The Future of Precision Medicine

Collaboration, Integration, Participationprecision medicine initiative

Today the White House hosted the Precision Medicine Initiative (PMI) Summit, celebrating the first year since the President’s announcement of the Precision Medicine Initiative. The entire team at DNAnexus shares President Obama’s sense of excitement as we reflect upon what’s been accomplished; even as we roll our up sleeves and get busy doing the hard work the lies ahead. John Holdren, Director of the White House Office of Science and Technology kicked off the event announcing the progress of a few remarkable initiatives 1) the NIH advancing cancer clinical trials through the development of large research cohorts, 2) the Million Veteran Program which has enrolled 150,000 vets to date and is now open to active duty women and men, and 3) the precisionFDA community platform for NGS assay evaluation and regulatory science, which just launched its first “Consistency Challenge”.

There were a number of inspirational stories from patients and families recalling their own struggle with disease and how precision medicine aided in diagnosis and treatment. It is so rewarding to see real-life examples of how genomic sequencing is being used to diagnose genetic disorders in the clinic and advance treatment and, ultimately, help patients lead healthy and happy lives.

What resonated most for us from the White House PMI panel was the President’s remarks on the healthcare system. Although it is a system labeled for “health care”, it is actually a “disease care” system. The U.S. healthcare system has been designed based on patient passivity; patients wait until they are sick and then it’s the doctor’s job to treat the disease/condition. Instead, we need to transform the healthcare industry to play a more active role in health and get health information into the hands of consumers. This will allow patients to remain healthy and keep disease from manifesting in the first place.

In order to make the President’s PMI a reality, we need to make anonymized patient data available to researchers and to merge information from different studies in order to advance medical research. We believe in a secure and unified platform; one that connects thousands of scientists around the world. True scientific breakthroughs are possible when researchers are able to collaborate openly, securely, and transparently around petabyte-sized datasets.

It’s been a remarkable twelve months for DNAnexus. , We’ve had the opportunity to contribute to a range of efforts expected to advance the science of precision medicine and accelerate its translation into tangible clinical benefits. Examples include:

Looking ahead, we believe that the realization of precision medicine’s promise requires the intelligent integration of genetic data with electronic health record data and a range of other data types. Successfully doing this requires the technology to effortlessly collaborate around large volumes of data in a secure and compliant fashion – which DNAnexus provides. But meaningful progress also requires the commitment to share relevant data, which we believe is developing, especially as (a) stakeholders increasingly recognize the scientific advantages of collaboration as opposed to a history of secrecy and data silos; (b) stakeholders begin to appreciate the ease and security of cloud computing in this process; (c) patients appropriately demand and belatedly receive more ownership of their own (damn!) data, and can easily elect to contribute that data to scientific research.

We’ve been privileged to be so deeply involved in the mission of precision medicine, and are excited by the opportunities to drive this work forward. As a business, and as a U.S. business, we are excited to see President Obama’s vision for precision medicine and improved health care align with our own.

precisionFDA: Why It Matters

Screen Shot 2015-12-15 at 9.32.57 AMI hadn’t intended to write about precisionFDA going live – this post by Dr. Taha Kass-Hout and Elaine Johanson of the FDA provides a terrific summary, and this post by Angela Anderson of DNAnexus offers valuable additional context. However, I found myself today so excited by this project and what it represents that I can’t resist offering a few additional thoughts about what makes this initiative so special.

First, it addresses an important problem in the field: the analytic validity of NGS tests. The ready availability of relatively inexpensive sequencing has enabled us to contemplate diagnostic sequencing at a scale that would have been difficult to imagine even a decade ago. At the same time, the drive to apply sequencing in different clinical contexts raises a critically important question: do I trust this test? A key starting point for clinical interpretation of DNA data is to agree on the sequence itself. If your procedure and analysis reports that a particular sequence in a DNA sample is “GATCGATC” and my procedure and analysis of the same DNA says the sequence is “GATTGATC,” then we’ve got a problem. precisionFDA will allow users to compare approaches, figure out what’s working, and determine where refinements might be needed.

Second, precisionFDA represents a novel and forward-thinking approach to regulation. Rather than envisioning governmental regulators as the folks who will define and then impose a specific set of performance standards, precisionFDA instead sees the government as providing the platform that will enable the NGS community to evolve the standards on their own — organically and transparently.

