commercializing diagnostics


When an Exome Test Is Part of the Therapy and Not a Diagnostic: John West on Personalis and Personalized Cancer Vaccines

About six years ago there was a wave of genome interpretation startups getting their first rounds of funding. One of them was Personalis, a company founded by a well known group of Stanford geneticists and bioinformaticians.

John West is the CEO of Personalis, and he joins us today to talk about how the company is participating in the dramatic shift in drug development toward immuno oncology drugs. Our listeners might remember John from his days at Solexa where he served as CEO and presided over the sale of the company to Illumina.

At the same time Personalis came on the scene, the first drug that would harness the immune system to fight cancer was being approved by the FDA, Yervoy by Bristol-Myers Squibb. This was the first of four drugs known as checkpoint inhibitor drugs. These four drugs have had spectacular success and together generate revenue of over 6 billion per year, a level which has doubled in the past year.

John and Personalis are working with biotech companies on a new generation of immuno therapies known as personalized cancer vaccines. These new drugs are actually custom synthesized for each patient after an “immunogram” or genetic workup of the tumor has been done. We know today that tumor growth is driven mostly by neoantigens, or new antigens which arise from mutations that happen after the cancer first appears, says John. So an immunogram done by Personalis must look at all the genes (over 20,000) and not just the original driver mutations. An immunogram could only be done in the last few years with the latest developments in next gen sequencing and algorithm creation.

How far along are these new personalized cancer vaccines? And what is the commercialization challenge for Personalis?

“We are essentially an integral part of the therapy,” says John. "So we don’t think of it as a diagnostic test. We think about it as the initial part of the manufacturing of the therapy."

Biomarker Panel to Predict Type 1 Diabetes

When we talk precision medicine on Mendelspod, we’re usually talking about oncology. But today we shift our focus to diabetes.

Raghu Mirmira is an MD PhD at Indiana University who is working on a panel of biomarkers that would predict Type 1 diabetes. That’s right. Predict.

Having already found a DNA biomarker candidate which detects dying beta cells using the new technology of digital PCR, Raghu is now working to improve the panel with other metabolites.

Will we some day have a Myriad Genetics for diabetes? Raghu says, yes. But he warns that we must also develop new treatment options to go along with a predictive blood test.

“Before we get to the point where this is a commercially available test, we need to be doing further studies to figure out what’s the outcome of individuals who test in a particular way. And what kind of interventions could improve those outcomes in some way.”

October 2016 with Nathan and Laura

Today’s show was recorded on Halloween, which now feels so yesterday. Forgive us for some spookiness.

What doesn’t feel so yesterday is the launch this past month of Helix, a company spun out of Illumina that aims to add exomes to the lineup of direct-to-consumer testing. Nathan points out their model for delivering data incrementally through various apps. Laura questions how Helix will vet the apps.

This month the genomics community gathered in Vancouver for the annual American Society for Human Genetics conference. The commentators give their highlights. Then we double back on a genetic counseling conference from last month and a big topic that we missed in our last show: population screening for BRCA.

It’s a bird, it’s a plane, it’s a turducken gone crazy. . . . . No, actually, says Nathan, “it’s a virus inside a spider costume for Halloween inside a bacterium inside a fly!"

With FDA Guidance on LDTs Still Not Out, What Are Labs Doing?

As we get closer to the election and the end of 2016, the debate over LDT regulation has gone quiet. At this time last year, there was one hearing after another, first in the Senate, then in the House. The FDA’s Jeffrey Shuren was called before congress and drilled over the nuances of the guidance as well as asked when it would be released. He said, in the first half of 2016.

Though there has been no guidance released, the FDA has continued sending letters out to individual labs, requesting certain LDTs be approved before the labs market them. In March of this year, the FDA put a couple labs and two Texas hospitals on notice that were marketing “high risk” unregulated diagnostics. This surprised many in the laboratory community. These tests were diagnostics to detect the Zika virus, and any delay could negatively impact public health. The FDA told the labs they expected them to submit a request for emergency authorization (EUA).

So what are labs across the country doing? What are they supposed to be doing? Are they shying away from developing new LDTs? Are they proactively working to develop 'clinical validity’ for their tests, something they haven’t had to do under CLIA (the current regulatory statue for labs), but would be required to pursue by the FDA?

