using a trillion points of data to deliver precision … a trillion points of data to deliver...

Using a Trillion Points of Data to Deliver Precision Medicine

Atul Butte MD, PhD Director Institute for Computational Health Sciences Professor of Pediatrics University of California San Francisco, CA

Dr. Atul Butte is the Director of the new Institute for Computational Health Sciences (ICHS) at the University of California, San Francisco, and a Professor of Pediatrics. Dr. Butte trained in Computer Science at Brown University, worked as a software engineer at Apple and Microsoft, received his MD at Brown University, trained in Pediatrics and Pediatric Endocrinology at Children's Hospital Boston, then received his PhD from Harvard Medical School and MIT. Dr. Butte has authored nearly 200 publications, with research repeatedly featured in Wired Magazine, the New York Times and the Wall Street Journal. Dr. Butte is also the principal investigator of ImmPort, the archival and dissemination repository for clinical and molecular datasets funded by the National Institute of Allergy and Infectious Diseases. In 2013, Dr. Butte was recognized by the White House as an Open Science Champion of Change for promoting science through publicly available data. Other recent awards include the 2014 E. Mead Johnson Award for Research in Pediatrics, 2013 induction into the American Society for Clinical Investigation, the 2012 FierceBiotech IT “Top 10 Biotech Techies”, and the 2011 National Human Genome Research Institute Genomic Advance of the Month. Dr. Butte is also a founder of three investor-backed data-driven companies: Personalis, providing clinical interpretation of whole genome sequences; Carmenta, discovering diagnostics for pregnancy complications; and, NuMedii, finding new uses for drugs through open molecular data.

Annual Quality Congress, Plenary Session, Sunday, October 4, 2015 Using a Trillion Points of Data to Deliver Precision Medicine Objective: Reflect on the power of “big data” and how it will drive healthcare in the 21st century and beyond.


Atul Butte, MD, PhD

October 4, 2015 1


[email protected]

@atulbutte

@ImmPortDB

Atul Butte, MD, PhD

Director, Institute for Computational Health Sciences

University of California, San Francisco

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

– Ansh Labs

– Prevendia

– Samsung

– Assay Depot

– Regeneron

– Verinata

– Pathway Diagnostics

– Geisinger Health

– Covance

– Wilson Sonsini Goodrich & Rosati

– 10X Genomics

– Medgenics

– GNS Healthcare

– Gerson Lehman Group

– Coatue Management

• Corporate Relationships

– Northrop Grumman

– Aptalis

– Thomson Reuters

– Intel

– SAP

– SV Angel

• Speakers’ bureau

– None

• Companies started by students

– Carmenta

– Serendipity

– NuMedii

– Stimulomics

– NunaHealth

– Praedicat

– MyTime

– Flipora

Kilo

KiloMega

KiloMegaGiga


Atul Butte, MD, PhD

October 4, 2015 2

KiloMegaGigaTera

KiloMegaGigaTeraPeta

KiloMegaGigaTeraPetaExa

KiloMegaGigaTeraPetaExa

Zetta

Already nearly 1.6 million microarrays publicly‐available!

Doubles every 2‐3 years!

Butte AJ. Translational Bioinformatics: coming of age. JAMIA, 2008.


Atul Butte, MD, PhD

October 4, 2015 3

Yes, even a high‐school student can use public data to design a new diagnostic!

Marina Sirota

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 LiuMatt CooperBruce Ling

New markers for preeclampsia

Linda LiuBruce Ling

Matt Cooper

Liu LY, …, XB Ling, Butte AJ. BMC Medicine, 2013.


Atul Butte, MD, PhD

October 4, 2015 4

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)

Rat colonoscopy Rat with Inflammatory Bowel Disease

Inflammatory Bowel Disease

After Anti‐seizure Drug

Dudley JT, Sirota M, ..., Pasricha J, Butte AJ. Science Translational Medicine, 2011.

