1. NCI’s Genomics Data Commons (GDC) & NCI Cloud Pilots
9/15/2018
NCI’s Genomics Data Commons (GDC) & NCI Cloud Pilots
Tanja Davidsen, PhD
NCI Center for Biomedical Informatics and IT
March, 2017
National Cancer Institute

3. The NCI Genomic Data Commons
Provide the cancer research community with a unified data repository that enables data sharing across cancer genomic studies in support of precision medicine
One of the NCI resources supporting this vision in the NCI Genomics Data Commons which will provide….

4. The NCI Genomic Data Commons
Support the receipt, quality control, integration, storage, and redistribution of standardized genomic data sets derived from cancer research studies
Available data
NCI Funded cancer genomics datasets
User submissions
Data searching and retrieval/downloading
Harmonization of raw sequence (alignment and variant calling) of all GDC data
Application of state-of-the-art methods of generating derived data
Developed, supported, and hosted by U. Chicago
The GDC achieves this goal
knowledge network supporting the import and standardization of genomic and clinical data from cancer research programs.
Genomic Data Commons

5. NCI Genomic Data Commons
a unified data repository for the research community
NCI Genomic Data Commons
Data Storage
Retrieval, Submission, & Harmonization
Researchers

6. NCI Genomic Data Commons
The GDC went live on June 6, 2016 with approximately 4.1 PB of data.
This includes:
2.6 PB of legacy data
1.5 PB of “harmonized” data
577,878 files about cases (patients), in 42 cancer types, across 29 primary sites.
10 major data types, ranging from Raw Sequencing Data, Raw Microarray Data, to Copy Number Variation, Simple Nucleotide Variation and Gene Expression.
Data are derived from 17 different experimental strategies, with the major ones being RNA- Seq, WXS, WGS, miRNA-Seq, Genotyping Array and Expression Array.
Foundation Medicine announced the release of 18,000 genomic profiles to the GDC at the Cancer Moonshot Summit.

7. GDC: Data Submission & Harmonization
Data Harmonization

8. GDC: Data Retrieval GDC Website Data Transfer Tool Data Portal
Visualization Tools
Legacy Archive {
"data": {
"hits": [
{"project_id": "TCGA-SKCM”,"primary_site": "Skin”}
, {"project_id": "TCGA-PCPG”,"primary_site": "Nervous System”}
, {"project_id": "TCGA-LAML”,"primary_site": "Blood”}
, {"project_id": "TCGA-CNTL”,"primary_site": "Not Applicable”}
, {"project_id": "TCGA-UVM”,"primary_site": "Eye”}
GDC API
API URL
Endpoint
URL parameters
Query parameters 8

9. Content in the Genomic Data Commons
TCGA ,353 cases
TARGET ,178 cases
Current
~58,000 cases
Foundation Medicine 18,000 cases
Cancer studies in dbGaP ~4,000 cases
MMRF ~1,000 cases
Coming soon
NCI-MATCH ~3,000 cases
Clinical Trial Sequencing Program ~3,000 cases
Planned (1-3 years)
Cancer Driver Discovery Program ~5,000 cases
Human Cancer Model Initiative ~1,000 cases
APOLLO – VA and DoD ~8,000 cases
GDC launched with two of the major NCI genomic data sets, TCGA and TARGET.

10. The NCI Cancer Genomics Cloud Pilots
Understanding how to meet the research community’s need to analyze large-scale cancer genomic and clinical data

11. NCI Cancer Genomics Cloud Pilots
Cloud Pilots provide:
Access to large genomic data sets without need to download
Access to popular pipelines and visualization tools
Ability for researchers to bring their own tools and pipelines to the data
Ability for researchers to bring their own data and analyze in combination with NCI genomic data
Workspaces, for researchers to save and share their data and results of analyses
Democratize access to NCI-generated genomic and related data, and to create a cost-effective way to provide scalable computational capacity to the cancer research community.
These pilots were initiated two years ago based on our awareness that the traditional model of data download and management by every research group was no longer scalable and the NCI wanted to explore the effectiveness of co-locating data and compute in a cloud environment for access and analysis. The overall goals is to…..

12. NCI Genomic Data Commons
GDC/Cloud Pilot Ecosystem
Researchers
Broad FireCloud
ISB CGC
SBG CGC
Cancer
Genomic Data
NCI Genomic Data Commons
NCI Cloud Pilots
Data Storage
Retrieval, Submission, & Harmonization
Data Compute
Analysis, Workflows, & Pipelines

13. Three NCI Genomics Cloud Pilots
PI: Gad Getz
Google Cloud
Firehose in the cloud including Broad best practices workflows
Broad Institute
PI: Ilya Shmulevich
Leverage Google infrastructure; Novel query and visualization
Institute for Systems Biology
PI: Deniz Kural
Amazon Web Services
Interactive data exploration; > 30 public pipelines
Seven Bridges Genomics

14. Broad Institute Cloud Pilot
Targeted at users performing analyses at scale.
Modeled after their Firehose analysis infrastructure developed for the TCGA program.
Users can upload their own data and tools and/or run the Broad’s best practice tools and pipelines on pre-loaded data.

15. Institute for Systems Biology Cloud Pilot
Closely tied with Google Cloud Platform tools including BigQuery, App Engine, Cloud Datalab, Google Genomics, and Compute Engine
Level-3 TCGA data in BigQuery allows fast SQL-like queries across the entire dataset
Web interface allows scientists to interactively compare and define cohorts
PI / Biologist
web access
Computational Research Scientist
Python, R, SQL
Algorithm Developer
ssh, programmatic access
ISB-CGC Web App
Google Cloud Console
Google APIs
ISB-CGC APIs
Compute Engine VMs
Cloud
Storage
BigQuery
Genomics
Local Storage
ISB-CGC
Hosted Data
Controlled-Access Data
Open-Access Data
User Data

16. Seven Bridges Genomics Cloud Pilot
Built upon the SBG commercial cloud-based genomics platform
Graphical query interface to identify hosted data of interest
Includes a native implementation of the Common Workflow Language specification for creating user-defined workflows

17. Timeline & Extension
Selection
Design/Build I
Design/Build II
Evaluation
Extension
Jan 2014
Sept 2014
April 2015
Jan 2016
Sept 2016
One year contract extension for all three NCI Cloud Pilots
Continue to make all current tools and data available for an additional year
Build on the tools/analyses available
Continue to make the platform, pipeline, and tools portable (Dockerization, Workflow languages - CWL/WDL)
New datasets added (including pediatric cancer data)
New datatypes added: Proteomics, Imaging data, multiple genome builds
Overall ~2.5 PB of data in extension

18. Community Evaluation of the Cloud Pilots
Cloud Credits
Storage and compute credits are available to researchers through a tiered system to use the Cloud Pilots
Grant supplements
Support NCI grantees to serve as beta-testers and conduct genomic analysis relevant to their research on one or more Cloud Pilots
DREAM Challenge
Crowd-based competition to identify the optimal methods for detecting and quantifying mRNA fusions and isoforms from RNA-Seq data