UCSC Press Release: Human genome project draws on UCSC computer scientists expertise toassemble genome data

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June 26, 2000
Contact: Tim Stephens (831) 459-2495; stephens@cats.ucsc.edu
Human genome project draws on expertise of UCSC computer scientists to analyze and assemble genome data
For Immediate Release
SANTA CRUZ, CA--In an intensive effort over the past few months, researchers at the University of California, Santa Cruz, created a powerful new computer program and used it to assemble the "working draft" of the human genome announced today by leaders of the international Human Genome Project.
At a press conference in Washington, D.C., Francis Collins, director of the National Human Genome Research Institute at the National Institutes of Health, and other leaders of the Human Genome Project public consortium today announced that the consortium has assembled a working draft of the sequence of the human genome--the genetic blueprint for a human being. (See NIH news release at http://www.nih.gov/news/pr/jun2000/nhgri-26.htm.)
The public release of this working draft is a landmark achievement, although much work remains to be done. The Human Genome Project involves a public consortium of more than 1,000 scientists at institutions in the United States and Europe. David Haussler, professor of computer science and director of the Center for Biomolecular Science and Engineering at UC Santa Cruz, joined the project early this year. Haussler has been working closely with Eric Lander, director of the Genome Center at MIT's Whitehead Institute, who is directing the computational analysis of the human genome data.
"The analysis performed by Haussler's group at UC Santa Cruz was a crucial contribution to generating this working draft of the human genome sequence," Lander said.
Five laboratories, including Lander's group, have generated most of the raw data, determining the sequences of chemical building blocks that make up the DNA in human chromosomes. The human genetic code is spelled out in roughly 3 billion DNA subunits, called bases, 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 automated sequencing machines.
The sequencing procedures yielded sequences for many random fragments of DNA from each region, providing a total of about 400,000 sequenced fragments of human DNA. Having obtained the sequences of these random fragments, however, the researchers faced a major challenge in trying to reassemble them to represent the sequences of each of the 23 human chromosomes as accurately as possible.
"The computational analysis we performed was to try to determine the proper order and orientation of each piece and to join overlapping pieces of the sequence together," Haussler said.
Jim Kent, a graduate student in biology at UCSC who has a background in computer science, designed and wrote most of the software used to perform the analysis, and he did it in a remarkably short time frame. "He has done a phenomenal job of creating the software to do this very complex operation," Haussler said.
The working draft generated by this analysis incorporates all of the sequence data available as of June 15. It covers 85 percent of the genome and is 99.9 percent accurate. The researchers will continue to fill in the remaining gaps and improve the order and orientation of the fragments as more sequence data becomes available. They will also begin analyzing the working draft to locate the genes buried within the genome sequence.
Haussler's analysis relied on information from a variety of sources in addition to the raw sequence data. In particular, a map developed by Robert Waterston, director of the Genome Sequencing Center at Washington University in St. Louis, one of the five main sequencing sites, served as an invaluable guide in putting the pieces together, Haussler said. Waterston's map provided an approximate location on the chromosomes of each small piece of DNA, plus information about how it might overlap with neighboring pieces.
Greg Schuler, a scientist at the National Center for Biotechnology Information (NCBI), also provided vital steps in the analysis of the genome sequence data. NCBI manages a variety of public databases of biological information and is responsible for storing and organizing the information gathered by the Human Genome Project. The human genome databases are also maintained at the European Bioinformatics Institute (EBI) in Cambridge, England. NCBI and EBI are both major contributors to the computational analysis of the human genome data.
Haussler is working closely with the Ensembl project, a genome analysis effort led EBI's Ewan Birney and including scientists at the Sanger Centre, a major genome research center in Cambridge. "Our collaboration with the Ensembl group has been great," Haussler said. He is also working with a team at Neomorphic, a Berkeley-based genomics company, led by vice president for bioinformatics David Kulp. Neomorphic is working with other groups in the Human Genome Project to locate and classify genes within the genomic DNA sequences. The company has exclusive license to a computer program called Genie, initially developed by Haussler, Kulp, and others, which Neomorphic has refined into a powerful set of gene-finding tools. Genie was used to identify genes in the genome of the fruit fly, Drosophila melanogaster, which was sequenced last year.
"Initial runs of Genie on the working draft of the human genome have already produced evidence for many tens of thousands of genes," Kulp said.
The ultimate goal of the Human Genome Project is to identify and understand the function of all of the genes contained within the human genome. This information will be a boon to biomedical researchers, helping them to identify genes related to specific diseases, to understand how genetic variations affect susceptibility to diseases and responses to drugs, and to design new drugs. Of the human diseases known to be linked to specific genes, 95 percent are associated with genes that have already been located in the working draft of the genome.
"We are going through a portal, opening a door to a new world," Haussler said. "When I saw the fragments from Jim Kent's first assembly of the genome come flying across my computer screen, I thought, 'This is it…this is our genome.' It is hard to describe the sense of wonder I felt."
In addition to Kent, Haussler's team at UCSC includes Nick Littlestone, a visiting scientist at the Center for Biomolecular Science and Engineering; Scott Kennedy, a graduate student in mathematics; Patrick Gavin, who just graduated from UCSC with a B.S. in computer science; and systems consultant Paul Tatarsky.
Haussler expects to perform a new analysis soon incorporating all of the additional sequence data available since June 15. He and his collaborators will be trying to get a handle on how many genes there are, where they are located, what their structures are, and what their functions might be.
"The analysis of the genes is the most challenging part of this whole undertaking, and it is also the most interesting because that is where the potential lies for making major discoveries," Haussler said.