Finally, the ability to design, refine, and deploy this platform in such a rapid and agile fashion reflects in part the value of well-conceptualized public-private partnerships, in this case between the FDA and DNAnexus. By intentionally leveraging the skills and capabilities of a company like ours, the FDA was able to implement and realize their exciting and ambitious vision.

The ultimate success of the precisionFDA platform will of course depend upon how well it serves the community it is intended to support. However, it’s hard to think of a more auspicious beginning, and my hope would be that success here will encourage more leaders to evaluate the potential of public/private partnerships to deploy platforms that leverage the power of a distributed innovation community to address important shared challenges.

Highlights from Festival of Genomics California 2016

PrecisionFDA, Explore Your Genome Giveaway, & Treadmills

Last week, we had the pleasure of attending Festival of Genomics California. We hope you were able to catch some of the truly inspiring talks from the plenary speakers, such as Karen Nelson from J. Craig Venter Institute, Manolis Kellis from MIT Computational Biology Group, and Carlos Bustamante from Stanford University School of Medicine.

Our big story at the conference was about precisionFDA – an open source platform to advance regulatory science about NGS-based analytic tools and datasets. DNAnexus is under contract with the FDA Office of Health Informatics to assist the FDA in preparation for a December 15th launch by developing the precisionFDA portal and assisting in the engagement of the genomics community. At the Festival, we organized a panel moderated by Omar Serang and George Asimenos who led a discussion involving Deanna Church, Personalis; Michael Eberle, Illumina; Kevin Jacobs, 23andMe; and Justin Zook, NIST.

We kicked off a closed panel discussion with a video overview of precisionFDA.

George showed screenshots of the precisionFDA platform, highlighting examples of how the community will be able to use the platform, including the variant call comparison tool that can compare results between a test dataset and a benchmark/reference dataset, and separate out true positives, false positives and false negatives.

From there, the panel delved into a lively discussion. Deanna pointed out that only roughly 1500 out of the 4000 genes that have some clinical relevance are represented in their entirety in the Genome in a Bottle/National Institute of Standards (NIST) and Technology NA12878 dataset. Therefore, the precisionFDA community needs to spend time expanding that sample, not just adding more samples to the community’s database. Michael stressed the importance of pedigrees in validating variants in a reference sample.

Kevin made a passionate speech for how the community needs to focus on conventions. How can we possibly enter an era of precision medicine if we are still unable to agree on where the human genome exons are located? Researchers use computers and algorithms to calculate the results with binary formats, however the reality is the computer is only doing what the human researcher tells it to do, and since humans are not very precise, how can we be confident in our results? Justin stressed the importance that NIST should not be the standards-making body for dictating these standards, they need to be developed and agreed upon by a community.

In addition to its variant call comparison functionality, the precisionFDA platform will allow participants to conduct in-silico experiments using software and publish their conclusions in the form of electronic notes that can be placed with their experiments and reference the data and analyses. Using this feature, participants have the opportunity to showcase to the community their views on certain “hot” topics such as “the utility of simulations”.

Be sure to visit precision.fda.gov and follow us on @precisionFDA to get the latest. The platform will be accepting applications for membership in the community beginning December 15th!

Explore Your Genome Giveaway!
In addition, we also want to thank Sure Genomics for joining us in our booth to demo their product and discuss how the DNAnexus Platform analyzes their customer’s whole genome sequencing data. During the festival Sure Genomics and DNAnexus announced two lucky winners that will have their genomes sequenced and analyzed by Sure Genomics.  Each winner will receive a complimentary Personal DNA Kit, personal DNA report mapping key markers, and one-year free storage.   

Day 1 Winner:  Alain C., Insilico
Day 2 Winner:  Jennifer P., Kapa Biosystems

Congratulations Alain & Jennifer!

Returning Winners of Race the Helix Treadmill Challenge
FoG CA Race the HelixBlazing fast. That’s the only way DNAnexus runs, whether in the cloud or on the treadmill. DNAnexus repeated its June victory in Boston to win the Race the Helix Treadmill Challenge in California.

We also want to thank all those that stopped by our booth. We look forward to seeing everyone again next year at Festival of Genomics Boston.