The Need for Specialized Application Programming Interfaces for Human Genomics R&D Initiatives

"DNA Molecule Display, Oxford University", Image by allispossible.org.uk

“DNA Molecule Display, Oxford University”, Image by allispossible.org.uk

The term of art for the onscreen workspaces containing the sophisticated tools used by software developers and engineers is called the application programming interface (API).¹ It is where code is written, assembled, tested and revised.

Scientists working on various aspects of the human genome have recently expressed a comparable need for the development of specialized APIs to assist in a wide range of projects in their field.² A very informative and compelling  piece about this by Prakash Menon (CEO of BaseHealth) entitled Developing An Application Programming Interface for the Genome was posted on VentureBeat.com on June 27, 2015. I will sum up, annotate, and then pose some questions that will not require their own specialized API to be considered.

The article begins by citing to a quote from Gholson Lyon, a genomics scientist at the Cold Spring Harbor Laboratory in New York, about the existing lack of a “killer app to interact” with DNA. He very recently raised this in another article entitled Apple Has Plans for your DNA by Antonio Regalado, posted on May 5, 2015 on MIT’s technologyreview.com. (The article appears in print in the July/August 2015 issue of MIT’s Technology Review.) This fascinating piece is about Apple’s new ResearchKit, an open source medical research framework for researchers to create iPhone apps for medical studies.³ Such an API technology, as Gholson described it, would make access and interpretation the genome universal, as well as make it more “programmable”.  (I highly recommend reading both Menon’s and Regalato’s articles together in their entirety.) 

Menon parses the three waves of genomics computing in the following manner:

  • First Wave:  During the 1990’s, this was the “sequencing era” when the human genome was first fully mapped. Rapid technological advances have enabled scientists to do this increasingly faster and cheaper. This has resulted in the emergence of the field of personalized medicine where diagnostics and treatments are designed by using more accurate genomic data of patients.
  • Second Wave: The current state of genomic technologies with faster (termed “high-throughput”), more accurate, and less expensive genome sequencing for treating diseases.
  • Third Wave: This is currently evolving with an emphasis is upon “integrating genomic data with other types of data”. This will soon permit advances such as “connect variants to environmental, lifestyle, dietary, and activity” data for the benefit of people who are well as well as those who are suffering from genetically based illnesses.

He believes that creating APIs for genomic science to be used by “developers everywhere” would put genomic data into a “wider context” and, in turn, enable new insights to be integrated into daily medical practice. Furthermore, timely innovations become more likely. As he sees this situation, the genome is a “database that we have constructed and curated”, and as such requires new interfaces to obtain the most value from its vast contents.

This also raises the prospect of genomic APIs becoming yet another addition in a growing conceptual framework dubbed the “API Economy”. (See Six Ways to Get a Grip on the API Economy by Serdar Yegulap, posted on InfoWorld.com on April 20, 2015, for a concise summary and the latest indicators of this emerging trend.)

Perhaps the Fourth Wave of genomics computing will be ushered in by a new generation of software and hardware developers who will “think about personalization at the molecular level”, and not require any further involvement by skilled bioinformatics specialists.

The author acknowledges the need for “privacy, security and the ethical implications” of his proposals, but believes that the potential benefits will result in these concerns being resolved.

Potential new software-driven innovations from Menon’s proposed genomic APIs include:

  • Pharmacy systems that integrate with a patient’s genomic data so that prescribed drugs are the best choices for the individual, including a reduction in side effects.
  • Improved organ and bone marrow donor matching systems.
  • Optimizing food ingredients, supplements and diets, as well as activity and rest periods.
  • Adding genomic data to “build worlds around each player” in online games.

In Menon’s assessment of these four waves, he sees the third wave presently “playing out” and the fourth wave arriving but “it’s not yet widely distributed”.Today, the first genomic APIs are starting to appear. In the US, developers are immersing themselves in the key concepts of molecular biology to more fully enable their work. He further predicts that in the next wave of “billion-dollar businesses” will involve the human genome, only some of which will be specifically in health care.

As to the needs and desires of individuals concerning their genomic data, Menon believes that they want to use it for their own advantage, combine and compare it with the data of others, and to create “wholly new capabilities”.  Indeed, we have seen already numerous applications of genomic data that could not possibly have been imagined by James Watson and Francis Crick, the Nobel Prize winning discoverers of the structure of DNA.

My questions are as follows:

  • Should genomics APIs be developed and circulated on a fully open source basis? If so, what intellectual property issues may still arise and how, and by whom, should they be settled, arbitrated or litigated?5
  • Will developers from other fields, as well as non-affiliated scientifically curious individuals, be drawn into using the APIs for original research and development projects?
  • What, if any, scientific, ethical and regulatory guidelines might be needed as oversight for genomic APIs?
  • Will such APIs lead to a surge in startup company formation in genomics and other related biotechnology businesses?
  • Are there unique elements of design and functionality in genomic APIs that might lead to innovations in API development in other fields? That is, is there some form of beneficial and/or symbiotic effect that may emerge?

 


1 An API for the depository of TED Talks was recently discussed in the May 13, 2015 Subway Fold post entitled IBM’s Watson is Now Data Mining TED Talks to Extract New Forms of Knowledge.

2.  See also the June 12, 2015 Subway Fold post entitled Scientists Are Developing Massive Storage Systems Based Upon Minute Amounts of DNA and Polymers for a related story on using DNA as a dramatically different information storage medium.

3.  For a full exploration of current efforts and proposals to use smartphones as medical platforms, please see the March 3, 2015 Subway Fold post entitled Book Review of “The Patient Will See You Now”. To follow this area of development on a daily basis I highly recommend following the book’s author, Dr. Eric Topol, on Twitter at @EricTopol.