#####
Editor's note: You may contact Haussler at (831) 459-2105 or haussler@cse.ucsc.edu.

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June 26, 2000 Contact: Tim Stephens (831) 459-2495; stephens@cats.ucsc.edu Human genome project draws on expertise of UCSC computer scientists to analyze and assemble genome data For Immediate Release SANTA CRUZ, CA--In an intensive effort over the past few months, researchers at the University of California, Santa Cruz, created a powerful new computer program and used it to assemble the "working draft" of the human genome announced today by leaders of the international Human Genome Project. At a press conference in Washington, D.C., Francis Collins, director of the National Human Genome Research Institute at the National Institutes of Health, and other leaders of the Human Genome Project public consortium today announced that the consortium has assembled a working draft of the sequence of the human genome--the genetic blueprint for a human being. (See NIH news release at http://www.nih.gov/news/pr/jun2000/nhgri-26.htm.) The public release of this working draft is a landmark achievement, although much work remains to be done. The Human Genome Project involves a public consortium of more than 1,000 scientists at institutions in the United States and Europe. David Haussler, professor of computer science and director of the Center for Biomolecular Science and Engineering at UC Santa Cruz, joined the project early this year. Haussler has been working closely with Eric Lander, director of the Genome Center at MIT's Whitehead Institute, who is directing the computational analysis of the human genome data. "The analysis performed by Haussler's group at UC Santa Cruz was a crucial contribution to generating this working draft of the human genome sequence," Lander said. Five laboratories, including Lander's group, have generated most of the raw data, determining the sequences of chemical building blocks that make up the DNA in human chromosomes. The human genetic code is spelled out in roughly 3 billion DNA subunits, called bases, 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 automated sequencing machines. The sequencing procedures yielded sequences for many random fragments of DNA from each region, providing a total of about 400,000 sequenced fragments of human DNA. Having obtained the sequences of these random fragments, however, the researchers faced a major challenge in trying to reassemble them to represent the sequences of each of the 23 human chromosomes as accurately as possible. "The computational analysis we performed was to try to determine the proper order and orientation of each piece and to join overlapping pieces of the sequence together," Haussler said. Jim Kent, a graduate student in biology at UCSC who has a background in computer science, designed and wrote most of the software used to perform the analysis, and he did it in a remarkably short time frame. "He has done a phenomenal job of creating the software to do this very complex operation," Haussler said. The working draft generated by this analysis incorporates all of the sequence data available as of June 15. It covers 85 percent of the genome and is 99.9 percent accurate. The researchers will continue to fill in the remaining gaps and improve the order and orientation of the fragments as more sequence data becomes available. They will also begin analyzing the working draft to locate the genes buried within the genome sequence. Haussler's analysis relied on information from a variety of sources in addition to the raw sequence data. In particular, a map developed by Robert Waterston, director of the Genome Sequencing Center at Washington University in St. Louis, one of the five main sequencing sites, served as an invaluable guide in putting the pieces together, Haussler said. Waterston's map provided an approximate location on the chromosomes of each small piece of DNA, plus information about how it might overlap with neighboring pieces. Greg Schuler, a scientist at the National Center for Biotechnology Information (NCBI), also provided vital steps in the analysis of the genome sequence data. NCBI manages a variety of public databases of biological information and is responsible for storing and organizing the information gathered by the Human Genome Project. The human genome databases are also maintained at the European Bioinformatics Institute (EBI) in Cambridge, England. NCBI and EBI are both major contributors to the computational analysis of the human genome data. Haussler is working closely with the Ensembl project, a genome analysis effort led EBI's Ewan Birney and including scientists at the Sanger Centre, a major genome research center in Cambridge. "Our collaboration with the Ensembl group has been great," Haussler said. He is also working with a team at Neomorphic, a Berkeley-based genomics company, led by vice president for bioinformatics David Kulp. Neomorphic is working with other groups in the Human Genome Project to locate and classify genes within the genomic DNA sequences. The company has exclusive license to a computer program called Genie, initially developed by Haussler, Kulp, and others, which Neomorphic has refined into a powerful set of gene-finding tools. Genie was used to identify genes in the genome of the fruit fly, Drosophila melanogaster, which was sequenced last year. "Initial runs of Genie on the working draft of the human genome have already produced evidence for many tens of thousands of genes," Kulp said. The ultimate goal of the Human Genome Project is to identify and understand the function of all of the genes contained within the human genome. This information will be a boon to biomedical researchers, helping them to identify genes related to specific diseases, to understand how genetic variations affect susceptibility to diseases and responses to drugs, and to design new drugs. Of the human diseases known to be linked to specific genes, 95 percent are associated with genes that have already been located in the working draft of the genome. "We are going through a portal, opening a door to a new world," Haussler said. "When I saw the fragments from Jim Kent's first assembly of the genome come flying across my computer screen, I thought, 'This is it…this is our genome.' It is hard to describe the sense of wonder I felt." In addition to Kent, Haussler's team at UCSC includes Nick Littlestone, a visiting scientist at the Center for Biomolecular Science and Engineering; Scott Kennedy, a graduate student in mathematics; Patrick Gavin, who just graduated from UCSC with a B.S. in computer science; and systems consultant Paul Tatarsky. Haussler expects to perform a new analysis soon incorporating all of the additional sequence data available since June 15. He and his collaborators will be trying to get a handle on how many genes there are, where they are located, what their structures are, and what their functions might be. "The analysis of the genes is the most challenging part of this whole undertaking, and it is also the most interesting because that is where the potential lies for making major discoveries," Haussler said. ##### Editor's note: You may contact Haussler at (831) 459-2105 or haussler@cse.ucsc.edu. 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