Anti‐seizure drug works against a rat model of inflammatory bowel disease

Psychiatric Drug Imipramine Shows Significant Activity Against Small Cell Lung Cancer

Vehicle control Imipramine

p53/Rb/p130triple knockoutmodel of SCLC

Mice dosed after tumor formation

Joel DudleyNadine Jahchan

Julien SageAlejandro Sweet‐Cordero

Joel NealNuMedii

Mazen NasrallahPeter Marinkovich

Mårten Winge

Unpublished


Atul Butte, MD, PhD

October 4, 2015 5

Unpublished

Need more drugs for more diseases

Public big data available

NIH fundingData analyzed,

method designed

Company launched, ARRA, StartX,

Stanford license, first deal

Claremont Creek, Lightspeed ($3.5

million)

Credit: Whitehead Institute and MIT Credit: Oxford Nanopore Technologies and Wired

Credit: Euan Ashley, Russ Altman, Steve Quake, Lancet


Atul Butte, MD, PhD

October 4, 2015 6

Credit: Russ Altman and team

Human genome sequence can be used to predict drug adverse events

Credit: Rong Chen, Optra Systems, and Personalis, Inc.

Important genome differences “locked up” in publications


Collect the “big data” of findings across publications to analyze the “big data” of the genome


Credit: Rong Chen, Optra Systems, and Personalis, Inc. Credit: Rong Chen and Alex Morgan, Lancet


Atul Butte, MD, PhD

October 4, 2015 7

Maybe the genome can be used to

suggest (promote?) preventative health

strategies?

Credit: Rong Chen, Alex Morgan, Joel Dudley, Lancet Credit: Rong Chen, Alex Morgan, Joel Dudley, Lancet

Credit: Rong Chen, Alex Morgan, Joel Dudley, Lancet

Nicholas Volker

With daily weight and

intake measures,

I have lost 50 pounds (22 kg) in the past 2 years!

Future blood tests will be performed in

non‐traditional outlets.

Where will the data live?


Atul Butte, MD, PhD

October 4, 2015 8

Medical devices can be funded and designed by internet technologists!

Where will the data live? Public data can drive health defining mobile apps

The cost of delivered care is becoming public.

How will the public respond?

immport.niaid.nih.gov

Jeff WiserPatrick DunnSanchita Bhattacharya

The next big open data?

Raw clinical trials data

Download 100+ studies

today


Atul Butte, MD, PhD

October 4, 2015 9

Institute for Computational Health SciencesHow can we expect health care professionalsto review 6 billion pieces of data in a 15 minute encounter?

We already ask health care professionalsto review 1 GB of data in 15 minutes…



… but we give them tools to help them do this!

What is Big Data in Biomedicine?


Atul Butte, MD, PhD

October 4, 2015 10

Algorithms?

Programmers?

Databases?

High‐performance computers?

Mobile?

Big Data in Biomedicine is…

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…

Hope

Big Data in Biomedicine is

Collaborators• Jeff Wiser, Patrick Dunn, Mike Atassi / Northrop Grumman

• Ashley Xia and Quan Chen / NIAID

• Takashi Kadowaki, Momoko Horikoshi, Kazuo Hara, Hiroshi Ohtsu / U Tokyo

• Kyoko Toda, Satoru Yamada, Junichiro Irie / Kitasato Univ and Hospital

• Shiro Maeda / RIKEN

• Alejandro Sweet‐Cordero, Julien Sage / Pediatric Oncology

• Mark Davis, C. Garrison Fathman / Immunology

• Russ Altman, Steve Quake / Bioengineering

• Euan Ashley, Joseph Wu, Tom Quertermous / Cardiology

• Mike Snyder, Carlos Bustamante, Anne Brunet / Genetics

• Jay Pasricha / Gastroenterology

• Rob Tibshirani, Brad Efron / Statistics

• Hannah Valantine, Kiran Khush/ Cardiology

• Ken Weinberg / Pediatric Stem Cell Therapeutics

• Mark Musen, Nigam Shah / National Center for Biomedical Ontology

• Minnie Sarwal / Nephrology

• David Miklos / Oncology

Support• Lucile Packard Foundation for Children's Health

• NIH: NIAID, NLM, NIGMS, NCI; NIDDK, NHGRI, NIA, NHLBI, NCATS

• March of Dimes

• Hewlett Packard

• Howard Hughes Medical Institute

• California Institute for Regenerative Medicine

• Luke Evnin and Deann Wright (Scleroderma Research Foundation)

• Clayville Research Fund

• PhRMA Foundation

• Stanford Cancer Center, Bio‐X, SPARK

• Tarangini Deshpande

• Sam Hawgood

• Keith Yamamoto

• Isaac Kohane

Admin and Tech Staff

• Mary Lyall

• Mounira Kenaani

• Kevin Kaier

• Boris Oskotsky

using a trillion points of data to deliver precision … a trillion points of data to deliver...

Documents