genomic medicine


10 Genomics Questions for the Presidential Candidates

ScienceDebate.org has just released 20 science questions for the presidential contenders.  We thought we'd send in our own list of 10 genomics related questions.  Here they are:

 

1.  Will you get your genome sequenced, and 

   A.  Donald, will you show us what percentage of Neanderthal you have?

   B.  Hillary, will you show us the variants you keep on your private home server?

 

2.  If Obama could be cloned, should his clone be able to run for another term?

 

3.  Which of the following would make the best Moonshot:

A Maniacal Commitment to Science: Peering into Regeneron’s Genetics Center with Jeff Reid

Today we feature a pharma company that has been around for some time but recently getting more media coverage for the impressive scale of their new genetic center. Regeneron Pharmaceuticals, insiders joke, has been an overnight success that took 25 years.

One might think every big pharma company has their own genetic center for internal R & D. But today’s guest, Jeff Reid, Executive Director of Genome Informatics at the Regeneron Genetic Center (RGC), says that actually deep genetic research is often outsourced.

In just two years, the RGC has built an impressive sequencing lab and announced large partnerships with healthcare systems and academic centers that rival major government projects. One such collaboration with Geisinger Health System involves the sequencing of 100,000 genomes. Already, the RGC has sequenced over 100,000 exomes and has plans to sequence 500,000.

“What we’re doing is quite different,” says Jeff. "We are envisioned as a large scale academic genome center embedded in a pharma company."

Jeff says the strategy is to not only go wide with studies of large numbers of patients for the purpose of finding very rare variants, but to go deep as well. Big numbers can be distracting, he points out, saying that some times they get more insight off a small project, such as the treatment of children with a rare genetic disease.

“There are strategies all across the spectrum of project size,” he says.

Set up in an age when compute and data storage are no longer an issue, the RGC has become the first large scale genetic center to be entirely in the cloud. What is the major informatics challenge for Jeff and the center? And what does having such a large scale genome center mean about Regeneron and where we are today with genomic medicine?

The Days of Miracle and Wonder: Laura Hercher on Genetic Counseling, Part 2

We often hear at conferences that there are too few genetic counselors. And that this bottleneck is constraining the delivery and promise of genomic medicine. Is this true?

It is 100% true, says Laura Hercher of Sarah Lawrence College in the second part of our interview on genetic counseling.

“We graduate just under 300 genetic counselors a year. And last year at our annual meeting [National Society of Genetic Counselors], there were posted over 600 jobs. We’re producing jobs at a much greater rate than we’re producing counselors.”

The interview moves to a broader discussion about how society goes about keeping up with the increasing amount and power of genomic technologies, such as new gene editing techniques. Laura reads an excerpt of her recent piece at the DNAExchange.com

“There is no simple solution to this, but the battle begins with how we define ‘we’. Genetics needs to remind us of what we share as often as it tells us how we are different. Many of you are out there every day fighting battles you may not recognize as part of a larger war: battling insurance companies for access, battling to bring diversity to our biobanks and clinical trials, supporting a new vision of family, in which our 99.9% shared DNA is enough, and we are not defined by the fraction that is identical by descent. We are educators in a field that is an agent of change, and so it falls to us to work for an ever more expansive and inclusive definition of ‘we’. Without that, we risk that the amazing technology of the genomic age will be perverted into a tool for doubling down on the things that divide us.

These are the days of miracles and wonder

This is the long distance call

The way the camera follows us in slo-mo

The way we look to us all

The way we look to a distant constellation

That’s dying in a corner of the sky

These are the days of miracle and wonder

And don’t cry baby don’t cry

Don’t cry

The Days of Miracle and Wonder: Laura Hercher on Genetic Counseling, Part 1

They’ve been called the “unsung heroes” of our age. They are primarily women. And when the trend for most of us is to become specialists, they have been generalists.

Today we begin a special series on genetic counselors. Our first guest, a genetic counselor herself, is a name familiar to our audience. Laura Hercher is one of our regular month-in-reviewers, and today it’s all about her. She is on the faculty at Sarah Lawrence College where the first genetic counseling program was begun in 1969 and where half of the nation’s genetic counselors have been trained.

