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International Cancer Genome Consortium

International Cancer Genome Consortium. Cancer A Disease of the Genome. Challenge in Treating Cancer: Every tumor is different Every cancer patient is different. Goals of Cancer Genome Research. Identify changes in the genomes of tumors that drive cancer progression

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International Cancer Genome Consortium

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  1. International Cancer Genome Consortium

  2. CancerA Disease of the Genome • Challenge in Treating Cancer: • Every tumor is different • Every cancer patient is different

  3. Goals of Cancer Genome Research • Identify changes in the genomes of tumors that drive cancer progression • Identify new targets for therapy • Select drugs based on the genomics of the tumor

  4. Systematic studies of cancer genomes • High rate of abnormalities > often 10,000 mutations per cancer - minority are “driver” mutations - vast majority are “passengers” • Heterogeneity within and across tumor types • Sample quality matters

  5. ‘Next Generation’ sequencing instruments are providing new opportunities for comprehensive analyses of cancer genomes • Capacity of new instruments 100,000 to 1,000,000 times that of instruments used for Human Genome Project • Drastic decrease in costs per genome • Applications: DNA, RNA, chromatin (i.e. epigenome)

  6. Sequencing Evolution/Revolution 1990: thousand bases/day 2000: million bases/day 2010: billion bases/day

  7. International Cancer Genomics Strategy MeetingOctober 1–2, 2007 Toronto (Canada) 22 countries represented 120 participants 34 Genome or Cancer Center Directors 24 Representatives from funding agencies 62 Scientists selected to represent ethics, technologies, statistics, informatics, pathology, clinical oncology and cancer biology

  8. Rationale for an International Consortium The scope is huge, such that no country can do it all. Coordinated cancer genome initiatives will reduce duplication of effort for common tumors 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. The ICGC will accelerate the dissemination of genomic and analytical methods across participating sites, and the user community.

  9. ICGC Goal To obtain a comprehensive description of genomic, transcriptomic and epigenomic changes in 50 different tumor types and/or subtypes which are of clinical and societal importance across the globe. - 500 tumors per tumor type > 25,000 cancer genomes!

  10. Commitments for > 10,000 tumor genomes! New RFAs/projects in development April 2010: World Map of Comprehensive Cancer Genome Projects

  11. ICGC Cancer Genome Projects

  12. SELECTED FEATURES OF ICGC (April 2010)

  13. The level of organization is at the specific cancer type or subtype. A particular cancer may be investigated by an individual research lab/center or by a collaborative research group, across jurisdictions. The key to inclusion of a project in the ICGC is that it should take a comprehensive, genome-wide approach to the analysis of that tumor type (or sub-type). The ICGC is open to many organizations willing mount a comprehensive analysis of at least one cancer type or subtype, and that agree to carry out their efforts according to ICGC policies. Basic Tenets

  14. Organization HCC Lung NSCLC Colon CLL GBM Breast Her+ etc.

  15. Study Design and Statistical Issues Every cancer genome project should state a clear rationale for its choice of sample size, in terms of the desired sensitivity to detect mutations. The target number is 500 samples per tumor type/subtype. Fewer than 500 samples will be acceptable for rare and homogeneous tumors; more than 500 samples may be required for tumors that demonstrate considerable heterogeneity

  16. Tumor Types and Subtypes • The ICGC aims to study cancers of all major organ systems • Studies will cover adult and childhood / adolescent cancers • Guidelines have been developed for ICGC participants for the selection of Cancer Genome Projects

  17. Biobanking needs for ICGC and Cancer Research This is HARD! Sample collection can easily be rate limiting Much of sample collection needs to be prospective Quality assessment is critical A committee of clinical and pathology experts (with representation from different institutions) is needed to draft and oversee the specific guidelines that will apply for every tumor type or sub-type. All samples have to be reviewed by two or more reference pathologists. Patient-matched control samples, representative for the germline genome, are mandatory to discern “somatic” from “inherited” mutations. Clinical annotation of specimens are critical, ranging from exposures to outcomes

  18. ICGC Consent and Privacy Protection Policies ICGC membership implies compliance with Core Bioethical Elements for samples used in ICGC Cancer Projects ICGC acknowledges that the informed consent process used by ICGC members will necessarily differ according to local, socio-cultural and legal requirements To minimize the risk of patient/individual identification, the ICGC has established the policy that datasets be organized into two categories, open and controlled-access.

  19. Data Releases

  20. Genome Analyses Mandatory: Genomic DNA analyses of tumors (and matching control DNA) are core elements of the project. Complementary (Recommended): Additional studies of DNA methylation and RNA expression are recommended on the same samples that are used to find somatic mutations. Optional: Proteomic analyses Metabolomic analyses Immunohistochemical analyses

  21. Genome Analyses Whole genome shotgun analyses (long-term goal) Interim, large-scale, catalogues of somatic mutations Sequencing of all coding exons and other genomic regions of particular biological interest for point mutations. Analysis of low genome coverage of paired-end reads for rearrangements. Genotyping arrays, to detect copy number changes, LOH and breakpoint information. Analyses of DNA Methylation Expression Analyses: protein coding genes, non-coding RNAs, notably microRNAs.

  22. ICGC Data Coordination Centre Mission • Establish common standards, data models, reference datasets • Develop and maintain ICGC web portal for data dissemination • Protect sensitive data • Coordinate data releases • Provide support and training

  23. ICGC Database Model

  24. Access mechanisms for Controlled Data

  25. Data Access Compliance Office (DACO)

  26. 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. Note: Users of the data (including Consortium members) may elect to perform further research that would add intellectual and resource capital to ICGC data and elect to exercise their IP rights on these downstream discoveries. However, ICGC participants and other data users are expected to implement licensing policies that do not obstruct further research: (http://tinyurl.com/4rslvy). ICGC Intellectual Property Policy

  27. ICGC Data Release Policies The members of the International Cancer Genome Consortium (ICGC) are committed to the principle of rapid data release to the scientific community. The individual research groups in the ICGC are free to publish the results of their own efforts in independent publications at any time.

  28. Data users are free to use data that targets specific genes & mutations without any restrictions. • ICGC member projects may, if they choose, impose a publication moratorium period that will only limit other data users from publishing global analyses. All data shall become free of a Publication Moratorium when either the data are published by the ICGC member project or 1 year after the specified quantity of data on which the initial global analyses will be carried out (e.g. genome dataset from 100 tumors per project) have been released via the ICGC portal or other public databases. • In all cases data shall be free of any restriction 2 years after its initial release. Data Release, Data Tiers & Publications Working Group

  29. ICGC Data Generation has started (April 2010)

  30. http://icgc.org

  31. “OPEN” ICGC Data sets in DCCApril 2010

  32. Additional “OPEN” Data sets in DCC, April 2010

  33. Reference cancer genome used by ICGC to compare methods is available via DCC COLO-829 malignant melanoma cell line

  34. ICGC Marker Paper Nature 464, 993-998 (15 April 2010)

  35. The International Cancer Genome Consortium can be the hub of the wheel, but it’s not all of cancer research! Translating into new interventions, tests, and public health strategies will require biological and clinical studies, changes in health care practices, and TIME!

  36. The Work The Consortium Funding/Projects An Idea 2007 Discussions 1 project The Launch 2008 A Plan Ethics A Working Consortium 8 projects Samples Pathology 2009 Data Management Data Access A Consortium sharing ideas and expertise 10 projects Data 3-4 more… Data Analysis 2010 A Consortium coordinating and collaborating Rare/Childhood Cancers

  37. 3rd Workshop of the International Cancer Genome Consortium (ICGC)Madrid, Spain – March 2010

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