genomic medicine


Current Version of LDT Draft Guidance Means Much Fewer and Lower Quality Tests for Patients, Says Elaine Lyon of ARUP

Guest:

Elaine Lyon, Former President, AMP; Medical Director of Molecular Genetics, ARUP Laboratories Bio and Contact Info

Listen (4:37) What is at stake here?

Listen (6:16) Is your message being heard?

Listen (8:03) Current guidance would shut down two thirds of current tests

Listen (2:33) What would be the best outcome with guidance?

Today we begin a Special Report on LDTs Series. LDTs, or Laboratory Developed Tests, have been used in healthcare for years to aid in diagnosis and treatment of illness. In the age of genomics, the number of these tests has boomed and become ever more complex. It was not until last year that the FDA, who had long been suggesting it, put out the first version of a draft guidance, or terms of regulation for LDTs. Implementation is expected to take about ten years.

Last week the FDA held a community feedback workshop at the NIH and heard from dozens of stakeholders from around the country. Today we’re joined by one of the speakers at the workshop, Elaine Lyon, the Medical Director of Molecular Genetics at ARUP Laboratories. Elaine was the President of AMP or Association of Molecular Pathologists for 2014.

Elaine joined us on the program last year just before the FDA issued the guidance to make the argument that actually what her lab performs are LDPs or Laboratory Developed Processes and not tests. Because they are processes that require a medical professional, this service is more akin to the practice of medicine and therefore not to be regulated by the FDA, she believes.

Nonetheless, guidance has been issued, and it looks like it will go forward. Elaine and other stakeholders around the community have given their input. Will they be heard? What is Elaine’s best hope for an outcome that will work for laboratories across the country and satisfy the FDA?

Stay tuned for interviews with Liz Mansfield of the FDA and the feedback of other stakeholders in this ongoing series.

Setting Better Expectations for Genomic Medicine: Geoff Ginsburg, Duke University

Guest:

Geoffrey Ginsburg, Director, Duke Center for Applied Genomics and Precision Medicine Bio and Contact Info

Listen (6:58) Genomic medicine occuring across the lifespan

Listen (2:40) What have been the key events since the Human Genome Project?

Listen (7:12) What do you make of opt-out databases?

Listen (9:57) What role will EMRs play in genomics?

Listen (3:07) What drives your optimism?

Genomic medicine is now being adopted across human lifespan, says Geoff Ginsburg in today’s interview.

Geoff is the director for Duke’s Center for Applied Genomics and Precision Medicine and joins us for the next installment in our series, Genomic Medicine Today: Where Are We?

Geoff starts by listing the various applications of genomics in medicine from prenatal screening to oncology to pharmacogenetics. He says that too much was promised too early with the first Human Genome Project, but he is optimistic that we are now setting better expectations and healthcare is seeing the benefits of genomics.

“We’re certainly not at the full realization of genomic medicine, but there are clear sign posts that it’s being applied to clinical medicine,” he says.

What role will electronic medical records play in taking genomics into mainstream clinical practice, we ask Geoff, and how are we doing with the consent issue?

Podcast brought to you by: Omicia - Offering end-to-end genome interpretation and reporting solutions to help diagnostic labs and research institutions unlock the potential of individualized medicine.

Test Driving Genomic Medicine: Thomas Quertermous, Stanford

Guest:

Thomas Quertermous, Director of Research, Division of Cardiovascular Medicine, Stanford University Bio and Contact Info

Listen (7:45) Close, but not quite there

Listen (5:34) How good are the commercial bioinformatics providers?

Listen (8:19) The challenge of education

Listen (5:12) Genetics and heart disease

Listen (2:55) Where do you put the price for whole genome interpretation?

Listen (2:32) Are long reads a big deal?

Thomas Quertermous co-chairs a pretty spectacular committee at Stanford. Called the Dean’s Panel on Clinical Genomic Testing, the committee makes the call on which genetic tests are ready for prime time in the clinic. Thomas joins us to launch our new series, Genomic Medicine Today: Where Are We?

