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APPLYING INTEGRATED INFORMATICS AND MODELING TO PREDICT GENETIC AND ENVIRONMENTAL FACTORS UNDERLYING MENTAL HEALTH AND ILLNESS
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The Conte Center for Computational Neuropsychiatric Genomics is a cross-‐disciplinary and multi-‐institutional effort involving seven universities that include The University of Chicago, Northwestern University, The University of Illinois at Chicago, Harvard University, Stanford University, Columbia University, and the University of Haifa in Israel. The overarching goal of the Center is to identify the genetic and environmental risk and protective factors that underlie mental health and disease, including autism, schizophrenia, bipolar disorder, major depression, anxiety disorder, and psychopathology. Our team develops and applies drastically new mathematical and computational strategies to infer causal relationships among genetic variation, environmental variables and psychiatric phenotypes. We achieve this by combining the statistical power of large genetic and pharmacogenomic datasets, text-‐mining strategies and review of electronic medical records. Computational predictions are then experimentally validated using high-‐throughput biochemical, genomic and proteomic strategies, as well as the development of in vitro and animal models.
CONTE LEADERSHIP
ALTMAN, Russ Stanford University APRISON, Barry The University of Chicago COOK, Edwin H. Jr. University of Illinois at Chicago COX, Nancy The University of Chicago GERSHON, Elliot The University of Chicago GROSSMAN, Robert The University of Chicago KOHANE, Isaac Harvard University KUMAR, Ravinesh The University of Chicago LAHEY, Benjamin The University of Chicago LIU, Chunyu University of Illinois at Chicago MORIMOTO, Richard Northwestern University NICOLAE, Dan The University of Chicago PELEG, Mor University of Haifa RABADAN, Raul Columbia University RZHETSKY, Andrey The University of Chicago SHAH, Nigam Stanford University STRANGER, Barbara The University of Chicago WHITE, Kevin The University of Chicago
CONTE SCIENTIFIC ADVISORY BOARD 2014
DENNY, Joshua Vanderbilt University EGGAN, Kevin Harvard University RICE, John Washington University in St. Louis SEBAT, Jonathan University of California San Diego SULLIVAN, Patrick University of North Carolina at Chapel Hill
SCHEDULE AT A GLANCE Mon, May 5, 2014 (Hyatt Hyde Park, 5225 S Harper Ave) 7:00-‐9:00 Kick-‐Off Reception Tues, May 6, 2014 (International House at The University of Chicago, 1414 E 59th St) 8:30-‐9:15 Continental Breakfast (Home Room) 9:15-‐9:30 Opening Remarks (Assembly Hall)
Welcome (Ravinesh Kumar) / Round-‐table Introductions 9:30-‐11:00 Project and Core Updates and Highlights (Assembly Hall)
9:30-‐10:00 Project 4: Integrated Informatics (Andrey Rzhetsky, UChicago) 10:00-‐10:30 Project 3: Molecular Networks (Nancy Cox, UChicago) 10:30-‐11:00 Project 2: Electronic Health Records (Nigam Shah, Stanford)
11:00-‐11:10 Coffee Break 11:10-‐12:10 Project and Core Updates and Highlights (Assembly Hall)
11:10-‐11:40 Project 1: Pharmacogenomics (Russ Altman, Stanford) 11:40-‐12:10 Core C: Mental Health Phenotypes (Robert Gibbons, UChicago) 12:10-‐12:15 Rapid Fire Poster Highlights 12:15-‐1:00 Lunch (Home Room) / Poster Session (Assembly Hall) 1:00-‐1:30 Open Meetings 1:30-‐3:00 Core Updates and Highlights (Assembly Hall)
1:30-‐2:00 Core C: RNAi in Human Neurons (Kevin White, UChicago) 2:00-‐2:30 Core C: CRISPR in C. Elegans (Rick Morimoto, Northwestern) 2:30-‐3:00 Core B: Conte Data Cloud (Robert Grossman, UChicago)
