Baltimore, MD | October 5-6, 2015

The Intersection of Data Privacy, Innovative Partnerships, Genetics and Ongoing Laboratory Hurdles

The Personalized/Precision Medicine Blog

The official blog of the Annual Personalized and Precision Medicine Conference provides readers with information, insight and analysis regarding the field of personalized and precision medicine, genomics, genomic interpretation and the evolution of healthcare in the post-genomic era.

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John Waslif

John Waslif

John Waslif is the Managing Director of Arrowhead Publishers and Conferences and the Producer of their Annual Personalized Medicine Conference, which brings together multiple stakeholders, including payers, molecular diagnostics companies, genome analysis/interpretation companies, clinicians and many others in order to provide attendees with a holistic view of the personalized and precision medicine landscape.

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Guest Blogger: Anya Schiess, MBA, General Partner, Co-Founder, Healthy Ventures (Ms. Schiess will be giving a presentation entitled "Healthy Ventures: A New VC Perspective" at the 7th Annual Personalized and Precision Medicine Conference in Baltimore on October 5-6, 2015.

For genomics to achieve its expected market growth, the industry will evolve from custom hardware/software/applications, where companies are almost fully vertically integrated, into an ecosystem where entrepreneurs can leverage each other’s innovations. The total amount of genome sequence data generated is doubling every 7 months and the market is expected to quintuple, to over $15 billion, by 2020 1,2. While some skeptics doubt the every day utility of genomic information, it’s difficult to argue that with so much data generated, new clinically important applications will be discovered. Commercializing new applications will require a re-organization of the industry.
As industries evolve, they often fragment. The early computer companies were vertically integrated, manufacturing everything from the processors to the software applications. As it matured, the industry fragmented into layers, and specialized companies came to dominate their layer. Early examples include Intel and microprocessors, and Microsoft and operating software. Recently, we’ve seen the same fragmentation with web infrastructure businesses, e.g. Twilio and cloud communications, AWS and cloud storage, Slack and managed collaboration. 
The genomics industry will do the same. First, we are seeing the hardware/software separation with the sequencing layer led by Illumina, and the computing layer led by AWS. Next, we will see bioinformatics fragment. For example, Spiral Genetics and data compression, DNAnexus and genome assembly, Bina (Roche) and data processing, SolveBio and the reference data layer. The companies that currently own the customer channel – like Invitae, Counsyl, and Foundation Medicine – will go from vertical integration to a focus on the application layer, outsourcing the rest of the stack. This will free tremendous working capital to focus on the new applications enabled by the data explosion. Without focusing on the new apps, these pioneers of genomic testing will be disrupted by nimbler competitors building the future. We’ll also see new categories of applications like genomic interpretation apps and pharmaceutical R&D applications. These will be built on top of an outsourced, fragmented, and more nimble stack.
At Healthy Ventures, we are investing into this fragmentation. We love companies that are creating the infrastructural backbone for the new genomics industry. We look for layers/fragments least likely to be commoditized and where the time-to-maturity is shorter; examples of which include the reference data layer. The company must have more than just a product; it must have the vision and ability to ‘own’ its layer, creating a durable business with a large absolute market, like OneCodex is doing in microbial genomics. Perhaps most difficult, the company must be relevant today, in a highly concentrated market with few end-users doing very high throughput analysis, and also relevant tomorrow in a much larger, but much more distributed market where bioinformaticists are in short supply yet everyone has access to a sequencer.
  1 Stephens, Zachary D, et al. “Big Data: Astronomical or Genomical?” PLOS Biology, 7 July 2015.
  2 Genetic testing for cancer alone is expected to be $9B. Source: Foundation Medicine.
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Guest Bloggers: Ron Eisenstein, Partner, Nixon PeabodyDavid Resnick, JD, Partner, Nixon Peabody (Mr. Resnick will be giving a presentation entitled "Balancing Public and Private Intellectual Property Interests in a Post Mayo-Myriad Age: What is Likely to Be Patentable in Diagnostics - and What Should Be Patentable - to Best Serve the Public Interest" at the 7th Annual Personalized and Precision Medicine Conference in Baltimore on October 5-6, 2015.

