genomic medicine


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
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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

The FDA on LDT Draft Guidance Notice to Congress

Guests:

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.

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

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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.

Delivering Genomic Medicine: Challenges in Data Visualization and Reporting - Panel Event Set for June 5th in Oakland

Mendelspod and Chempetitive Group are pleased to team up and bring you another evening of networking with a panel discussion, "Delivering Genomic Medicine: Challenges in Data Visualization and Reporting." Join us after work in Oakland on Thursday, June 5th for drinks, bites and discussion.
 

Sample Prep for Clinical Sequencing with Sami Amr, Partners Center

Guest:

Sami Amr, PhD, Director of the Sequencing Core, Partners HealthCare Center for Personalized Genetic Medicine (PCPGM)

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Listen (8:30) How is NGS sample prep improving in clinical applications?

Listen (3:22) Will we get to a one-touch system?

Listen (5:12) Panel or exome?

Listen (4:12) Lab tech proficiency

To finish up our NGS 2014 series, we're joined by Sami Amr, Director of the Sequencing Core at Harvard's Partners Center. Sami and his colleagues are using NGS for ever more clinical applications. How must sample prep improve as genomics goes clinical? Will we ever get to a one-touch system? Which sequencing platform does Sami prefer? These are some of the questions the hands-on lab director addresses in today's 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.

The Whiplash Culture of DTC Genomics with Anne Wojcicki, 23andMe

Guest:

Anne Wojcicki, CEO, 23andMe

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Listen (5:39) What was your personal reaction to the FDA letter?

Listen (5:34) What is the appropriate level of regulation?

Listen (3:30) Results roulette?

Listen (1:06) What is the path forward with the FDA?

Listen (4:17) How do you go about deciding next steps?

Listen (3:48) Audience: What about international options?

Anne Wojcicki is a fighter. Seen by many in our industry as a leader in delivering genomics to the masses, she now has a more complicated job as CEO of 23andMe.

On November 22 of last year, the FDA sent a letter to Anne and her team in Mountain View telling them to stop marketing their popular genetic testing service. It's a day, Anne says, she'll remember well.

In one of the few interviews she has given since the letter, Anne shares her reaction to it.

"There was a lot of shock. And I think it took a while to settle in to really understand what the implications of the letter were," she says at the top of the interview.

Though some see her as standing strong for the right of the average person to see their genomic profile, yet others in the industry feel Anne and her company are undermining the potential of personalized medicine by delivering an inferior product. Today we ask Anne just what she thinks is the appropriate level of regulation and what is her response to those who say that the 23andMe test is merely genetic "results roulette."

Confirming that the company is working diligently to comply with the requests of the FDA, Anne says she leans on a team that has become used to a "whiplash culture." And while she admits that the company could do a better job of labeling the product, she nevertheless asserts that the "current regulatory process was not ready for us." She's of the opinion that the company can again offer the health related testing.

Today's show reveals a CEO who remains undeterred in her mission while acknowledging a more complex way forward.

"This is not the simple path. It's a fight. And I'm really honored to be part of that fight and driving a change. But I have more headaches than I used to," she says at the conclusion.

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

Rare Disease Horizons: The Hope of New Research and Technology, Part I: Genomics with Dr. Eric Topol

Guests: Eric Topol, MD, Cardiologist, Genetic Researcher, and Technologist

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Listen (4:55) DNA sequencing has come a long way since the Human Genome Project

Listen (5:01) How should patients know if they should get their genome sequenced?

Listen (3:29) What are the challenges to getting your genome sequenced and interpreted?

Listen (4:15) What hope does genomics offer to those with rare disease?

We start the series with a show about genomics, because this is often where a diagnosis begins--looking at the patient’s genome for causal mutations. Dr. Topol is a highly sought after expert who helps families with patients of a rare disease at the renowned Scripps Institute in La Jolla, CA. He’s also the author of a book, The Creative Destruction of Medicine, which describes the impact of new technologies such as DNA sequencing and mobile smartphones to change forever the practice of medicine.

                   

For more info, get the free eBook from Rare Genomics Institute

"Rare Disease Horizons: The Hope of New Research and Technology" is underwritten by the Rare Genomics Institute.

                            

 

 

Finding the Sweet Spot in Regulating Genomic Medicine

New technologies and the possibilities they bring to improve human life always come in fits and starts.

Genomic medicine is no exception.  The overdriven tools space of next generation sequencing has created a bursting spring season in genomics research.  New studies linking “this” biomarker with “that” phenotype bloom with a force of nature leading some to make bold predictions about man’s ability to conquer his own form.  We can smell eternity.



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