3:00-‐3:05 Rapid Fire Platform Highlights (Assembly Hall) 3:05-‐3:15 Coffee Break 3:15-‐4:15 P50 Next Round Planning Meeting (Coulter Lounge) 3:15-‐4:15 Conte Cloud Workshop (Assembly Hall) 4:15-‐6:00 Open Meetings 6:00-‐9:00 Dinner (Pizza Capri, 1501 East 53rd St, Chicago) Wed, May 7, 2014 (International House at The University of Chicago, 1414 E 59th St) 8:30-‐9:30 Continental Breakfast 9:30-‐9:45 Core Updates and Highlights (Assembly Hall)
9:30–9:45 Core A: Education and Outreach (Barry Aprison, UChicago) 9:45-‐11:00 Conte Trainee Talks (Assembly Hall) 9:45-‐10:00 Kaanan Shah (UChicago) 10:00-‐10:15 Bethany Percha (Stanford) 10:15-‐10:30 Rachel Melamed (Columbia) 10:30-‐10:45 Assaf Gottlieb (Stanford) 10:45-‐11:00 Judith Somekh (UHaifa) 11:00-‐11:15 Coffee Break 11:15-‐12:00 Conte Associates Talks (Assembly Hall) 11:15-‐11:30 Lea Davis (UChicago) 11:30-‐11:45 Sek Won Kong (Harvard) 11:45-‐12:00 Steven Bagley (Stanford) 12:00-‐1:00 Lunch 12:30-‐1:00 Scientific Advisory Board (SAB) Meeting (Tiffin Room) 1:00-‐1:30 SAB Evaluation Meeting with Project/Core Leaders (Tiffin) 1:30 Closing Reception (Home Room)
FULL SCHEDULE Monday May 5, 2014 Kick-‐off Reception, Hyatt Hyde Park | 5225 S. Harper Ave, Chicago IL Tuesday May 6, 2014 International House at The University of Chicago | 1414 E. 59th St, Chicago IL 8:30-‐9:15 Continental Breakfast (Home Room) 9:15-‐9:30 Opening Remarks (Assembly Hall) Welcome Ravinesh Kumar, PhD, Conte Director of Research, The University of Chicago Round-‐table Introductions 9:30-‐11:00 am Project and Core Updates and Highlights (Assembly Hall) 9:30-‐10:00 am Project 4: Integrated Modeling of Multiple Data Types Andrey Rzhetsky, PhD, The University of Chicago 10:00-‐10:30 Project 3: Data Integration and Disease Risk Modeling in the Context of Molecular Networks and Genetic Associations Nancy Cox, PhD, The University of Chicago 10:30-‐11:00 Project 2: Modeling the Temporal Succession of Phenotypes and Environmental Cues Nigam Shah, PhD, Harvard University 11:00-‐11:10 Coffee Break (Assembly Hall) 11:10-‐12:10 Project and Core Updates and Highlights (Assembly Hall) 11:10-‐11:40 Project 1: A Comprehensive Network of Neuropsychiatric Drugs-‐Genes-‐Phenotypes Russ Altman, MD, PhD, Stanford University 11:40-‐12:10 Core C: The Future of Mental Health Measurements: Computerized Adaptive Tests Robert Gibbons, PhD, The University of Chicago 12:10-‐12:15 Rapid Fire Poster Highlights (Assembly Hall) 12:15-‐1:00 Lunch (Home Room) | Poster Session (Assembly Hall)
FULL SCHEDULE (continued) 1:00-‐1:30 Open Meetings 1: 30-‐3:00 Core Updates and Highlights (Assembly Hall) 1:30-‐2:00 Core C: Combinatorial RNAi in Human Neurons Kevin White, PhD, The University of Chicago 2:00-‐2:30 Core C: CRISPR Technology in C. Elegans Rick Morimoto, PhD, Northwestern University 2:30-‐3:00 Core B: High Performance Informatics & Conte Protected Data Cloud Robert Grossman, PhD, The University of Chicago 3:00-‐3:05 Rapid Fire Platform Highlights (Assembly Hall) 3:05-‐3:15 Coffee Break (Assembly Hall) 3:15-‐4:15 P50 Next Round Planning Meeting (Coulter Room) 3:15-‐4:15 Conte Cloud Workshop (Assembly Hall) 4:15-‐6:00 Open Meetings 6:00-‐-‐9:00 Dinner Pizza Capri (1501 East 53rd St, Chicago) Tuesday May 6, 2014 International House at The University of Chicago | 1414 E. 59th St, Chicago IL 8:30-‐9:30 Continental Breakfast (Home Room) 9:30-‐9:45 Core Updates and Highlights (Assembly Hall) 9:30-‐9:45 Core A: Education, Training and Outreach Initiatives Barry Aprison, PhD, The University of Chicago 9:45-‐11:00 Conte Trainee Talks (Assembly Hall) 9:45-‐10:00 Unique Patterns of Variability Around Mendelian Genes Kaanan Shah, PhD, The University of Chicago
