Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
In this issue...
Also available in pdf.
1997 Santa Fe Highlights
Human Genome Project Administration
In the News
Software and the Internet
Meeting Calendars & Acronyms
JGI Comes of Age: Goals, Progress, and Challenges Outlined
Scientific Director Branscomb Offers "State of JGI" Message
JGI is committed to immediate and full public data release, with data and quality assessments computed automatically and presented in a common internal Web interface. Monthly goals and results are available on the JGI Web site.
Branscomb highlighted the importance of an ongoing review of sequencing priorities in terms of amount, quality, and cost, noting the inevitability of some problematic trade-offs. Plans are under way for JGI to participate in sequence-evaluation programs with other major sequencing centers, and Branscomb pledged JGI to objective cost reporting and predicted cost-efficiencies comparable to those of the rest of the community. An 11-member external board advises JGI on managerial, strategic, technical, and scientific matters. JGI also seeks input from "end users" of genomic information, governmental policymakers, and the academic community.
Sequencing Strategies and Goals
The three laboratories have significant experience in both directed and random (shotgun) sequencing strategies:
To reach the 20-Mb sequencing goal, 45% will be done at both Berkeley and Livermore and the remaining 10% at Los Alamos. A rate increase to around 35 Mb is projected by the end of FY 1998.
The sequencing goal for FY 1999 is 20 to 24 Mb of high-quality sequence and an additional 70 to 80 Mb of draft sequence. Branscomb observed that sequencing goals and cost economies will not be achieved unless, within 3 to 4 years, PSF is generating well above 100 Mb of Bermuda bases per year.
A Consensus Strategy for PSF
Branscomb emphasized the need for well-designed informatics that integrates (within a single functional entity) support for the work at the different sites, especially PSF. Four goals for informatics are to achieve as much uniformity as possible in practices and tools, provide seamless management of and access to critical data across all sites, maintain organizational and administrative unity and coherence, and define a uniform role for informatics and computational approaches in support of quality maintenance.
Beyond Production Sequencing
Branscomb pointed to another trade-off for high-quality and high-productivity sequencing goals: Postpone originally planned efforts to "functionalize" the sequence data (that is, annotate it with additional, experimentally derived information to make it more useful to biologists). Investigators are exploring ways to do comparative sequencing in the mouse at a much lower level of redundancy and quality to locate and sequence mouse-human conserved regions accurately enough to learn their biological significance. In the first year, researchers will perform a small amount of mouse physical mapping to support future mouse-human comparative genomic sequencing if it proves affordable. DOE OBER also has funded a pilot project to functionalize fruit fly sequences. "The practical challenge," Branscomb said, "is to find out what scaleable methods can be devised to annotate fly sequence data for about $1000 per gene or less. It's an interesting challenge."
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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.