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.
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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.

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.

Welcome to Rick Williams

Williams, a Medical Sciences graduate of Oxford University, has advanced degrees in law, public administration and business.  He served in the Army from 2002 to 2010 in various capacities as an infantry officer in Afghanistan and Iraq.  Following his military service he spent two years as a specialist focusing on tribal engagement and negotiation in Eastern Afghanistan.  His interest in the mental health of veterans grows out of his own personal experiences with soldiers under his command battling PTSD, depression, and suicide.

Great WebEx for Genomics Group - another one tomorrow at 11 am (a repeat) - References

Thanks for everyone that participated! Special thanks to Larry Meyer, Head of Clinical Genomics at the VA, who provided some very useful information - Larry - we want you to be part of our group!

Here are the references, plus some on multiple deployments increasing the risk of PTS:

SUICIDE:

1. Bush, N.E. et al. Suicides and Suicide Attempts in the U.S.Military, 2008–2010. Suicide and Life-Threatening Behavior. 2013; 43(3): 262-273.

No questions have been added to this group.

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

First whole genome analysis of a Veteran

Attached is a poster  from Gholson Lyon, M.D., Ph.D. of the Cold Spring Harbor Laboratory, Stony Brook University and the Institute for Genomic Medicine at the Utah Foundation for Biomedical Research. This individual had a serious psychiatric illness which required deep brain stimulation.

Genomics and Big Data_PART 3

Folks-

This is the last part of this somewhat lengthy document that I am going to post. I apologize, because some of the pagination is not as indicated as 'Genomics and Big Data_PART 1', and I have left out some text and the Appendices and Glossary. If anyone wants a full version this document, please contact me by email (beware - it is in excess of 100 pages in length).

Genomics and Big Data_PART 1

This will be the introductory part of a long report that I completed in response to a 'big data' study being performed by MITRE for the U.S. Army. It will be released in phases, with some text redacted. Here is the Executoive Summary. See link below for the first part of the PDF. - Gerry Higgins

 

EXECUTIVE SUMMARY