Biomedicine from Stethoscope to Computer
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Philip Bourne runs programs at the NIH that support computational and quantitative sciences for biomedical discovery. He discussed his career path from chemistry PhD to his current role leading data science efforts. He is motivated by enabling open data sharing to accelerate cures, harnessing citizen science through games, and realizing the promise of precision medicine through large cohorts and mobile technologies. If successful, precision medicine could lead to more targeted treatments based on an individual's genomic data within a decade.
Biomedicine from Stethoscope to Computer
- 1. Biomedicine – from Stethoscope to Computer Philip E. Bourne NIH Associate Director for Data Science Emerging Researchers National Conference in STEM February 20, 2015
- 2. What I do… I run a program at the NIH which supports projects that advance the contribution of the computational and quantitative sciences to biomedical discovery. I also run a research lab at the NIH where we do computational biology with an emphasis on protein structure.
- 3. How I think I got here… • I embrace change • I make and keep lots of friends and colleagues • I keep questioning assumptions • I follow my heart • I learned to live with regret • I try to make the most of every day • I go after the big problems • I give back to the scientific community and society Google “PLOS Ten Simple Rules”
- 4. The Life of One Scientist – The Early Years So That You Might Not Make the Same Mistakes • My high school teacher Mr. Wilson said I would be a failure at chemistry • My PhD is in chemistry • The opportunity to live in different places shaped my life • Good friends are forever
- 6. Always Loved Computing Circa 1974
- 7. Postdoctoral Work – The Molecular Basis of How the Body Works • Regrets: never learnt another language
- 8. Post Doc
- 9. Some Things Stay with You Your Whole Life 9
- 10. Senior Scientist HHMI Columbia University New York • Driven not by career but wanting to live in New York City
- 11. ~1990 Got Involved with The Human Genome • Was only possible by applying computers to problems in biology • Developed algorithms to support physical and genetic mapping of Chromosome 13
- 12. Went to UCSD to Apply Computers to Big Biological Problems In 1993 possibly the best place in the world to do computational biology
- 13. Eventually…. I Fell in Love with the Data Problem
- 14. Numberofreleasedentries Year The Growth of Data is A Major Driver in Biology
- 15. Realized that there is still more work for me to do… it isn’t all in the lab… and it is in Washington, D.C. New Job! Associate Director for Data Science (ADDS) at the National Institutes of Health (NIH) Mission: To accelerate and support the integration of the computational and quantitative sciences and the biomedical sciences. I also got to move my lab to the NIH – my group’s research in protein structure biology continues here in the D.C. area and with collaborations all over the world.
- 16. WHAT MOTIVATES ME TODAY? 3 VIGNETTES
- 17. 1. Josh Sommer and Chordoma Disease http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation#fullprogram
- 18. Josh Sommer – A Remarkable Young Man Co-founder & Executive Director the Chordoma Foundation http://sagecongress.org/Presentations/Sommer.pdf
- 19. Chordoma • A rare form of brain cancer • No known drugs • Treatment – surgical resection followed by intense radiation therapy http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG
- 26. Open Data leads to faster cures Collaboration • Open Data generates collaborations and supports Team Science • Collaborations bring in more researchers Big Data • More researchers create more data • More researchers create different types of data Faster Cures • Computational Science helps biologists do more with all that Big Data • Big Data leads to new discoveries.
- 27. Drug Discovery
- 28. The Worst of Times Source: http://www.pharmafocusasia.com/strategy/drug_discovery_india_force_to_reckon.htm
- 29. Here is One Reason Why • Tykerb – Breast cancer • Gleevac – Leukemia, GI cancers • Nexavar – Kidney and liver cancer • Staurosporine – natural product – alkaloid – uses many e.g., antifungal antihypertensive Collins and Workman 2006 Nature Chemical Biology 2 689-700
- 30. Bioinformatics – Reverse Engineering Drug Discovery Characterize ligand binding site of primary target (Geometric Potential) Identify off-targets by ligand binding site similarity (Sequence order independent profile-profile alignment) Extract known drugs or inhibitors of the primary and/or off-targets Search for similar small molecules Dock molecules to both primary and off-targets Statistics analysis of docking score correlations … Xie and Bourne 2009 Bioinformatics 25(12) 305-312
- 31. 2. HARNESSING SOCIETY FOR SCIENCE A Team of scientists is great but….what if ordinary people could help us do science. Computer games are the key.
