American Academy of Microbiology report proposes initiative to interpret genome data

While large-scale genomic sequencing technologies over the past decade have given scientists databases filled with the complete genomes of hundreds of organisms, not enough is being done to interpret all that data by assigning functions to sequenced genes (annotation), according to a report released today by the American Academy of Microbiology. An Experimental Approach to Genome Annotation proposes a new initiative to help address this challenge.

“Roughly 40% of predicted genes have not been assigned even tentative functions. It is rare in science to be able to clearly delineate the boundaries of current knowledge, but that is exactly where genomics stands today,” according to the report. “The annotation initiative proposed in this document will extend those boundaries and will likely lead to new applications and new progress in healthcare, biodefense, energy, the environment and agriculture.”

Given the current lack of a reliable source of functional annotation data, the report recommends that a centralized genome annotation initiative be established in the United States. A key component of this initiative is the development of a centrally organized database of peer-reviewed, experimentally verified gene annotations, tied to catalogs of genes that have yet to be annotated and known biochemical functions for which a gene has yet to be found.

Additionally, the report cites lack of available funding as a primary reason that progress in this field has been so slow. The report recommends that the new annotation initiative provide flexible funding to support experiments that will test annotation predictions, including nontraditional funding mechanisms such as smaller awards to a greater number of laboratories and awards to support student research.

The report is based on the findings of a colloquium convened by the Academy in Washington, DC in July 2004. A group of distinguished scientists, including microbiologists, biochemists and bioinformatics specialists gathered to address the critical challenges of genome annotation and to seek ways to accelerate progress in the field of genome annotation.

“The genome sequences that exist today are a great available resource, and the potential impact they represent to us, if annotated accurately, though combined experimentation and bioinformatics, has yet to be explored,” says colloquium chair Richard Roberts of New England Biolabs in Beverly, Massachusetts.