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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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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NIH is Off and Running 
NIH would seem to be wasting no time in getting President Obama’s Precision Medicine Initiative off the ground. Having begun planning in February, it announced just two days ago, the formation of a panel of precision medicine experts to lead initial steps towards designing the project. Notably absent in any of the announcements to date is how the government will succeed in engaging Americans. Perhaps these experts will propose engagement strategies behind these closed doors? Even if so, are they the right folks to create the ticket to success? There is, after all, no initiative without Americans’ enthusiastic support. So, engagement is of vital importance. 
Wherefore Public Engagement? 
Citizen science and crowd sourced funding have proven successful strategies for engaging/exciting average folk in/about scientific research But they can’t hold a candle to what celebs have done for public awareness of genetics. And yes, of course I’m thinking about Angelina Jolie, who isn’t? She certainly has been credited with doing ‘ a lot’ to raise awareness about the clinical benefit of BRCA testing and preventative actions. Face it, if you want to get something noticed, America’s beloved celebs –perhaps- do it best. Well, maybe not because they’re so genius at it but because when they talk we pay attention.  And so, how will the government grab enough attention to get its million DNA donors? 
Will Engaging Be Fun? 
While commentators have questioned the government’s technological ability to successfully undertake the project, the challenge of recruiting a million folks- I mean regular folks-to complete the project is a timely manner is a bit, dare I say, thought provoking. Clinical research is serious business, to be sure. Yet, the American appetite for fun and fluff suggests that a successful engagement strategy will need to appeal to this appetite. 
I can well imagine the public’s imagination being captivated by Apple announcing that all I phone 7 (for example) purchasers will get, free of charge, a spit cup to submit a DNA sample along a finger print protected new app that contains their genome sequence, on the condition that purchasers share their genome, albeit it encrypted and secured, with government researchers. New IPhone 7 users would then –literally- have their genome at their fingertips, but so too would the initiative. I can also imagine great public interest resulting from a Justin Beiber public service announcement saying he’ll give away a million (of the same) spit cups to fans so they can see if they have predispositions to Beiber- like reckless behavior, so as to encourage young people to behave engage sensibly, while giving his image a more mature make over.  
And so, in the context I just sketched, I’m wondering what the government will come up with to engender public enthusiasm-that is enthusiasm which converts to participation. I admit I don’t recall any federal efforts to engage the public, save for the military marketing, replete with catchy jingles. Remember ““Uncle Sam wants YOU for the U.S. Army”?
(The 1917 poster was used to recruit soliders for both WW I and WW II). Or, the catchy jingle “Be all you can be: Join the Army”? So, does NIH need a genome slogan and a genetic jingle? Maybe. Perhaps they should hire Jon Stewart can write the slogan and Jay Z the jingle… 
Let’s Talk Ethics
Sarcasm aside, engaging the public will be more challenging than in countries with universal health insurance and a national health service, like the UK or Iceland. Yes, our fragmented health care system poses obvious technological complexities that must be solved to enable access to clinical-phenotypic- data. Arguably, equally, if not more important, is the issue of how access to the project participation will be ferreted out given the that there are people who do and don’t have insurance, those whose medical records are and aren’t digitized, who are or aren’t proficient in English, who do or don’t believe that their genetic risks are preordained by God, etc.  In other words, the million-person cohort needs to be diverse. The project needs to collect data from people who live in all types of different geographical places, and situations. But how will diverse be defined? What will be inclusion/exclusion criteria? Will the inclusion criteria exclude persons whose medical record is not digitized? That is, those with a paper record can’t participate? Will those without health insurance be ineligible? What database biases could ensue from the implementation of said criteria?  
Difference is important to democracy. It’s also vital for genetics research. So, integral to study design, are some important ethical considerations. For one, is excluding individuals who lack an EHR or even health insurance from participating fair or even ethically defensible?? 
Thinking More Globally
Many have worried about personalized medicine becoming available only to the rich. This argument is based on the high cost of new diagnostics and therapeutics. A more fundamental issue is whether it’s ethically defensible to interject certain exclusion criteria, and interject bias dataset. As I’ve argued elsewhere the principle of beneficence may require maximal data sharing to permit genomic benefit sharing amongst all persons, not just an entitled few. If the initiative’s data set excludes persons lacking an EHR or lacking insurance, we will be faced, in my view, with the unfortunate consequence that not only will enthusiastically engaged persons will be ineligible to participate, but also a bias that could limit generated knowledge in some important ways. If true, such a bias lead to some adverse impacts. That said, for a western industrialized country, this would be an unfortunate consequence because it will evince the possibility that the principles of democracy, and social justice, will not extend to precision medicine.
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Nearly 30 years after the start of planning for the Human Genome Project, 25 years after the Project began, and 12 years after it’s completion was announced, genomic research progress is becoming impactful. Lives are being radically changed for the better thanks to more precise, diagnostics and targeted treatments. Patients are starting to get the right medicine in the right dose at the beginning of treatment, not halfway through. However, although tumor profiling is regularly done to determine which of available cancer treatments is most appropriate, and pharmacogenetic/pharmacogenomic testing is more available thanks to an increasingly crowded market, personalized medicine has yet to help the majority of patients, e.g. those suffering from common and complex diseases.

