precision medicine


Move Over PDL1: New Test Combo Adds RNAseq to Better Track Immune Escape

Reports from ASCO, the nation’s biggest cancer conference, this year again were full of stunning stories about the success of older and new immuno therapies. The race has never been hotter for biomarkers to target patient groups. Most of this new class of drugs--which harnesses the immune system to go after the cancer--inhibit an immune checkpoint called programmed cell death protein 1 or PDL1. So frontline cancer treatment these days typically includes a test for the PDL1 biomarker. But there are a breadth of potential targets in the immune system that promise to make this class of cancer drug even more effective.

Today we talk with Mark Gardner, CEO of OmniSeq, who has just received approval from New York State (the company is in Buffalo) to launch their new Immune Report Card.

“The biology is complicated. Even for folks that are PDL1 high, in the majority of cases those patients are not going to respond to these drugs. The average number of responders is 20-30%. So we know something else is going on. It turns out we’ve known some of the mechanisms for how the tumors are achieving "immune escape.” What we’ve not had the ability to do is to simultaneously measure across the range of hypotheses for how that tumor is escaping."

Omniseq's Immune Report Card includes mutational burden and MSI testing, which is common practice today. The two additional “legs” of the report are copy number variation for PDL1 as well as RNAseq.

Deep Omics Profiler, Mike Snyder, Now Turns to Wearables

Mike Snyder is well known in the genomics community for his iPOP (integrated personal omics profiling) study. Profiling himself with hundreds of thousands of measurements each day over a period of seven years and a group of a hundred others for about three years, he and his team at Stanford have shown that sequencing and other omics data can be used to predict Type II diabetes, cancer, heart problems and other disease. He’s also published numerous papers comparing NGS instruments. Now he is expanding iPOP with a whole new set of tools: over the counter wearable devices.

Though Fitbit’s sales may be down, Mike says wearables are hot. His team has found that there are over 1,000 health related wearable devices on the market today. He predicts that we will all be wearing them, using data that will be centralized onto the "dashboard" of our smart phones to drive our health decisions.

Those who have used wearables have used them mostly as “activity monitors,” and they tire of the devices after about three months. His lab, says Mike, is looking at wearables differently by using them as “health monitors.”

“The power of these devices is that they will measure continuously your basic physiological parameters, and we think that complements the other sorts of data that we’ve been collecting quite nicely. We actually think these devices can be used to tell when you’re getting sick.”

Just as when omics data predicted his own onset of Type II diabetes, Mike says wearables data helped him quickly diagnose his contraction of Lyme disease. The data in the recent two year study also showed when three others were getting sick—their heart rates went way up over baseline.

What about all the wild goose chases and the chance for hypchondria?

“I’m a believer in letting the data tell us what’s going on,” he says. "I didn’t know my blood oxygen level dropped on flights. In hindsight, it makes a lot of sense. And that’s what everyone says, 'it makes a lot of sense.' But most people didn’t know that. This could be a big issue for those with pulmonary illnesses.”

We end with a brief discussion of Mike’s new book: “Genomics and Personalized Medicine: What Everyone Needs to Know."

  

Known for Medical Devices, 116 Yr Old BD Makes a Bold Move in Genomics

Talk to someone who attended this year’s AGBT, and you’ll know the big buzz was about single cell genomics. One of the exciting new platforms came from a new player in the genomics space and yet from a very old company.

Founded at the end of the 19th Century, Becton Dickinson (BD) has been one of America’s great medical device innovators. They made the first syringe designed specifically for insulin injections. Their BD Vacutainer became the standard for blood collection in the U.S. They designed the first “intelligent” insulin pump. At this year’s AGBT conference, BD showed up with a new genomics division announcing their new Resolve(TM) Single-Cell Analysis Platform.

Today we talk with the VP of BD Genomics, Stephen Gunstream. Stephen says life science researchers already know BD through the BD Biosciences unit which over the past thirty years has been perfecting flow cytometry for their single cell analyzers and sorters. Acknowledging that BD has been going through “a culture shift the past five to ten years,” Stephen says their history with flow cytometry made their recent move into single cell genomics tools a natural one.

“People talk about a resurgence in single cell genomics, but I wouldn’t really call it a resurgence,” says Stephen. "We’ve been analyzing cells for 30 years with flow cytometry. What has really changed is that the capabilities of next gen sequencing has allowed us to do this in a highly parallel manner at a cost which is a lot more affordable.”

So how will BD stand out in a rapidly maturing marketplace? What research does Stephen think the new platform will most impact? And perhaps most importantly, will BD with their century old history of experience with clinical products be able to significantly help guide genomics research products into the clinic?

Can You Name the World’s Largest Single Disease Research Charity?

Let’s take a break from the US and head over to the UK, home of the world’s largest single disease medical research charity.

Cancer Research UK (CRUK) raises five hundred million pounds a year for research and drug discovery into any and all of the two hundred plus types of cancer. The charity is extremely well integrated into U.K. culture, and uniquely English in that the donations are mostly small and come from all corners of society. A third of CRUK’s funding comes from donations averaging £10 or less.

Allan Jordan is head of chemistry for the drug discovery unit of CRUK. On today’s show he says that the democratic funding of the charity gives them a great deal of flexibility to do early stage drug discovery. Whereas a big pharma or biotech has to devote their resources to limited assets, or drugs, CRUK is able to spend more on basic biology research and follow the science into any type or cancer or multiple cancers.

