Pichai Raman on behalf of cBioPortal Team Wednesday, May 25, 16 cBioPortal+ Cancer Visualization & Analytics Application for Research | Translational Science | Clinical Decisions Pichai Raman on behalf of cBioPortal Team Wednesday, May 25, 16

Outline History& Overview Data and Application usage Key Functionality & Features Security & Authentication Coming Attractions

History & Overview Original cBioPortal developed at MSKCC for TCGA data and other large-scale cancer profiling efforts Lowers barrier to access and visualize complex genomic data for research cBioPortal Development now shared across 5 teams : DFCI, MSKCC, Princess Margaret, and CHOP, the Hyve cBioPortal+ : CHOP Implementation has a focus on Pediatric cancer data sets

History & Overview Excels at visualization & presentation of multiple data types in an integrated manner

Data and Application Usage Used Extensively at MSKCC with > 5000 Users a week Type Total MSKCC CHOP Studies 113 91 22 Samples 24026 21334 2692 Data sets are being added on a weekly basis from various sources. Processed through reproducible best practice pipelines.

Data and Application Usage MSKCC currently houses a number of data sources. Used Extensively at MSKCC with > 5000 Users a week SU2C CBTTC BUT WE ARE ADDING MORE TARGET EGA/dbGaP

Key Functionality & Features cBioPortal+ has a number of visualizations based on one of three entry points Study View Display of frequent / recurrent mutations or lesions within a study When creating virtual co-horts of molecular subtypes will be able to quickly identify “potental” drivers Sample View Get an overview of all of a patients genetic lesions, connections to Path Reports, clinical trials, drugs, etc.. Has COSMIC data as well as internal statistics to aid in determining if a mutation is likely causal Gene View Look at gene data (mutation / expression etc..) across or within study Correlate genes to other genes within a study or compare to normal tissue expression Can be used to identify targets for immunotherapy

Key Functionality & Features cBioPortal+ has a number of visualizations based on one of three entry points Study View Display of frequent / recurrent mutations or lesions within a study When creating virtual co-horts of molecular subtypes will be able to quickly identify “potental” drivers Sample View Get an overview of all of a patients genetic lesions, connections to Path Reports, clinical trials, drugs, etc.. Has COSMIC data as well as internal statistics to aid in determining if a mutation is likely causal Gene View Look at gene data (mutation / expression etc..) across or within study Correlate genes to other genes within a study or compare to normal tissue expression Can be used to identify targets for immunotherapy

Mutation Lollipop View Recurrent hotspot identification Height indicates frequency Annotates with COSMIC, cBioPortal Frequencies, and predicts whether mutation event is damaing

Tumor vs Normal Immunotherapy Target Discovery Color indicates significance P-value Cutoff P-value, Tumor vs Normal Median Tumor Expression Visualization for RNA-Seq or Microarray data, with ability to look at raw, log, or z-score normalizations and p-value showing differential

Other Gene View Visuals Mutual Exclusivity Correlation PPI Networks

Key Functionality & Features cBioPortal+ has a number of visualizations based on one of three entry points Study View Display of frequent / recurrent mutations or lesions within a study When creating virtual co-horts of molecular subtypes will be able to quickly identify “potental” drivers Sample View Get an overview of all of a patients genetic lesions, connections to Path Reports, clinical trials, drugs, etc.. Has COSMIC data as well as internal statistics to aid in determining if a mutation is likely causal Gene View Look at gene data (mutation / expression etc..) across or within study Correlate genes to other genes within a study or compare to normal tissue expression Can be used to identify targets for immunotherapy

Descriptive statistics on cohort Summary Page Overview Recurrent CNV Recurrent Mutations Descriptive statistics on cohort

Selection of Samples Survival Plot Select Genes and all samples with a mutation become a group for Survival Plot

Clinical Data Table Tabular view to find Samples Clinical data sortable and searchable Can click on sample to get to sample view

Key Functionality & Features cBioPortal+ has a number of visualizations based on one of three entry points Study View Display of frequent / recurrent mutations or lesions within a study When creating virtual co-horts of molecular subtypes will be able to quickly identify “potental” drivers Sample View Get an overview of all of a patients genetic lesions, connections to Path Reports, clinical trials, drugs, etc.. Has COSMIC data as well as internal statistics to aid in determining if a mutation is likely causal Gene View Look at gene data (mutation / expression etc..) across or within study Correlate genes to other genes within a study or compare to normal tissue expression Can be used to identify targets for immunotherapy

Clinical Trials and additional tabs Patient Summary Page Add to Harvest Cart Mutation & CNA table Clinical Trials and additional tabs Genome View

Patient View Harvest Cart Integration Clicking submit takes you to CBTTC Harvest application with desired samples loaded Samples Added to the bucket can be accessed via the HARVEST CART tab

Gene Target & FDA approval also listed Patient View Drugs Tab Gene Target Gene Target & FDA approval also listed

Other Patient View Visuals Tissue Images Pathology Report Clinical Data

Security & Authentication User User Authentication Provided by Google Group CBTTC SU2C Public Data Set 1 Data Set 2 Data Set 3 Data Set 4 Data

Coming Attractions Timeline – Multiple samples per patient Support for PDX Variant Annotation & Prioritization More simplified clinical interface Isoform level information Connection to raw data and processing pipelines 30+ Active Developers from CHOP, MSKCC, DFCI, Princess Margeret, and the Hyve

Acknowledgements cBioPortal Consortium MSKCC DFCI Princess Margeret The Hyve CBTTC Collaborators Adam Resnick Alex Felmeister Tyler Rivera Jena Lilly Angela Waanderers Philip Allman CHOP cBioPortal+ Team Karthik Kalletla Anna Lu Kaitlyn Money CHOP/DBHi Collaborators Deanne Taylor Asif Chinwalla John Maris & SU2C

Thank You Visit Us : www.cbioportalplus.org Follow Us : @cBioPortal_Plus