Some lab directors, such as today’s guest, say they haven’t changed a thing and are in “wait and see” mode. John Longshore is the Director of Molecular Pathology for the Carolinas Pathology Group and Carolinas HeathCare System, an integrated health network with more than 40 hospitals. He’s optimistic that laboratories are being heard on Capitol Hill and that it won't come down to FDA guidance. Referring to a recent Senate HELP meeting in September 2016 on the topic of LDTs, he says he's confident "that we will have regulation through congressional legislation rather than FDA guidance.”

The debate continues . .

Digital PCR Opens Up New Liquid Biopsy Opportunity in Melanoma Treatment: David Polsky, NYU

The history of science is also a history of toolmaking. And nowhere is this more true than in modern biology. New instruments in the lab allow biologists additional modes of discovery, new levels of quantification, and the opportunity to pursue new and old questions with more data.

David Polsky is a dermatologist and researcher at NYU’s Langone Medical Center. Last week he received a grant from the NCI for readying a new liquid biopsy test that tracks the progression of melanoma for the clinic. Until now, there has been no blood based marker that was able to track melanoma as there is with other cancers such as prostate cancer and the PSA (prostate specific antigen) score. This new test, which could be a major breakthrough for the treatment of melanoma, targets seven mutations which occur in 70% of melanoma patients. These mutations are found in cell free, circulating tumor DNA.

In today’s interview, David points out that the test is possible only with the advent of digital PCR and its ability to measure DNA more with absolute quantification and sensitivity. We knew these mutations before, but just couldn't measure them.

“Droplet digital PCR has been a major breakthrough in our ability to detect rare events and also to quantitate them with accuracy and precision. Those two features are absolutely critical,” says David.

David and his group have been collaborating on the test with Bio-Rad, who makes the ddPCR instruments and designed these tests, and with Molecular MD. Clinical trials with Bristol-Meyers Squibb are expected. Now, with the preliminary science published, the NCI grant will go towards developing analytical and clinical validation so that the test might be commercially available for patients soon.

CEO of ABC Diagnostics Takes a Hint from Allergan's Saunders

We found the following wadded up next to a trash can:

CEO Blog: Another Social Contract with Patients

Lately, there has been zero focus on the price of diagnostics.  Damnit.  Drug companies get all the attention.   And the profits.  I’m writing out a new social contract for diagnostics companies. 

It’s often said that 50% of solving a problem is in first of all defining the problem.   This holds true for medicine as well.  If a patient pays $100,000 for a medication, we should get paid $100,000 for the correct diagnosis.  Period.

June 2016 with Nathan and Laura: GMO Labeling, Misspelling CRISPR, Sequenom Patent Loss, SmidgIon

Today's show was recorded July 1st, the first day that Vermont’s GMO labeling law went into effect. Just how big a win was this for the anti-GMO crowd, we ask our two commentators, Nathan Pearson and Laura Hercher. They have a surprisingly optimistic take, suggesting that the GMO labeling could become a positive marketing tool.

Laura says the scale and ease of CRISPR vs the older technology of zinc fingers is like going from manuscript writing to the printing press. She insists, therefore, that the approval of the first ever CRISPR trial is a big deal even though we’ve already been doing the same cell replacement therapy with zinc fingers. She also points out that the new trial is funded by Sean Parker’s foundation which is moving along at a Silicon Valley pace.

"The tech industry has never had their moment where it killed someone to move too fast.”

Last week the Supreme Court killed off Sequenom’s patent for prenatal screening. After Laura and Theral hotly debate whether there should be such patents, Nathan suggests there is a right balance.

“It’s sort of like tuning a carburetor,” he says. "Patents can encourage people to invest, but they can also inhibit the development of technology.”

And lastly, DNA has a new mascot. It’s called the SmidgIon.

Sequenom Patent Loss a Threat to Personalized Medicine, Says Kevin Noonan

It’s a non-decision with big implications. On Monday, the Supreme Court turned down an appeal by Sequenom in their patent case with Ariosa. The rebuff by the highest court kills Sequenom’s prenatal screening test patent for good.