The goal of this series is to find out just what practical progress we’ve made in commercializing whole genome sequencing. What are the success cases? How many are there really? What are the obstacles and keys to progress?

TQ, as he's known in the industry, recently co-authored a paper published in the Journal of the American Medical Association (JAMA) that provided a snapshot of just where we’re at today with genomic medicine. The conclusion? We’re close, but not quite there.

The key to clinical whole genome sequencing, he suggests, is to come to it with the question of "what you hope to learn from the adventure."

“I think it’s good if you start with a goal and try to stick to that goal rather than create an all encompassing analysis of the genome," he says in today’s interview.

As for challenges, TQ says that we need better healthcare informatics solutions, and always, better education at the provider level.

What are his thoughts on the leading commercial solutions for whole genome interpretation, and does it really cost $100,000? What does TQ think about the rise of long read sequencing led by PacBio this past year?

Join us as we begin a new series probing the front lines of clinical genomics.

Podcast brought to you by: Omicia - Offering end-to-end genome interpretation and reporting solutions to help diagnostic labs and research institutions unlock the potential of individualized medicine.

Faces of Leadership in Diagnostics: Mara Aspinall

Guest:

Mara Aspinall, Founder, DxInsights

Bio and Contact Info

Listen (2:43) DxInsights and EPEMED

Listen (3:53) Diagnostics 5.0

Listen (2:43) International School of Biomedical Diagnostics

Listen (3:43) FDA Guidance on LDTs: the right time? the right move?

Listen (3:53) Angelina Jolie: a teaching moment

Listen (4:17) What translational gap?

Listen (1:56) Educating payers

You could call her Ms. Dx Education. Mara Aspinall has served as CEO of diagnostics companies big and small, but she’s also spent a great deal of time building a diagnostics community. Some of the early meetings of the Personalized Medicine Coalition took place in her home.

Recently Mara has stepped up her efforts in diagnostics education: that of the industry players, of physicians, and also of the next generation. She’s a co-founder of DxInsights, a new non-profit focused on better education that has already put on their first conference. DxInsights recently announced a partnership with EPEMED, or the European version of the Personalized Medicine Coalition, to create a new Knowledge Center. She is perhaps most proud of helping to create a new International School of Biomedical Diagnostics which has enrolled their first graduate students this year. This school is a first of its kind, pulling faculty expertise from various organizations in Southern Arizona as well as Dublin City University.

“We have medical school students requesting that sequencing--and what I call “Diagnostics 5.0”-- be a part of their curriculum, and it has not been,” she says in today’s interview.

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Mara is a supporter of the FDA’s recent move on LDTs, saying that the current system for diagnostics has not been working. She thinks new regulation that levels the playing field among the various players will help to spur business and innovation because it offers a more predictable path to market.

We end with her thoughts on physician and payer education.

Podcast brought to you by: Slone Partners - Premier talent. Delivered.

'Moving Target Science:' Jonathan Brody on Pancreatic Cancer

Guest:

Jonathan Brody, Assoc Professor of Surgery, Thomas Jefferson University

Bio and Contact Info

Listen (8:17) BRCA testing being used for pancreatic cancer as well

Listen (3:31) The Tennis Ball Bucket Challenge

Listen (6:25) Moving target science

Listen (7:23) A seamless infrastructure

Listen (5:03) Patient consent

Look for Jonathan Brody, a scientist at Thomas Jefferson University, on Google, and you’ll likely find a picture of doctors having buckets of tennis balls dropped on their heads.

Based obviously on viral “Ice Bucket Challenge,” the “Tennis Ball Bucket Challenge” was a way for Jonathan and his colleagues to bring awareness to the lack of funding for pancreatic cancer. Though the outlook for pancreatic cancer patients is much bleaker than for those with breast or prostate cancer, funding into pancreatic cancer research is much lower. Jonathan makes sense of the connection.

