Download Clinical Decisions

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
•
cBioPortal Development now
shared across 5 teams : DFCI,
MSKCC, Princess Margaret, and
CHOP, the Hyve
•
Lowers barrier to access and
visualize complex genomic
data for research
•
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
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.
Used Extensively
at MSKCC with
> 5000 Users a
week
Data and Application
Usage
MSKCC currently
houses a number of
data sources.
SU2C
CBTTC
TARGET
EGA/dbGaP
Used Extensively
at MSKCC with
> 5000 Users a
week
BUT WE ARE
ADDING MORE
Key Functionality &
Features
cBioPortal+ has a number of visualizations based on
one of three entry points
Study View
Sample View
Gene View
Display of frequent /
recurrent mutations or
lesions within a study
Get an overview of all of
a patients genetic lesions,
connections to Path
Reports, clinical trials,
drugs, etc..
Look at gene data (mutation
/ expression etc..) across or
within study
When creating virtual cohorts of molecular
subtypes will be able to
quickly identify
“potental” drivers
Has COSMIC data as well
as internal statistics to aid
in determining if a
mutation is likely causal
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
Sample View
Gene View
Display of frequent /
recurrent mutations or
lesions within a study
Get an overview of all of
a patients genetic lesions,
connections to Path
Reports, clinical trials,
drugs, etc..
Look at gene data (mutation
/ expression etc..) across or
within study
When creating virtual cohorts of molecular
subtypes will be able to
quickly identify
“potental” drivers
Has COSMIC data as well
as internal statistics to aid
in determining if a
mutation is likely causal
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
Median
Tumor
Expression
P-value,
Tumor vs
Normal
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
PPI Networks
Correlation
Mutual Exclusivity
Key Functionality &
Features
cBioPortal+ has a number of visualizations based on
one of three entry points
Study View
Sample View
Gene View
Display of frequent /
recurrent mutations or
lesions within a study
Get an overview of all of
a patients genetic lesions,
connections to Path
Reports, clinical trials,
drugs, etc..
Look at gene data (mutation
/ expression etc..) across or
within study
When creating virtual cohorts of molecular
subtypes will be able to
quickly identify
“potental” drivers
Has COSMIC data as well
as internal statistics to aid
in determining if a
mutation is likely causal
Correlate genes to other
genes within a study or
compare to normal tissue
expression
Can be used to identify
targets for
immunotherapy
Summary Page
Overview
Recurrent
Mutations
Recurrent
CNV
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
Sample View
Gene View
Display of frequent /
recurrent mutations or
lesions within a study
Get an overview of all of
a patients genetic lesions,
connections to Path
Reports, clinical trials,
drugs, etc..
Look at gene data (mutation
/ expression etc..) across or
within study
When creating virtual cohorts of molecular
subtypes will be able to
quickly identify
“potental” drivers
Has COSMIC data as well
as internal statistics to aid
in determining if a
mutation is likely causal
Correlate genes to other
genes within a study or
compare to normal tissue
expression
Can be used to identify
targets for
immunotherapy
Patient Summary Page
Add to
Harvest
Cart
Mutation
& CNA
table
Clinical Trials
and additional
tabs
Genome
View
Patient View
Harvest Cart Integration
Samples Added to the
bucket can be accessed via
the HARVEST CART tab
Clicking submit takes you
to CBTTC Harvest
application with desired
samples loaded
Patient View
Drugs Tab
Gene Target & FDA approval
Gene Target
also listed
Other Patient View Visuals
Tissue Images
Pathology Report
Clinical Data
Data
Group
User
Security & Authentication
CBTTC
Data Set 1
Data Set 2
User Authentication
Provided by Google
SU2C
Public
Data Set 3
Data Set 4
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