Jul 07 2016

Bioinformatics is a vocation. Not a job.

by at 10:57 am

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.

  1. AMIA’16 – 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.
  1. Cyberattack Response! – 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!
  2. 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.
  3. 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 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.
  4. Know Your TumorSM – Patients with pancreatic cancer can obtain molecular tumor profiling through the Pancreatic Cancer Action Network’s Know Your TumorSMprecision 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.
  5. Moonshot – 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!

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May 20 2014

Do not blink

by at 4:58 pm

Blink and you will miss a revolution! This is indeed true in the field of biomedical informatics today as it transforms healthcare and clinical translational research at light speed. Two recent conferences – AMIA’s Translational Bioinformatics (#TBICRI14) and BioIT World (#BioIT14) brought together national and international informatics experts from academia, industry and non-profit organizations to capture a snapshot of scientific trends, marvel at the progress made and the opportunities ahead. I hope to give you a glimpse of my personal journey at these two conferences with references to additional information should you decide to delve deeper.

Stanford Professor and creator of PharmGKB, Russ Altman’s (@Rbaltman) presented the year in review, a cherished event at the annual AMIA TBI conference, which highlighted the 42 top papers in the field. He started with the warning letter from the FDA to Ann Wojcicki, CEO, 23andMe to stop marketing the consumer gene testing kit that is not FDA cleared; and followed with a Nature commentary by Robert Green and Nita Farahany asserting that the FDA is overcautious on consumer genomics. The authors cited data from over 5000 participants that suggested that consumer genomics does not provoke distress or inappropriate treatment. Russ then reviewed Harvard professor John Quackenbush’s (@johnquackenbush) Nature Analysis paper, which showed that the measured drug response data from two large-scale NIH funded pharmacogenomics studies were highly discordant with large implications for using these outcome measures to assess gene-drug interactions for drug development purposes. Large-scale database curation related shout outs included Pfizer-CTD’s manual curation of 88,000 scientific articles text mined for drug-disease and drug-phenotype interactions published by David et al., in the Journal Database; and the DGIdb: mining the druggable genome by Griffith et al., in Nature Methods.  Russ’s crystal ball for 2014 predicts an emphasis on non-European descent populations for discovery of disease associations, crowd-based discovery using big data, and methods to recommend treatment for cancer based on genomes and transcriptomes.

The 7 AM birds-of-a-feather session on “researching in big data” facilitated by Columbia’s Nick Tatonetti (@nicktatonetti) engaged a vocal group of big data proponents where we discussed the definition (the four V’s – velocity, volume, veracity and variety), processing (MapReduce/Hadoop, Google APIs), visualizing (d3.js) and sharing of massive biomedical datasets (no-sql databases to cloud based resources). New analytical tools were presented including netGestalt from Vanderbilt for proteogenomic characterization of cancer; PhenX toolkit from NIH for promoting data sharing and translational research; SPIRIT from City of Hope for protocol decision trees, eligibility screening, and cohort discovery and many others.

Method presentations included an integrated framework for pharmacogenomics characterization of oncological drugs, and novel NGS analysis methods on the Amazon cloud, by ICBI members Krithika Bhuvaneshwar and Brian Conkright, respectively. A keynote lecture given by Richard Platt described PCORI’s PCORnet coordinating center, a newly established consortium of 29 networks that will use electronic health data to conduct comparative effectiveness research and the 18-month schedule to get the consortium up and running. Zak Kohane, Director, Center for Biomedical Informatics at Harvard Medical School kicked his keynote lecture out of the park again. He described, among other things, the critical role of translational bioinformaticians in translating big data to clinically usable knowledge. The entire conference proceedings can be found here.

Last week, BioIT World started with an excellent keynote by John Quackenbush where he described his journey as the co-founder of Genospace. As digital architects of genomic medicine, the company aims to improve the progress and efficacy of healthcare in the genomic age. John finished his talk by emphasizing that the most important “omics’ in precision medicine is econOMICS, especially given that the first slide of most everyone who talks about precision medicine these days is one that shows the drop in cost per megabase of DNA sequence compared to Moore’s law. On the other hand, Stephen Friend, President of Sage Bionetworks, discussed during his keynote provocative questions such as “why not have a GitHub for data?” and “can we have sponsors such as Gates and NIH push open data access for programs they fund?” BioIT world this year had 13 parallel tracks covering a wide range of topics from cloud computing to cancer informatics.

I attended talks including transSMART – a community driven open source platform for translational research by Roche and the transSMART foundation; the Pan-Cancer analysis of whole genome projects by Lincoln Stein of the Ontario Institute for Cancer Research; and MetaboLYNC – a cloud based solution for sharing, visualizing, and analyzing metabolomics data by the company Metabolon, Inc. Diagnosis and treatment in elderly patients presents a unique set of challenges because of their extensive clinical history, altered physiology and physiological response both to diseases and treatments, patterns of behavior and access to appropriate medical care. A talk by Michael Liebman, IPQ analytics and Sabrina Molinaro, Institute of clinical physiology, Italy highlighted the application of big data to address the complexity in treatment of elderly patients with diabetes and hypertension.

I had the wonderful opportunity to chair a session on “Clinical genomics data within cloud computing environments” and shared our experience at Georgetown as we build a cancer cloud in collaboration with University of Chicago and the Globus Genomics team.

With so many exciting talks and demonstrations of terrific progress in informatics at both conferences, I did feel that I could not blink lest I should miss something of extreme importance. I welcome you to check out the rest of the newsletter to catch up on exciting events and activities at ICBI. Let’s continue the conversation – find me on e-mail at sm696@georgetown.edu or on Twitter at @subhamadhavan

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