clinical genomics


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.

The Progress of Clinical Genomics in Sweden with Ulf Gyllensten

Guest:

Ulf Gyllensten, Professor, Department of Immunology, Genetics, and Pathology, Uppsala University, Sweden Bio and Contact Info

Listen (4:24) What are your goals at the National Genomics Infrastructure?

Listen (4:42) PacBio revolutionizing HLA typing

Listen (4:01) Getting the word about long reads out to clinicians

Listen (3:17) What would you like to see from sequencing companies in the future?

Listen (8:03) An update on clinical genomics in Sweden

Listen (5:02) The Road Show

For our final show in the series on long read sequencing, we move to Sweden and talk to Ulf Gyllensten, Co-Director of the National Genomics Infrastructure.

Ulf and his team use all the major sequencing platforms, and one of their jobs at the NGI is to compare the platforms. In today’s interview, he tells of the goals at the NGI and how new long read technology from PacBio is opening up new applications.

Some of these applications are clinical, and Ulf gives an update on clinical genomics in Sweden where regulation and privacy concerns are much more straight forward than they are here in the U.S.

Podcast brought to you by: Pacific Biosciences - providers of long read sequencing solutions based on their Single Molecule Real Time technology.

After a Decade on the Sidelines, Gene Myers Back into Sequencing, Excited about Long Reads

Guest:

Gene Myers , Founding Director, Systems Biology Center, Max Planck Institute Bio and Contact Info

Listen (6:10) What have you been up to since the Celera days?

Listen (4:08) Last decade more about technology than science

Listen (3:53) Wanting to do science not medicine

Listen (4:10) Not many saying it, but short reads have given crappy results

Listen (4:43) Near perfect assemblies now possible

Listen (3:19) Future of sequencing

Gene Myers is an algorithmicist best known for his time at Celera where he developed BLAST, perhaps the most widely used bioinformatics tool ever.

But then Gene got bored with sequencing projects.

“There was this focus on trying to make sequencing the human genome cheaper,” Gene says in today’s interview. "And we knew that eventually technology would win that one. You didn’t have to be much of a visionary to see that.”

Gene argues that it’s been simply a matter of “turning the crank” over the past decade since the first human genome was sequenced. Scientists have been going from organism to organism, and staring at the human genome for genotype-phenotype correlations. Yes, sequencing has gotten much cheaper, and that is important for medicine. But Gene wasn't interested in medicine. He wanted to move on to new science.

So what has Gene been up to? And why is he getting back into sequencing after a decade on the outside?

The answer has to do with long reads.

Podcast brought to you by: Pacific Biosciences - providers of long read sequencing solutions based on their Single Molecule Real Time technology.

Has the Race to the $1,000 Genome Proceeded at the Expense of Quality? New Series on The Rise of Long Read Sequencing

According to a 2010 article in Bio-IT World, the term $1,000 Genome has been around since 2001.  The University of Wisconsin’s David Schwartz claims to have coined the term at an NHGRI retreat during a breakout session.  Whatever its origin, the $1,000 Genome soon became the target for the rapid development of next-gen sequencing (NGS).

Can We Do DTC Genomics Right? Misha Angrist, Part II

Guest:

Misha Angrist, Author, Assoc. Professor, Duke Institute for Genomic Sciences

Bio and Contact Info

Listen (7:03) Presidential bioethics commissions do not have a good record

Listen (5:06) Questioning FDA priorities

Listen (4:31) Not the best arguments in FDA letter to 23andMe

Listen (3:26) Can we do DTC genomics right?

Listen (4:49) Thoughts on A Troublesome Inheritance

Listen (4:30) Self censorship

Today we continue with part two of our interview with Duke Assoc. Professor and author, Misha Angrist, mostly centered around the issue of regulating genomic medicine.

Misha questions recent FDA actions, such as the clamp down on 23andMe.

"I'm generally pretty hard on the FDA," he says.

Misha has a "complex view" about the FDA's letter last November to 23andMe. While he thinks 23andMe "dropped the ball" and went too far in interpreting consumers' genomic data, he also thinks the FDA used the wrong arguments in their letter ordering the DTC company to discontinue its health related testing.

He lauds 23andMe's hiring of Jill Hagenkord as CMO, saying that she "gets it."

We finish with Misha's response to Nick Wade's new book, A Troublesome Inheritance: Genes, Race, and Human History.

Editor's Note: Since this interview was recorded, the 23andMe blog put out an update saying that the FDA had accepted their submission for a new 510(k) application.

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

Some Glimpses into the Challenges of Data Visualization Panel Event

Big Data might offer tremendous breakthroughs in healthcare and personalized medicine.  But with the new amounts of terabytes and petabytes flooding organizations today, old architectures aren't able to keep up.

