Includes bibliographical references and index.

Front Cover; Collaborative Genomics Projects: A Comprehensive Guide; Copyright Page; Contents; 1 Introduction; Overview of the Cancer Genome Atlas; Scope, Implementation, and Applicability of This Guide; Policy Considerations; References; 2 Gathering Project Requirements; Introduction; Establish the Purpose of the Project; Identify Key Stakeholders; Set Project Milestones; Design a Pipeline for the Project; Examples of Pipeline Activities; Conclusion; References; 3 Communications Strategies; Introduction; Why Develop a Communications Strategy?; A Note on Press Releases

A Communications Strategy Applies Tactics to Share MessagesHow to Develop a Communications Strategy; Step 1: Audiences: Who Are the Audiences and Stakeholders?; Step 2: Challenges: What Are Their Concerns?; Step 3: Consideration: Are the Audience's Concerns Valid?; Step 4: Messaging: What Should Be Said in Response?; Step 5: Tactics: What Is the Best Way to Reach the Audience?; Step 6: Priority: Which Audiences and Messages Are Most Important?; Step 7: Tactic Evaluation: Were the Communications Messages Received?; Step 8: Strategy Evaluation: Are the Tactics Working?

Project and Policy Changes: A Part of Strategy EvaluationExamples from Communications Strategies; Communications Devices: Symposia and Visual Identity; Annual Scientific Symposia; Visual Identity; Conclusion; References; 4 Pipeline: Sample Acquisition; 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; Implications of Using a Centralized IRB

Implications of Honoring Individual IRB Approval RulingsIdentify Potential Tissue Source Sites; Establish Contractual Obligation and Payment Plans for Tissue Source Sites; Management of Clinical Data Collection; Sharing Clinical Data; Practical Considerations for Clinical Data Collection and Management; References; 5 Pipeline: Data Generation; Introduction; Building a Data Generation Model; What Data Types Should Be Generated?; What Technologies and Methods Should Be Employed to Generate Data?; Who Will Be Generating the Data?

Establishing a Data Generation Pipeline and Quality Control MeasuresProper Tracking of Data Generation; Conclusion; References; 6 Pipeline: Data Storage and Dissemination; 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; 7 Pipeline: Data Analysis; Introduction

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.

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