By now most people have read about the U.S. Court of Appeals for the Federal Circuit's long awaited decision in Ariosa v. Sequenom. Whether or not you agree with the decision, almost all, including the Federal Circuit, agree that the technology in question revolutionized prenatal diagnostics. Sequenom developed the relevant technology to use fetal DNA in the mother’s blood to detect genetic abnormalities. This technological advance allowed diagnostic tests, for example, screening for Down’s Syndrome, to be done with a small sample of the mother’s blood, avoiding the serious risks of amniocentesis.  

The parties agreed that the underlying discovery upon which the patent (6,258,540,) was based was that a small portion of maternal blood from a pregnant woman contains cell-free fetal DNA (cffDNA). This cffDNA was found in serum and plasma, portions of the blood previously discarded in any analysis of maternal blood samples. It was this cffDNA obtained from a minimally-invasive blood draw performed on the mother that could be used to determine if the fetus had certain birth defects. The parties further agreed that the patent does not claim cffDNA or paternally inherited DNA themselves. Rather, the patent claims methods of using cffDNA. The district court, on summary judgment, had found that since the claims used conventional methods such as PCR amplification, the claims were  directed to a natural phenomenon and not eligible for patent protection  under 35 U.S.C. 101 in light of the Supreme Court's decision in Mayo. On June 12th, the Federal Circuit affirmed this decision. 
Many patent practitioners have denounced the decision. One argument is that it flies in the face of common sense. If serum and plasma were routinely discarded, their use can hardly be considered conventional. 
Others will point to Judge Linn's strange concurrence. After explaining why this case differs from Mayo, and that the claims were worthy of patent protection, he states that he is constrained by the Mayo decision to find the claims unpatentable. As Judge Linn points out, what he and the others are relying on is dicta, a judge's editorializing.  While persuasive, dicta is not binding. 
Second, Judge Linn ignores the Supreme Court's subsequent opinions in Myriad and Alice.  In Myriad the Court found that altering a natural material, even in a conventional manner, was sufficient for patent eligibility. In Alice the Court discussed how significant contributions to the field could result in patent eligibility.  Finally, while mentioning that the Mayo Court had pointed to the claims in Diamond v. Diehr as involving conventional steps that when considered as a whole integrated the statutory exception (an algorithm) and transformed the method into a patent eligible invention, Judge Linn failed to explain why the present claims failed to accomplish the same transformation. 
So what are we supposed to make of this decision? Some will just "go fishing" and stop trying to get method patents, certainly method directed to diagnostics. Indeed, practitioners have seen a decrease in filings of patent applications directed to diagnostics over the last few years. There has also been a decrease in patent litigation.  In fact, one recent study suggests that the decline in patent litigation is a result of the Supreme Court's recent decisions on patent eligibility. 
While no one wants unnecessary litigation, the question is what effect these decisions will have on health care and other scientific advances. We know for certain that these decisions will hurt licensing revenue for universities and nonprofits. Their impact on investment for the biotech industry will be somewhat more nuanced.  While innovators are likely to be negatively impacted by less valuable patent protection, others in the industry will enjoy reduced concern about being blocked by patents.  Will this help the consumer? Maybe. The current structure of the biotech industry places substantial emphasis on private investment. That investment is based upon a robust U.S. patent system that, for a limited time, blocks others from offering competing products  and undercutting attempts to recoup the costs of R&D.  
One can ask whether Seqenome would have made the same investment if it knew that others would be able to offer competing tests without the same development costs. What about Myriad Genetics? If there had been no Myriad to undertake the substantial clinical testing burden, would we have the data that permits women with "bad" tests to take preemptive action and prevent the development of breast cancer?  These are the questions that industry is likely to be prosposing to Congress in the coming weeks and months. The outcome of such efforts is unclear. 
The pharmaceutical industry has not helped itself by providing opponents with opportunities to criticize the effects of patents, such as substantially raising the cost of medications that have been in use for years. As a result of the current state of patent law, the research community may need to look to a different system of funding translational research. Given the climate in DC for at least the last decade, we know the money is unlikely to come from the government. 
In view of the problems with starting a new paradigm, we suggest that the patent system, even with decisions like Ariosa and Myriad, remains the most viable alternative. While the Federal Circuit's most recent decision in Ariosa does not help, it does not change the fact that the Supreme Court held that some patents involving laws of nature or natural phenomenon remain patent eligible. Certainly it does not affect alternative claiming strategies. For example, kit claims, device claims, or even method of treatment claims remain viable approaches. 
One key to successfully obtaining meaningful patent protection is to truly understanding how a given method will be used commercially and focusing the claims fairly narrowly to provide narrow but essential protection. Remember that claims which may no longer issue in the United States are still valid in Europe and many other countries. Additionally, if the most dire predictions prove true, a legislative solution becomes increasingly likely.  Moreover, the Federal Circuit could hear the Ariosa case en banc. Alternatively, the Federal Circuit could reach a different decision in other cases having different records. Such things have happened before.  
While the pendulum on patent eligibility has taken a fairly significant swing in the direction of patent ineligibility, history suggests that these pendulum swings a constant readjustment of competing concerns and that the situation is unlikely to be static. We suggest you stay tuned. 
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Genomic sequencing is moving into clinical care, but this technological advance threatens to outpace our ability to use it effectively in clinical practice and to address the associated health policy issues. A key issue is whether payers will cover sequencing and what evidence will be needed to document its value. The TRANSPERS (Ctr for Translational & Policy Research on Personalized Medicine) Center at UC San Francisco has just released a Policy Primer for Genomic Sequencing, the press release for which can be viewed here: 