This is largely because the US government does not yet have large studies linking genomic to clinical data.  Numerous other countries, however, do. The British 100,000 genomes project, the Saudi Arabia’ Genome Mapping Project, the Genome of the Netherlands, with similar efforts starting up in Belgium, and other European Countries are cases in point. Many reasons for the US lag have been cited, including the lack of data management standards and system inter-operatability. Notably, the private sector is leading the way.  The largest current repository is privately owned, by 23 & Me (800,000 samples), Craig Venter is spearheading the Microbes and Metabolites Fuel an Ambitious Aging Project, which will sequence a million genomes, and some pharmaceutical companies are establishing in house sequencing projects, i.e.“The Search for Exceptional Genomes”).


Recognizing the medical power of personalized medicine to prevent, treat and in some cases cure disease, President Obama announced that the US will get into the game with a $215 million dollar precision medicine initiative to expand initial successes into a large-scale effort. While the initiative will use data from existing cohort studies, widespread participation, including the public and the breadth of stakeholders, is vital to the 2nd core objective of creating a research database of 1 million genomes with related clinical and other types of information which will generate a new taxonomy of disease based on what the National Academy of Science researchcalls an information commons and knowledge network of disease and treatments.

Excitement is high and planning began within weeks of the initiative’s announcement. The NIH hosted a two day workshop where experts, representing a broad range of diverse disciplines and white papers, presentations and thoughts about opportunities, challenges and strategies for successful implementation, 2500 viewers engaged through WebEx. Regulatory officials recently announced plans to use the $10 million expected to build full or hybrid cloud storage, open-source data sharing platforms and Google-like search tools.


It is easy to get excited about this new initiative, particularly because it promises to propel precision medicine efficiently and effectively. But, combining and mining data from disparate third party sources will be no small feat, particularly considering the adoption process of electronic medical records and existing interoperatability problems in linking existing databases. Cautious optimism may be prudent, given that existing smaller scale sequencing projects are moving at a snail’s pace or stalling out. The Million Veteran Program, ( launched in 2011, intends to combine individual genetic information to determine associations between genetics and health status to better screen, diagnose, and prognose disease and develop targeted treatments, only recently (less than 6 months ago) awarded the genomic analyses contract. As of last year at this time, i.e. three years into the project, only 200,000 veterans had enrolled. To be fair, though, a recent report indicates that the Project already has 343,000 samples and has partially analyzed 200,000 participants[CI6] ( Progress has been, in other words, slow. If you are unaware of the project’s status, that could be because the government has said little. Another relatively large scale project, the National Children’s Study, which was designed to collect 100,000 genomes at birth, and slated to start next year, was shut down at the end of last year based on a report that found that the design was not feasible. Congressional battles about funding issues did not help matters. These events will hopefully inform planning efforts so that the current initiative will not succumb to the same.

Pundits have expressed concern about the government’s ability to manage such a large dataset given technological failures of The insurance exchange site crashed and shut down for 5 hours upon launch. A technological glitch related to income verification prevented an unknown number of public from submitting applications and a hacker claimed to have obtained 70,000 records containing personal identifying information.


A separate concern is whether the initiative will permit broad based data sharing. Currently, while publicly funded research is deposited into publicly accessible databases, as a practical matter only research institutions with the resources to devote to filing laborious applications can hope to gain access. Small labs and institutions with far lower operating budgets cannot devote scarce resources to securing access to data, and thus their research is severely limited. Without data access, they simply cannot pursue certain research and thus talented researchers are beginning to redirect their careers to plant and animal genomes, since they are more readily accessible.


Public engagement is clearly vital. And media coverage may be greasing the skids for success. After all, when the President of the United States announces a biomedical initiative in his (or perhaps some day her) State of the Union address, many take notice;  When USA Today reports on details of the initiative, its clear that precision medicine is trying to make its way into every home in America;


If the precision medicine initiative can overcome both of these impediments, it will have achieved a great deal. Good planning is a start and timely execution important. If the initiative succeeds in being transparent, engaging the public and enabling broad based data sharing then a new paradigm of open and collaborative research will have been established. Such will undoubtedly propel precision medicine significantly forward and ideally support precision medicine efforts underway in various places around the globe. 

The opportunity for thoughtful public input is great given the discussions that will occur at the plethora of upcoming precision medicine conferences. Hopefully, the NIH and the FDA will invite public comment, because the discussions that will occur at precision medicine conferences are likely to generate valuable insights.

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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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