April 14, 2003
UCSC Genome Browser provides portal to finished
human genome sequence
By Tim Stephens
As leaders of the Human Genome Project announced the project's successful
completion at a press conference today in Bethesda, Md., UCSC bioinformatics
researchers made the completed reference sequence of the human genome
publicly available on the web-based UCSC Genome
The international effort to sequence the 3 billion DNA letters
in the human genome is considered by many to be one of the most
ambitious scientific undertakings of all time.
This was also the first site to make the initial working draft of
the human genome publicly available in June 2000.
The UCSC Genome Browser provides a web-based "microscope"
for exploring the human genome sequence and is used daily by thousands
of biomedical researchers throughout the world, said David Haussler,
a Howard Hughes Medical Institute investigator and holder of the UC
Presidential Chair in Computer Science.
"We have now built the browser on top of the finished genome sequence.
That sequence will serve as a new foundation for medicine and human
biology, and our browser will form the most popular portal to explore
our shared genetic heritage," said Haussler, who directs UCSC's
Center for Biomolecular Science and Engineering (CBSE).
The center's Genome Bioinformatics Group worked long hours to get the
browser ready for today's announcement of the finished sequence. HHMI
postdoctoral researcher Terrence Furey led an effort to ensure that
the locations of as many known genes as possible were identified in
the genome sequence.
CBSE research scientist James Kent, who earlier assembled the first
working draft of the human genome, created the UCSC Genome Browser.
The browser displays the genome in alignment with dozens of annotation
tracks contributed by researchers at UCSC and collaborators worldwide.
"We have 51 annotation tracks aligned with the genome sequence,
so the browser is very rich in information," said Fan Hsu, director
of proteomics at CBSE.
The browser is now maintained by a team of engineers led by Kent. It
is linked to key additional resources at the European
Bioinformatics Institute and the National
Center for Biotechnology Information.
In addition to Haussler, Kent, Furey, and Hsu, many other members of
the UCSC Genome Bioinformatics Group worked long hours to ensure the
success of the UCSC Genome Browser and human genome data releases. They
include Matt Schwartz, Angie Hinrichs, Heather Trumbower, Donna Karolchik,
Chuck Sugnet, Mark Diekhans, Ryan Weber, Robert Baertsch, Yontao Lu,
Krishna Roskin, and several other graduate students in the Haussler
As the focus of the human genome research community shifts from sequencing
to sequence analysis, the UCSC Genome Browser is well positioned to
fill an essential role in uncovering the causes, treatments, and prevention
of disease and in exploring our shared genetic heritage, Haussler said.
"The Human Genome Sequencing Consortium has given us an extraordinary
gift. The finished human genome sequence is like a finely polished mirror,
reflecting ourselves at the molecular level with unprecedented scope
and accuracy," he said.
"I am extremely proud that the UCSC Genome Bioinformatics Group
has been able to play a role in this great achievement."
The international effort to sequence the 3 billion DNA letters in the
human genome is considered by many to be one of the most ambitious scientific
undertakings of all time, even compared to splitting the atom or going
to the moon.
"The Human Genome Project has been an amazing adventure into ourselves,
to understand our own DNA instruction book, the shared inheritance of
all humankind," said Francis Collins, director of the National
Human Genome Research Institute (NHGRI) and leader of the Human Genome
Project since 1993.
"All of the project's goals have been completed successfully
well in advance of the original deadline and for a cost substantially
less than the original estimates," Collins said.
The flagship effort of the Human Genome Project has been producing
the reference sequence of the human genome. The international consortium
announced the first draft of the human sequence in June 2000. Since
then, researchers have worked tirelessly to convert the "draft"
sequence into a "finished" sequence.
Finished sequence is a technical term meaning that the sequence is
highly accurate (with fewer than one error per 10,000 letters) and highly
contiguous (with the only remaining gaps corresponding to regions whose
sequence cannot be reliably resolved with current technology). That
standard was first achieved for a human chromosome when a team of British,
Japanese, and U.S. researchers produced a finished sequence for human
chromosome 22 in 1999.
The finished sequence produced by the Human Genome Project covers about
99 percent of the human genome's gene-containing regions, and it has
been sequenced to an accuracy of 99.99 percent.
In addition, to help researchers better understand the meaning of the
human genetic instruction book, the project took on a wide range of
other goals, from sequencing the genomes of model organisms to developing
new technologies to study whole genomes. As of April 14, 2003, all of
the Human Genome Project's ambitious goals have been met or surpassed.
"Never would I have dreamed in 1953 that my scientific life would
encompass the path from DNA's double helix to the 3 billion steps of
the human genome. But when the opportunity arose to sequence the human
genome, I knew it was something that could be done--and that must be
done," said Nobel Laureate James Watson, president of Cold Spring
Harbor Laboratory in Cold Spring Harbor, N.Y. "The completion of
the Human Genome Project is a truly momentous occasion for every human
being around the globe."
The International Human Genome Sequencing Consortium included hundreds
of scientists at 20 sequencing centers in China, France, Germany, Great
Britain, Japan and the United States. The five institutions that generated
the most sequence were: Baylor College of Medicine, Houston; Washington
University School of Medicine, St. Louis; Whitehead Institute/MIT Center
for Genome Research, Cambridge, Mass.; the Department of Energy's Joint
Genome Institute, Walnut Creek, Calif.; and The Wellcome Trust Sanger
Institute near Cambridge, England.
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