Submitted by Ayanna Monteverdi on Thu, 07/27/2017 - 09:43
The life science tools space is flourishing. Biomedical research output is at an all time high. Today’s guest says there are over 40,000 papers published each year on cancer biomarkers.
But very few of those become commercialized tests. Why?
Many had hoped the FDA would step in and save the diagnostics industry from itself, from a race to the bottom when it came to being able to reproduce clinically relevant tests. But that’s obviously on hold. In the meantime, others are stepping in. And there is one government agency which has no regulatory authority but some power to help out.
Kenneth Cole is the group leader for developing bioassay methods and standards at the National Institute of Standards and Technology. His group has just created a new set of standards and methods for HER2 testing which is available to the clinical lab community to help improve their own assays. It’s been said on the program that this very common test for use in cancer therapy has a false positive rate of 20 percent. That's too many patients getting told the wrong thing.
Ken’s group is now going to work on EGFR and other common tests, and they can help the testing community in several ways. First of all, Ken says, they have a “the luxury of being able to focus in on the measurement techniques and on examining all the sources of variability in an assay." They also work on characterizing cell lines, which have become “an essential part of modern biology.” Ken says a big part of the work at NIST is the education of the community and of the new crop of scientists.
Do you have an assay you’d like help with? Ken is easy to reach, and NIST welcomes your requests. They have set up many partnerships from loose collaborations to projects with IP protection.
Often the best place to find solutions is in going back to the basics.
Submitted by Ayanna Monteverdi on Thu, 04/13/2017 - 10:58
Rubbing shoulders at molecular medicine conferences these days one senses a sigh of relief when you talk about laboratory developed tests (LDTs). With the FDA’s decision to put regulation on hold coupled with the expected confirmation of Scott Gottlieb as FDA commissioner, those in the lab testing business seem to be confidently settling back to the status quo. And those who were arguing that all we need is a “beefed up” CLIA to hold labs to better testing standards don’t appear to be motivated to do so anymore.
Several questions arise when it comes to LDTs. First of all, if regulation was truly important for enabling this revolution we call precision medicine, then why couldn’t the Obama administration get it issued? In other words, is the status quo so bad? Secondly, without the FDA even threatening to regulate, will we see the “beefed up” CLIA that many labs argued is the best way forward? Without the stick of the FDA, is the carrot gone too?
Russell Garlick is the CSO of SeraCare, a private company that has worked to improve clinical laboratory standards for over thirty years. The company recently added a new business unit for precision medicine diagnostics, and Russell was brave enough to come on today and address these questions.
As for the status quo being good enough, Russell isn't happy.
“Many of the organizations undertaking clinical trials to recruit oncology patients have lost confidence because LDTs in one geography of the United States don’t perform the same as in other parts of the United States,” he says.
Russell has worked many years with labs on IVDs--the already regulated group of diagnostic tests. He sounds disappointed that the FDA has dropped their focus on LDTs, but is hopeful that existing organizations, such as the College of American Pathologists, or even private companies such as SeraCare might step in and seize an opportunity to improve things.
“There’s a lot of status quo. And frankly it’s a little bit disappointing,” he says, “because the laboratories can benefit from [improved standards]. It’s that inertia to do something new and different."
Submitted by Ayanna Monteverdi on Sun, 02/19/2017 - 20:01
First of all, watch the video below.
A Santa Cruz company is now previewing a nanopore device that could be a major disruptor in molecular testing. The device is the size of a glucometer and could take all kinds of testing—perhaps someday even cancer-tracking liquid biopsies—into the home with its ease of use and ability to work with thousands of different assays.
Two Pore Guys, named for the pores not the guys, is a spinout from UC Santa Cruz and one of a growing biotech community on the west side of Santa Cruz, CA. The company has yet to do beta testing and is focused now on scaling up manufacturing of the small, relatively simple devices. CEO, Dan Heller, says Two Pore Guys has no plans to develop their own tests but will stay focused on the platform.
“We could make ten or fifteen assays and go to market with them, but why not let others make thousands and thousands of assays?” Dan asks. "They’ve already spent billions of dollars and decades developing primers or capture molecules for antibodies. Why not just give it a new life and let them sell it into the market? It's a revenue share."
So what tools might this replace? Dan lists the standard lab machines for PCR, HPLC, and mass spec. “There’s many uses of existing lab equipment that could be done on our device more quickly, cheaply, easily,” says Dan.
Based on recently developed nanopore technology, the small device looks remarkably straight forward. A molecule—just about any molecule-- is pulled through a nanopore by an electric current. The impedance of the current is the measure of the molecule. Though the device does not currently sequence DNA, its possibilities to replace other large life science tools does seem all the more real in a time when Oxford Nanopore’s small sequencing devices--also partly developed at UCSC—are proving themselves powerful tools.
Listening to Dan, the broad range of molecules and applications becomes dizzying: diagnostic testing such as liquid biopsy tests for cancer (the company is currently doing a study with UC San Francisco for a KRAS liquid biopsy test), infectious disease, border security, agriculture, animal health, and environmental testing.
It leaves us with this question in the end: why was this not done before?
Submitted by Ayanna Monteverdi on Thu, 11/17/2016 - 12:17
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.”
Submitted by Ayanna Monteverdi on Wed, 10/19/2016 - 10:08
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.”
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.
Submitted by Ayanna Monteverdi on Thu, 06/30/2016 - 12:04
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.
Submitted by Ayanna Monteverdi on Wed, 06/29/2016 - 11:45
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."
Submitted by Ayanna Monteverdi on Fri, 06/24/2016 - 10:27
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.
Submitted by Ayanna Monteverdi on Wed, 05/18/2016 - 22:10
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.