Atul Butte remote presentation on 2019-02-05 for Accelerating biology 2019: Towards Thinking Machines, in Pune India

1. Translating a Trillion Points of Data into
Diagnostics, Therapies and New Insights
in Health and Disease
atul.butte@ucsf.edu
@atulbutte
Atul Butte, MD, PhD
Priscilla Chan and Mark Zuckerberg Distinguished Professor
Director, Bakar Computational Health Sciences Institute, UCSF
Chief Data Scientist, University of California Health (UC Health)

4. Kilo
Mega
Giga
Tera
Peta
Exa
Zetta

5. @chr1sa
bit.ly/endscience

6. @affymetrix

7. bit.ly/genedata

8. bit.ly/geobrca

9. http://www.nap.edu/catalog.php?record_id=13284

10. Marina Sirota

12. Protein

13. Cancer markers
Haeberle H, Dudley JT, …,
Butte AJ, Contag CH. Neoplasia, 2012.

14. Cancer markers
Transplant Rejection markers
Chen R, …, Butte AJ.
PLoS Computational Biology, 2010.

15. Preeclampsia: large cause of maternal and fetal death
• Incidence
• 5-8% of all pregnancies in the U.S. and worldwide
• 4.1 million births in the U.S. in 2009
• Up to 300K cases of preeclampsia annually in the U.S.
• Mortality
• Responsible for 18% of all maternal deaths in the U.S.
• Maternal death in 56 out of every 100,000 live births in US
• Neonatal death in 71 out of every 100,000 live births in US
• Cost
• $20 billion in direct costs in the U.S. annually
• Average hospital stay of 3.5 days
Linda Liu
Bruce Ling
Matt Cooper

17. New blood markers for preeclampsia
Linda Liu
Bruce Ling
Matt Cooper
@MarchofDimes
bit.ly/preeclamp

18. Need a
diagnostic for
preeclampsia
Public big data
available
March of Dimes
Center for
Prematurity
Research
Data analyzed,
diagnostic
designed
SPARK grant
($50k)
Life Science
Angels, other
seed investors
($2 million)
@CarmentaBio
progenity.com
bit.ly/carm_prog

19. @MatthewHerper
bit.ly/newdrug1

21. Cancer Discovery 2013, 3:1.
Psychiatric Drug Imipramine Shows Significant Activity
Against Small Cell Lung Cancer
Vehicle control Imipramine
p53/Rb/p130
triple knockout
model of SCLC
Mice dosed after
tumor formation
Joel Dudley
Nadine Jahchan
Julien Sage
Alejandro Sweet-Cordero
Joel Neal
@NuMedii

22. Bin Chen
Wei Wei
Li Ma
Bin Yang
Mei-Sze Chua
Samuel So
Gastroenterology, 2017

23. Need more drugs
for more diseases
Public big data
available
NIH funding
Data analyzed,
method designed
Company launched,
ARRA, StartX,
Stanford license,
first deal
Claremont Creek,
Lightspeed ($3.5
million)
@NuMedii

24. The next big open data: clinical trials
Download 300+ studies today
Drug repositioning, new patient subsets,
digital comparative effectiveness, more!
immport.org
Sanchita Bhattacharya
Elizabeth Thomson

27. • Founded 2015
• 49 affiliated faculty members from UCSF’s four
top-ranked schools
– 5 in National Academy of Medicine
– 1 in National Academy of Science
– 2 in the American Society for Clinical Investigation
– 3 NIH Director’s Awards
– 2 Sloan Foundation fellows
– 1 HHMI faculty scholar
– 1 MacArthur Foundation fellow
– 1 Chan/Zuckerberg faculty fellow

28. Build the strongest team in the world in
biomedical computation and health data analytics
• Academic affinity home for faculty and staff
• Research and development (and spin out technologies)
• Develop new educational plans
• Bring the best new computational and informatics faculty members
to UCSF
• Organize infrastructure and operations
• Build and use our new data assets for precision medicine

29. University of California
• 10 campuses and 3 national labs
• ~200,000 employees, ~250,000 students/yr
UC Health
• 18 health professional schools (6 med schools)
• Train half the medical students and residents in
California
• ~$2 billion NIH funding
• $11.4 billion clinical operating revenue
• 5000 faculty physicians, 12000 nurses
• UCSF and UCLA are in US News top 10
• 5 NCI Comprehensive Cancer Centers, 5 NIH CTSA

30. UC Health Data Analytics Platform
Combining healthcare data from across the
six University of California medical schools and systems
Health Data Warehouse

