atul butte's presentation at lincs 2013
DESCRIPTION
Dr. Butte describes how his lab uses open public dataTRANSCRIPT
New uses of drugs from a trillion points of data
Atul Butte, MD, PhD
Chief, Division of Systems Medicine, Department of Pediatrics, Genetics,and by courtesy, Medicine, Pathology, and Computer Science
Center for Pediatric Bioinformatics, LPCH
Stanford University
@atulbutte
Disclosures• Scientific founder and
advisory board membership– Genstruct– NuMedii– Personalis– Carmenta
• Past or present consultancy– Lilly– Johnson and Johnson– Roche– NuMedii– Genstruct– Tercica– Ecoeos– Ansh Labs– Prevendia– Samsung– Assay Depot– Regeneron– Verinata– Geisinger
• Honoraria– Lilly– Pfizer– Siemens– Bristol Myers Squibb– AstraZeneca
• Corporate Relationships– Aptalis– Thomson Reuters
• Speakers’ bureau– None
• Companies started by students– Carmenta– Serendipity– NuMedii– Stimulomics– NunaHealth– Praedicat– MyTime– Flipora
Over 1.2 million microarrays available
Doubles every 2-3 years
Butte AJ. Translational Bioinformatics: coming of age. JAMIA, 2008.
Public big data = retroactive crowd-sourcing
Available Cancer Types # Cases Shipped by BCR # Cases with DataDate Last Updated (mm/dd/yy)
Acute Myeloid Leukemia [LAML] 200 200 6/24/2013
Adrenocortical carcinoma [ACC] 80 0
Bladder Urothelial Carcinoma [BLCA] 201 184 7/5/2013
Brain Lower Grade Glioma [LGG] 296 271 7/3/2013
Breast invasive carcinoma [BRCA] 1007 961 7/5/2013
Cervical squamous cell carcinoma and endocervical adenocarcinoma [CESC] 163 163 7/5/2013
Colon adenocarcinoma [COAD] 439 425 6/28/2013
Esophageal carcinoma [ESCA] 63 63 7/5/2013
Glioblastoma multiforme [GBM] 514 510 6/28/2013
Head and Neck squamous cell carcinoma [HNSC] 427 376 7/3/2013
Kidney Chromophobe [KICH] 66 66 7/5/2013
Kidney renal clear cell carcinoma [KIRC] 512 512 7/3/2013
Kidney renal papillary cell carcinoma [KIRP] 158 144 6/28/2013
Liver hepatocellular carcinoma [LIHC] 152 128 7/3/2013
Lung adenocarcinoma [LUAD] 500 499 7/3/2013
Lung squamous cell carcinoma [LUSC] 500 494 7/5/2013
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma[DLBC] 18 18 7/3/2013
Mesothelioma [MESO] 0 0
Ovarian serous cystadenocarcinoma [OV] 572 570 7/5/2013
Pancreatic adenocarcinoma [PAAD] 71 62 7/3/2013
Pheochromocytoma and Paraganglioma [PCPG] 0 0
Prostate adenocarcinoma [PRAD] 248 201 7/5/2013
Rectum adenocarcinoma [READ] 169 168 6/28/2013
Sarcoma [SARC] 111 75 7/5/2013
Skin Cutaneous Melanoma [SKCM] 357 336 7/5/2013
Stomach adenocarcinoma [STAD] 343 325 7/3/2013
Testicular Germ Cell Tumors [TGCT] 0 0
~300 Diseases and Conditions
20k+ Genes
Blue: gene goes down in diseaseYellow: gene goes up in disease
Human Disease Gene Expression Collection
Butte AJ, Kohane IS. Nature Biotechnology, 2006, 24:55.Butte AJ, Chen R. Proc AMIA Fall Symposium, 2006.Chen R, Butte AJ. Nature Methods, 2007.Dudley J, Tibshirani R, Deshpande T, Butte AJ. Molecular
Systems Biology, 2009.Shen-Orr S, ... Davis MM, Butte AJ. Nature Methods, 2010.
