Collaborative genomics projects : a comprehensive guide

✍ Scribed by Sheth, Margi; Zenklusen, Jean C.; Zhang, Jiashan

• Publisher: Academic Press is an imprint of Elsevier
• Year: 2016
• Tongue: English
• Leaves: 128
• Edition: First edition
• Category: Library

✦ Synopsis

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 collaborators
• Describes lessons learned through TCGA to prepare for potential roadblocks
• Evaluates policy considerations that are needed to avoid pitfalls
• Recommends strategies to make project management more efficient

✦ Table of Contents

Content:
Front-matter,CopyrightEntitled to full textChapter 1 - Introduction, Pages 1-5
Chapter 2 - Gathering Project Requirements, Pages 7-14
Chapter 3 - Communications Strategies, Pages 15-29
Chapter 4 - Pipeline: Sample Acquisition, Pages 31-41
Chapter 5 - Pipeline: Data Generation, Pages 43-49
Chapter 6 - Pipeline: Data Storage and Dissemination, Pages 51-58
Chapter 7 - Pipeline: Data Analysis, Pages 59-67
Chapter 8 - Quality Control, Auditing, and Reporting, Pages 69-72
Chapter 9 - Project Closure, Pages 73-79
Conclusion, Pages 81-83
Appendix A - Glossary of Terms, Pages 85-90
Appendix B - TCGA Workflow Diagrams, Pages 91-95
Appendix C - Publication Guidelines as of July 14, 2015, Pages 97-101
Appendix D - Mutation Annotation Format (MAF) Specification, Pages 103-110
Appendix E - MAGE-TAB, Pages 111-113
Appendix F - Data Use Certification Agreement, Pages 115-125
Appendix G - TCGA Analysis Working Group Charter, Pages 127-132
Index, Pages 133-136