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FULL SCHEDULE (continued) 10:00-‐10:15 A Fast and Flexible Approach to the Discovery of Relationships in Biomedical Text Bethany Percha, PhD Candidate, Stanford University 10:15-‐10:30 Discovery of Seasonal Patterns in Incidence of Disease from EHR Data and Comparison Between Hospital Systems Rachel Melamed, PhD Candidate, Columbia University 10:30-‐10:45 Drug Side Effects: How to Predict Them and How to Deal with So Many Predictions Assaf Gottlieb, PhD, Stanford 10:45-‐11:00 Using Dynamic Model-‐Based Systems Biology for Exploring the ASD-‐IBD Connection Judith Somekh, PhD, University of Haifa, Israel 11:00-‐11:15 Coffee Break (Assembly Hall) 11:15-‐12:00 Conte Associates Talks (Assembly Hall) 11:15-‐11:30 Defining the Inverse Axis of Risk in Complex Traits Lea Davis, PhD, The University of Chicago 11:30-‐11:45 Reducing False Positive Incidental Findings with Ensemble Genotyping and Logistic Regression-‐Based Variant Filtering Methods Sek Won Kong, PhD, Harvard University 11:45-‐12:00 Comparing Disease Synergism and Protection in Two Electronic Medical Record Systems using Inferred Genetic Overlap Steven Bagley, MD, Stanford University 12:00-‐1:00 Lunch (Home Room) 12:30-‐1:00 Scientific Advisory Board (SAB) Meeting (Tiffin Room) 1:00-‐1:30 SAB Evaluation Mtg w/ Project & Core Leaders (Tiffin Rm) 1:30 Closing Reception (Home Room)
POSTERS AT A GLANCE (Poster Board #) #1 ALLIEY-‐RODRIGUEZ, Ney The University of Chicago
Copy Number Variants and their Impact on Counseling for Mental Disorders #2 APRISON, Barry The University of Chicago Conte Center Education, Outreach, and Training Initiatives #3 ARCHER, Chase The University of Chicago The MicroWestern Array for Analysis of Protein Targets #4 CHEN, Chao Central South University China
Integration of miRNA-mRNA Networks to Elucidate the Molecular Complexity of Psychiatric Disorders
#5 CHEN, Lin The University of Chicago
A Unified Framework for Two-Stage Gene-Environment Interaction Tests with Adaptive Filtering
#6 CIRYAM, Prajwal Northwestern University
Proteome Metastability in Health, Aging, and Disease #7 COOK, Edwin H., Jr. University of Illinois at Chicago
Heterogeneity in 5-Httlpr Genotype-Phenotype Effects #8 COOK, Edwin H., Jr. University of Illinois at Chicago Pharmacogentics Study of Serotonin Transporter and 5HT2A Genotype in Autism #9 FORDE, Martin The University of Chicago
High-Throughput Combinatorial RNAi Screening in Human Neurons to Validate Candidate Genes for Neuropsychiatric Disorder
#10 GILETA, Alex The University of Chicago Genome-wide Association Study of Incentive Salience in Outbred Rats #11 GRENNAN, Kay The University of Chicago
Molecular Network Analysis Enhances Understanding of the Biology of Mental Disorders
#12 GUTER, Steve University of Illinois at Chicago
The Autism Diagnostic Observation Schedule, Module 4: Revised Algorithm and Standardized Severity Scores-A Replication Study in an NDAR sample
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#13 GUTER, Steve University of Illinois at Chicago National Database for Autism Research (NDAR): An Overview
#14 IM, Hae Kyung The University of Chicago
Predicting the Transcriptome to Probe the Biology of Complex Traits - PrediXcan #15 LI, Jian Northwestern University HSF1 Controls Two Proteostasis Networks Essential for Development #16 LYTTLE, Christopher The University of Chicago Introduction to MarketScan®
#17 OPAL, Mark The University of Chicago RAMAKER, Marcia Selective Serotonin 2C Receptor Antagonists Induce Fast-Acting Antidepressant Effects and Neuronal Remodeling
#18 PATTERSON, Maria The University of Chicago
