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1. Status and Update of the International Cancer Genomics Consortium (ICGC) June 1st 2015 B.F. Francis Ouellette francis@oicr.on.ca Senior Scientists & Associate Director, Informatics and Biocomputing, Ontario Institute for Cancer Research, Toronto, ON Associate Professor, Department of Cell and Systems Biology, University of Toronto, Toronto, ON. 2. ONTARIO INSTITUTE FOR CANCER RESEARCH You are free to: Copy, share, adapt, or re-mix; Photograph, film, or broadcast; Blog, live-blog, or post video of; This presentation. Provided that: You attribute the work to its author and respect the rights and licenses associated with its components. Slide Concept by Cameron Neylon, who has waived all copyright and related or neighbouring rights. This slide only ccZero. Social Media Icons adapted with permission from originals by Christopher Ross. Original images are available under GPL at; http://www.thisismyurl.com/free-downloads/15-free-speech-bubble-icons-for-popular-websites 3. ONTARIO INSTITUTE FOR CANCER RESEARCH 3Module #: Title of Module 4. ONTARIO INSTITUTE FOR CANCER RESEARCH 5. ONTARIO INSTITUTE FOR CANCER RESEARCH Disclaimer I am on the SAB of many NIH funded projects (SGD, Galaxy, GenomeSpace, and HMP2), as well as on the Science, Industry Advisory Committee of Genome Canada. I do not (and will not) profit in any way, shape or form, from any of the brands, products or companies I may mention. 6. ONTARIO INSTITUTE FOR CANCER RESEARCH @bffo francis@oicr.on.caE-mail 7. ONTARIO INSTITUTE FOR CANCER RESEARCH 8. ONTARIO INSTITUTE FOR CANCER RESEARCH International Cancer Genome Consortium 9. ONTARIO INSTITUTE FOR CANCER RESEARCH http://www.csb.utoronto.ca/ 10. ONTARIO INSTITUTE FOR CANCER RESEARCH http://bioinformatics.ca/ 11. ONTARIO INSTITUTE FOR CANCER RESEARCH 12. ONTARIO INSTITUTE FOR CANCER RESEARCH 13. ONTARIO INSTITUTE FOR CANCER RESEARCH http://bioinformatics.ca/workshops/2014 14. ONTARIO INSTITUTE FOR CANCER RESEARCH E-mail: course_info@bioinformatics.ca Web: http://bioinformatics.ca 15. ONTARIO INSTITUTE FOR CANCER RESEARCH Cancer A Disease of the Genome Challenge in Treating Cancer: Every tumor is different Every cancer patient is different 16. ONTARIO INSTITUTE FOR CANCER RESEARCH Johns Hopkins > 18,000 genes analyzed for mutations 11 breast and 11 colon tumors L.D. Wood et al, Science, Oct. 2007 Wellcome Trust Sanger Institute 518 genes analyzed for mutations 210 tumors of various types C. Greenman et al, Nature, Mar. 2007 TCGA (NIH) Multiple technologies brain (glioblastoma multiforme), lung (squamous carcinoma), and ovarian (serous cystadenocarcinoma). F.S. Collins & A.D. Barker, Sci. Am, Mar. 2007 Large-Scale Studies of Cancer Genomes 17. ONTARIO INSTITUTE FOR CANCER RESEARCH Heterogeneity within and across tumor types High rate of abnormalities (driver vs passenger) Sample quality matters Consent and controlled data access is complicated Lessons learned 18. ONTARIO INSTITUTE FOR CANCER RESEARCH International Cancer Genome Consortium Collect ~500 tumour/normal pairs from each of 50 different major cancer types; Comprehensive genome analysis of each T/N pair: Genome Transcriptome Methylome Clinical data Make the data available to the research community & public. Identify genome changes GATTATTCCAGGTAT GATTATTGCAGGTAT GATTATTGCAGGTAT 19. ONTARIO INSTITUTE FOR CANCER RESEARCH Rationale for the ICGC The scope is huge, such that no country can do it all. Coordinated cancer genome initiatives will reduce duplication of effort for common and easy to acquire tumor samples and and ensure complete studies for many less frequent forms of cancer. Standardization and uniform quality measures across studies will enable the merging of datasets, increasing power to detect additional targets. The spectrum of many cancers varies across the world for many tumor types, because of environmental, genetic and other causes. The ICGC will accelerate the dissemination of genomic and analytical methods across participating sites, and the user community 20. ONTARIO INSTITUTE FOR CANCER RESEARCH ICGC Goals, Structure, Policies & Guidelines http://goo.gl/sPGLQN 21. ONTARIO INSTITUTE FOR CANCER RESEARCH Primary Goal: coordinate efforts to reach goals (50 tumours) 22. ONTARIO INSTITUTE FOR CANCER RESEARCH http://docs.icgc.org/dcc-data-element-specifications 23. ONTARIO INSTITUTE FOR CANCER RESEARCH Primary Goal: be comprehensive http://goo.gl/BE7KH1 24. ONTARIO INSTITUTE FOR CANCER RESEARCH Analysis Data Types Germline variants (SNPs) Simple Somatic Mutations (SSM) Copy Number Alterations (CNA) Structural Variants (SV) Gene Expression (micro-arrays and RNASeq) miRNA Expression (RNASeq) Epigenomics (Arrays and Methylation) Splicing Variation (RNASeq) Protein Expression (Arrays) 25. ONTARIO INSTITUTE FOR CANCER RESEARCH Primary Goal: generate highest quality http://goo.gl/FXCvi9 