One of the holy grails of biology is the ability to predict the functional characteristics of an organism from what we know about its genome and its environment.
In 1995, researchers sequenced the complete genome of an organism for the first time. Each year since then has brought faster and cheaper gene sequencing methods and technologies. Yet despite these advancements, scientists still do not understand the functions of all the genes in any organism, or exactly how the information in genes is converted into physical characteristics.
Why is it so complicated? What tools and technologies are needed to uncover the universal principles relating to the genotype-phenotype connection? What are the next steps to advance the field of functional genomics?
Functional genomics attempts to make use of the data produced by genome and RNA sequencing projects to describe gene and protein functions and interactions—and ultimately, to answer questions about how DNA is translated into physical characteristics.
In February 2020, the National Academies of Sciences, Engineering, and Medicine convened a workshop to explore the current state of functional genomics, and ways to advance the field over the next 10-20 years. Speakers and participants at Next Steps for Functional Genomics: A Workshop discussed goals, strategies, and technical needs to allow functional genomics to contribute to the advancement of basic knowledge and its applications to benefit society. Through speaker presentations and group discussions, a number of clear themes emerged for the next steps in functional genomics.
Get an introduction to the workshop in this short video, with opening remarks by:
Through speaker presentations and group discussions, a number of clear themes emerged for the next steps for functional genomics, including:
Although it has been valuable in the past to focus time and resources on a small number of “model organisms,” the field has now reached the point where it is not only feasible, but necessary to study many and varied organisms to uncover the universal principles relating to the genotype-phenotype connection.
Learn more in this workshop presentation on defining model systems by Paul Katz of the University of Massachusetts Amherst:
The workshop’s exploration of pursuing work and tool development on a broad range of research organisms continued in the following workshop talks:
Keynote: Predicting Current and Future Sources of Variation in Quantitative Traits
Patricia Wittkopp, University of Michigan
Determining and Defining “Model” Systems for Diverse Functional Genomics Applications
Panel Discussion
Case Studies on Building Functional Genomics Tools in Diverse Systems:
Functional genomics investigators depend on a wide variety of tools and resources. While some of these tools can be developed by the researchers themselves, productivity would be higher if the researchers were supported by, for example, online databases, groups who generate -omics information on various organisms, and others in the field who are developing new tools and improving on existing tools.
Learn more about the training needs of future genotype-to-phenotype researchers in this workshop panel discussion on addressing challenges in education.
Functional genomics research is generating an increasingly huge amount of data. These data are valuable, but pose major challenges, including validating and integrating the data as well as properly training and rewarding those who create, maintain, and work with the resulting large databases.
In this workshop video, Alexis Battle of Johns Hopkins University discusses work to use gene expression data to understand the genetic variation that is associated with disease.
The workshop’s exploration of the challenge of big data continued in the following workshop talks:
Knowledge Guided Analysis on the Cloud: Challenges and Opportunities
Saurabh Sinha, University of Illinois Urbana-Champaign
Pros and Cons of Consortia and Large Databases
Panel discussion
This panel discussion explored the pros and cons of consortia and large databases:
More discussion of this theme can be found in the following workshop recordings:
Interpreting and Validating Results from High-Throughput Screening Approaches
Panel Discussion
Challenges and Successes of Integrating Large Datasets
Panel discussion
Dealing with some of the complex questions that arise in functional genomics requires genomicists and molecular biologists to collaborate with scientists from other fields, such as mathematics, physics, computational biology, physiology, and behavioral biology.
In this workshop presentation, Rahul Satija of the New York Genome Center discussed a method his laboratory is developing for integrating different datasets on cellular identity to gain a more holistic view of cell function. This integration technique could be used to assemble a reference atlas of cell function to help interpret new sources of data and facilitate comparisons between different model species—and thus boost collaboration.
More discussion of this theme can be found in the following workshop recording:
Understanding the Contributions of the Non-Protein-Coding DNA to Phenotype
Francois Spitz, University of Chicago
Next Steps for Functional Genomics: A Workshop summarizes the presentations and discussions from this February 2020 workshop, which brought together experts to determine the current state of the science of functional genomics, and what is needed to move the field forward.