The Conte Protected Data Cloud (Conte-PDC): A Secure Cloud Architecture Enabling Analysis of Big Data for the Neuropsychiatric Genomics Community
#19 PRILUTSKY, Daria Harvard University
Gene Expression as a Higher-Throughput Readout for iPSC-Derived Neurons to Study Autism
#20 SENGUPTA, Subhajit NorthShore University Health System
Are Normal Cells Mosaic?-A Statistical Model for Cell Genomes #21 SHAH, Nigam Stanford University
Common & Distinct Patient-Reported Symptoms in Autism & Schizophrenia: Preliminary Findings from PatientsLikeMe, an Online Patient-Powered Research Network (PPRN)
#22 ZHU, Yitan NorthShore University Health System
Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data
PARTICIPANT LIST ALLIEY-‐RODRIGUEZ, Ney The University of Chicago Research Associate nalliey@bsd.uchicago.edu ALTMAN, Russ Stanford University Professor russ.altman@stanford.edu APRISON, Barry The University of Chicago Education Director baprison@bsd.uchicago.edu ARCHER, Chase The University of Chicago Scientific Director ctarcher@uchicago.edu BAGLEY, Steven Stanford University Research Engineer steven.bagley@stanford.edu BLAIR, David The University of Chicago MD/PhD Candidate daveblair@uchicago.edu BROWN, Adam The University of Chicago PhD Student asbrown16@gmail.com CAMACHO, Camilla The University of Chicago PREP Scholar cbcamacho@peds.bsd.uchicago.edu CHEN, Chao University of Illinois at Chicago Associate Professor chenchaor@gmail.com CHEN, Lin The University of Chicago Assistant Professor lchen@health.bsd.uchicago.edu CIRYAM, Prajwal Northwestern University MD/PhD Student p-‐ciryam@fsm.northwestern.edu COOK, Edwin University of Illinois at Chicago Professor ecook@psych@uic.edu COX, Nancy The University of Chicago Professor ncox@bsd.uchicago.edu DAVIS, Lea The University of Chicago Research Associate lea.k.davis@gmail.com
DENNY, Joshua Vanderbilt University Associate Professor josh.denny@vanderbilt.edu FORDE, Martin The University of Chicago Research Technologist mforde84@gmail.com FOSTER, Ian The University of Chicago Professor foster@anl.gov GERSHON, Elliot The University of Chicago Professor egershon@yoda.bsd.uchicago.edu GIBBONS, Robert The University of Chicago Professor rdg@uchiacgo.edu GILETA, Alex The University of Chicago PhD Student alex.gileta@gmail.com GONZALES, Natalia The University of Chicago Graduate Student ngon@uchicago.edu GOTTLIEB, Assaf Stanford University Postdoctoral Fellow assafgo@stanford.edu GREENWAY, Matthew The University of Chicago Research Programmer mgreenway@uchiago.edu GREENAN, Kay The University of Chicago Research Technologist kgrennan@uchicago.edu GROSSMAN, Robert The University of Chicago Professor robert.grossman@uchicago.edu GUTER, Stephen University of Illinois Project Coordinator sguter@psych.uic.edu HEATH, Allison The University of Chicago Research Associate aheath@uchicago.edu IM, Hae Kyung The University of Chicago Research Associate haky@uchicago.edu JI, Yuan The University of Chicago Associate Professor YJi@health.bsd.uchicago.edu KONG, Sek Won Harvard University Associate Scientist swkong@enders.tch.harvard.edu
KUMAR, Ravinesh The University of Chicago Research Director rakumar@uchicago.edu LAHEY, Benjamin The University of Chicago Principal Investigator blahey@heath.bsd.uchiago.edu LI, Jian Northwestern University Postdoctoral Fellow jian.li@northwestern.edu LIU, Chun-‐Yu University of Illinois at Chicago Associate Professor liucy@uic.edu LYTTLE, Christopher The University of Chicago Director, Methods Core clyttle@bsd.uchicago.edu MELAMED, Rachel Columbia University PhD Candidate rdm2114@columbia.edu MORIMOTO, Richard Northwestern University Professor r-‐morimto@northwestern.edu NICOLAE, Dan The University of Chicago