Next Steps for Functional Genomics: Proceedings of a Workshop (2020)
Chapter: Front Matter
Next Steps for
Functional Genomics
PROCEEDINGS OF A WORKSHOP
Robert Pool, Steven M. Moss, and Frances Sharples, Rapporteurs
Board on Life Sciences
Division on Earth and Life Studies
THE NATIONAL ACADEMIES PRESS
Washington, DC
www.nap.edu
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This activity was supported by the National Science Foundation under Award Number 1927620. Any opinions, findings, conclusions, or recommendations expressed in this publication do not necessarily reflect the views of any organization or agency that provided support for the project.
International Standard Book Number-13: 978-0-309-67673-1
International Standard Book Number-10: 0-309-67673-8
Digital Object Identifier: https://doi.org/10.17226/25780
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Suggested citation: National Academies of Sciences, Engineering, and Medicine. 2020. Next Steps for Functional Genomics: Proceedings of a Workshop. Washington, DC: The National Academies Press. https://doi.org/10.17226/25780.
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PLANNING COMMITTEE ON NEXT STEPS FOR FUNCTIONAL GENOMICS: A WORKSHOP
GENE E. ROBINSON (NAS, NAM), Chair, University of Illinois at Urbana-Champaign
PHILIP N. BENFEY (NAS), Duke University
CHARLES DANKO, Cornell University
EMMA FARLEY, University of California, San Diego
TRUDY F. C. MACKAY (NAS), Clemson University
TERRY MAGNUSON (NAM), University of North Carolina at Chapel Hill
LAUREN O’CONNELL, Stanford University
ANDREA SWEIGART, University of Georgia
Staff
STEVEN M. MOSS, Associate Program Officer, Board on Life Sciences
FRANCES SHARPLES, Board Director, Board on Life Sciences
KOSSANA YOUNG, Senior Program Assistant, Board on Life Sciences
BOARD ON LIFE SCIENCES
JAMES P. COLLINS, Chair, Arizona State University
A. ALONSO AGUIRRE, George Mason University
VALERIE H. BONHAM, Ropes & Gray LLP
DOMINIQUE BROSSARD, University of Wisconsin–Madison
NANCY D. CONNELL, Johns Hopkins Center for Health Security
SEAN M. DECATUR, Kenyon College
JOSEPH R. ECKER, Salk Institute for Biological Studies
SCOTT V. EDWARDS, Harvard University
GERALD EPSTEIN, National Defense University
ROBERT J. FULL, University of California, Berkeley
MARY E. MAXON, Lawrence Berkeley National Laboratory
ROBERT NEWMAN, Independent Consultant
STEPHEN J. O’BRIEN, Nova Southeastern University
LUCILA OHNO-MACHADO, University of California, San Diego
CLAIRE POMEROY, Albert and Mary Lasker Foundation
MARY E. POWER, University of California, Berkeley
SUSAN RUNDELL SINGER, Rollins College
LANA SKIRBOLL, Sanofi
DAVID R. WALT, Harvard Medical School
PHYLLIS M. WISE, University of Colorado Boulder
Staff
FRANCES SHARPLES, Director
KATIE BOWMAN, Senior Program Officer
ANDREA HODGSON, Program Officer
JO HUSBANDS, Senior Scholar
KEEGAN SAWYER, Senior Program Officer
AUDREY THEVENON, Program Officer
STEVEN M. MOSS, Associate Program Officer
JESSICA DE MOUY, Senior Program Assistant
KOSSANA YOUNG, Senior Program Assistant
Reviewers
This Proceedings of a Workshop was reviewed in draft form by individuals chosen for their diverse perspectives and technical expertise. The purpose of this independent review is to provide candid and critical comments that will assist the National Academies of Sciences, Engineering, and Medicine in making each published proceedings as sound as possible and to ensure that it meets the institutional standards for quality, objectivity, evidence, and responsiveness to the charge. The review comments and draft manuscript remain confidential to protect the integrity of the process.
We thank the following individuals for their review of this proceedings:
JULIA BAILEY-SERRES, University of California, Riverside
EMMA FARLEY, University of California, San Diego
MARC HALFON, University at Buffalo-SUNY
STEVEN HENIKOFF, Fred Hutchinson Cancer Research Center
Although the reviewers listed above provided many constructive comments and suggestions, they were not asked to endorse the content of the proceedings nor did they see the final draft before its release. The review of this proceedings was overseen by JASPER RINE, University of California, Berkeley. He was responsible for making certain that an independent examination of this proceedings was carried out in accordance with standards of the National Academies and that all review comments were carefully considered. Responsibility for the final content rests entirely with the rapporteurs and the National Academies.
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Contents
Importance of Functional Genomics
Workshop Outline and Objectives
2 THE GENOTYPE–PHENOTYPE CHALLENGE
Concluding Remarks and Summary
3 CASE STUDIES ON BUILDING FUNCTIONAL GENOMICS TOOLS IN DIVERSE SYSTEMS
Understanding the Genotype–Phenotype Connection in Monkeyflowers
Microbial Communities and Their Interactions on Cheese Rinds
Neurogenetics of Sociality and Relationships
Genetic Interrogation of Diverse Plants
4 UNDERSTANDING THE CONTRIBUTIONS OF NON-PROTEIN-CODING DNA TO PHENOTYPE
Functional Genomics of Adaptation in Sticklebacks
Phylogenetics of Flightless Birds
Role of Chromatin Folding in Gene Expression
5 ADVANCING RESEARCH ON THE ENVIRONMENTAL REGULATION OF GENE FUNCTION
Factors Shaping Variation in Social Behavior
How Environmental Factors Influence a Complex Phenotype
Environmental Regulation of Gene Function in Agriculture
Environmental Factors Affecting Quantitative Traits in Drosophila
6 PREDICTING CURRENT AND FUTURE SOURCES OF VARIATION IN QUANTITATIVE TRAITS
Discovering the Genetic Basis of a Change: An Example
Exploring the Regulation of Gene Expression
7 INTERPRETING AND VALIDATING RESULTS FROM HIGH-THROUGHPUT SCREENING APPROACHES
Lessons on Design and Validation from a CRISPR Loss-of-Function Screen on KRAS-Mutant Cancers
Using Functional Genomics to Understand Development
Validating Results from High-Throughput Enhancer Screens
Harnessing Genetic Diversity to Understand Maintenance of Pluripotency in Embryonic Stem Cells
8 LARGE DATABASES AND CONSORTIA
ChRO-seq: A New Technique for Interpreting Genome Sequence
Using Gene Expression to Understand the Genetics of Disease
A Cloud-Based Platform for Genomics Data Mining
9 BIG-PICTURE CHALLENGES IN RESEARCH, EDUCATION, AND TRAINING
Determining and Defining “Model” Systems
Societal and Ethical Implications of Functional Genomics Research
10 FUTURE OF FUNCTIONAL GENOMICS
Breakout Group Discussions on the Future of Functional Genomics
Comments from the Town Hall Discussion
Closing Remarks and Final Overview
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7-3 Display of how the sequences of the enhancers ETS and GATA encode for tissue-specific expression
7-4 Mediation analysis, called the “steps method,” which contains four logical statements
8-1 Representation of ChRO-seq data and interpretation of those data
8-2 Representation of how to identify “anchors” across datasets
9-1 Ethical dimensions of consideration behind choosing a research organism
