Don't Work: Marty Tenenbaum, Cancer Commons


Marty Tenenbaum, Founder, Cancer Commons

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Listen (4:28) Why Cancer Commons?

Listen (6:07) Four reasons why clinical trials don't work

Listen (6:57) How do we go about changing the system?

Listen (4:35) What do you mean by Rapid Learning Community?

Listen (4:48) What obstacles do Cancer Commons partners face in sharing more data?

Listen (1:24) The difference between a cancer researcher and a patient is a diagnosis

"At the end of the day, we're all patients," says Marty Tenenbaum, Founder of Cancer Commons, in today's interview.

Marty is a tough cookie. He's a survivor of metastatic melanoma--not a fun one--and he's been getting traction around the biomedical research industry.

Here's the thing. Marty's survival was really by chance.

Cancer has been called the "great equalizer," and Marty is fond of saying that "the only difference between a cancer researcher and a cancer patient is a diagnosis." He is on a mission to work with researchers, doctors, policy experts, and patients to improve the system so that success is not just an accident.

But how does one who is not a researcher or leader in the industry go about that? Marty sees the best opportunity in changing the way clinical trials work. In today's interview, he lays out four reasons why the current system fails patients. And he offers his ideas to fix it.

This is where Cancer Commons comes in. Already a successful web entrepreneur, Marty is attempting to break down the walls between trials and patient care with a new "clearing house" for cancer patients. Ideally, he sees a system that would allow for a "trial of one"--where a patient in treatment has access to an experimental therapy. The goal would be to focus on the patient's own recovery and not only some future patient. Important also would be that much more of the patient's data would be available to expedite research and medical therapy.

A good deal of the funding for Cancer Commons has come from Marty's own pockets. He did well as an entrepreneur. And then he survived a tough cancer. He's now devoting all his resources to creating a new paradigm that puts the patient not at the end, but at the beginning of the process,so that many more patients will have the chance he did.

Podcast brought to you by: BioConference Live's "Cancer: Research, Discovery and Therapeutics" - taking place online Oct 16-17, 2013. Register for free now.

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."

Putting the Bench Next to the Bedside: Laurence Cooper, MD Anderson Cancer Center


Laurence Cooper, MD, PhD, MD Anderson Cancer Center

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Listen (4:55) When clinical science and bench research is one and the same

Listen (10:40) Single cell genomics enabling next level of immunotherapy

Listen (5:00) Marrying immunotherapy with gene therapy - Four clinical trials

Listen (4:18) Is this a new model for drug development?

Listen (8:30) Why has the war on cancer taken so long?

Laurence Cooper is one of those rare MD and PhD hybrids-what he calls a "'super nerd." Specializing in immunotherapy at MD Anderson Cancer Center, Dr. Cooper is a pediatric oncologist with a very important resource: he also runs a laboratory where he's able to study the basic biology underlining his patients' cancers.

"Clinical science and bench research are one and the same," he affirms in the interview.

This concept is nothing new. But that a doctor is able to treat his patients with therapy developed in his own laboratory is very rare.

Today's show with Dr. Cooper is the final program in our series on single cell genomics. He explains how the new tools for looking at and manipulating individual cells are transforming immunotherapy. Today, treatment for childhood leukemia has become much more targeted and way less toxic.

And Dr. Cooper is not limited only to naturally occurring stem cells in a donor to transplant to his patients. With genetic engineering, his lab is able to create or reengineer specific cell types for transplant. Currently the lab has four clinical trials going which enable Dr. Cooper and his team to treat his own patients with the latest therapies that are developed in the lab.

This marriage between the clinic and the lab is a powerful example of the translation of biomedical science. Could it be a model for drug development?

That depends a lot on funding, concedes Dr. Cooper. His lab is funded by MD Anderson, but also in large part through NIH grants. The interview ends with a discussion on funding for the "war on cancer" with a provocative comparison to the "war on terror."

On 9/11, 3,000 people died. Yet every two days, that many people die from cancer. Dr. Cooper wonders why "the outrage of 9/11 has not yet translated into outrage of still having 3,000 people die every two days."

We hope to have Dr. Cooper back on the program soon as part of our series on the "war on cancer."

Podcast brought to you by: Fluidigm - The leader in single-cell genomics and maker of the C1™ Single-Cell Auto Prep System. The path less traveled just got easier.

