2014 Conte Annual Scientific Retreat Agenda

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 [email protected] ALTMAN, Russ Stanford University Professor [email protected] APRISON, Barry The University of Chicago Education Director [email protected] ARCHER, Chase The University of Chicago Scientific Director [email protected] BAGLEY, Steven Stanford University Research Engineer [email protected] BLAIR, David The University of Chicago MD/PhD Candidate [email protected] BROWN, Adam The University of Chicago PhD Student [email protected] CAMACHO, Camilla The University of Chicago PREP Scholar [email protected] CHEN, Chao University of Illinois at Chicago Associate Professor [email protected] CHEN, Lin The University of Chicago Assistant Professor [email protected] CIRYAM, Prajwal Northwestern University MD/PhD Student p-‐[email protected] COOK, Edwin University of Illinois at Chicago Professor ecook@[email protected] COX, Nancy The University of Chicago Professor [email protected] DAVIS, Lea The University of Chicago Research Associate [email protected]

DENNY, Joshua Vanderbilt University Associate Professor [email protected] FORDE, Martin The University of Chicago Research Technologist [email protected] FOSTER, Ian The University of Chicago Professor [email protected] GERSHON, Elliot The University of Chicago Professor [email protected] GIBBONS, Robert The University of Chicago Professor [email protected] GILETA, Alex The University of Chicago PhD Student [email protected] GONZALES, Natalia The University of Chicago Graduate Student [email protected] GOTTLIEB, Assaf Stanford University Postdoctoral Fellow [email protected] GREENWAY, Matthew The University of Chicago Research Programmer [email protected] GREENAN, Kay The University of Chicago Research Technologist [email protected] GROSSMAN, Robert The University of Chicago Professor [email protected] GUTER, Stephen University of Illinois Project Coordinator [email protected] HEATH, Allison The University of Chicago Research Associate [email protected] IM, Hae Kyung The University of Chicago Research Associate [email protected] JI, Yuan The University of Chicago Associate Professor [email protected] KONG, Sek Won Harvard University Associate Scientist [email protected]

KUMAR, Ravinesh The University of Chicago Research Director [email protected] LAHEY, Benjamin The University of Chicago Principal Investigator [email protected] LI, Jian Northwestern University Postdoctoral Fellow [email protected] LIU, Chun-‐Yu University of Illinois at Chicago Associate Professor [email protected] LYTTLE, Christopher The University of Chicago Director, Methods Core [email protected] MELAMED, Rachel Columbia University PhD Candidate [email protected] MORIMOTO, Richard Northwestern University Professor r-‐[email protected] NICOLAE, Dan The University of Chicago Professor [email protected] OPAL, Mark The University of Chicago Postdoctoral Fellow [email protected] PALMER, Abraham The University of Chicago Associate Professor [email protected] PATTERSON, Maria The University of Chicago Postdoctoral Fellow [email protected] PERCHA, Bethany Stanford University PhD Candidate [email protected] PITT, Jason The University of Chicago PhD Student [email protected] PRILUTSKY, Daria Harvard University Postdoctoral Fellow [email protected] RAMAKER, Marcia The University of Chicago Postdoctoral Fellow [email protected]

REED, Patrick The University of Chicago PhD Student [email protected] RICE, John University of Washington in St. Louis Professor [email protected] RZHETSKY, Andrey The University of Chicago Professor [email protected] SEBAT, Jonathan University of California San Diego Associate Professor [email protected] SENGUPTA, Subhajit NorthShore University HealthSystem Postdoctoral Fellow [email protected] SHAH, Kaanan The University of Chicago Postdoctoral Fellow [email protected] SHAH, Nigam Stanford University Assistant Professor [email protected] SOMEKH, Judith University of Haifa, Israel Postdoctoral Fellow [email protected] STALLCUP, Kathyrn Chicago Biomedical Consortium Executive Director k-‐[email protected] SULLIVAN, Patrick The University of North Carolina at Chapel Hill Professor [email protected] WANG, Kanix The University of Chicago PhD Candidate [email protected] WHITE, Kevin The University of Chicago Professor [email protected] ZHU, Yitan NorthShore University HealthSystem Research Scientist [email protected]

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

Documents

2014 Conte Annual Scientific Retreat Agenda