Collaborative Genomics Projects: A Comprehensive Guide

Collaborative Genomics Projects: A Comprehensive Guide contains operational procedures, policy considerations, and the many lessons learned by The Cancer Genome Atlas Project. This book guides the reader through methods in patient sample acquisition, the establishment of data generation and analysis pipelines, data storage and dissemination, quality control, auditing, and reporting.

This book is essential for those looking to set up or collaborate within a large-scale genomics research project. All authors are contributors to The Cancer Genome Atlas (TCGA) Program, a NIH- funded effort to generate a comprehensive catalog of genomic alterations in more than 35 cancer types.

As the cost of genomic sequencing is decreasing, more and more researchers are leveraging genomic data to inform the biology of disease. The amount of genomic data generated is growing exponentially, and protocols need to be established for the long-term storage, dissemination, and regulation of this data for research. The book's authors create a complete handbook on the management of research projects involving genomic data as learned through the evolution of the TCGA program, a project that was primarily carried out in the US, but whose impact and lessons learned can be applied to international audiences.

Establishes a framework for managing large-scale genomic research projects involving multiple collaboratorsDescribes lessons learned through TCGA to prepare for potential roadblocksEvaluates policy considerations that are needed to avoid pitfallsRecommends strategies to make project management more efficient

• Chapter 1. Introduction
  • Abstract
  • Overview of the Cancer Genome Atlas
  • Scope, Implementation, and Applicability of This Guide
  • Policy Considerations
  • References
• Chapter 2. Gathering Project Requirements
  • Abstract
  • Introduction
  • Establish the Purpose of the Project
  • Identify Key Stakeholders
  • Set Project Milestones
  • Design a Pipeline for the Project
  • Conclusion
  • References
• Chapter 3. Communications Strategies
  • Abstract
  • Introduction
  • Why Develop a Communications Strategy?
  • How to Develop a Communications Strategy
  • Project and Policy Changes: A Part of Strategy Evaluation
  • Examples from Communications Strategies
  • Communications Devices: Symposia and Visual Identity
  • Conclusion
  • References
• Chapter 4. Pipeline: Sample Acquisition
  • Abstract
  • Introduction
  • Define the Sample Set for the Project
  • Establish a Central Biospecimen Processing Facility
  • Establish Sample Qualification Metrics
  • Sample Processing and Distribution to Data Generation Centers
  • Establish Consent Protocols
  • Handling Institutional Review Boards in Multi-Center Studies
  • Identify Potential Tissue Source Sites
  • Establish Contractual Obligation and Payment Plans for Tissue Source Sites
  • Management of Clinical Data Collection
  • References
• Chapter 5. Pipeline: Data Generation
  • Abstract
  • Introduction
  • Building a Data Generation Model
  • Establishing a Data Generation Pipeline and Quality Control Measures
  • Proper Tracking of Data Generation
  • Conclusion
  • References
• Chapter 6. Pipeline: Data Storage and Dissemination
  • Abstract
  • Introduction
  • Creation of Centralized Data Management Center
  • Define Standard Data and Metadata Formats
  • Collect, Store, and Version Data and Metadata
  • Implement Quality Control Measures for Submitted Data
  • Put in Place Appropriate Security and Access Controls
  • Redistribute Data and Metadata Tailored to Diverse Project Stakeholders and End Users
  • Conclusion
  • References
• Chapter 7. Pipeline: Data Analysis
  • Abstract
  • Introduction
  • Preconceived Questions to Answer
  • Establishment of Data Analysis Teams
  • Analysis Structure and Methodology
  • Practical Considerations
  • Conclusion
  • References
• Chapter 8. Quality Control, Auditing, and Reporting
  • Abstract
  • Introduction
  • Establish Quality Metrics for Each Component of the Pipeline
  • Ensure Ethical Management of Samples, Information, and Derived Data Sets
  • Provide Quality Reports to Stakeholders to Help Improve Processes
  • Example of a Quality Management Issue
  • Conclusion
• Chapter 9. Project Closure
  • Abstract
  • Introduction
  • Levels of Closure
  • Budgetary Considerations
  • Conclusion
  • References
• Conclusion
  • Flexibility
  • Transparency
  • Collaboration
  • Communication
  • Reference
• Appendix A. Glossary of Terms
• Appendix B. TCGA Workflow Diagrams
• Appendix C. Publication Guidelines as of July 14, 2015
  • Use of TCGA Data in Publications and Presentations Prior to Initial TCGA Global Analysis Publication
  • Use of TCGA Data in Publications and Presentations after Initial TCGA Global Analysis Publication
  • Use of TCGA Data for Research Purposes Other Than Publication and Presentation
  • TCGA Program Attribution in Publications and Presentations
• Appendix D. Mutation Annotation Format (MAF) Specification
• Appendix E. MAGE-TAB
• Appendix F. Data Use Certification Agreement
  • Introduction and Statement of Policy
  • Terms of Access
  • Appendix 1
• Appendix G. TCGA Analysis Working Group Charter
  • Purpose
  • Organization and Function
  • Membership
  • Benefits of DWG/AWG Participation
• Index