NIH Awards $1 Million to UNC for Genome Fingerprint Scanning Program
Bethesda, Maryland The National Center for Research Resources
(NCRR), a component of the National Institutes of Health (NIH),
announced today it will provide more than $1 million over three
years to the University of North Carolina at Chapel Hill to further
develop and make more widely available a Genome Fingerprint Scanning
(GFS) program. The tool allows researchers to match mass spectrometry
data directly to raw, unannotated genetic sequences to identify
proteins and locate novel genes. Proteomics, the study of how proteins
interact and respond to changing conditions in complex systems,
is increasingly being used to help decipher diseases such as cancer,
diabetes, and Alzheimer's.
"This powerful genome fingerprint scanning tool will allow
researchers to overcome a major bottleneck that has hampered their
capacity to make full use of the vast information generated by sequencing
dozens of genomes," said NCRR Director Judith L. Vaitukaitis,
M.D. "This is the equivalent of being able to harness a whole
library of information without an index."
Current software for protein identification is limited mainly to
those for which a gene or protein entry exists in one of the public
databases. Protein identification cannot be effectively performed
for organisms whose annotations are incomplete, missing, or incorrect.
By contrast, the GFS program is capable of matching mass spectrometry
data from proteomic studies directly to raw, or even unfinished,
genome sequences. The program has already been used to identify
novel proteins in Francisella tularensis, the bacterium that causes
the infectious disease tularemia, and in Tetrahymena thermophila,
a model organism for studies of cellular and molecular biology.
"This support from NCRR will allow us to transform our Genome
Fingerprint Scanning program from an experimental, beta-quality
tool, into a free, widely-used resource that will benefit the global
proteomics community," said Morgan C. Giddings, Ph.D., assistant
professor at the University of North Carolina at Chapel Hill School
of Medicine and the GFS project director.
An enhanced GFS program will greatly assist researchers who are
studying proteins to better understand complex diseases. The most
common approach compares proteins expressed in diseased versus normal
tissues to determine proteins whose expression levels or forms are
significantly changed, indicating a potential role in the disease.
One example is a recent study identifying some of the important
regulatory gene clusters controlling glucose responsiveness in a
key metabolic pathway affecting diabetes. Another is the discovery
of the genes producing many abnormal regulatory proteins found in
This grant will allow Giddings and her team to upgrade the project's
current Web site, http://gfs.unc.edu,
to include numerous enhancements for end users of the program. They
plan to greatly improve the program's output to include peptide
maps that users can browse overlaid on a genome, expand the list
of built-in searchable genomes, provide a multi-genome simultaneous
search capability, and automate both updates of the genome databases
and distribution of the computing load to ensure rapid response
times. In addition, Giddings intends to enhance the GFS to extend
its applicability to large, multi-exon genes. She also will make
the program, developed on Unix under the Macintosh operating system,
available for Linux, Microsoft Windows and other common platforms;
and will develop documentation aimed at all user levels.
NCRR is part of the National Institutes of Health, an agency
of the Department of Health and Human Services. NCRR is the nation's
leading federal sponsor of resources that enable advances in many
areas of biomedical research. NCRR support provides the scientific
research community with access to a diverse array of biomedical
research technologies, instrumentation, specialized basic and clinical
research facilities, animal models, genetic stocks, and such biomaterials
as cell lines, tissues, and organs. Additional information about
NCRR can be found at www.ncrr.nih.gov.