Genomics

 

Genomic data can provide tremendous insight into variant alleles that predict disease risk, polymorphisms that determine drug efficacy and toxicity, and guide the course of therapeutic interventions. The goal of this group is to develop an implementation plan that addresses the following objectives:

 

 

  1. Develop the optimal technical strategy to embed or access genomic data, in the context of Protected Health Information (PHI), in the Electronic Health Record. This will include lessons learned from other implementations that have been successful, and involve stakeholders from federal health IT, academia and commercial entities, and provide a "safe harbor" in which to discuss different methodologies.
  2. Determine the most usable approach to present genomic data to the clinician in the Electronic Health Record, using decision support systems that support rapid, accurate and certain diagnostic and therapeutic determinations.
  3. Enable data exchanges from Disease Registries, NCBI resources, and other databases that allow the clinician and others to become more informed about important genotype-phenotype correlations.
  4. Focus on the immediate health needs of Veterans returning from combat, through HIE and other forums that utilize the OSEHRA, which focus on PTSD and TBI, cutting through and integrating silos of significant data repositories, which may exist in research, provider, payor and vendor environments.
  5. Develop an infrastructure that will be flexible enough to accommodate future advances in all "omics" domains that may provide value for patient care.
  6. Provide a platform where clinicians and patients can discuss pertinent health information.
  7. Ensure that PHI is adequately protected, so that mHealth applications can be used by the clinician for more efficient tracking of patient status.
  8. Facilitate the process of ordering gene and genome-based tests from the Electronic Health Record using a simple approach for easy and secure access to commercial providers of gene-based LDTs and IVDs.
  9. Provide a "blue-button" for the Veteran and members of the U.S. military to access their own gene-based test results and genomic data.
  10. Provide epidemiologists, pharmaceutical scientists and medical device manufacturers, and academic researchers access to a wealth of genomic information at the back end, using appropriate controls for the de-identification and anonymization of PHI, to perform better clinical and basic research that will not only improve medical outcomes for Veterans, but for the society as a whole.

Group Email: 

genomics@groups.osehra.org
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Invitation to connect on LinkedIn

LinkedIn ------------ I'd like to add you to my professional network on LinkedIn. - Dr. Gerry Dr. Gerry Higgins Vice President, Pharmacogenomic Science at AssureRx Health, Inc. Washington D.C. Metro Area Confirm that you know Dr. Gerry Higgins: https://www.linkedin.com/e/ntu41d-hwmzvcsd-3o/isd/5885608115881136128/94Tt6U_x/?hs=false&tok=3WE9gXt1OFT6g1 -- You are receiving Invitation to Connect emails. Click to unsubscribe:

Whole genome sequencing: Bioethics and clinical interpretation

I posted some documents that I could obtain permission for, as well as references for those that I could not..

-Gerry

Recommended reading:

[1] Dewey, F.E. et al.Clinical interpretation and implications of whole-genome sequencing. JAMA. 311(10):1035-1044 (2014)          doi:10.1001/jama.2014.1717.

[2] Jacob, H.J. et al. Genomics in clinical practice:Lessons from the front lines. Science Transl. Med. 5(194): 1-5 (2013).

Easy-to-use bioinformatics tools and resources

Folks-

Just a small slice of what is out there. This was part of the supplementary information part of a paper that I submitted with Dr. Brian Athey, chair of computational medicine and bioinformatics, University of Michigan Medical School.

Draft text, web links and references.

-Gerry

My experience at the fall 2013 Cold Spring Harbor Lab course 'Advanced Sequencing Technologies & Applications’

Folks-

I thought some folks might be interested. I have been doing Sanger sequencing since 1980, but this course was a blast, even for a fossil such as myself.

Boinformatics, including Python, Perl, etc is easy, compared to other software programming that I have attempted...

-Gerry Higgins

Seeking Contribution to a Wiki-'Omics' and other important issues

Greetings all-

I am writing from the Cold Spring Harbor Lab, where I am in the 'Advanced Sequencing' program, led by Elaine Mardis (Washington University), Dick McCombie (CSHL), Mike Zody (Broad Institute) and others. We have a great course wiki, and I have the outline of one I would like to post for this group.

Pictures from the OSEHRA Summit

In the spirit of "openness", I took a collection of pictures throughout the OSEHRA event, all of which are available for download at no cost.  (BTW, I have a lot of pictures of participants in addition to the speakers).

You will find them on my website at http://www.kenrubinphotography.com    Look at the "Featured" albums.

To download, select the images you like from the OSEHRA event and choose "Buy".  You will not be charged.

Comments welcomed and appreciated.

Next Genomics Group WebEx has been scheduled

2 will be held next week:

(1) Monday, June 17th at 1 pm; and

(2) Tuesday, June 18th at 11am.

We will joined by members of Veterans advocacy groups, including the VFW, American Legion, Disabled American Veterans, Vietnam Veterans of America, Iraq and Afghanistan Veterans of America, as well as senior members of special operations.

The focus will be on how we can support the Million Veteran Program, given the current state-of-the-art in genomics.

Results of first WebEx from the Genomics Advisory Panel

This was a first organizational meeting that was sparsely attended, but we had great contributions from Dr. Jessica Tenenbaum (Duke Bioinformatics Core) and Dr. Gholson Lyon (Cold Sping Harbor Laboratory; Stony Brook University and Utah Foundation for Biomedical Research).

These are the major outcomes from the meeting that we feel need to be addressed:

(1) Engage with experts in the integration of 'omic' data into the electronic health record - the HL7 clinical genomics was mentioned. We need to identify existing approaches, standards, file formats, etc in a thorough manner.

New member of Genomics Advisory Panel

I am honored to add the following indviudal to the Genomics Advisory Panel of the 'genomics group' of OSEHRA. Dr. Tenebaum is also head of the 'genomics group' for the American Medical Informatics Association (AMIA), and has done 'breakthrough' research in the context of the MURDOCK study and many other research projects  - Gerry

tranSMART gets tremendous coverage at Bio-IT world in Boston

For more information, see: http://www.transmartfoundation.org/site/home  

 I would like to talk about tranSMART, an open source community for pre-competitive data sharing for pharmaceutical companies, biotechnology companies and academic researchers. Some recent advances:

1.      A 501(c) organization – the ‘tranSMART Foundation’ (see www.transmartfoundation.org) has been set-up at the University of Michigan.

No questions have been added to this group.

Presidential Commission for the Study of Bioethical Issues report on Privacy and Progress in Whole Genome Sequencing

Executive Summary of report excerpted below.  Full Report Included in Link.

Over the course of less than a decade, whole genome sequencing has progressed from being one of our nation’s boldest scientific aspirations to becoming a readily available technique for determining the complete sequence of an individual’s deoxyribonucleic acid (DNA)—that person’s unique genetic blueprint.

Standards for Integration of Genomic Data into Electronic Health Records

These are still evolving, but HL7 and ANSI have provided some great resources. This page will provide a resource for links to specific technical guidelines.

I have added some more links that may be of interest:

 

Open-source EHR standards initiative       http://www.openehr.org 

International Standards Organization ISO   http://www.iso.org/iso/iso_technical_committee.html?commid=54960