The KHIT Blog: Omics update: National Human Genome Research Institute Health IT news

Wednesday, September 2, 2015

Omics update: National Human Genome Research Institute Health IT news

Well, this bears watching.

NIH grants seek best ways to combine genomic information and EHRs
Researchers seek to better understand genomic basis of disease, provide tailored care to patients

Bethesda, Maryland, Tues., September 1, 2015 - A dozen awards from the National Institutes of Health will support research that incorporates DNA sequence information into electronic medical records. The goal of research conducted by the Electronic Medical Records and Genomics (eMERGE) network is to better understand the genomic basis of disease and to tailor medical care to individual patients based on their genomic differences.

The grants, administered by the National Human Genome Research Institute (NHGRI), represent the third phase of the eMERGE program, and focus on moving genomics research closer to clinical application by identifying the potential medical effects of rare genomic variants (inherited differences in the DNA code) in about 100 clinically relevant genes. The activity of such genes can affect a person's health, and might affect treatment choices.

"The newly funded projects are focused on discovering genes and gene variants with clinical implications by using the latest sequencing technologies to examine rare and common variants suspected to relate to disease risk and treatment effects," said Rongling Li, M.D., Ph.D., program director for eMERGE in the Division of Genomic Medicine at NHGRI, a part of NIH. "The other important component of these grants is implementing what researchers learn about these gene variants into medical settings to improve patient care."

Researchers will look at the best ways to provide DNA test results to physicians and patients, she said, and ways in which doctors might use this information to improve clinical treatment and practice. These funded researchers will also examine the psychological and economic effects on patients and families, and the effects on healthcare systems, in using this information...

Full article w/grantee information here. I'm seeing a total of $52,405,228 in awards (I may be overcounting, given the somewhat unclear way the monies are reported).

I direct you to a number of my prior posts on the "Omics" topical issues:

"It's not so elementary, Watson." Developments in Health IT (June 29th)

"Personalized Medicine" and "Omics" -- HIT and QA considerations (July 16th)

Are EHRs obsolete? (Aug 6th)

"Personalized Medicine" - will Health IT be up to the task? (Aug 16th)

Three core (compound) questions, really:

Will commercial ("clinical") "omics" assays be sufficiently, uniformly accurate and precise?

Will clinical staff be adequately up to speed on "omics" dx analytics and tx options, and how will all of this fit into workflows?

Will Health IT capacity and functionality on the street suffice uniformly, or will we have a digital "omics divide" for a long time?

Another question comes to mind. Are we seriously proposing to import raw gene sequence information into EHRs as "structured data" rather than just document-oriented PDF summary reports (e.g., attachments that are essentially faxes by any other name) -- i.e., the the way we now handle imaging study radiologists' "impression" narratives? (I have yet to see my prostate OncoType dx results, but I'm sure it simply comprises a brief summary genetic "impression" written by my urologist's assay vendor's genetic analyst.)

Above, a snippet of genetic sequence "raw data." I rather doubt that many physicians would have any interest in or diagnostic need to see stuff like this. It seems to me that the utility may well run the other way, i.e., correlating the myriad patient data elements routinely captured in EHRs (e.g., Pt Demographics, FH, SH, PMH, CC, Vitals, Active dx's, Active Rx's, HPI, H&P, ROS, Labs/Imaging, specialist consults, etc) with Omics data. The old word "registry" comes to mind.

UPDATE: eMERGE

"The eMERGE Network brings together researchers with a wide range of expertise in genomics, statistics, ethics, informatics, and clinical medicine from leading medical research institutions across the country. Each center participating in the consortium is uniquely situated to provide critical resources to this highly collaborative and productive network. Each site combines abiobank or study cohort with extensive genomic data and access to clinical data derived from electronic medical records. Sites are geographically dispersed and have diverse patient populations, including two sites focusing specifically on pediatrics."

eMERGE is a national network organized and funded by the National Human Genome Research Institute (NHGRI) that combines DNA biorepositories with electronic medical record (EMR) systems for large scale, high-throughput genetic research in support of implementing genomic medicine. eMERGE studies and pilots genomic medicine translation through discovery, implementation, tools, and policy. During Phase I and II, the Network deployed more than 40 electronic phenotype algorithms across more than 55,000 subjects with dense genomic data. Returning clinical results has been implemented or planned for pilot at sites across the Network. A large-scale survey of patient attitudes regarding data sharing is being sent to 90,000 clinic patients across the country. A multicenter pilot of returning genome sequence information to electronic medical records (EMRs) for use in healthcare is almost complete. Themes of genomics, bioinformatics, genomic medicine, ethnics, data sharing, privacy, and community engagement are of particular relevance to eMERGE.

eMERGE was initiated in 2007 and included five biorepositories linked to EMRs. The network demonstrated that EMR phenotyping to develop cohorts for genome-wide studies was a robust approach to genetic discovery, defined approaches for enhancing privacy of shared EMR data, and engaged patients and communities in consent and data sharing. eMERGE expanded to include 7 clinical sites in 2011 and 2 pediatric sites in 2012.

eMERGE is openly interested in collaborations. Current external collaborations include the US Air Force, ENCODE, IGNITE, and the larger ELSI (Ethical, Legal, and Social Issues) community. eMERGE is dedicated to developing tools, identifying best practices, and communicating results for participant consent, data sharing, and returning genomic research results,to benefit the broader medical and scientific communities and the general public.

Interesting, all of it.
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More to come...