31. • Combined EHR data from UCSF, UCLA, UC Irvine, UC Davis,
UC San Diego, and UC Riverside
• Total 15 million patients with an MRN, basic diagnosis data
• Central database built using OMOP (not Epic) as a data backend
– Structured data from 2012 to the present day
– 5.2 million patients with “modern” data
– 101M encounters, 307M procedures, 283M med orders, 684M vital signs,
453M lab test results, 422M diagnosis codes
– Claims data from our self-funded plans now included
– Continually harmonizing elements
• Quality and performance dashboards 31
The University of California has an
incredible view of the medical system

32. Hanna Paik
Jae Hyun
bit.ly/2DZLsvr

33. Hanna Paik
Jae Hyun
bit.ly/2DZLsvr

34. What is Big Data in Biomedicine?

35. Algorithms?
Programmers?
Databases?
High-performance computers?
Mobile?
What is Big Data in Biomedicine?

36. Predicting the disease before it strikes
Explaining the rare disease that defies experts
Finding drugs for diseases lacking attention
Making sure we do the right thing for patients
An amazing platform for biomedical innovation
Big Data in Biomedicine is…

37. Hope
Big Data in Biomedicine is

38. UC Clinical Data Warehouse Team
Executive Team
• Atul Butte
• Joe Bengfort
• Michael Pfeffer
• Tom Andriola
• Chris Longhurst
Steering Committee
• Lisa Dahm
• Mohammed Mahbouba
• David Dobbs
• Kent Andersen
• Ralph James
• Jennifer Holland
• Eugene Lee
ETL Team
• Albert Dugan
• Tony Choe
• Michael Sweeney
• Timothy Satterwhite
• Ayan Patel
• Niranjan Wagle
• Ralph James
• Joseph Dalton
Data Harmonization
• Dana Ludwig
• Daniella Meeker
Data Quality
• Momeena Ali
• Jodie Nygaard
Business Analyst
• Ankeeta Shukla
Hardware
• Sandeep Chandra
• Jeff Love
• Scott Bailey
• Kwong Law
• Pallav Saxena
Support
• Elizabeth Engel
• Jack Stobo
• Michael Blum
• Sam Hawgood

39. Collaborators
• Alejandro Sweet-Cordero, Julien Sage /
Pediatric Oncology
• Elizabeth Thomson, Patrick Dunn / Northrop
Grumman
• Gabe Rosenfeld, Quan Chen / NIAID
• Andrei Goga / UCSF Oncology
• Mallar Bhattacharya / UCSF Pulmonary
• Minnie Sarwal / UCSF Nephrology
• Geoffrey Gurtner / UCSF Surgery
• Roberta Diaz Brinton / Arizona
• Carol Bult / Jackson Labs
• David Stevenson, Gary Shaw / Stanford
Neonatology
• Takashi Kadowaki, Momoko Horikoshi, Kazuo
Hara, Hiroshi Ohtsu / U Tokyo
• Kyoko Toda, Satoru Yamada, Junichiro Irie /
Kitasato Univ and Hospital
• Shiro Maeda / RIKEN
• Mark Davis, C. Garrison Fathman /
Immunology
• Russ Altman, Steve Quake / Stanford
Bioengineering
• Euan Ashley, Joseph Wu / Stanford Cardiology
• Mike Snyder, Carlos Bustamante, Anne Brunet
/ Stanford Genetics
• Jay Pasricha / Stanford Gastroenterology
• Rob Tibshirani, Brad Efron / Stanford Statistics
• Hannah Valantine, Kiran Khush/ Stanford
Cardiology
• Mark Musen, Nigam Shah / National Center for
Biomedical Ontology
• Sam So, Ken Weinberg, David Miklos /
Stanford Oncology

40. Support
Admin and Tech Staff
• Kristin Haynes
• Mounira Kenaani
• Kevin Kaier
• Boris Oskotsky
• Mae Moredo
• Ada Chen
• University of California, San Francisco
• Priscilla Chan and Mark Zuckerberg
• Bakar Family
• NIH: NIAID, NLM, NIGMS, NCI, NHLBI, OD; NIDDK, NHGRI, NIA, NCATS, NICHD
• California Governor’s Office of Planning and Research
• March of Dimes
• Juvenile Diabetes Research Foundation
• Howard Hughes Medical Institute, California Institute for Regenerative Medicine
• Hewlett Packard, L’Oreal, Progenity, Genentech
• Scleroderma Research Foundation
• Clayville Research Fund, PhRMA Foundation, Stanford Cancer Center, Bio-X, SPARK
• Tarangini Deshpande
• Kimayani Butte
• Talmadge King and Mark Laret and Jack Stobo
• Sam Hawgood and Keith Yamamoto
• Isaac Kohane