DOE '99 Oakland Highlights
Meeting Intro
HGP Progress, Challenges
Joint Genome Institute
JGI Facility Opening
Sequencing
Device Speeds Sequencing
Chromosome 19 Genes
Functional Genomics
Sample Prep System
Informatics
Education & Bioethics
Microbial Genomes
Next Meeting Feb. 2000

Genome Project
Accelerated Timetable
FY1999 Budgets
JGI Refits Facility
Progress

In the News 
 Drosophila Near Completion
Directors, Researchers Receive Awards
Chromosomes 21, 22 Near Finish
Human MHC Region Sequenced
Mouse Probes Aid Mapping
Genetic Testing Committee
DOE Labs & Biomedicine
Biomedical Engineering Proposals
Drug Firms Create SNP Resource
SBIR 1999 Awards
HUGO News
1999 Hollaender Winners

Microbial Genomics 
EcoCyc Database for E. coli
Developing EcoCyc
Thermotoga Sequence
Clostridium Sequenced
Microbial Gene Finder
Neisseria Sequence
Microbial Web Sites

Ethical, Legal, and Social Issues
Education, Counseling Foundation
 ELSI Studies
ELSI Retrospective
Protecting Privacy

Informatics 
MGI 2.2 Released
DNA Repository

Web, Other Resources, Publications 
Metabolic Pathways
New Staden Package
PDB Newsletter
Polymorphism Database
Bacterial Protein Database
DOE BER Publications
HGP Information Web
Biotechnology Business Webs
Behavioral Genetics
Office of Science Reports
Articles on Genetics

Funding 
Genome Research Funding

Meeting Calendars & Acronyms 
Genome & Biotech Meetings 
Training Courses & Workshops 
Acronyms 

HGN archives & subscriptions 
HGP Information home

HGP Grantees Report Progress, Challenges

Report from 1999 DOE Genome Meeting

Some 360 researchers, program managers, and invited guests gathered in California on January 12-16 for the DOE Human Genome Program workshop. Plenary presentations and posters described a wide spectrum of accomplishments and activities, highlights of which are reported below.

Joint Genome Institute
Achievements, Future Plans Presented

A contingent of researchers from JGI reported on the challenges and triumphs involved in merging the sequencing capabilities of three national laboratories into a single, smoothly functioning unit while meeting much higher sequencing goals. Efforts were highly successful, and all objectives were reached as planned, with over 20 Mb of sequence submitted to GenBank in October 1998.

JGI converged the disparate sequencing processes of the three centers of Lawrence Berkeley, Lawrence Livermore, and Los Alamos national laboratories at the Production Sequencing Facility (PSF) in Walnut Creek, California. The team took up residence in one of the new buildings in December 1998, and Secretary of Energy Bill Richardson was keynote speaker at the April 19 formal PSF dedication (see box at right).

Some details of JGI presentations follow (for JGI update, see "HGP Sequencing Progress", and Web site).

Clone Resources
Jan-Fang Cheng reported that about 71.7 Mb of sequence-ready maps were generated in FY 1998 for target regions of chromosomes 5, 16, and 19, and some 3500 unique genes have been mapped to these regions. The goal for FY 1999 was to develop maps for over 250 Mb to allow production of a draft sequence of the three chromosomes by March 2000. The JGI mapping teams then plan to generate similar maps for the mouse genome in regions syntenic with these human chromosomes.

Clones containing target regions are isolated from 10x-coverage BAC libraries via a combination of colony hybridization and PCR approaches using STSs obtained mostly from public databases. Minimally overlapping clones that represent contiguous regions (contigs) of the chromosome are selected for sequencing. Contigs, expanded by end-sequence STS walking, are oriented by STSs developed from known genes and ordered genetic and RH markers. All clones are sized by pulsed-field gel electrophoresis, and their chromosome map locations are confirmed by FISH. Detailed information on STS and restriction maps is available on the Web site.

Quality Control and Assurance
Norman Doggett described the robust system of quality control and assessment processes for sequence generated at JGI. He emphasized JGI's commitment to quality, with more than 95% of all finished bases having Phrap scores over 40 and at least 95% of all bases covered in reads from both strands (or 2 chemistries). To ensure correct assembly, JGI validates the data before submitting the sequence to GenBank and performs postsubmission quality assessment. Validation includes visual inspection of all bases with Phrap values of 30 or less and comparison of the final assembled sequence to 3 independent high-resolution restriction fingerprints.

Informatics
Meeting JGI's ambitious FY 1998 goals was something of a "miracle of elasticity" of the preexisting separate systems at member laboratories, according to Tom Slezak. He noted the complex efforts now under way as the laboratories work toward merging into a single PSF informatics system without interfering with production pressures. The long-term goal is to make information available in a single view through the entire process, from mapping to submission, while allowing for multiple viewing methods.

"Data silos" in various locations currently are hard to connect, but eventually physical maps will become sequence maps as all marker and annotation data are merged. Querying, navigating, and displaying data soon will require seamless links to information on function, structure, and experimental results. Slezak emphasized the importance of implementing an infrastructure for functional genomics informatics.

The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v10n3-4).