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Translating a Trillion Points of Data into
Therapies, Diagnostics,
and New Insights into Disease
atul.butte@ucsf.edu
@atul...
Conflicts of Interest
• Scientific founder and
advisory board membership
– Genstruct
– NuMedii
– Personalis
– Carmenta
• H...
Kilo
Mega
Giga
Tera
Peta
Exa
Zetta
@affymetrix
bit.ly/genedata
Preeclampsia: large cause of maternal and fetal death
• Incidence
• 5-8% of all pregnancies in the U.S. and worldwide
• 4....
New blood markers for preeclampsia
Linda Liu
Bruce Ling
Matt Cooper
@MarchofDimes
bit.ly/preeclamp
Need a
diagnostic for
preeclampsia
Public big data
available
March of Dimes
Center for
Prematurity
Research
Data analyzed,...
@nanopore
@wired
Whitehead Institute
Credit: Euan Ashley, Russ Altman, Steve Quake, Lancet
Credit: Rong Chen, Optra Systems, and Personalis, Inc.
Credit: Rong Chen, Optra Systems, and Personalis, Inc.
Maybe the genome
can be used to
suggest (promote?)
preventative health
strategies?
Credit: Rong Chen, Alex Morgan, Joel Du...
Need to use
genomes to
predict
disease
Publications
available for
curation
Stanford
donor
funding
Science
curated,
methods...
@MatthewHerper
bit.ly/newdrug1
b
Bin Chen
Wei Wei
Li Ma
Bin Yang
Mei-Sze Chua
Samuel So
Gastroenterology, 2017
Need more drugs
for more diseases
Public big data
available
NIH funding
Data analyzed,
method designed
Company launched,
A...
Build the strongest team in the world in
biomedical computation and health data analytics
• Academic affinity home for fac...
The next big data: clinical data
What is Big Data in Biomedicine?
Algorithms?
Programmers?
Databases?
High-performance computers?
Mobile?
What is Big Data in Biomedicine?
Predicting the disease before it strikes
Explaining the rare disease that defies experts
Finding drugs for diseases lackin...
Hope
Big Data in Biomedicine is
UC Clinical Data Warehouse Team
Executive Team
• Atul Butte
• Joe Bengfort
• Michael Pfeffer
• Tom Andriola
• Chris Longhu...
Collaborators
• Alejandro Sweet-Cordero, Julien Sage /
Pediatric Oncology
• Elizabeth Thomson, Patrick Dunn / Northrop
Gru...
Support
Admin and Tech Staff
• Mary Lyall
• Mounira Kenaani
• Kevin Kaier
• Boris Oskotsky
• Mae Moredo
• Ada Chen
• Unive...
Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte
Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte
Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte
Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte
Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte
Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte
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Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte

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Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease - by Atul Butte

  1. 1. Translating a Trillion Points of Data into Therapies, Diagnostics, and New Insights into Disease atul.butte@ucsf.edu @atulbutte Atul Butte, MD, PhD Director, Institute for Computational Health Sciences UCSF Distinguished Professor of Pediatrics University of California, San Francisco
  2. 2. Conflicts of Interest • Scientific founder and advisory board membership – Genstruct – NuMedii – Personalis – Carmenta • Honoraria for talks – Lilly – Pfizer – Siemens – Bristol Myers Squibb – AstraZeneca – Roche – Genentech – Warburg Pincus • Past or present consultancy – Lilly – Johnson and Johnson – Roche – NuMedii – Genstruct – Tercica – Ecoeos – Helix – Ansh Labs – Prevendia – Samsung – Assay Depot – Regeneron – Verinata – Pathway Diagnostics – Geisinger Health – Covance – Wilson Sonsini Goodrich & Rosati – Orrick – 10X Genomics – Medgenics – GNS Healthcare – Gerson Lehman Group – Coatue Management • Corporate Relationships – Northrop Grumman – Aptalis – Allergan – Astellas – Thomson Reuters – Intel – SAP – SV Angel – Progenity – Illumina • Speakers’ bureau – None • Companies started by students – Carmenta – Serendipity – Stimulomics – NunaHealth – Praedicat – MyTime – Flipora – Tumbl.in
  3. 3. Kilo Mega Giga Tera Peta Exa Zetta
  4. 4. @affymetrix
  5. 5. bit.ly/genedata
  6. 6. 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
  7. 7. New blood markers for preeclampsia Linda Liu Bruce Ling Matt Cooper @MarchofDimes bit.ly/preeclamp
  8. 8. 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
  9. 9. @nanopore @wired Whitehead Institute
  10. 10. Credit: Euan Ashley, Russ Altman, Steve Quake, Lancet
  11. 11. Credit: Rong Chen, Optra Systems, and Personalis, Inc.
  12. 12. Credit: Rong Chen, Optra Systems, and Personalis, Inc.
  13. 13. Maybe the genome can be used to suggest (promote?) preventative health strategies? Credit: Rong Chen, Alex Morgan, Joel Dudley, Lancet
  14. 14. Need to use genomes to predict disease Publications available for curation Stanford donor funding Science curated, methods designed Company launched, Stanford license MDV, Lightspeed, Abingworth ($20 million) Same 3 plus Wellington Shields ($22 million) Series C ($33 million)
  15. 15. @MatthewHerper bit.ly/newdrug1 b
  16. 16. Bin Chen Wei Wei Li Ma Bin Yang Mei-Sze Chua Samuel So Gastroenterology, 2017
  17. 17. 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
  18. 18. 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
  19. 19. The next big data: clinical data
  20. 20. What is Big Data in Biomedicine?
  21. 21. Algorithms? Programmers? Databases? High-performance computers? Mobile? What is Big Data in Biomedicine?
  22. 22. 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…
  23. 23. Hope Big Data in Biomedicine is
  24. 24. 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
  25. 25. 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
  26. 26. Support Admin and Tech Staff • Mary Lyall • Mounira Kenaani • Kevin Kaier • Boris Oskotsky • Mae Moredo • Ada Chen • University of California, San Francisco • Priscilla Chan and Mark Zuckerberg • 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 • Luke Evnin and Deann Wright (Scleroderma Research Foundation) • Clayville Research Fund, PhRMA Foundation • Stanford Cancer Center, Bio-X, SPARK • Tarangini Deshpande • Kimayani Butte • Sam Hawgood, Keith Yamamoto • Isaac Kohane

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