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Uptake of genomic and precision medicine is hindered in part by an undereducated health care workforce. Last Spring, UCSF launched the first large-scale open online course on this topic for health care providers to an international audience of 13,000. 
The course aims to provide participants with baseline knowledge of genomics, an overview of the clinical applications of genomic medicine, the skills to evaluate the clinical validity and utility of new tests, and an appreciation of the associated ethical and social issues inherent in this field. 
Precision Medicine has the potential to change fundamentally how health care is practiced, but requires a health care workforce that understands the complexities of this field. As one of the instructors of the course, Jeanette McCarthy’s research on the genetic underpinnings of infectious and chronic diseases has led to over 50 publications in peer-reviewed journals.
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Foley & Hoag’s Bruce Quinn, MD, Ph.D., a national expert on Medicare policy and health reform has offered his thoughts on the FDA’s recent notice of intent to issue draft guidance for regulation of lab-developed tests (LDTs) in a couple of forums recently. Here are the urls:

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New discoveries in genomics research are exciting to physicians because they can see that genomics targeting may provide greater effectiveness in patient treatments. In collaboration with the Genomics Medicine Institute (GMI) at El Camino Hospital and Genetic Alliance, NCHPEG (National Coalition for Health Professionals Education in Genetics) has developed a CME curriculum on genomic medicine.

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The 6th Annual Personalized & Precision Medicine Conference is pleased to announce that Dr. Paul Billings, Chief Medical Officer at Omicia, Scientific Advisory Board member of the FDA, member of the Genomic Medicine Advisory Committee at the Dept. of Veterans Affairs, and the National Academy of Sciences Institute of Medicine’s Roundtable on Genomics has joined the speaking faculty for the 2014 conference to be held on October 29 & 30, 2014 in San Francisco, CA.

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Direct-to-consumer (DTC) genomic services have generated controversy over when it is appropriate to provide genetic results to individuals. Critics have argued for restrictive regulation of such services, and even their prohibition, on the grounds of the harm they may pose to consumers. However, others argue that these services offer consumers the ability to make better-informed health decisions based on increased understanding of genetic risks. 

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