4.  This point invokes master sci-fi writer William Gibson’s often quoted line “The future is here already — it’s just not very evenly distributed.

5.  The United States Supreme Court declined to hear an appeal of a case involving Google and Oracle concerning the ownership of an API . See Supreme Court Declines to Hear Appeal in Google-Oracle Copyright Fight by Quentin Hardy, in the June 29, 2015 edition of The New York Times for full coverage.

 

Book Review of “The Patient Will See You Now”

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Image by NEC-Medical-137

There was great sorrow across the world on Friday, February 27, 2015 over the passing of Leonard Nimoy. (The link is to his obituary in The New York Times.) He was a renowned and prolific actor, director, photographer and poet. He will forever be best known for his remarkable portrayal of Mr. Spock on the original Star Trek series and later on in the franchise’s other shows and movies (two of which he directed). I will greatly miss him as someone who has faithfully followed Star Trek through every single adventure on the small and large screens.

I heard the sad news just shortly after I had finished reading The Patient Will See You Now: The Future of Medicine is in Your Hands by Eric Topol (Basic Books, 2015). The coincidence of these two events took on a significant meaning for me. This is because some of the tech portrayed as pure science fiction in ST has, over the 48 years of the franchise’s existence, actually came into being, while Dr. Topol’s book now proposes using smartphones to as medical testing and communication devices to revolutionize health care delivery and informatics. In part but with some major distinctions, this will be somewhat akin to the tricorder used by the crew of The Enterprise. (See also, the XPrize competition that the semiconductor company Qualcomm is running to award $10 Million for the creation of a working tricorder.)

Just as the many iterations of the Starship Enterprise undertook long voyages into new and distant parsecs of space, so too does Dr. Topol (who is a cardiologist, professor of genomics and the director of the Scripps Translational Science Institute in California as shown on the book jacket), take his readers deeply into the realms of science, technology, bioethics, economics and policy. Notwithstanding the complex inter-relationships among these topics and his well-considered proposal to use smartphones as the basis for an integrated medical platform, he manages to explain and present all of this in a highly accessible and imaginative manner. I would thus add to his lengthy list of accomplishments that he is a very effective communicator of what might otherwise have been as dry as bio-inactive dust text in the hands of another writer. His presentation in his book indeed shows an expert touch in balancing the art of his prose with the science of his profession.

So, what is all this new-fangled medical/techno-network hub(ub) about anyway? At the core of his book, Dr. Topol proposes to extend and enhance the capabilities of iPhones, Android phones and the like so that patients and doctors can use them to perform medical tests such as, among many others, checking blood pressure, cardio functions, blood and genomic factors, and even as a form of microscope. This data can then be readily uploaded for analysis and recommended treatments. This new configuration could potentially be far cheaper and faster than current methods for similar results. More importantly, this would help to democratize medicine whereby the patient owns and controls the distribution of his or her personal medical data.

In careful detail, Dr. Topol expands the notion of this alternative platform outward in assessing and proposing the benefits to everyone in the US healthcare system. This could enable the gathering and unlocking of massive troves of medical data for research and analytics to produce more accurate and meaningful test results, improve proactive preventative health programs, reach under-served communities, and perhaps reduce spiraling costs and intractable bureaucracies. He addresses the timely and critical concerns of privacy and security that generating such massive amounts of highly sensitive data would surely entail. As well, such a system might raise the incentives for the medical establishment to develop more universal standards and greater interoperability for electronic medical records systems.

Dr Topol’s other critical theme is that his proposals would redefine the balance of control between the doctor to the patient. Hence the title of his book that inverts the traditional announcement in the doctor’s waiting room of “the doctor will see you now” into a new construct where the patient has new-found precedence in their care and data. As part of his call for this transformations, he repeatedly mentions the eternal persistence of doctors’ “paternalism” as being both an anachronism and an impediment to trying to improve the healthcare system. He has a, well, healthy skepticism about this still prevalent artifact and believes it can be effectively routed around by empowering patients with the ever-increasing numbers and capabilities of their smartphones.

It would be difficult for anyone to disagree that the US healthcare system is in dire need of change for a multitude of scientific, economic and political reasons. Bravo for Dr. Topol in challenging his own profession’s conventional wisdom and proposing a truly bold plan to disrupt it and make it more responsive to the needs of patients. Rather than being an all or nothing proposition, his plan can  also be viewed as an opening gambit to incrementally move these possibilities forward.

The science and technology needed to start implementing and networking some of these systems already exist in part or in full. The bits and bytes are likely the easier part of this equation. The genuinely hard part is finding the broad-based consensus, will and the resources to get it done. This book eloquently and persuasively lays out the policy and particulars for anyone in the medical industry, medical education, government and regulatory agencies, insurance industry, pharmaceutical companies, and consumers to consider and then perhaps begin doing something.

Not only does Dr. Topol have his finger on the pulse of today’s patient needs, he likewise has it on the entire medical establishment. He has used his experience and insight to write a 290-page prescription for a new alternative treatment to re-energize an ailing system that deserves the reader’s serious consideration. Who knows? It may well be the beginning of a new path for us to try in an effort to live longer and prosper.

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For two additional recent reviews of this book I recommend clicking through to ‘The Patient Will See You Now,’ by Eric Topol, reviewed by Sandeep Jauhar, in the February 13, 2015 edition of The New York Times, and Doctor Android reviewed by David A. Shaywitz in the January 12, 2015 edition of The Wall Street Journal (subscription required).