Like many other fields, there are different schools of thought when it comes to genetic counseling. In today's show, Laura says that the older method was for the counselor to decide what genetic data was good for the patient. It was thought that "genetic information is super explosive, and you have to treat it like non-exploded ordnance all the time and be very very careful what you give out."

Now, Laura says, the trend in genetic counseling matches that in the world at large "where people expect a free flow of information," and more is left up to the patient. "The early studies we've gotten have suggested that people can handle information."

What makes a good counselor? And is there a difference between counseling in the clinical setting and counseling for industry?

These are a few of the questions we cover in Part 1 of the interview.

Listen to Part 2.

A Precision Medicine Platform Comes of Age: Jonathan Hirsch, Syapse

Today’s show with Jonathan Hirsch, the President and co-founder of Syapse begins a couple years ago. We first featured him on the program in January of 2014 with the headline, Is this the Omics-to-Clinic Site We’ve All Been Waiting For?

It turns out, in many respects it is. Syapse has had some big wins with some of the more progressive healthcare companies in the U.S., including Intermountain and Stanford. This year Syapse announced the creation of the Oncology Precision Network for data sharing in cancer care among several major institutions. The company even got a shout out from Vice President Biden in one of the recent White House confabs.

Over the years we’ve featured various bioinformatics and clinical informatics companies who had the aim of bringing omics data to the clinic. Syapse is emerging as a leader in that field demonstrating strong traction, particularly in cancer care. Today Jonathan explains the company’s Precision Medicine Platform, on top of which sits their oncology application.  He gives an example of just how this platform is changing cancer care at Intermountain in St. George, Utah, a small town with some big expertise.

And has the Veep’s Cancer Moonshot been changing things up?

“Everyone focuses on the money, but it’s not about the money,” Jonathan says. "It’s about how you use the power of the presidency to knock heads together and bring people together in collaborative relationships that they might otherwise not have entered. We’ve seen a measurable change in attitudes around clinical data sharing from this initiative."

FDA’s Liz Mansfield on New NGS Guidances

On July 6th, as part of the President’s Precision Medicine Initiative, the FDA issued two new draft guidances for the oversight of next gen sequencing (NGS) tests. The first guidance is for using NGS testing to diagnose germline diseases. In the second, the FDA lists guidelines for building and using genetic variant databases.

To help us understand just what the guidance is and what led to its release, we’re joined by Liz Mansfield, the Deputy Office Director for Personalized Medicine at the FDA.

It’s unusual for the FDA to issue guidance around a single technology, but Liz says that NGS is “transformative” and is eclipsing so many of the older technologies. The biggest challenge is that NGS is a technology used for discovery and has the power to test for so many things at once.

How does the new NGS guidance relate to the much talked about guidance on LDTs that came out a couple years ago? And does the new guidance represent a more incremental, step by step approach for the FDA in dealing with the explosion of today’s molecular testing field?

“No, it’s not an attempt to break down into smaller bites the issue on LDTs. It’s to address this particular technology, regardless of who the developer is,” says Liz.

The two guidances are for very specific purposes and Liz anticipates further NGS guidances to be issued in the future. For example, guidelines for dealing with somatic mutations rather than germline mutations.

After the Genomes: Season 1

Image source:  HBO.com

Andy: Surprise! The human genome is still as boring as it always was.

Chris: Oh, come on, you didn’t get turned on by that BAM file?

Andy: Hi, I’m Andy. 

Chris: Hi, I’m Chris, and this is “After the Genomes!”

Andy: Each week for the next three weeks, we’ll be looking back on Game of Genomes, an ongoing series at STAT News written by science journalist, Carl Zimmer.

How Is the Brexit Impacting Genomics? with Clare Turnbull and Hadyn Parry

Today's guests have been separately on the program recently. And we've asked them, both Brits, to come back on for a discussion of the Brexit. Clare Turnbull is Clinical Lead for the 100K Genomes Project Cancer Program at Genomics England. Hadyn Parry is the CEO at Oxitec, a company based in Oxford which is already selling their genetically engineered mosquitos into Brazil to deal with viral diseases like Zika and Dengue Fever.