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Brave New Health

Commonwell Health Alliance

Another important read (pdf)

I love this kind of stuff. It sustains and humbles me. "As politicians, advertisers, salesmen, and propagandists for various political, economic, moral, religious, psychic, environmental, dietary, and artistic doctrinaire positions know only too well, fallible human minds are easily tricked, by clever verbiage... Common language—or at least, the English language—has an almost universal tendency to disguise epistemological statements by putting them into a grammatical form which suggests to the unwary an ontological statement. A major source of error in current probability theory arises from an unthinking failure to perceive this."

Quotes

"An economist is a person who sees something that works in practice and tries to figure out whether it will work in theory."

- J.D. Kleinke, medical economist
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"The only person who enjoys change is a baby with a wet diaper."

"Every misspent dollar in our health care system is part of somebody's paycheck.

- Brent James, M.D., M.Stat

“We could do healthcare, at markedly higher quality, for everyone in this country, without rationing or denying anybody the care that they need, without having the government dictate how doctors practice or whether hospitals could expand, at half the cost we do it now.”

- Health Care Futurist Joe Flower

Most of the sciences, unlike parts of medical science, are not concerned with the impossible. There is not complementary and alternative physics, or chemistry, or biochemistry, or engineering. These disciplines compare their ideas against reality, and, if the ideas are found wanting, abandoned."

- Mark A. Crislip, MD

"Q: How much alcohol is too much?
A: More than your doctor drinks."

- a physician I once heard speak during a CME presentation

“Just because science doesn’t know everything, doesn’t mean you get to fill in the gaps with whatever fairy tale most appeals to you.”

- Dara O’Briain

'[I]t is one small step from using the computer for "helping" doctors to monitoring them, judging them, dictating to them what to do, and withdrawing payment for computer non-compliance. The use of computer data is a multi-edged sword. It can be used for the "good," facilitating diagnosis and treatment and making it more accurate and up-to-date, and for “evil,” invading privacy, inviting security breechs, and making decisions based on the opinions of remote authorities rather than those present at the patient-doctor encounter.'

- Richard Reece, MD

“[T]here ARE statistics which are non-political. Just because The Washington Post/Fox News reports the temperature is 75 degrees doesn’t mean it’s really snowing and sunscreen is a liberal/conservative plot. Even if you earn a living being ideological.”

- Michael L. Millenson

"It is a generally a fairly convincing argument that people shouldn’t have to be subsidized to undertake a change which is in their best interest.

The reconciliation seems to be that EHR is not supposed to make a doctor’s practice more efficient and higher quality. It is supposed to make the system of care more efficient and higher quality, which is not the same thing. Those of you who took calc recall that maximizing the total of variables is not achieved by maximizing any one variable and this is a perfect example of that.

Those of you have served in combat certainly noticed that too — if everyone works as a team the unit takes fewer casualties. If you try to save your own hide, you might, but at the expense of more casualties overall."

- Al Lewis

"There are two ideas to keep in mind about Bayesian reasoning and how we tend to mess it up. The first is that base rates matter, even in the presence of evidence about the case at hand. This is often not intuitively obvious. The second is that intuitive impressions of the diagnosticity of evidence are often exaggerated."

- Daniel Kahneman, "Thinking, Fast and Slow"

"Physicians apply advanced scientific knowledge, but they must do so without the favorable conditions that experimental scientists create for themselves. Multitasking is forced on physicians, often in chaotic environments and under severe time and resource constraints."

- Lawrence and Lincoln Weed, "Medicine in Denial"

"It’s time to stop the whining about Obama care and acknowledge we already have universal health care. We just pay for it in the stupidest way possible that ensures problems are that much more disastrous and complicated when they’re finally treated."

- Mark Hoofnagle, MD, PhD

"Every act of conscious learning requires the willingness to suffer an injury to one's self-esteem. That is why young children, before they are aware of their own self-importance, learn so easily."

- Thomas Szasz, MD
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"Of course, one reason that process metrics* are so popular is that processes are much easier to define and measure than outcomes."

- The Skeptical Scalpel
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"There is an “illusion of validity” for any random data point, a seductive sense that is colored by what we hope will be true. Mountains of pharmaceutical claims are often made from mere molehills of data."

- Danielle Ofri, MD
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"Joy empowers people. It is a source of energy that enables people to hope and plan and change their lives for the better. Spend some time around someone who is relentlessly negative and how do you feel–drained, right? More and more research shows that joy is not something that just happens to you, like a bolt of lightening out of the blue. Joy is, instead, a habit to cultivate. Negative thinking and despair are the crabgrass of our souls–weeds that take root and spread, sometimes to all areas of life. Joy, in contrast, is a soul’s rose–hardy when cared for, able to put down roots over time and withstand disease and extremes. Like a rose, however, your joy can become blighted from neglect or harsh conditions. We all need to tend to our joy–to prune away the badness, and to know that, even though it may look like a prickly bare root, if you invest time in a joyous outlook, gorgeous things will bloom, even in the harshest conditions."

- Dr. Jan Gurley
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"'Solutions' exist only in mathematics."

- Karen Martin
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"The issue of how to regulate clinical software is, in the long run, indistinguishable from the issue of how to regulate medicine. The only difference is that medicine is practiced in the open, without secrecy, subject to peer review, and under a merit-based state license."

- Adrian Gropper, MD
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"Economist, rope, tree: some assembly required."

- Source unknown

DISCLAIMER:

I write this blog wholly on my own time and my own dime. The views proffered are expressly my own as a concerned and active citizen/taxpayer (in addition to being the result of my substantive experience in the various IT fields), and in no way reflect any policy views of my former employer, notwithstanding that some of the thinking has indeed obviously been spurred by the implications of the work with which I have been doing for them.

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Wednesday, September 2, 2015

Omics update: National Human Genome Research Institute Health IT news

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