Genomics: GTL facilities follow directly from the science case—should one exist—for systems biology at DOE? Are there alternate models for some of the proposed effort that could more efficiently deliver the same scientific output?
In an era of flat or declining budgets, which aspects of the proposed Genomics: GTL program are the most meritorious? Which appear to have the highest ratio of scientific benefit to cost?
This report was prepared by the committee in response to that charge. To provide background information, the committee gives a brief introduction on genomics and the scientific advances that genomics has brought and describes DOE’s role in genomics research and its Genomics: GTL program in Chapter 1. In Chapter 2, the committee examines the role that the Genomics: GTL program could play in achieving DOE’s mission goals. The committee reviews the design of the program and its infrastructure plan in the last chapter.
Genomics is the study of the structure, content, and evolution of genomes and the analysis of the expression and function of genes and proteins at the level of the whole cell or organism (Gibson and Muse, 2002). Genomics has many subfields—including functional genomics, structural genomics, proteomics, and metagenomics—and it makes use of bioinformatics and other computational tools to study the global properties of genomes. Such genomic tools as high-throughput DNA sequencing, microarrays, and the polymerase chain reaction have revolutionized biomedical science. The first full genome sequence of a free-living organism, Haemophilus influenzae, was determined 10 years ago (Fleischmann et al., 1995). The process was expensive and took years to accomplish, but completion of the sequence established several important principles. It showed that the so-called shotgun assembly technique was workable and effective in sequencing whole genomes. And it became clear that our understanding of the genetic information in a microorganism was much less than expected—a lesson still true 10 years later, when as much as 30 percent of the open reading frames of new microbial genomes are found to have unknown function.
Genome sequencing was quickly applied to microorganisms with larger and more complex genomes, including the yeasts Saccharomyces cerivisiae and Schizosaccharomyces pombe, and then to a series of model organisms, including the nematode, fruit fly, mustard, and mouse. With each new organism came a greater understanding of the organization and function of genomes and the identification of new genes and metabolic pathways. With the completion of the draft human genome sequence in 2003, the basis for rapidly understanding much of the genome information through comparative genomics was in place.
The sequencing of the human genome has provided detailed genetic information about specific genes and pathways in humans and has opened vast possi-