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Announcements on the First Analysis of Genome Sequence
February 12, 2001
International Human Genome Mapping Consortium Publishes Physical Map of the Human Genome
Washington, D.C., Feb. 12, 2001
The Human Genome Project public consortium today announced that it has assembled
and published a nearly-completed physical map of the human genome - the genetic
blueprint for a human being. The map, which is more than 95 percent complete
and covers 96 percent of the genome, will appear in the Feb. 15 issue of the
journal Nature.
Organized by researchers at Washington University School of Medicine in St.
Louis, with contributions from laboratories throughout the world, the map provided
the basis for the selection of clones for sequencing, and in turn provided the
scaffold on which the draft human genome sequence was assembled. After the multiple
centers involved in the public effort sequenced pieces of DNA, these pieces
could be positioned with respect to one another to determine where particular
pieces fit with other pieces on a chromosome.
"If you have a large, complicated jigsaw puzzle of, say, a forest scene,
a number of trees may look alike," says John D. McPherson, Ph.D., corresponding
author of the paper. "Making this map was like simplifying that large puzzle
by dividing it up into many small puzzles, each containing one tree, then putting
all the pieces of the small puzzles together, and in turn putting all the small
puzzles together to make the whole forest. That way, you can build one tree
at a time, and then integrate them into the whole picture."
"In assembling the sequence, it is key to map the pieces back to their proper places in the genome," says Robert H. Waterston, M.D., Ph.D., the James S. McDonnell Professor of Genetics, professor of anatomy and neurobiology, head of the Department of Genetics and director of the Genome Sequencing Center at Washington University School of Medicine in St. Louis, the center that organized the physical mapping effort. "The physical map was a critical guide for the assembly of the human genome sequence."
The public effort to sequence the genome has relied on a map-based approach. The map was a key component in the construction of the working draft of the genome sequence that was announced June 26, 2000.
Mapping was important because approximately 50 percent of the genome is repetitive. Some regions of DNA have sequences that are up to 98 percent identical to one another even though they may be physically located millions of base pairs apart or even on different chromosomes.
"That's where we could have had problems without a map-based approach," says John D. McPherson, Ph.D., who is an associate professor of genetics and a co-director of the Washington University Genome Sequencing Center. "So many parts of the genome look exactly like other parts that if you work only with small pieces, it's tempting to try to stick similar pieces from different parts together. The physical map allows us to work with large pieces and to know where the little ones are supposed to go."
To make the map, the researchers used bacterial artificial chromosomes (BACs) - large segments of DNA (about 175,000 base pairs long) that are cloned into bacteria. Once human DNA is cloned into bacteria, it can be copied and analyzed. Analysis of those copies allows the clones to be placed in an overlapping series that covers most of the gene-containing portion of the 3.2 billion base pairs of the genome.
Early in the public mapping effort, each of the centers in the genome consortium worked on maps for particular chromosomes. But it soon became clear that making a fingerprint map of the entire genome would be greatly beneficial to the international effort, so the mapmakers joined together their data from around the world to create one accepted map, accessible to all.
During the last two years, mappers at Washington University have processed up to 20,000 BAC clones each week - more than 350,000 in all - recording the pattern each clone made when cut with different types of "restriction enzymes." Each type of restriction enzyme homes in on a short, specific sequence of base pairs and slices the DNA strand at that spot. Those patterns, called "fingerprints," distinguished DNA fragments from each other, revealing which clones contained identical stretches of DNA that could be overlapped.
In order to ensure a high level of accuracy in the final map, researchers created enough overlapping clones to cover the entire genome roughly 20 times. Representative clones were distributed to the various sequencing centers, which determined the order of base pairs in each BAC clone. Using sophisticated computer software and knowledge of each clone's map position, the sequences of the BAC clones were assembled back into an intact and complete genome.
The first pass netted a physical map consisting of 7,700 clusters of overlapping clones - or "contigs" - that combine together into one continuous stretch of the map. But since that time, the researchers have used a variety of means - including examinations of data in GenBank (an online repository of sequence data), more detailed analysis of fingerprints and fingerprints from additional clones - to increase the size of the contigs and, therefore, to reduce the number of gaps between contigs. On Oct. 7, 2000 - the cut-off date for incorporating data into the mapping paper - there were 1,246 contigs. In the four months since that data freeze, that number has fallen below 950.
The researchers continue to make progress and expect to have the map completed soon. The physical map continues to assist those researchers who are finishing the genome sequence and will provide a resource for years to come for researchers wanting to study particular genes.
The international Human Genome Mapping Consortium includes scientists at institutions in France, Germany, Japan, China, Great Britain, Canada and the United States.
The fingerprinting project was funded as part of the Human Genome Project sequencing initiative of the National Human Genome Research Institute ( at NIH). Researchers at the Keio University School of Medicine were supported in part by the Fund for Human Genome Sequencing Project from the JST and the Fund for "Research for the Future" Program from the Japan Society for the Promotion of Science. Researchers at the RIKEN Genomic Sciences Center are supported by the Special Fund for Human Genome Sequencing from the Science and Technology Agency of Japan and a Grant-in-Aid Scientific Research on Priority Area, "Genome Science" from Monbusho, Japan. Additional funding was provided by the National Cancer Institute (at NIH) and the U.S. Department of Energy and grants from the Max-Planck-Society and the Federal German Ministry of Education, Research and Technology as part of the German Human Genome Project.
The institutions that form the Human Genome Mapping Consortium include:- Washington University School of Medicine Genome Sequencing Center, St. Louis,
MO, USA
- The Sanger Centre at the Wellcome Trust Genome Campus, Hinxton, UK
- National Center for Biotechnology Information, NIH, Bethesda, MD, USA
- Whitehead Institute for Biomedical Research, MIT, Cambridge, MA, USA
- Albert Einstein College of Medicine, New York, NY, USA
- Baylor College of Medicine Human Genome Sequencing Center, Houston, Texas,
USA
- Roswell Park Cancer Institute, Buffalo, NY, USA
- University of Washington Multimegabase Sequencing Center, Seattle, WA, USA
- Fred Hutchinson Cancer Research Institute, Seattle, WA, USA
- Genoscope, Evry, France
- U.S. Dept. of Energy Joint Genome Institute, Walnut Creek, CA, USA
- Stanford Human Genome Center and Department of Genetics, Palo Alto, CA,
USA
- Center for Biomolecular Science and Engineering,University of California,
Santa Cruz, CA, USA
- British Columbia Cancer Research Center, Vancouver BC, Canada
- Department of Genome Analysis, Institute of Molecular Biotechnology, Jena,
Germany
- Department of Human Genetics and Pediatrics, University of California, Los
Angeles, CA, USA
- RIKEN Genomic Sciences Center, Saitama, Japan
- Department of Molecular Biology, Keio University School of Medicine, Tokyo,
Japan
- Max-Planck-Institute for Molecular Genetics, Berlin, Germany
Papers are available online at http://www.nature.com/genomics/
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