Democratizing Single Cell Genomics with Gajus Worthington, Fluidigm

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

Guest: Gajus Worthington, CEO, Fluidigm Bio and Contact Info

Chapters: (Advance the marker)

0:39 Looking at heterogeneity

6:18 How is your technology driving the study of single cells

13:35 Overcoming skepticism

18:29 The promise of IPS dependent on looking at cells separately

21:11 Single cell genomics will expand to every area of cell biology

25:31 Are you the next big Illumina?

30:01 BONUS: Chip holds as much plumbing as a one-thousand-room hotel

Gajus Worthington has a message. Molecular biologists have been studying the genetics of individual cells (single cell) for a long time. But the amount of manual labor required has been prohibitive to achieving sufficiently large data sets. Fluidigm, a tools company in South San Francisco, co-founded by Worthington, is changing that. Now a single micro fluidics chip that contains as much plumbing as a one-thousand-room hotel is driving the adoption of single cell genomics research. In today's interview, Worthington, also CEO of Fluidigm, explains the company's technology and some of its applications.

We've heard a lot lately about the heterogeneous nature of cancer tumors. But there is heterogeneity everywhere, including stem cells. "Some iPS (induced pluripotent stem) cells are more "gifted" than others," Worthington explains. "To make iPS achieve its promise, and the promise is amazing, you have to understand the mechanism by which these "gifted" cells go from one type to another." One assumes the company's name comes from the two words "fluidics" and "paradigm." Fluidigm's technology is enabling researchers to make a shift in paradigm necessary to go ever deeper into the complexity of biology. Will they be the next Illumina?

Message from a Patient: Whole Genome Sequencing Not Clinical Yet

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

Guests: Jay Lake, Sci-Fi Author Bio and Contact Info

Joseph Edward Lake, US Ambassador Bio and Contact Info

Listen (6:05) The term patient implies waiting - and waiting kills

Listen (3:34) The medical bureaucracy very challenging for a patient

Listen (7:30) Health is a privilege

Listen (10:46) Whole genome sequencing not clinical yet

Listen (2:13) Who is creating the future?

Today we begin a series, The Age of the Engaged Patient. Jay Lake is a sci-fi writer and compulsive blogger. He is also a patient. He joins us for today's program with his father, Joe, to talk about his struggle with colon and lung cancer. As is often the case with patient stories, patient can imply a team working together for the health of one individual.

Jake is very open about his cancer and his life as a patient. He blogs often about his daily medical experiences and has built up a large following in addition to his sci-fi fan base. "If I can use my storytelling skills to explain cancer, then I've beaten the disease," he exclaims in the interview. What do Jay and his dad think about the term patient? And what message does he have for our audience of life science researchers? Jay recounts his adventure with whole genome sequencing and is honest about how "painful and difficult" this aspect of his treatment has been.

Digital PCR 'Hits Its Stride'

Podcast brought to you by: Chempetitive Group - Who for more than a decade has helped science-based companies build and execute innovative marketing campaigns. "We love science. We love marketing. We love the idea of combining the two to make great things happen for your marketing communications."


George Karlin-Neumann, PhD, Director of Scientific Affairs" for Bio-Rad's Digital Biology Center Bio and Contact Info

Listen (5:00) Understanding Digital PCR

Listen (4:41) Advantages

Listen (1:40) Applications

Listen (3:40) Still room for Real Time PCR

Listen (3:14) First ever dPCR conference

Hanlee Ji, MD, Medical Oncologist, Hematologist / Oncologist in Stanford Bio and Contact Info

Listen (5:09) How is an oncologist using dPCR?

Listen (4:56) A physicians take on personalized medicine

Listen (5:32) Digital technologies already adopted in clinic and dramatically changing war on cancer

In May of this year Nature Methods published an article, “Digital PCR hits its stride.” What is this new technology? Will it replace more conventional methods such as Real Time PCR? And what new opportunities does this new disruptive technology open up?

To answer these questions, we’re joined by George Karlin-Neumann, Director of Scientific Affairs at Bio-Rad’s Digital Center and Hanlee Ji, a physician scientist at Stanford. George explains the exciting new technology and its advantages over Real Time PCR. Hanlee talks about the adoption of the technology in the clinic for the treatment of cancer.