“Patients [with pancreatic cancer] just have time to get angry and put up a fight. They don’t have time like breast cancer patients,” Jonathan points out in today’s show. "You go to a breast cancer run, and there’s hundreds and hundreds of survivors. You go to a pancreatic [cancer] fundraiser, and it’s really sad when they say, everyone who’s a survivor raise your hand. You might be lucky if it’s a big event, if there’s a dozen or so.”

Based in the Department of Surgery at Thomas Jefferson University, Jonathan is in a unique situation working with physician scientists to translate findings in cancer research directly into patient care. It’s what he calls moving target science. He shares his dream that one day we’ll look at cancer as we used to look at bacterial infections: diagnosis and tailored treatment.

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

Guest:

David Haussler, Director, Center for Biomolecular Science and Engineering, UCSC
Bio and Contact Info

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

The FDA on LDT Draft Guidance Notice to Congress

Guests:

Liz Mansfield, Deputy Office Director of Personalized Medicine, OIR, FDA
Bio and Contact Info

Katie Serrano, Deputy Director of the Division of Chemistry and Toxicology, OIR, FDA
Bio and Contact Info

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.

Join Us Next Week for a Discussion about the Challenges of Data Visualization and Reporting in Genomic Medicine

Next Thursday, June 5th, Mendelspod teams up again with Chempetitive Group to bring you an evening of networking and a special panel discussion.

"Delivering Genomic Medicine: Challenges in Data Visualization and Reporting"

When:  Thursday, June 5th

   Networking:  5 30 pm

   Panel Discussion:  6 15 pm

Where:  Omicia Inc, 1625 Clay St, Oakland, CA  94612

Applauding FDA Action against 23andMe, Stanford's Hank Greely Calls for More Guidance on Genetic Testing

Guest:

Hank Greely, Professor of Law, Stanford

Bio and Contact Info

Listen (5:00) What's the best argument for FDA regulation of genetic testing?

Listen (10:50) A health exceptionalist

Listen (7:06) What about a Consumer Reports for genetic testing?

Listen (5:05) A device or a report?

Listen (3:13) Tools in command

Listen (3:43) The genoscenti vs. the general public

Hank Greely is a law professor at Stanford who teaches a course on the FDA and keeps a close watch on the genomic revolution. Hank is concerned with the ethical, legal, and social implications of new biomedical technologies.

We're excited to have Hank join us as part of our series, Regulation and Genomic Medicine. He has developed one of the most clear voices on the question of whether the FDA should regulate genetic testing.

"The best argument for regulating 23andMe is that they're providing health information that is not very good," he starts out in today's interview.

We threw the best arguments against regulation that have come up in this series at Hank. For example, one researcher compared the state of bioinformatics and genome interpretation today with that of the early days of the computer. Was the computer good enough in the 80's, the researcher asked. No, but we still used it, he said.

Hank accepts this argument and agrees that the U.S. has been a more libertarian country than many countries around the world. But we make an exception for health, Hank says. Computers weren't used in the early days, he points out, for guiding cars through traffic.

But is the FDA being overly paternalistic? Are 23andMe's predictions really any different from using data from the Framingham studies?

"In health, I am much more paternalistic than I am with anything else," Hank says. When the information is of really weak power and dubious accuracy, I get still more paternalistic."

Hank is quick to point out that he's not for banning astrology, something that he calls "completely useless." He takes issue with the fact that 23andMe has sold itself as a health company.

"When something wraps itself in scientific and medical guise, and is presented as being scientifically correct, we have the right to demand that it actually is."

What about letting the market bring up the value of genetic testing on its own? Is a genetic test really a device or is it a report done by a professional? And are we doing too much sequencing for sequencing sake? Hank isn't one to avoid tough questions. At the same time, he doesn't deny that some truly impactful technology is here.

"I expect that within 10-15 years there's going to be whole genome sequences in the electronic medical records of most people in this country. If we learn to use them well, interpret them well, convey the information to the patients well, they hold real potential for improving public health. If we do it poorly, they could make things worse."

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



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