February 12, 2001
Contact: Tim Stephens (831) 459-2495; firstname.lastname@example.org
GRADUATE STUDENT LANDS A STARRING ROLE IN THE HUMAN GENOME PROJECT
For immediate release
SANTA CRUZ, CA˝They may as well go ahead and give Jim Kent his Ph.D. now, considering
his role in a scientific achievement destined for the history books. Kent, a graduate
student in biology at the University of California, Santa Cruz, designed and wrote
the computer program called GigAssembler used to put together the draft sequence
of the human genome published this week in Nature.
Kent will present his work at a symposium on Monday, sharing the stage with the likes
of Francis Collins, director of the National Human Genome Research Institute. (Note
to reporters: The Genome Symposium will take place on February 12 from 2:30 to
5:30 P.M. at the National Institutes of Health in Bethesda, MD, and will be webcast
Kent is not a typical biologist, having spent 15 years writing computer animation
software after earning his bachelor's and master's degrees in mathematics at UCSC.
As part of his initial graduate research in biology (studying gene expression in
the roundworm C. elegans), he wrote an impressive program that caught the
eye of professor of computer science David Haussler. Haussler, a Howard Hughes Medical
Institute investigator and a leader in the field of bioinformatics, soon began collaborating
with Kent. Shortly thereafter, Eric Lander, director of the Genome Center at MIT's
Whitehead Institute, asked Haussler to help analyze the human genome.
That project led to Kent's finest hour˝so far. Working flat out for a solid month
in the garage office behind his Santa Cruz bungalow, he wrote most of GigAssembler
in a mad rush. When the 80-hour work weeks began to take a toll on his wrists, he
used ice packs to control the pain. His efforts paid off.
Haussler led the team of UCSC researchers, including Kent, that used GigAssembler
to analyze data from the genome consortium's sequencing laboratories and piece together
a draft of the genome sequence. Running the program on a hastily built parallel-processing
cluster of 100 computer workstations, they finished just in time for Collins to announce
the completion of a working draft of the human genome at a White House press conference
in June 2000.
"The assembly process is kind of like solving a giant jigsaw puzzle, but it
is a much more complicated jigsaw puzzle than you ever imagined," Kent said.
When Kent decided to take on the task of assembling the genome, he faced a daunting
challenge. The human genetic code is spelled out in roughly 3 billion DNA subunits
arranged in specific sequences on the chromosomes. To determine those sequences,
Genome Project scientists divided the chromosomal DNA into about 25,000 small overlapping
regions for analysis by sequencing labs. The labs obtained sequences for many random
fragments of DNA from each region, providing a total of about 400,000 sequenced fragments.
These sequences then had to be assembled in the proper order and orientation to represent
the sequences of each of the 23 human chromosomes as accurately as possible.
Kent turned his attention to the problem shortly after passing his Ph.D. qualifying
exam in May 2000. "After my oral exams, I looked around and saw that the assembly
wasn't very far along. I had an idea that I was pretty sure would work, so I pursued
it," he said, then added, in a typical understatement, "It ended up being
a bigger project than I had thought."
Kent, Haussler, and other members of the UCSC team are coauthors on three scientific
papers on the human genome in the February 15 issue of Nature. They continue
to work on the task of completing the genome sequence, identifying gaps where new
sequencing data are needed, and updating the assembled sequence as new data become
available. Haussler's group has also been involved in the analysis of the genome
to predict locations of genes using a program called Genie, developed by his former
student David Kulp, now vice president of bioinformatics at Affymetrix. In addition,
one of Haussler's graduate students, Terrence Furey, has been working with a group
that is identifying the locations in the sequence of the dark bands that are used
as landmarks in cytogenetic studies of human chromosomes.
As an encore to GigAssembler, Kent created a web-based human genome browser that
has already proved quite useful to biomedical researchers. The browser is publicly
available at genome.ucsc.edu. The site gets
an average of 20,000 "hits" per day, Haussler said.
Kent has a story he likes to tell about how he ended up switching from computer animation
to biology. He had written graphics and animation programs for some of the first
personal computers in the 1980s, and later developed products for Atari and Autodesk.
But he finally got tired of keeping up with the constantly changing operating systems.
Windows 95 was the last straw, he said.
"The platform for software developers came on 12 CD-ROMs, and I said to myself,
heck, the whole human genome would fit on one CD-ROM, and it doesn't change every
three months," he said.
Little did he know that he would actually be the one to put the human genome onto
a CD-ROM disk. A human genome CD-ROM produced at UCSC was recently placed in the
National Millennium Time Capsule, to be housed at the National Archives for the next
"It is kind of odd to find myself in the middle of all this," Kent said.
"But it's always thrilling when you get something complicated to work, and there
is an awful lot of research that depends on having the genome sequence finished."
Of course, what Kent achieved with GigAssembler was entirely dependent on input from
many other scientists involved in the sequencing and analysis of the human genome.
In particular, a map of the genome developed by Robert Waterston, director of the
Genome Sequencing Center at Washington University in St. Louis, served as an invaluable
guide in putting the pieces together, Haussler said.
Haussler's team at UCSC was part of the genome analysis group led by Whitehead's
Lander. The key members of this group include Collins, Lander, Waterston, Ewan Birney
at the European Bioinformatics Institute in Cambridge, England, and Gregory Schuler
at the National Center for Biotechnology Information. A complete list of the members
of the genome analysis group, which includes scientists at more than a dozen institutions,
can be found in the Nature paper on sequencing and analysis of the human genome.
Editor's note: Reporters may contact Haussler
at (831) 459-2105
or email@example.com, and
Kent at (831) 459-4366.
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