Take the genome, for instance.  We know that there is a ton of valuable information in there.  But how does one go about looking at it?  Doctors have very little time as it is, and decision making becomes a burden becuase it takes days to get answers to questions, if at all.  And what about the opportunity to get genomic data to the lay person as 23andMe was doing?  

The Impossible Job of Genetic Counseling: Misha Angrist Part I

Guest:

Misha Angrist, Author, Assoc. Professor, Duke Institute for Genomic Sciences

Bio and Contact Info

Listen (7:25) New MA in Bioethics and Science Policy

Listen (7:58) Can we embrace NIPT without losing compassion for those with developmental disabilities?

Listen (3:24) How does the process of bioethics work?

Listen (7:41) The unsung heroines

Duke University's Institute of Genome Sciences and Policy will be gone on July 1st. It was announced earlier this year that the flagship institute will be broken up into several new programs. This gave us the perfect excuse to talk about science policy and bioethics challenges in a two part interview with an old Mendelspod friend, Misha Angrist. Misha is an associate professor at Duke and a well known author (Here is a Human Being: At the Dawn of Personal Genomics). He'll be working with Nita Farahany in the new Duke Science and Society Program which is introducing an MA in Bioethics and Science Policy later this fall.

Part I of Misha's interview begins with a discussion about the new masters degree, a first of its kind, and then moves on to a broader discussion of prenatal diagnostics (NIPT). Misha shares some of his concerns with the rapid uptake of prenatal testing, summing up with a question:

"Can we embrace NIPT without losing our compassion for people with developmental problems?"

Misha says he's not a bioethicist (why doesn't anyone want to call themselves a bioethicist?) but then offers some insight into the process of bioethics.

"One of the problems that bioethics has is that we like to traffic in the binary, that things are either/or, and we pit things against each other. That's not always appropriate."

But the meat of the interview has to be Misha's passion for the genetic counselor. Misha jokes about his own path as an "almost" genetic counselor, then goes on to say that:

"Genetic counselors are unsung heroes--or heroines, since the overwhelming majority of them are female. They have an impossible, thankless job. They have to deliver bad news very often to people who may or may not be prepared to hear it."

Stay tuned for Part II of the discussion where Misha shares his thoughts on 23andMe and the future of DTC testing.

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

Why Hasn't Clinical Genetics Taken Off?

Insiders to genomics are looking around and, generally over a tasty adult beverage, bemoan the lack of forward progress on the clinical side of adoption. Why haven clinical adoption rates gone up faster? What’s making this hard? I’ve become frustrated over the last few years, raising a significant amount of money across a number of companies, all trying to speed up the scale of adoption in the non-sick population. Looking back, looking around and seeing how the current landscape of startups and new activities in clinical genetics are being run, I’ve come to the following conclusions.

Clinical Genomics Takes Hold in Iowa: Colleen Campbell, IIHG

Guest:

Colleen Campbell, Assistant Director, University of Iowa - Iowa Institute for Human Genetics

Bio and Contact Info

Listen (2:35) How are you implementing genomic medicine?

Listen (3:17) Pharmacogenetic pilot with CYP219

Listen (8:24) How are you educating physicians?

Listen (2:32) Which patients are getting their exomes sequenced?

Listen (5:55) What are you doing with secondary and incidental findings?

Listen (1:30) Technical challenges?

Listen (3:33) History of IIHG

Today we take you to the front lines of clinical genomics.

Colleen Campbell is the assistant director at the Iowa Institute of Human Genetics (IIHG), a statewide resource devoted to understanding the extent and meaning of human DNA sequence variation. In March of this year, the IIHG at the University of Iowa began offering whole exome sequencing as well as some pharmacogenomic testing.

In today's interview, Colleen shares with us some practical stories outlining just how the IIHG is bringing genomics into the clinic. How did she and her colleagues go about deciding which pharmacogenomic tests to offer, and how are they dealing with the issue of incidental findings? As both a geneticist and a genetic counselor, Colleen offers a comprehensive, behind the scenes view on a story that is unfolding around the world.

At Mendelspod, we hear a lot about the challenge of educating clinicians on genomics. This has been a key area of focus for Colleen and her colleagues. The genomics team is engaging not only doctors but also nurses and the general community in new ways that could be a model for other clinics.

"Groups who are trying to implement these these kinds of tests need to think about educating the entire healthcare team," she says. "It's really important to educate everyone, from the person who greets the patient at the front desk to the nurses, the physicians, the genetic counselors, and the pharmacists--really anyone who's going to interact with the patient."

We end with a brief discussion about how the IIGH came about, and what are the next moves for Colleen and her team.

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



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