Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
|Available in PDF
In this issue...
DOE '99 Oakland Highlights
In the News
Ethical, Legal, and Social Issues
Web, Other Resources, Publications
Meeting Calendars & Acronyms
HGP Leaders Confirm Accelerated Timetable for Draft Sequence
New Sequencing Resources Aid Effort
In September, international leaders of Human Genome Project (HGP) sequencing confirmed a plan to complete a rough draft of the human genome by next spring, a year ahead of schedule. This accelerated pace is made possible by the commercialization of a new generation of automated capillary DNA sequencing machines and by BAC mapping resources generated from DOE-sponsored clone projects.
The rough draft will provide a scaffold of sequence across about 90% of the human genome. Remaining gaps will be closed and accuracy improved over the following 3 years to achieve a complete, high-quality human DNA reference sequence by 2003 [see HGN 10(1-2), 1 (www.ornl.gov/hgmis/publicat/hgn/v10n1/01goals.shtml)]. So far, about 13% of human sequence has been finished, and another 12% is available in draft form (genome.ornl.gov/GCat; www.ncbi.nlm.nih.gov/projects/genome/guide/human/).
About 60% of the draft sequence will be produced by six major NIH-funded sequencing centers, including those previously established at Washington University, St. Louis; MIT-Whitehead Institute; and Baylor College of Medicine. In July, laboratories at the University of Washington, Seattle; Genome Therapeutics Corp.; and Stanford University joined the NIH production sequencing effort.
The DOE-funded Joint Genome Institute (JGI) and the Sanger Center (United Kingdom) will generate about 10% and 30%, respectively, of the draft sequence. (See box, below right, for details on JGI sequencing.) France, Germany, and Japan are contributing significant amounts of human sequence, and China recently joined the worldwide project. To avoid duplicated work, each laboratory focuses on particular genomic regions (see Human Genome Sequencing Index).
Sequencing group members reaffirmed the policy of placing all sequence in publicly accessible databases within 24 hours of obtaining a continuous 1000- to 2000-base assembly. They also agreed that sequencing should continue to be based on a proven strategy using BAC clones containing DNA from known genomic locations.
BAC-End Sequences: Prime Resource
Data from the DOE-funded BAC-end sequencing projects at The Institute for Genome Research (TIGR) and the University of Washington, Seattle (UWS), are critical for achieving the new HGP goals. These projects are generating single-sequence reads from both ends of the human DNA insert in 450,000 BAC clones [HGN 10(1-2), 4 (www.ornl.gov/hgmis/publicat/hgn/v10n1/04bacend.shtml) and BAC Web page [no longer available].
In March, DOE increased its support of BAC-end sequencing projects to accelerate their completion and usefulness for guiding production sequencing. The BAC-end sequences, called sequence tag connectors (STCs), are valuable tools for eliminating redundant sequencing. They can direct researchers to particular BAC clones needed for extending a sequenced region along the chromosome and can identify clones representing genomic regions still not sequenced. STCs also can provide quality checks on sequence assemblies and are useful for spanning regions resisting standard sequencing biochemistry.
STC data will furnish researchers with markers spaced on average every 3000 to 4000 bases across the entire human genome, a 100-fold improvement over other current human genome maps. Detailed data on BACs are available at TIGR (www.tigr.org/tdb/humgen/bac_end_search/bac_end_intro.html) and UWS. The STC data resource is complemented by several other types of mapping information, including FISH mapping of BAC clones.
The electronic form of the newsletter may be cited in the following
The Human Genome Project (HGP) was an international 13-year effort, 1990 to 2003. Primary goals were to discover the complete set of human genes and make them accessible for further biological study, and determine the complete sequence of DNA bases in the human genome. See Timeline for more HGP history.
Published from 1989 until 2002, this newsletter facilitated HGP communication, helped prevent duplication of research effort, and informed persons interested in genome research.