5,178 compounds· 1,300 off-patent FDA-approved drugs· 700 bioactive tool compounds· 2,000+ screening hits (MLPCN and others)3,712 genes (shRNA + cDNA)· targets/pathways of FDA-approved drugs (n=900)· candidate disease genes (n=600)· community nominations (n=500+)15 cell types· Banked primary cell types· Cancer cell lines· Primary hTERT immortalized· Patient derived iPS cells· 5 community nominated
Lamb J, ..., Golub TR. Science, 2006. Sirota M, Dudley JT, ..., Sweet-Cordero A, Sage J, Butte AJ.
Science Translational Medicine, 2011.
Marina SirotaJoel Dudley
Validation methods are increasingly commoditized
Candidate anti-seizure drug against inflammatory bowel disease
Marina SirotaJoel Dudley
Sirota M, Dudley JT, ..., Sweet-Cordero A, Sage J, Butte AJ. Science Translational Medicine, 2011.
Anti-seizure drug works against a rat model of inflammatory bowel disease
Dudley JT, Sirota M, ..., Pasricha J, Butte AJ. Science Translational Medicine, 2011.
Marina SirotaJoel Dudley
Mohan M Shenoy Jay Pasricha
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
Anti-ulcer drug works for lung adenocarcinoma
• Human lung adenocarcinoma cell lines explanted into mouse models
• Followed growth 11 days
• Positive-control doxorubicin grew to 2x original volume
• Tumors in mice treated with vehicle grew to 3.25x original volume
• Not only did our compound work statistically better than control, it worked in a dose-dependent manner
• Tumors in mice treated with 50 mg/kg/day grew 2.8x
• Those treated with 100 mg/kg/day grew only 2.3x.
Joel DudleyMarina Sirota
Julien SageSirota M, Dudley JT,..., Sage J, Butte AJ. Science Translational Medicine, 2011,
Control With Cimetidine
Anti-depressant 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 SageJoel NealNuMedii
Cancer Discovery, 2013.
Drug development
NuMedii lands 1st deal to spin drug data into product gold San Francisco Business Times by Ron Leuty, Reporter
Date: Wednesday, October 3, 2012, 5:30am PDT - Last Modified: Wednesday, October 3, 2012, 6:27am PDT
Ron LeutyReporter- San Francisco Business Times
NuMedii Inc. is looking to make a big difference in drug
development with Big Data.
The Mountain View company co-founded by Stanford
University’s Atul Butte and his wife, former Affymetrix
executive Gini Deshpande, said Wednesday that it inked a
deal to help drug developer Aptalis Pharma Inc. find new
treatments for gastrointestinal disorders and cystic fibrosis.
Stanford University professor and NuMedii
co-founder Atul Butte.
October 3, 2012 4:02 pm by Deanna Pogorelc | 1 Comments
Pairing existing drugs with new disease applications, using not wet labs but
computers, has landed a Stanford startup its first contract with a pharmaceutical
company.
Using data to find new drug-disease matches wins startup NuMedii its first pharma deal
108 million substances x650,000 assays
1 billion points of data within a grid of 70 trillion cells
Five Lessons Learned• Public molecular data has incredible utility
– All public-funded data should eventually become publicly-available
– Consider mechanisms to promote secondary uses and computation
• Sufficient high quality data already exists to impact medicine
– More is better, but no reason to wait for more data
– Should never wait for perfect data, experiment, conditions
– Requiring perfection can even slow secondary use
• It’s not just about infrastructure, it’s about using it
– Too many tools. Those who build platforms use them too!
• Need to train students to initiate science with data
– High school higher education career changers
– Scaling through students
• Entrepreneurship from public-funded data is not a dirty word!
– Academics and industry can coexist and thrive together
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
• National Institutes of Health
• March of Dimes
• Hewlett Packard
• Howard Hughes Medical Institute
• California Institute for Regenerative Medicine
• Scleroderma Research Foundation
• Clayville Research Fund
• PhRMA Foundation
• Stanford Cancer Center, Bio-X
• Tarangini Deshpande
• Kimayani Butte
Admin and Tech Staff
• Susan Aptekar
• Rhonda Pisk
• Alex Skrenchuk