26. ONTARIO INSTITUTE FOR CANCER RESEARCH 27. ONTARIO INSTITUTE FOR CANCER RESEARCH Primary Goal: available to all 28. ONTARIO INSTITUTE FOR CANCER RESEARCH Primary Goal: available to all 29. ONTARIO INSTITUTE FOR CANCER RESEARCH Detailed Phenotype and Outcome data Region of residence Risk factors Examination Surgery Radiation Sample Slide Specific histological features Analyte Aliquot Donor notes Gene Expression (probe-level data) Raw genotype calls Gene-sample identifier links Genome sequence files ICGC Controlled Access Datasets Cancer Pathology Histologic type or subtype Histologic nuclear grade Patient/Person Gender, Age range, Vital status, Survival time Relapse type, Status at follow-up Gene Expression (normalized) DNA methylation Computed Copy Number and Loss of Heterozygosity Newly discovered somatic variants ICGC OA Datasets http://goo.gl/w4mrV 30. ONTARIO INSTITUTE FOR CANCER RESEARCH Secondary Goal: coordinate work to benefit productivity http://goo.gl/K5mHC3 31. ONTARIO INSTITUTE FOR CANCER RESEARCH https://icgc.org/icgc/committees-and-working-groups 32. ONTARIO INSTITUTE FOR CANCER RESEARCH Secondary Goal: disseminate knowledge http://goo.gl/ObcZXy 33. ONTARIO INSTITUTE FOR CANCER RESEARCH ICGC Goals, Structure, Policies & Guidelines http://goo.gl/sPGLQN 34. ONTARIO INSTITUTE FOR CANCER RESEARCH Policy ICGC membership implies compliance with Core Bioethical Elements for samples used in ICGC Cancer Projects: http://goo.gl/TFrCmK http://goo.gl/nYx6YG 35. ONTARIO INSTITUTE FOR CANCER RESEARCH POLICY: The members of the International Cancer Genomics Consortium (ICGC) are committed to the principle of rapid data release to the scientific community. http://goo.gl/TFrCmK 36. ONTARIO INSTITUTE FOR CANCER RESEARCH Publication Policy The individual research groups in the ICGC are free to publish the results of their own efforts in independent publications at any time (subject, of course, to any policies of any collaborations in which they may be participating). 37. ONTARIO INSTITUTE FOR CANCER RESEARCH Moratorium: http://www.icgc.org/icgc/goals-structure-policies-guidelines/e3-publication-policy 38. ONTARIO INSTITUTE FOR CANCER RESEARCH Publication Policy 39. ONTARIO INSTITUTE FOR CANCER RESEARCH Where do you find that information? We actually make it hard to find, but we are working on that! (this is an example of where ICGC would like to do what TCGA does!) http://cancergenome.nih.gov/publications/publicationguidelines 40. ONTARIO INSTITUTE FOR CANCER RESEARCH Policy on Intellectual Property All ICGC members agree not to make claims to possible IP derived from primary data (including somatic mutations) and to not pursue IP protections that would prevent or block access to or use of any element of ICGC data or conclusions drawn directly from those data. http://goo.gl/TCMXCl 41. ONTARIO INSTITUTE FOR CANCER RESEARCH 85 Projects 18 Jurisdictions 42 Cancer types Over 12,000 Cancer Genomes International Cancer Genome Consortium: February 2015 42. ONTARIO INSTITUTE FOR CANCER RESEARCH DCC Activities DCC activities are split between two groups: Software Development DCC portal Submission tool Biocuration (which also includes Content Management) Data level management Submitter handling Coordination with secretariat User support http://dcc.icgc.org/team 42 43. ONTARIO INSTITUTE FOR CANCER RESEARCH Data Validation ValidationValidation (dictionary) Validation (across fields) Validation (across fields) Validation (across fields) indexing Happy Users http://goo.gl/1EcyR 44. ONTARIO INSTITUTE FOR CANCER RESEARCH http://docs.icgc.org/methods 45. ONTARIO INSTITUTE FOR CANCER RESEARCH http://docs.icgc.org/dcc-data-element-specifications 46. ONTARIO INSTITUTE FOR CANCER RESEARCH ICGC Biocuration Helping submitters get their data to ICGC Progress reporting (data audit) Quality checks (coverage, correctness, etc.) Helping users get to the data Validate and check (and recheck) metadata on public repositories Test and integrate with other public repositories via standard data formats, ontologies. Documentation, documentation, and more documentation Training 46 47. ONTARIO INSTITUTE FOR CANCER RESEARCH ICGC datasets to date: https://dcc.icgc.org/projects/history 48. ONTARIO INSTITUTE FOR CANCER RESEARCH http://goo.gl/CekF6y Missing Clinical Data? 49. ONTARIO INSTITUTE FOR CANCER RESEARCH 49 http://goo.gl/CekF6y 50. ONTARIO INSTITUTE FOR CANCER RESEARCH 50 51. ONTARIO INSTITUTE FOR CANCER RESEARCH DACO Data Portal Info/help Login 52. ONTARIO INSTITUTE FOR CANCER RESEARCH http://dcc.icgc.org/ 53. ONTARIO INSTITUTE FOR CANCER RESEARCH http://dcc.icgc.org/ 55 projects Access to all data files (and more with DACO access) Faceted searches 54. ONTARIO INSTITUTE FOR CANCER RESEARCH https://dcc.icgc.org/projects 55. ONTARIO INSTITUTE FOR CANCER RESEARCH https://dcc.icgc.org/search 56. ONTARIO INSTITUTE FOR CANCER RESEARC