1. www.bioinformatics.ca NCRI Cancer Conference November 1, 2015

2. 2Module #: Title of Module

3. NCRI Workshop 2015 bioinformatics.ca The ICGC Data Portal Part 1: Data submission, processing and release

4. NCRI Workshop 2015 bioinformatics.ca ICGC Data Release Cycle Release 1 Data files Submission and Validation Time Data Annotation & ETL Sign off Portal Release Release 2 Data files Submission and Validation Sign offOpen Portal Release Data Annotation & ETL

5. NCRI Workshop 2015 bioinformatics.ca Data Type Submitted To the Data Coordination Center (DCC) – Simple somatic and germline mutation – Somatic copy number variation – Somatic structural mutation – Methylation – Gene expression (RNAseq, Arrays) – Protein expression – miRNA – Exon junctions To the European Genome Archive (EGA) and cgHub – Sequencing raw data (Fastq, BAM)

6. NCRI Workshop 2015 bioinformatics.ca Data Validation at Submission

7. NCRI Workshop 2015 bioinformatics.ca Data Annotation & ETL Pipeline Annotation – Mutation frequencies – Mutation gene consequences Amino Acid changes and their consequences for all gene & transcripts (e.g. frameshift) – Mutation functional impact – Gene Ontology terms, Reactome pathways, Cancer Gene Census – Germline mutations masking ETL pipeline – Annotated data indexed using an ElasticSearch cluster of 16 nodes

8. NCRI Workshop 2015 bioinformatics.ca THE ICGC Data Portal Part 2: Portal features highlights

9. NCRI Workshop 2015 bioinformatics.ca ICGC Data Portal

10. NCRI Workshop 2015 bioinformatics.ca Top 20 mutated genes with high functional impact SSMs in selected cancer projects Simple somatic mutation rate per donor across selected cancer projects

11. NCRI Workshop 2015 bioinformatics.ca Project Entity Page ALSO Most frequent mutations Most affected donors Publications Filter on high impact mutations ALSO Most frequent mutations Most affected donors Publications Filter on high impact mutations

12. NCRI Workshop 2015 bioinformatics.ca Gene Entity Page Pfam domains for all transcripts Frequencies by cancer projects

13. NCRI Workshop 2015 bioinformatics.ca Reactome Pathway Entity Page

14. NCRI Workshop 2015 bioinformatics.ca Permanent ID across releases Consequences for all transcripts Mutation Entity Page

15. NCRI Workshop 2015 bioinformatics.ca Genome Viewer

16. NCRI Workshop 2015 bioinformatics.ca Affected donors, mutated genes and mutations found simultaneously Download data files for filtered donors only Search data of interest by applying filters at Donor, Gene, and/or Mutation Search for donor files in external repositories (e.g. raw data) Current filters Export table

17. NCRI Workshop 2015 bioinformatics.ca Customized saved donor, gene and mutation sets Analyses: Enrichment Analysis Phenotype Comparison Set Operation Analyses: Enrichment Analysis Phenotype Comparison Set Operation

18. NCRI Workshop 2015 bioinformatics.ca File filters: Repository, Data Type, Experimental Strategy, File format, Access

19. NCRI Workshop 2015 bioinformatics.ca Acknowledgment Principal Investigator – Vincent Ferretti Project Manager – Francois Gerthoffert Lead bioinformatician – Junjun Zhang Software Architect and Tech Lead – Bob Tiernay Business Analyst – Phuong-My Do Software Developer – Dusan Andric – Terry Lin – Michael Moncada – Vitalii Slobodianyk

20. NCRI Workshop 2015 bioinformatics.ca The ICGC Data Portal Part 3: Live demo