Summer 2016 Newsletter
Bioinformatics is at the heart of modern day clinical translational research. And while experts define this as an interdisciplinary field that develops and improves methods and tools for storing, retrieving, organizing, and analyzing biological (biomedical) data – it is much, much more!
Bioinformatics helps researchers connect the dots between disparate datasets; improve extraction of signal from noise; predict or explain outcomes; and improves acquisition and interpretation of clinical evidence. Ultimately, it allows us to tell the real data stories.
To effectively tell these stories, and to see this all-encompassing domain in biomedical research and its true super powers, we must pursue bioinformatics as a vocation – or a calling – and not just a job.
Spring’16 has been a busy season for us Bioinformaticians at the Georgetown ICBI. I carefully curated six of our recent impact stories that you may find useful.
The perfect triangulation between clinical practitioners, researchers and industry can be seen at AMIA annual conferences. I was honored to chair the Scientific Planning Committee for this year’s AMIA Translational Bioinformatics (TBI) Summits, featuring sessions on the NIH Precision Medicine initiative, BD2K program, and ClinGen. I sat down with GenomeWeb’s Uduak Grace Thomas for a Q&A on this year’s Summit, which attracted over 500 informaticians. Come join us at the AMIA Joint Summits 2017 to discuss the latest developments in Bioinformatics.
We were in the middle of responding to NIH’s request for de-identified health record data for our Precision Medicine collaborative when MedStar Health, our health care partner’s computer systems, were crippled by a cyberattack virus. Thousands of patient records were inaccessible and the system reverted to paper records, seldom used in modern hospital systems. Thanks to the hard work and dedication of the IT staff, MedStar Health systems were restored within days with no evidence of any compromised data, according to the MedStar Health spokesperson. However, our research team had to act fast and improvise a way to fulfill the NIH’s data request. We ended up providing a complete synthetic linked dataset for over 200 fields. As our collaborator Josh Denny, a leader in the NIH Precision Medicine Initiative put it – “this experience you had to go through will help us be better prepared for research access to EHRs for nationwide clinical networks”. We sure hope so!
Amazon Web Service (AWS)
The AWS Public Sector Summit was buzzing with energy from an active ecosystem of users and developers in federal agencies, small and large businesses, and nonprofit organizations—a community created over just the past few years. It was enlightening for me to participate on a panel discussing Open Data for Genomics: Accelerating Scientific Discovery in the Cloud, with NIH’s Senior Data Science Advisor, Vivien Bonazzi, FDA’s former Chief Health Informatics Officer, Taha Kass-Hout and AWS’s Scientific Computing Lead, Angel Pizarro. Three take homes from the Summit - (1) a growing need for demand-driven open data; (2) concern over the future administration’s commitment (or lack thereof) to #opendata; and (3) moving beyond data storage, and the future of on-demand analytics.
Massive Open Online Course (MOOC) on Big Data
Want to begin demystifying biomedical big data? Start with this MOOC – to be available through Open edX late Fall. Georgetown University was recently awarded a BD2K training grant to develop an online course titled “Demystifying Biomedical Big Data: A User’s Guide”. The course aims to facilitate the understanding, analysis, and interpretation of biomedical big data for basic and clinical scientists, researchers, and librarians who have limited/no significant experience in bioinformatics. My colleagues Yuriy Gusev, Peter McGarvey and Bassem Haddad, who are leading the course, are recording interviews and lectures with experts on practical aspects of use of various genotype and phenotype datasets to help advance Precision Medicine.
Know Your TumorSM
Patients with pancreatic cancer can obtain molecular tumor profiling through the Pancreatic Cancer Action Network’s Know Your TumorSM precision medicine initiative. It is an innovative partnership with Perthera, a personalized medicine service company that facilitates the multi-omic profiling and generates reports to patients and physicians. Check out the results from over 500 KYT patients presented at AACR’16 by our multi-disciplinary team of patient coordinators, oncologists, molecular diagnostic experts and data scientists.
Latest announcement from VP Biden’s Cancer Moonshot program unveiled a major database initiative at ASCO’16. I had the opportunity to comment in Scientific American on the billions of bits of information that such a database would capture to help drive an individual’s precise cancer treatment. Continue to watch the Moonshot program if you are involved with cancer research or care continuum.
