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Human Genome: A Public Forum at UCSC

Fact Sheet

Bioinformatics and the Human Genome Project at UC Santa Cruz

Since December 1999, UC Santa Cruz scientists and engineers have been deeply involved in the assembly and analysis of the human genome. Leading this effort is David Haussler, a professor of computer science, Howard Hughes Medical Institute investigator, and director of the Center for Biomolecular Science and Engineering (CBSE). The CBSE is one of 19 centers around the world that make up the International Human Genome Mapping Consortium, a crucial component of the Human Genome Project.

UCSC's involvement in the Human Genome Project is due to Haussler's leadership in the field of bioinformatics, also known as computational biology. Bioinformatics applies the theories and tools of mathematics and computer science to the vast databases of biological information generated by DNA sequencing and other modern research techniques. A relatively new discipline, bioinformatics is playing an increasingly important role in the Human Genome Project, which aims to determine the complete DNA sequence of the human genome and identify all of the genes it contains. Haussler and his coworkers at UCSC have developed some of the most effective computational techniques for finding genes in DNA sequences.

The human genome is the chemical code that directs the production of proteins by our cells. These diverse proteins not only give us our physical attributes, but also contribute to many of our less tangible features, such as behavior, learning, and predisposition to disease. The "genome sequence" refers to the linear arrangement of some 3.2 billion subunits of DNA in our chromosomes. Since the launch of the Human Genome Project in 1990, genome centers all over the world have generated the raw sequence data by analyzing small fragments of human DNA.

Jim Kent, a graduate student in biology at UCSC and a member of the UCSC human genome team, wrote a computer program that assembled the sequenced fragments, creating a working draft sequence that spanned all 23 human chromosomes. UCSC was the first site to post the assembled human genome sequence on the Web, distributing it freely without any restrictions on use (see genome.ucsc.edu).

The assembled human genome sequence is referred to as a "working draft" because there are still gaps where DNA sequence is missing due to a lack of raw sequence data or ambiguities in the positions of the fragments. The draft sequence is regularly reassembled as new data become available. The Human Genome Project's ultimate goal of producing a "finished sequence" with no gaps and 99.99 percent accuracy is expected to be accomplished ahead of the 2003 target date. The UCSC team expects to play a significant role in this phase of the project as well.

In the meantime, the UCSC webservers process more than 50,000 requests for information each day from biomedical researchers worldwide who want to explore the genome sequence assembled at UCSC. Kent, with the help of other members of the UCSC team and other bioinformatics researchers at more than a dozen institutions, has created a genome browser to explore the working draft sequence. Scientists can use this browser as an interactive map of the genome to find genes, genetic markers, regions of similarity to other organisms, and many other useful features related to the genome sequence.

The initial annotation of the genome sequence represented on UCSC's genome browser has already led to a new understanding of the genome, as set forth in an array of papers published in the February 15 special issue of the journal Nature. In spite of this dramatic progress, exploration of the human genome has barely begun. The UCSC team is looking forward to the next phase in human genome research, which promises to deliver a much deeper understanding of how it all works.

The Human Genome Project is just one of many areas of biomedical research in which bioinformatics is providing valuable tools. Bioinformatics is an important component of one of the California Institutes for Science and Innovation recently established by Governor Gray Davis. The California Institute for Bioengineering, Biotechnology, and Quantitative Biomedical Research (QB3) will harness the quantitative sciences--mathematics, physics, chemistry, and engineering--to biomedicine to create fundamental new discoveries, products, and technologies for improving human health.

Haussler heads QB3's bioinformatics program, which will provide the mathematical and computational expertise essential for much of the institute's work. QB3 is led by UC San Francisco in collaboration with UC Berkeley and UC Santa Cruz. It is a cooperative effort among the three campuses and private industry. In addition to its research programs, the institute will train a new generation of students who will forge the union of the quantitative sciences and biomedical research.


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