precision medicine


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."

When Do We Move to Population Based Cancer Screening for Those with High Genetic Risk? Josh Schiffman, U of U

Last year when we were promised a soon-to-be-on-the-market, pan cancer, genetic based screening test, many of us were taken aback at the hubris. Not only does the science have a ways to go, there are deep ethical conflicts to work through. However, cancer screening based on a patient’s genetics is already being done in certain niche areas.

Josh Schiffman is a cancer researcher at the Huntsman Cancer Institute in Utah. He’s also a pediatric oncologist serving as the Medical Director of the Institute’s High Risk Pediatric Cancer Clinic. At the clinic, Josh and his colleagues put out a study where they demonstrated that early cancer surveillance in patients who have a rare disease called Li-Fraumeni Syndrome can dramatically increase overall survival.

Why Li-Fraumeni Syndrome? It turns out that patients from families with Li-Fraumeni Syndrome have only one working copy of the P53 gene, a well known protective mutation for cancer. Because of this genetic predisposition to cancer, these patients were screened early with whole body MRIs and other blood tests. For the study, patients whose tumors were found due to the early cancer screening were compared to those patients whose cancer was diagnosed because they presented with symptoms. The overall survival rate for those screened early was 100 percent compared to just 20 percent in the later group.

Should Josh’s work with this sub-population translate out to doing cancer screening for all based on known high risk cancer mutations? Josh says let’s do the study. As for the ethical concerns, he feels the landscape of cancer genetics has shifted.

“Many years ago we didn’t offer P53 screening to children, because there was nothing you could do about it,” he says in today’s interview. "But now that we’ve come a far way and technology has improved, if there is something we can do about it, then it makes more sense to do the test. So we believe very strongly that all children at increased risk [for cancer] should be tested."

A Sneak Peek into the Future of Clinical Genomics with Ben Solomon, Inova

We hear from some that soon each baby's genome will be sequenced at birth. This vast amount of genomic information will be stored in a person's medical record for life and be referenced for personalized healthcare, be it for a diagnostic, a prognostic, or a prediction. But others say that it is still way too early to be generating so much information on each person when we know so little about the genome. This camp argues that we should deal with patients on a case by case basis using a more targeted approach.

The Inova Translational Medicine Institute offers us a glimpse into questions such as the whole genome vs targeted approach. A unique not-for-profit research institute, they are using genomic information from patients in the Inova Health System’s five hospitals to move them closer to personalized medicine. With this direct access to patients, solid funding, and a location in the Washington/Baltimore government research hub, the institute is no doubt the envy of anyone working to implement genomics into the clinic. Add to that, Inova’s CEO is a former NCI director, John Niederhuber, who has hired some of the best and brightest in genomics.

We talk today with Ben Solomon, who was hired out of the NIH to be leader of the institute’s Medical Genomics Division. He says that one of their first studies looks at the genomes of over 1,000 pre-term birth babies and could be a model for clinical sequencing on a larger scale.

“We enroll folks about halfway through pregnancy," says Ben in today's show. "We generate whole genome sequencing on the baby when the baby is born, but we start collecting samples from mom and dad before the baby is born. Then we do whole genome sequencing on the full trio. And we follow them longitudinally, hopefully throughout their whole life. The oldest patients are four to five years old now. We re-consent them at a certain age.”

The study is an example of staying away from any bias that comes with looking for a particular disease. In fact, Ben says, in the age of genomics, the classical presentation of disease is drastically changing. A longitudinal study like this is about finding the "natural history" of many different conditions.

This particular study uses whole genome sequencing, but much of the work the institute does is targeted sequencing. Ben says that though it's often a blurred line, his team first determines whether the case is research or clinical. If it's a clinical setting, he says the first line approach is to go with a targeted panel, pointing out that the use of panels has grown tremendously over the past few years replacing the "one-off" genetic testing.

"A few years ago when someone was coming in with a question of hereditary breast and ovarian cancer, the standard was BRCA1 and BRCA2 testing. And very quickly that has changed into almost always larger panel testing. And even the panels offered are getting much larger."

Ben says there is often resistance to the growing size of panels - including from both genetics professionals as well as other clinicians and patients -because with larger panels, the likelihood of seeing variants of unknown significance increases and with that the challenge of interpretation.

This question of targeted vs whole genome leads to a discussion about how much genome interpretation Ben and his team do in house, demands of a bioinformatics infrastructure, and costs.

