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The US Department of Health and Human Services recently ruled that, “Oral history, journalism, biography, and historical scholarship activities that focus directly on the specific individuals about whom the information is collected” are specifically excluded from human subject regulation.
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National Library of Medicine Informatics Lecture Series
Title: Use of Clinical Big Data to Inform Precision Medicine
Speaker: Joshua Denny, MD
Date: Wednesday, November 4, 2015
Time: 2:00 pm – 3:00 pm
Location: Lister Hill Center Auditorium
This talk will be broadcast live and archived at http://videocast.nih.gov/
Abstract: Precision medicine offers the promise of improved diagnosis and more effective, patient-specific therapies. Typically, clinical research studies have been pursued by enrolling a cohort of willing participants in a town or region, and obtaining information and tissue samples from them. At Vanderbilt, Dr. Denny and his team have linked phenotypic information from de-identified electronic health records (EHRs) to a DNA repository of nearly 200,000 samples, creating a ‘virtual’ cohort. This approach allows study of genomic basis of disease and drug response using real-world clinical data. Finding the right information in the EHR can be challenging, but the combination of billing data, laboratory data, medication exposures, and natural language processing has enabled efficient study of genomic and pharmacogenomic phenotypes. The Vanderbilt research team has put many of these discovered pharmacogenomic characteristics into practice through clinical decision support. The EHR also enables the inverse experiment – starting with a genotype and discovering all the phenotypes with which it is associated – a phenome-wide association study (PheWAS). PheWAS requires a densely-phenotyped population such as found in the EHR. Dr. Denny’s research team has used PheWAS to replicate more than 300 genotype-phenotype associations, characterize pleiotropy, and discover new associations. They have also used PheWAS to identify characteristics within disease subtypes.
Brief Bio: Joshua Denny, MD is an Associate Professor in the Departments of Biomedical Informatics and Medicine at Vanderbilt University Medical Center. A primary interest of his lab has been development of the PheWAS method applied to EHRs to rapidly uncover genetic pleiotropy and highlight potential drivers of genetic associations with endophenotypes. He helps lead efforts for local and network pharmacogenetics implementation activities. He is part of the NIH-supported Electronic Medical Records and Genomics (eMERGE) network, Pharmacogenomics Research Network (PGRN), and Implementing Genomics in Practice (IGNITE) networks. He is past recipient of the American Medical Informatics Association New Investigator Award, Homer Warner Award, and Vanderbilt Chancellor’s Award for Research. Dr. Denny remains active in clinical care and in teaching students. He is also a member of the National Library of Medicine Biomedical Library and Informatics Review Committee.
Sign Language Interpreters will be provided. Individuals with disabilities who need reasonable accommodation to participate in this lecture should contact Ebony Hughes 301-451-8038 Ebony.Hughes@nih.gov or the Federal Relay (1-800-877-8339).
Event contact:
Jane Ye, Ph.D
Division of Extramural Programs
National Library of Medicine, NIH
301-594-4882
yej@mail.nih.gov
Community of Science (COS) Pivot database answers the growing demands on research developers to quickly discover the right funding opportunities and effectively collaborate with their colleagues.
Pivot combines a comprehensive, editorially maintained database of funding opportunities worth an estimated $33 billion with a unique database of 3 million pre-populated scholar profiles, drawn from Community of Scholars and Community of Science profiles. Its algorithm compiles pre-populated researcher profiles unique to an organization and matches them to current funding opportunities in the COS database. This allows users to search for a funding opportunity and instantly view matching faculty from inside or outside an institution. Conversely, a search for a scholar will link to matching funding opportunities.
On Demand Pivot Workshop, Thursday, October 22, 12:00 – 1:00, HS/HSL, Room 128. Drop-ins welcome!
Technology Brown Bag Forum at the Health Sciences & Human Services Library: 3D printing in health sciences, with special guest Dr. Gene Shirokobrod
3D printing in health sciences is becoming more and more common. Prosthetic limbs, drugs, and medical models are just a few of the uses and innovations. Join us for our next Technology Brown Bag as we explore 3D printing use cases connected to the UMB community. We will hear from special guest, Dr. Gene Shirokobrod, a faculty member from the UMB School of Medicine who co-founded a local company that produces a 3D printed physical therapy device, arc, for postural support.