Sequenom was first to market with their prenatal test that screened for chromosomal abnormalities, such as Trisomy 21. And there was nothing unusual in Sequenom’s receiving patent No. 6,258,540 for the test based on a novel discovery by researcher Dennis Lo showing that there was fetal DNA in the mother’s blood. The discovery sparked one of the fastest growing fields in the history of diagnostics.

The final result on this case has many in the field scratching their heads. If Sequenom can’t defend their patent for such a novel test, then what route should diagnostics companies take to protect their IP?

Today we’re joined by Kevin Noonan, a well known biotech patent lawyer and regular Mendelspod contributor, to discuss the case and what it means for our industry.

Kevin points out that in the precedent setting case of Mayo, the Supreme Court acknowledged that the case would end the patenting of many diagnostics, but expressly urged Congress to act and give the patent office more clarification. Until they do, Kevin says, companies are left with the only option of “hiding their technology” in order to get a return on their investment.

“We have this great age of personalized medicine that we’ve been hearing about since the Human Genome Project, which could die on the vine,” he says. "As a business person, you’re not gonna go into that business, you’re going to invest in the next “i” something because that you can protect. As a policy matter, it’s a horrible outcome."

Bringing Home Some Diagnostics Gold: Brad Gray, NanoString Show How It’s Done

You hear it everywhere. And it’s getting old. That "diagnostics is a tough slog.” That it’s the “redheaded stepchild of healthcare.”

And today’s guest doesn’t disappoint, repeating both these phrases. But Brad Gray and NanoString can claim some big “slogging" success. They’re coming out on top in diagnostics through some clever business strategy built on a solid platform. Made CEO at just 33 years of age, Brad has taken NanoString public and overseen a successful expansion from the research to the clinical market.

In his interview, you’ll hear Brad lay out the three pronged approach at NanoString. Starting as a spinout from Lee Hood’s Institute for Systems Biology, the company began in the life science tools space with their nCounter platform. The machine proved a favorite for cancer researchers because of its ability to look at single molecules of nucleic acid. When the company pole-vaulted into the clinical space, rather than set up their own lab and do the testing themselves--such as diagnostics pioneers, Myriad Genetics and Genomic Health--NanoString opted for a decentralized model. They did just the kind of thing that makes the FDA happy. They created a “push button simple” platform with kits so that clinical labs could do the testing themselves in a highly reproducible fashion.

But that’s not all. Under Brad’s leadership, the company has made several major companion diagnostics deals with big pharma. An agreement with Merck announced earlier this year delivered NanoString an upfront payment of $12 million. That’s a nice boost for a diagnostics company slogging away at reimbursement.

“The Merck deal is especially exciting because it’s the first major molecular diagnostics partnership in the field of immuno-oncology,” says Brad. "And the scale of it makes it the largest companion diagnostics deal ever announced, in economic terms.”

And what of the reimbursement slog for theirs flagship Prosigna breast cancer assay? NanoString can now boast Medicare coverage in all 50 states.

That’s about as good as it gets in our industry.

The Solid Future of Liquid Biopsies with Michael Nall, Biocept

There’s been lots in the news this past year about liquid biopsies—those non-invasive tests which locate biomarkers in a vial of blood. Much of that press (perhaps too much) has been about using these blood tests for cancer screening: predictive tests that could be available to consumers some time in the future.

But according to today’s guest, the real news about liquid biopsies is that they are in use now. Michael Nall is the CEO of Biocept, a company based in San Diego which has gone about as far as any organization in commercializing these non-invasive tests. They offer tests for many kinds of cancer, including breast, colon, prostate, and lung.

“The area we’re focused on really hasn’t gotten as much attention [as the cancer screening tests]. And yet it’s the nearest term and the biggest unmet medical need today: how do you help patients who have been diagnosed with cancer and who are progressing?” says Michael in today’s interview.

Biocept stands out in the space for not only their comprehensive line of testing, but for their demonstration of just how to commercialize these tests. The company has thirteen salespeople around the country who call directly on clinics. They are focused on two niches: cases where the cancer has metastasized in the bones or the brain and cases where not enough or no solid biopsy can be obtained.

Most importantly, Biocept has succeeded in getting paid for their tests using the same existing CPT codes that are used for the solid tumor tests.

Will we soon see a time when the liquid biopsy is the preferred test? How is Biocept preparing for impending FDA regulation? Hear this early success story for a pioneer in a rapidly growing field.




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