There are very few conditions,” says Allan about his drug discovery unit in Manchester. "We don’t have to be specific about any particular disease area; we don’t have to be experts in one disease at the expense of all others. We can tap into that UK-wide expertise and network that can help us understand the biology.”

How is the charity working with the UK's national healthcare system? And does Allan hear the same kind of skepticism that we hear in the U.S. about precision medicine in oncology?

Luke Timmerman on His New Biography of Lee Hood

There is tons of life science journalism. Our coffee tables and inboxes fill up each week with that quarterly or that daily. We sift through headlines and product advertisements to assess what’s going on in our industry. It’s our job to know. In this age of several-times-per-day newsletters and 24 hrs a day Twitter, we catch what we can.

And occasionally, we come across a carefully written piece or a well done interview, and we take a moment to realize with some awe the history that is being made in our industry.

Occasionally. Which is why a new book out by veteran biotech journalist and the guest of today’s show, Luke Timmerman, is such a rare treat.

Hood is a thrilling ride through the life of the visionary biologist, Lee Hood, told by someone who is not afraid to show the shiny and the not so shiny. From his boyhood in Montana to being chair of the biology department at Caltech where he oversaw the invention of the automated DNA sequencer, to being recruited to Seattle by Microsoft’s Bill Gates, Hood’s journey becomes the perfect vehicle for Timmerman to probe into the messy corners of science and put an intimate, human face on the history of biotech. Covering Hood’s move to the University of Washington as a young Seattle based reporter, Timmerman has known Lee Hood for several years. It's a full scale biography, efficiently and confidently written with an insider's perspective and access. Timmerman says it's an “unofficial biography,” meaning Hood was supportive of the project, but Timmerman had full freedom.

Playing historian has been somewhat of a fantasy for the long time journalist.

"There are things that are happening in the moment which a journalist can call people on, but you don’t really get the whole story. There’s only so much people can say and there are not a whole lot of documents that come available when you’re on deadline. But when you’re a biographer, and you have the luxury of time, and people have moved on, things become a lot less sensitive. People become more willing to talk, and a whole lot of documents become available through the public record.”

Who is this man, Lee Hood, and how has he impacted our industry? In the book, we read of the time when Hood holds a press conference to announce his team has done it—they’ve got an automated DNA sequencer. But, standing at perhaps the pinnacle of his career, Hood forgets to mention the "team" part. It’s a flaw that will go on to haunt what by any measure has been a remarkably successful career.

What impact has the subject made on the author? And what does Timmerman hope for the book?

To round out the interview, we get Timmerman’s thoughts on his new gig, the Timmerman Report, and the recent Sarepta decision by the FDA.

August 2016 with Nathan and Laura

It’s the end of summer and end of another month. Joining us to discuss the genomics headlines of August are Laura Hercher and Nathan Pearson.

A recent study demonstrating that breast cancer patients with low genomic risk may not need chemotherapy is just what precision medicine is all about, isn’t it? Theral and Laura think the study is a big deal. Nathan’s not so sure.

Nathan is convinced though that Eurocentric studies have implicit racism. Laura agrees, saying the lack of racial diversity in biological databases is a major weakness that we must face head on.

Also, the FDA issued a report supporting Oxitec’s GM mosquitos for use in Florida. Laura is on board with the science but warns about smugness on the part of the scientific community. And George Church’s lab released a reengineered e. coli. Nathan imagines a new genomic language of 2 letter codons.

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."

Gene and Tonic, July 8, 2016: 49ers Going into Genetic Testing

Just two years at their new home in Silicon Valley and not far down the road from 23andMe, the San Francisco 49ers are offering their fans genetic testing and the chance to donate blood to advance human genome research.

Announcing a partnership with the company ORIG3N, the 49er Chief Operating Officer, Ethan Casson, says that “this is the first agreement of its kind where a major sports organization can give back to the human genome some of what the genome has given to professional football players.”

Medicine and the Limits of Science with Michel Accad, MD

Are drug prices really too high? If so, how do we bring them down? Is precision medicine and the use of molecular profiles really making a difference in healthcare today?

These are questions that regularly haunt our industry and the journalists who cover it. But there will be no answers until we face the grand question of all, what today's guest calls the most nagging question in medicine: What is health?

Today we begin a new series focused on just this question.

When I came across Michel Accad’s recent blog, Why I Don’t Believe in Science, of course it provoked me to click. Either he would be a terrible nutcase, in which case I'd lose the time it takes to discover this, or it might turn out to be one of those disturbing points of the day when we have to actually do some thinking. What I found was a cardiologist based in San Francisco who was doing some deep philosophical thinking about medicine today. And, obviously, one savvy enough to get some click through. It turns out Michel does believe in science, but he doesn’t share the pervasive view that medicine is a continuum of science.

What are his thoughts about precision medicine? What is his definition of health?

We always jump at the chance to have a medical doctor on the program, and a doctor who is also a philosopher is a double treat. Today's interview takes us down a different path than our typical shows, and we'd like to invite the audience to send us your feedback by clicking here.

February 2016: Mosquitos, Preprints, and that Rocking White House Summit

It’s time again to look back on another month with Nathan and Laura.



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