Flipping Drug Development Upside Down: Niven Narain, BERG Health

The promise of rational drug design has driven pharma companies for years. The history of the industry has been one of trial and error, or “guess and check”, as scientists often say. Companies have screened thousands and thousands of compounds looking for one that might work—the proverbial needle in the haystack. With the arrival of molecular profiling and an explosion in understanding of basic biology, many in our field have hoped to make drug development more predictable: to start with the biology, and with the aid of new computing power, design a drug to work in a specific biological setting. But instead we've been making the haystack bigger. When will we see a tipping point where more drugs than not are derived through logic rather than luck? Though there have been great examples—Merck’s Truspot being the first and Novartis’ Gleevec perhaps the best known—rational drug design still remains a mostly unfulfilled promise.

BERG Heatlh, a Boston based pharma company, is working to change that with their AI platform and a new “back to biology” approach. Today we talk with BERG CEO, Niven Narain, who also is a co-founder of the company.

“We’re flipping the entire [drug development] model upside down,” Niven says. "We’re going to ask the patient biology what has gone wrong and generate as much of the omics data as we can from that patient. We then correlate that to their histories and health records in a population based way and compare it to healthy individuals. Out of that analysis we derive potential drug candidates and biomarkers.”

BERG has secured a considerable amount of press with the attention grabbing headline, “company using AI to cure cancer.” Backed by billionaire Carl Berg, the company can’t be faulted for thinking small. But are they doing anything different than other pharma companies? In today’s interview, Niven says they are looking at 15 trillion data points on a single sample. And the scientific approach is perhaps more robust that we’ve seen in the past. Rather than relying on the latest biomarker studies, the company takes a non-biased approach by letting the patient’s data create it’s own picture of the biology.

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.

Framingham for the Modern Era: Josie Briggs on the Precision Medicine Initiative

Josie Briggs is Director of the National Center for Complementary and Integrative Health (NCCIH) at the NIH. She is also currently serving as interim director of the president’s new Precision Medicine Initiative (PMI).

What has happened since the president announced the initiative, what is the proposed timeline going forward, and how much money will there be for the project ongoing?

Josie answers these questions and more in today’s show, comparing the PMI to the well known Framingham Heart Study, probably the nation’s greatest longitudinal study to date. As with the Framingham study, the NIH is hoping that the PMI will engage the general public in biomedical research.

“Having the interest of the public in clinical research, and having people sign up and be engaged and say that they want to be a part of this is, to me, a very important component. In some disease areas, it’s striking how few people participate in clinical research. This is — and the president’s enthusiasm is part of it — this is a way for there to be broader engagement in clinical research,” says Josie.

Defending the Value of Biotech Innovation in California: Sara Radcliffe, CLSA

Earlier this year, the California Life Sciences Association (CLSA) launched, becoming the first statewide policy and advocacy group for biotech. The new nonprofit, a merger between BayBio and the California Healthcare Institute, is led by CEO Sara Radcliffe, former Executive VP of Health at the international Biotechnology Industry Organization (BIO) in Washington.

Sara steps into this new role at a time when biotech is booming in the state and in the nation. Yet she will face some difficult challenges ahead:  drug prices are going through the stratosphere,  drawing increasing ire from the general public and state and national goverments while diagnostic test makers see their often patchy reimbursement being further reduced.  Facing a new statewide ballot initiative that aims to fix drug pricing and an upcoming drug cost transparency bill scheduled for the next legislative session, how will Sara defend CLSA members, such as Gilead and Celgene, who are charging ever higher drug prices? And what will she do for a promising yet underpaid diagnostics industry?

Welcome to California, Sara.  How does she like the Bay Area so far?   “It’s a much more laid back environment,” she says at the end of the interview. "Washington can be quite a staid environment. So I’m enjoying the entrepreneurial atmosphere."

 

 

Woodstock for Genomics? Richard Lumb and Carl Smith on this Month’s Festival

If you haven’t already, check out the inaugural Festival of Genomics being held in Boston later this month.

Billed as “a rigorous, fun, and transformational forum,” the unusual get-together will feature the who’s who on the genomics speaking circuit, including Craig Venter, George Church, and Eric Green. Based more on a music festival than a science conference, the Festival of Genomics offers a chance for folks from all around the genomics community to perhaps connect in a new way. And did I mention the disruptive price? Tickets are going for as low as $150 to enable more diverse attendance.

Who is this new media company, Front Line Genomics, that is producing the show? And what is their goal?

We talk to CEO, Richard Lumb, and Managing Editor, Carl Smith about the new company, the first festival, and their overall vision.

“We’d love the festival to be something that people genuinely look forward to and think: ah great, time to get out of the office and have some fun, meet old friends and see what new exciting research and new opportunities are out there,” says Carl in today’s show.

The Festival of Genomics takes place at the Boston Convention Center, June 22-24.

 

The Genomics Grinch

One of the handy tools a journalist can use is a sharp pin.  It’s quite helpful when encountering over inflated balloons, such as the politican’s ego,  a financial bubble, or the hype around going to war.   When the pin is used at the right time, and on the right target, there is no question that the resulting “pop” is heard by everyone.  



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