Professor nicolae@galton.uchicago.edu OPAL, Mark The University of Chicago Postdoctoral Fellow mopal@uchicago.edu PALMER, Abraham The University of Chicago Associate Professor aap@uchicago.edu PATTERSON, Maria The University of Chicago Postdoctoral Fellow maria.t.patterson@gmail.com PERCHA, Bethany Stanford University PhD Candidate blpercha@stanford.edu PITT, Jason The University of Chicago PhD Student pittjj@uchicago.edu PRILUTSKY, Daria Harvard University Postdoctoral Fellow Daria_Prilutsky@hms.harvard.edu RAMAKER, Marcia The University of Chicago Postdoctoral Fellow mjramaker@uchicago.edu
REED, Patrick The University of Chicago PhD Student pjr314@gmail.com RICE, John University of Washington in St. Louis Professor john@zork.wustl.edu RZHETSKY, Andrey The University of Chicago Professor arzhetsk@medicine.bsd.uchicago.edu SEBAT, Jonathan University of California San Diego Associate Professor jsebat@ucsd.edu SENGUPTA, Subhajit NorthShore University HealthSystem Postdoctoral Fellow subhajit06@gmail.com SHAH, Kaanan The University of Chicago Postdoctoral Fellow kshah2@medicine.bsd.uchicago.edu SHAH, Nigam Stanford University Assistant Professor nigam@stanford.edu SOMEKH, Judith University of Haifa, Israel Postdoctoral Fellow ysomekh@gmail.com STALLCUP, Kathyrn Chicago Biomedical Consortium Executive Director k-‐stallcup@northwestern.edu SULLIVAN, Patrick The University of North Carolina at Chapel Hill Professor patrick_sullivan@med.unc.edu WANG, Kanix The University of Chicago PhD Candidate kanixwang@uchicago.edu WHITE, Kevin The University of Chicago Professor kpwhite@uhicago.edu ZHU, Yitan NorthShore University HealthSystem Research Scientist zhuyitan@gmail.com
CONTE PROTECTED DATA CLOUD WORKSHOP Allison Heath, Ph.D. and Ney Alliey-‐Rodriguez, Ph.D. (The University of Chicago) May 6, 2014; 3:15-‐4:15 pm This workshop will introduce participants to the fully-‐up and operational Conte Cloud that is available to all Conte investigators. The Conte Cloud is a Bionimbus based cloud computing infrastructure that is currently comprised of 200 cores and 225 terabytes of raw storage. Topics discussed at this working group may include:
• What resources are available? How to gain access to the Conte Cloud? How to upload your own data to the Conte Cloud?
• How does cloud computing differ from standard clusters; how does the Conte Cloud differ from other cloud resources?; security and computing over protected data
• Basic workflow; logging into the Open Science Data Cloud console; launching VM; SSH to VM; computing
• Discussion of data sets available to all users: metadata and query services • What analysis programs and tools are of general interest to the Conte
community?; interest in community-‐maintained VMS? • Can we implement a pipeline for all NHGRI GWAS result to test for
enrichment with every GWAS? • General discussion on next steps, expansion, and new features
ACKNOWLEDGMENTS
Funding Agencies • National Institute of Health; P50MH9467 • Chicago Biomedical Consortium; L-‐004 • Psychiatric Genetics Training Grant; NIH T32 GM07197
Scientific Program • Ravinesh Kumar, Russ Altman, Kevin White, Andrey Rzhetsky
Program Booklet
• Ravinesh Kumar
Scientific Advisory Board • John Rice, Patrick Sullivan, Jonathan Sebat, Kevin Eggan, Joshua Denny
Event Management • Patty Coen, Great Chicago Events • Elena Menarini, Great Chicago Events
International House
• Jeanette Drake • Patricia Guadalupe Nieves
Audio-‐Visual Assistance • Anthony Vieceli, Plus One AV
Catering
• Rachel Brown, Phoenix Catering
Pizza Capri • Max Taleb
Hyatt Place
• Briana Pickett
Program Editing • Martin Forde
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