Thursday, October 29, 2015
Health Sciences & Human Services Library
Distance Ed Room
Noon to 12:45p
Technology Brown Bag Forum at the Health Sciences & Human Services Library: 3D printing in health sciences, with special guest Dr. Gene Shirokobrod
3D printing in health sciences is becoming more and more common. Prosthetic limbs, drugs, and medical models are just a few of the uses and innovations. Join us for our next Technology Brown Bag as we explore 3D printing use cases connected to the UMB community. We will hear from special guest, Dr. Gene Shirokobrod, a faculty member from the UMB School of Medicine who co-founded a local company that produces a 3D printed physical therapy device, arc, for postural support.
Thursday, October 29, 2015
Health Sciences & Human Services Library
Distance Ed Room
Noon to 12:45p
The HS/HSL recently updated the PCs and the monitors in its three library classrooms. Some of PCs and monitors that were removed were donated to Vivien T. Thomas Medical Arts Academy (VTTMAA). VTTMAA provides an academic program that encourages students to enter careers in health. The rest of the equipment will be given to the Office for Community Engagement at the University of Maryland, Baltimore. The Office for Community Engagement will use them to assist the Baltimore community at its UMB Community Engagement Center soon to be located at the BioPark on North Poppleton St.
With unique historical collections worth millions of dollars, staff at the HS/HSL weren’t taking any chances this past Friday as rain continued and Hurricane Joaquin began its slow trip up the east coast. After Governor Hogan announced a state of emergency, the library team sprang into action, unfurling over 2000 square feet of protective plastic. Rich Behles, Historical and Special Collections Librarian and Preservation Officer remarked, “We’ve had leaks in the historical collection stacks before. Knowing we were heading into a very wet weekend, where staff wouldn’t be monitoring the situation in the Woodward Historical Suite, we decided we would rather be safe than sorry.” And all that was well, ended well. There were no leaks, drips or precipitation of any type.
In February 2013, The White House Office of Science and Technology Policy issued a memorandum to all agency and department heads directing federal agencies with more than $100 million in annual research and development spending to establish plans for increasing public access to peer-reviewed scientific publications and digital data resulting from federally funded research.
Following the NIH Public Access Policy’s lead, the Centers for Disease Control and Prevention, as well as the Agency for Healthcare Research and Quality, will now require authors of peer-reviewed journal articles arising from agency funding to be deposited into a central repository using the NIH Manuscript Submission System. All articles must be electronically accessible to the public within 12 months of publication. For the CDC, the policy applies to all manuscripts published after July 15, 2013. For AHRQ, publications from research funded from February 2015 onward must be submitted. Beginning October 2015, digital data arising from these funding agencies must also have a data management plan available.
Faculty librarians at the HS/HSL can assist researchers in determining their compliance status and provide support in taking steps to deposit federally funded research articles into the central repository. Please visit our website for detailed instructions on the process or contact us at nihcompliance@hshsl.umaryland.edu.
The Library Genie is back! Last year he asked for your 3 library wishes and you responded. We can happily say that 3 library wishes were granted.
The Library Genie will be accepting wishes from October 1 to 31.
Now is your chance to let us know. Submit your 3 wishes to the Library Genie today! Your wishes will be anonymous, but if you’d be willing to talk more with us about your wishes you can include your name and e-mail address.
Thanks for your input and happy wishing!
From October 13th to October 23rd, NCBI will present the first iteration of NCBI NOW, a free online experience aimed at those new to next generation sequencing (NGS) analysis. Enrollment in this course is limited to the first 1,000 participants who sign up through the ORAU Portal: https://oraulearning.org/?partition=ncbi. Since enrollment is on a first-come, first-served basis, please only sign up for this educational opportunity if you will be able to participate fully.
Learners will watch 6-7 videos (average video duration: 45-60 minutes) online during the first 7 days of the course. These videos will cover the basics of NGS data, preprocessing, quality control and alignment strategies for both DNA-Seq and RNA-Seq, as well as a brief discussion of downstream analysis. Additionally, we will demonstrate how to leverage BLAST tools for NGS analysis.
Next, participants will apply a selection of RNA-Seq alignment algorithms over three days (1-2 hours per day), mapping RNA-Seq data to GRCh38 chromosome 20. Finally, participants will compare the results of these mappers for specific genes. Throughout the course, participants will be able to post questions at Biostars; experts from NCBI and elsewhere will be available online to answer questions.
Learners will emerge from the course equipped to map their own RNA-Seq or DNA-Seq data to the human genome, understand the options for downstream analysis, and use their understanding of the basic steps of data processing to interact more effectively with bioinformatician collaborators.