It is personally gratifying to see Bioinformaticians, BioIT professionals, and data scientists continue to solidify their role as an integral part of advancing biomedicine. I have yet to meet a bioinformatician who thinks of her/his work as just a job. Engage your bioinformatics colleagues in your work, we will all be better for it!
Let's continue the conversation:
Oncore Clinical trial management system launch
We are working with clinicians, researchers and administrators at Georgetown-MedStar Health to implement the Oncore CTMS for clinical research studies
I2b2 clinical research
We are working with Georgetown-Howard Universities CTSA to enable access to de-identified MedStar health record datasets through i2b2 for cohort discovery and translational research
We are collaborating with the National Center for human factors research at MedStar health to apply human factors engineering approaches to our precision medicine software development project
We are building tools to support exploration and analysis of cancer patient molecular diagnostic data for new hypothesis generation and decision support
ICBI is delighted to welcome new team members, collaborators and students
Dr. Shaojun Tang joined ICBI as a new faculty member in January 2016. His research primarily focuses on the development of tools and methods for the analysis of cancer immunotherapy data, including breast cancer and melanoma datasets. Dr. Tang is also interested in the study of multi-'omics' data using various machine learning tools.
Simina M. Boca, Maki Nishida, Michael Harris, Shruti Rao, Amrita K. Cheema, Kirandeep Gill, Haeri Seol, Lauren P. Morgenroth, Erik Henricson, Craig McDonald, Jean K. Mah, Paula R. Clemens, Eric P Hoffman, Yetrib Hathout and Subha Madhavan. Discovery of metabolic biomarkers for Duchenne Muscular Dystrophy within a natural history study. PLOS ONE, April 15, 2016
ICBI in the Community
ICBI members participated in the following
MACE2K: Molecular and Clinical Extraction: A Natural Language Processing Tool For Personalized Medicine. S. Rao, K. Vijay-Shanker, V. Sharma, S. Boca, K. Ross, M. Harris, P. McGarvey, R. Beckman, C. Wu, S. Madhavan. Curating the Clinical Genome, Hinxton, United Kingdom 2016
Retrospective Analysis of Patient Molecular Profiles to Inform Cancer Precision Medicine. B. Conkright, S. Rao, S. Boca, R. Beckman, J. Marshall, S. Madhavan, AMIA Joint Summits 2016
Combining Protein Annotation and Genome Variation. P. McGarvey, M. Harris, S. Rao, H. Huang, S. Madhavan, C. Wu, M. Martin, A. Nightingale, A. Bateman, the UniProt Consortium. AMIA Joint Summits 2016
viGEN – A Novel Bioinformatics Pipeline for Viral RNA Detection and Quantification in Human RNAseq Data. K. Bhuvaneshwar, L. Song, Y. Gusev. AMIA Joint Summits 2016
Molecular profiling of TOPO1: A way to evaluate irinotecan treatment in colorectal cancer. JM. Cunningham, P. Prins, B. Conkright, S. Boca, S. Rao, A. Gabrielson, A. Oseran, R. Beckman, M. Al-hajeili, S.Madhavan, J. Marshall. In ASCO Annual Meeting Proceedings 2016 Feb 1 (Vol. 34, No. 4_suppl, p. 546).
Trastuzumab Treatment and Cardiotoxicity in Breast Cancer Patients, Simina Boca. AMIA Joint Summits 2016
Quantifying the Impact of Precision Medicine, Robert Beckman, Ruesch Center for the Cure of Gastrointestinal Cancers Advisory Board, March 3, 2016.
Dynamic Precision Medicine Strategies for Cancer May Improve Patient Outcomes, Robert Beckman, Molecular and Computational Biology Department, University of Southern California, Los Angeles, California, February 12, 2016.
Clinical and Statistical Considerations in Design of Basket Trials. Robert Beckman. Drug Information Association (DIA) Key Opinion Leader (KOL) Lecture Series, online lecture, February, 2016.
Biomedical Informatics Driving Clinical & Translational Team Science, Subha Madhavan, Joint Team Science Symposium, D.C, April 12, 2016.
Amazon Web Services Summit. Subha Madhavan, June 20, 2016
ICBI Consultation and Support