- 32. Nature’s Reductionism There are ~ 20300 possible proteins >>>> all the atoms in the Universe 11.2M protein sequences from 10,854 species (source RefSeq) 38,221 protein structures yield 1195 domain folds (SCOP 1.75)
- 33. Bridging fields to support innovationSometimes biomedical research is mind-numbingly BORING! How can we manage time-intensive, low-skill tasks without biologist burn out??? Crowdsourcing?
- 34. Research Games for Citizen Science
- 35. Think Tank: Game Developers and Biomedical Researchers 9 biomedical researchers & 10 game developers December 9-10, 2014 @ NIH To address challenges of how these two communities collaborate, exchange data science & visualization expertise, and develop games for enabling and performing biomedical research
- 36. 3. PRECISION MEDICINE For the first time in history health care is patient centric.
- 37. President Obama’s State of the Union Address: January 20, 2015
- 38. “And that’s why we’re here today. Because something called precision medicine … gives us one of the greatest opportunities for new medical breakthroughs that we have ever seen.” President Barack Obama January 30, 2015
- 41. Precision Medicine Concept is not new • Consider prescription eyeglasses, blood transfusions… • Prospects for broader application raised by recent advances in basic research, technology development, genomics, proteomics, metabolomics, EMRs, Big Data, mHealth, etc. • Reinforced by 2011 National Research Council report What is needed now • Development of rigorous research program to provide scientific evidence needed to turn concept into reality • Recruitment of the best and brightest from multiple disciplines to join the team
- 42. Precision Medicine Initiative: The Time Is Right Ten Years Ago Now – 2014 (most recent data) Cost of sequencing a human genome $22,000,000 $1000 - $5000 Amount of Time to Sequence a Human Genome 2 years <1 day Number of smart phones in the United States 1 million (<2%) 160 million (58%) EMR Adoption, (% providers) 20-30% >90% Computing Power n n x 16
- 43. Precision Medicine: What Success Might Look Like 50-year-old woman with type 2 diabetes visits her doctor • Now – Though woman’s glucose control has been suboptimal, doctor renews her prescription for drug often used for type 2 diabetes – Continues to monitor blood glucose with fingersticks and glucometer, despite dissatisfaction with these methods
- 44. Precision Medicine: What Success Might Look Like 50-year-old woman with type 2 diabetes visits her doctor • Future: + 2 years – Volunteers for new national research network • Sample of her DNA, along with her health information, sent to researchers for sequencing/analysis • Can view her health/research data via smartphone – Agrees to researchers’ request to track her glucose levels via tiny implantable chip that sends wireless signals to her watch, researchers’ computers • Using these data, she changes diet, medicine dose schedule
- 45. Other Diseases: What Success Might Look Like 50-year-old woman with type 2 diabetes visits her doctor • Future: + 5 years – Receives word from her doctor about a new drug based upon improved molecular understanding of type 2 diabetes – When she enters drug’s name into her smartphone’s Rx app, her genomic data show she’ll metabolize the drug slowly • Her doctor alters the dose accordingly
- 46. Other Diseases: What Success Might Look Like 50-year-old woman with type 2 diabetes visits her doctor • Future: + 10 years – Celebrates her 60th birthday and reflects with her family about how proud she is to be part of cohort study – Her glucose levels remain well controlled; she’s suffered no diabetes-related complications – Her children decide to volunteer for cohort study
- 47. NIH… Turning Discovery Into Health @pebournephilip.bourne@nih.gov