The first question we throw at them is whether they are still in shock over the outcome of the vote. Clare resides in London, and Hadyn in Oxford—both places that voted overwhelmingly to remain in the European Union. In fact, Hadyn says he doesn’t know a single person who voted “leave.”

Clare says Genomics England is funded through 2020, so in the short term, the 100K Genomes Project is secure. She also has a role in academia where most genomics research takes place. There, she says, they are being hit with an immediate impact. 10-15% of grant funding in the British system comes from the EU.

“People are on grants which are running. People have won grants that not yet been awarded. And people are looking to collaborate on grants in the medium term future. And one becomes a pretty unattractive collaborator on an international, pan-European grant when it’s uncertain whether or not we’ll be in the EU. The uncertainty is pretty immediate,” says Clare.

Hadyn says the uncertainty is certainly affecting business in the short term. But points out that in the longer term, the UK is solid. They have a great tradition of science, and they have four of the top ten universities in the world. And their entrepreneurial culture is strong. It’s much easier to do a startup biotech company in the UK than in the rest of Europe.

“The longer term, I’m quite comfortable with,” he says. "It’s all about the uncertainty in the short term. The sooner we move to understanding the rules of the game, the sooner the short term uncertainty can be removed.

For now, both see a country still in shock and denial.

Know Then Thyself: Kari Stefansson, deCODE genetics

Kari Stefansson is a name well known in the field of human genetics. His founding of deCODE genetics in his native Iceland in 1996 took our field into a new frontier with the unique opportunity to work with not only a homogenous population but also to integrate with a large centralized healthcare database. It also surfaced a huge ethical debate about genomic privacy.

We’re very happy to welcome Kari to the program for the first time to talk about his vision for deCODE now that the company has been bought by Amgen. The company has continued to publish papers revealing major findings of rare variants associated with common diseases. Just last month Kari and deCODE published a paper in the NEJM with the discovery of a gene called ASGR1. The gene lowers the risk of heart disease by a substantial 34%.

Kari is passionate about discovery for the sake of discovery.

“All life on earth is rooted in information that lies in the simple code of As and Gs and Cs and Ts of DNA,” he reminds us. “Some of our discoveries are knowledge for the sake of knowledge. It is man studying man.”

But he also points out that as soon as they made the discovery of the ASGR1 heart-protective gene, researchers at Amgen went to work immediately on a drug discovery program. And, he says, he knows that many other pharma companies have already begun similar programs.

deCODE is perhaps best known though for their project to create a genomic database unlike any in the world. And for the ethical issues this has brought up. Last year deCODE announced that they had sequenced enough individuals to impute the genomes for the entire population of Iceland. This could lead to a new kind of preventative healthcare system that would be a model for other countries everywhere. It’s also left Kari and his colleagues scratching their heads over whether, for example, they have a social obligation to find out who in Iceland carries the dangerous BRCA mutations.

He shares some dramatic statistics that reveal their dilemma:

"Women who carry this mutation have 86% probability of developing a lethal cancer. They have 72% probability of developing breast cancer. They have a life expectancy that is twelve years shorter than non-carriers. They are three times more likely to die before the age of 70 than the non-carriers. And most of this risk could be mitigated by preventative surgery, for example.”

The interview goes well over our typical target of 20 minutes. But Kari is a deliberate thinker and an eloquent speaker. Enjoy.

Mukherjee Mess-up, the Secret Harvard Meeting, and Success in Gene Therapy: May 2016 with Nathan and Laura

Today we look back on the genomics headlines over the past month (and a few days). To do this we’re joined by our regular commentators, Nathan Pearson and Laura Hercher.

First we take on the science journalism kerfuffle of the year. When Pulitzer Prize winning author, Siddhartha Mukerjee, got epigenetics wrong in his New Yorker piece, scientists came out en masse to denounce it. Nathan reassures us that scientists aren’t afraid of writers.

Then on to that secret meeting at Harvard, HGP-Write. Laura gives it two thumbs down, saying it’s very normal for folks to be scared of the idea of synthesizing a human genome from scratch. So don’t make it more scary with a secret meeting and total lack of transparency.

Finally, we review some positive success stories for gene editing, specifically some gene therapies which have been approved or undergoing new trials.



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