1. www.bioinformatics.ca CCRC Cancer Conference November 8, 2015

2. 2Module #: Title of Module

3. CCRC Workshop 2015 – Module 2 bioinformatics.ca The ICGC Data Portal Part 1: Data submission, processing and release

4. CCRC Workshop 2015 – Module 2 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. CCRC Workshop 2015 – Module 2 bioinformatics.ca Data Type Submitted To the Data Coordination Center (DCC) – Simple somatic mutations and germline variants – Copy number somatic mutations and germline variants – Structural somatic mutations and germline variants – DNA methylation – Gene expression (RNA-Seq, microarrays) – Protein expression – miRNA – Exon junctions To the European Genome Archive (EGA) and CGHub – Raw sequencing data (FASTQ, BAM)

6. CCRC Workshop 2015 – Module 2 bioinformatics.ca Data Validation at Submission

7. CCRC Workshop 2015 – Module 2 bioinformatics.ca Data Annotations & ETL Pipeline Annotations – Mutation frequencies – Mutation consequences protein changes and their consequences for genes & transcripts (e.g. amino acid substitution, frameshift, nonsense-mediated decay etc) – Mutation functional impact High impact mutation prediction by FatHMM – Gene Sets: Gene Ontology terms, Reactome Pathways, Cancer Gene Census ETL data processing pipeline – Annotations and data are transformed and indexed using an ElasticSearch to support highly integrated search

8. CCRC Workshop 2015 – Module 2 bioinformatics.ca THE ICGC Data Portal Part 2: Portal feature highlights

9. CCRC Workshop 2015 – Module 2 bioinformatics.ca ICGC Data Portal https://dcc.icgc.org Quick keyword search Major functional sections

10. CCRC Workshop 2015 – Module 2 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 Facets

11. CCRC Workshop 2015 – Module 2 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. CCRC Workshop 2015 – Module 2 bioinformatics.ca Gene Entity Page Pfam domains for all transcripts Frequencies by cancer projects mutations

13. CCRC Workshop 2015 – Module 2 bioinformatics.ca Reactome Pathway Entity Page

14. CCRC Workshop 2015 – Module 2 bioinformatics.ca Permanent ID across releases Consequences for all transcripts Mutation Entity Page View the mutation in Genome Viewer

15. CCRC Workshop 2015 – Module 2 bioinformatics.ca Genome Viewer

16. CCRC Workshop 2015 – Module 2 bioinformatics.ca 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 Facets: filter + count Save the current donors

17. CCRC Workshop 2015 – Module 2 bioinformatics.ca Customized saved donor, gene and mutation sets Analyses: Enrichment Analysis Phenotype Comparison Set Operation Analyses: Enrichment Analysis Phenotype Comparison Set Operation

18. CCRC Workshop 2015 – Module 2 bioinformatics.ca File filters: Repository, Data Type, Experimental Strategy, File format, Access

19. CCRC Workshop 2015 – Module 2 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. CCRC Workshop 2015 – Module 2 bioinformatics.ca The ICGC Data Portal Part 3: Live demo