NEW YORK (GenomeWeb) – President Obama today announced plans to launch a $215 million precision medicine initiative to leverage advances in genomics, informatics, and health information technology to accelerate biomedical discoveries in the hopes of yielding more personalized medical treatments for patients in the US.
The public-private initiative, which will be included in the President's 2016 budget proposal to be released next week, will provide new funding to the National Institutes of Health, the National Cancer Institute, the US Food and Drug Administration, and the Office of the National Coordinator for Health Information.
That funding will help those agencies to, among other things, develop a voluntary national research cohort of more than 1 million people, obtain sequencing data for as many of those individuals as possible, identify genomic drivers of cancer, improve how next-generation sequencing-based tests are evaluated and marketed, and develop methods for managing and analyzing large patient data sets while protecting individual privacy.
"Precision medicine is about moving beyond this one-size-fits-all kind of approach to medicine and instead approaching disease prevention and treatment by taking into account individual differences in people's genes, their microbiomes, their environments, and their lifestyles," Jo Handelsman, associate director for science at the White House Office of Science and Technology Policy, said yesterday in a press briefing previewing today's announcement. "The idea is to give clinicians tools to better understand the mechanisms underlying a patient's condition, and to better predict which treatments will be most effective and safe."
The largest part of the initiative will provide $130 million to the NIH to help develop a national research cohort of a million or more volunteers whose data — including medical records, genetic and metabolomic profiles, microbiomes, and environmental and lifestyle information — will contribute to a further understanding of disease and help establish a new way of doing research through engaged participants and open, responsible data sharing, the White House said.
In addition, the NCI will be budgeted for $70 million to scale up efforts to understand the genetic basis of cancer by expanding genetically based clinical trials, exploring fundamental aspects of cancer biology, and establishing a national "cancer knowledge network" that will generate and share new knowledge.
Meantime, $10 million will be earmarked for the FDA to help it acquire additional tools and expertise to develop high-quality, curated databases that will be used in its efforts to evaluate next-generation sequencing technologies and ensure their accuracy, reliability, and safety for patients.
And, finally, the initiative calls for a $5 million investment in the ONC to support the development of interoperability standards and requirements that address patient privacy and enable the secure exchange of data across systems.
"This concept of precision medicine — that is, prevention and treatment strategies that take individual differences into account — is not entirely new," NIH Director Francis Collins said during the briefing. "But for much of medicine, this kind of personalizing just has not been possible. We just didn’t know enough. That's all changing now, and at an unprecedented pace, which makes now the right time to launch this initiative."
Collins pointed to advances over the past several years in basic research, data science, mobile connectivity, use of electronic medical records, and "perhaps most dramatic of all in terms of the scale, the decline in the cost of DNA sequencing. It cost us $400 million for that first genome, and now a genome can be sequenced for a cost approximating $1,000. That's more than 100,000-fold drop in 15 years."
Regarding the NIH's plan to create a longitudinal cohort of more than 1 million patients, Collins noted that the agency and its partners will not need to start from scratch, but will instead tap into already-established cohorts, both public and private.
"We are aware that there is something like 200 cohorts that have already been put in place that have at least 10,000 participants," Collins said. "They're in different sorts of shape as far as the kind of information that's already been collected. But there is a wealth of potential there."
Collins noted that a large part of this cohort effort will be trying to piece together many of these existing cohorts, and he said that this could be aided by existing projects such as the Electronic Medical Records and Genomics (eMERGE) program, which aims to combine electronic medical records technologies with DNA biorepositories for use in large-scale, high-throughput genomics research projects.
In terms of the types of existing cohorts that could be tapped into, Collins mentioned the attractiveness of the cohorts generated so far under Kaiser Permanente's Research Program on Genes, Environment, and Health, which includes more than 430,000 adult members of Kaiser's system in Northern California and has generated a 100,000-individual cohort in partnership with the University of California, San Francisco. However, Collins stressed that the NIH will be encouraging new participants to volunteer to help build the national cohort.
Another large part of the cohort effort will be attempting to obtain sequencing data for as many of the participants as possible. Although the cost of sequencing has dropped dramatically in recent years, this component of the initiative remains a major hurdle.
"We would love to have whole-genome sequence [data] on all the participants in the cohort, but the expense has to be considered, and where are we going to find those funds?" Collins said. Although it now costs about $1,000 to sequence a whole genome, "that curve is coming down, and that is actually quite reassuring," Collins added. "It will take us, of course, a matter of some time to assemble this cohort. Our expectation would be that, as it's being assembled, the cost [of sequencing] would be coming down, and so ultimately the goal would be to have a full-genome sequence on as many of the cohort as are comfortable."
Another important aspect of the national cohort project will be its interactive nature. "The precision medicine initiative is not just about scale," Collins said. "It's also intended to be a new model of research, one in which people who participate are true partners — not subjects, not even patients — partners."
To that end, the ONC is charged with developing new and better ways to ensure secure data exchange with patients' consent, and the initiative overall will be committed to protecting patients' privacy by launching a "multi-stakeholder process" that will solicit input from patient groups, bioethicists, privacy and civil liberties advocates, technologists, and other experts to identify legal and technical issues.
Summarizing, Collins noted that although the cohort initiative will likely yield its greatest benefits many years into the future, "there should be some successes in the relatively near future, as well, especially in the areas of cancer, and the field called pharmacogenomics — how to provide the right drug at the right dose to the right patient at the right time. This initiative will provide a wonderful platform for finding out how to apply that strategy to more and more people."
On the regulatory side, FDA Commissioner Margaret Hamburg noted during the briefing that the agency's funding would primarily be used to improve the way it oversees the marketing of new types of precision medicine technologies, particularly NGS.
"Our current market review approaches for evaluating a test's analytical and clinical performance are designed around a more traditional one test-one disease paradigm," Hamburg said. "In contrast, next-generation sequencing produces a massive amount of data, potentially bearing on a huge range of diseases, conditions, and risk factors that will be better handled using a new approach."
She noted that the FDA is currently in the process of considering what that approach should be, referring to the fact that the agency has scheduled a public meeting on Feb. 20 to discuss the challenges of regulating NGS technologies. Ahead of the meeting, last year the agency issued a white paper to lay out its current thinking and provide the basis for future discussion.
Hamburg also noted that the agency already has some experience regulating NGS technologies: In December 2013 it cleared Illumina's MiSeqDx — the first sequencing platform to gain such clearance — as well as two associated cystic fibrosis assays.
As Hamburg discussed just this week at the Personalized Medicine World Conference in Mountain View, Calif., and reiterated during yesterday's briefing, the FDA employed a "practical approach" to assessing the MiSeqDx.
"For analytic performance, we looked at how accurately the instrument sequenced a representative set of genetic variants across the genome rather than requiring data on every possible variant," she said. "Doing so avoided years of data gathering and unnecessary delay in the public's access to the benefits of this technology while still assuring its accuracy and reliability."
She noted that the agency took a similar tack in assessing the cystic fibrosis tests. "We didn't require that [Illumina] collect new independent data supporting each mutation's association with disease in order to demonstrate clinical performance," she said. Instead, Illumina was able to use existing information by referring to a "well-curated, shared database of cystic fibrosis mutations" — Johns Hopkins University's curated cystic fibrosis database of variants
"This database is really a model of patient participation, because it was created with support from the Cystic Fibrosis Foundation," Hamburg noted. Using its funding, the FDA intends to "advance the development of high-quality, curated databases akin to the one that was used in the review of the two Illumina tests for cystic fibrosis," she said.