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DOE Joint Genome Institute Exceeds DNA Sequencing Goal U.S. HGP

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DOE Joint Genome Institute Exceeds DNA Sequencing Goal U.S. HGP LOGY P BIO H YS IC Y S R T S I E T M H E I H C C S E N S G IC IN T E A ER RM ING INFO ISSN: 1050–6101, Issue No. 44 Vol. 10, Nos. 1–2, February 1999 In This Issue U.S. HGP on Fast Track for Early Completion Genome Project U.S.HGPonFastTrack..............1 n September 1998, advisory commit- The U.S. HGP began officially in 1990 DOE Joint Genome Institute ..........1 Itees at DOE and NIH approved new as a $3-billion, 15-year program to New 5-Year Goals...................3 5-year goals aimed at completing the find the estimated 80,000 human Faster Sequencing with BACs .........4 Human Genome Project (HGP) 2 years genes and determine the sequence of SNPMarkers......................6 earlier than originally planned in the 3 billion DNA building blocks Who’s Sequencing the Human Genome? 6 1990. The target date of 2003 also will that underlie all of human biology 1999 Oakland Workshop Proceedings...6 mark the 50th anniversary of Watson and its diversity. The early phase of Genomics Progress in Science ........6 and Crick’s description of DNA’s fun- the HGP was characterized by efforts Private-Sector Sequencing............7 GeneMap ’98 ......................7 damental structure. to create the biological, instrumenta- tion, and computing resources neces- The new plan was published in the In the News sary for efficient production-scale October 23, 1998, issue of Science, EMSL Remote Access ...............7 DNA sequencing. The first 5-year C. elegans Sequence ................8 which also cited the contributions of plan was revised in 1993 due to DOE BER Research.................9 international partners. These part- remarkable technological progress, Hollaender Fellows..................9 ners include the Sanger Centre in the and the second plan projected goals SBIR 1998 Awards ..................9 United Kingdom and research centers Mouse Resources .................10 Mouse Consortium .................10 in Germany, Japan, and France. (see Five-Year Plan, p. 2) Chlamydia Genome Analysis .........11 HUGO Office Merger ...............11 DOE Joint Genome Institute Exceeds Microbial Genomics Superbug Deinococcus radiodurans ...12 DNA Sequencing Goal Microbial Genome News ............12 ELSI he DOE Joint Genome Institute million “finished” bases and 40 million Eric Lander, HGP Science ...........13 T(JGI) surpassed its sequencing goal “draft” bases. [“Finished” sequence has Mark Rothstein, Genetic Privacy ......14 of 20 Mb of human DNA for FY 1998, been checked for accuracy, with gaps James Wilson, Gene Therapy ........15 marking almost a tenfold increase in filled in to form a continuous stretch LeRoy Walters, Gene Therapy ........16 production over the previous year. of DNA across a chromosomal region.] The JGI sequencing effort is targeting Radio and TV Programs.............17 “With this milestone, JGI rises to third Courses and Curriculum.............17 chromosomes 5, 16, and 19. position worldwide in terms of its total Proteomics contribution of human DNA sequence “We are seeking to break the 100-Mb Looking at Proteins.................18 to public databases and signals great barrier in the year 2000,” said JGI Proteomics News ..................19 promise for completion of the entire Director Elbert Branscomb. With 1998 Genetics in Medicine [Human Genome] project in 5 years,” worldwide sequencing capacity at Organization for Rare Disorders.......19 noted Martha Krebs, Director of the about 200 Mb per year, all major Genetics in Medicine News . 15, 16, 19, 20 DOE Office of Science. sequencing laboratories are ramping Informatics up production. At least 600 Mb of Software Programs..............11,20 Further dramatic increases are sequence is expected for 1999. GDB and Other Databases ..........21 expected as JGI’s main sequencing Publications ......................21 efforts move to its new facility in Wal- JGI, established at the end of 1996, is a consortium of scientists, engineers, Web, Other Resources, Publications nut Creek, California, half of which and support staff from the Lawrence 1999 Oakland Workshop Web Site .....6 has just been occupied. When the sec- Berkeley, Lawrence Livermore, and Gene Logic License ................11 ond half is completed in March 2000, Los Alamos national laboratories Calendars .......................22 about 200 staff members will main- tain around-the-clock operations. [HGN 8(2), 1; www.ornl.gov/hgmis/ Funding.........................23 publicat/hgn/v8n2/01doe.html; JGI Subscriptions, Acronyms ..........24 JGI’s sequencing goal for the current sequencing goals and progress: fiscal year is 70 Mb, including 30 www.jgi.doe.gov].◊ Human Genome News issues become available on the Web soon after going to press. Archived issues are also available. 2 Human Genome News 10(1–2) February 1999 Genome Project According to Ari Patrinos, DOE Asso- Five-Year Plan (from p. 1) To find out “Who’s Sequencing the Human ciate Director for Biological and Envi- Genome,” see p. 6. through FY 1998. The latest plan was ronmental Research, “Although we developed during a series of individ- have as our primary goal the finished ual and joint DOE and NIH work- sets of full-length cDNA clones and ‘Book of Life’ by the end of 2003, we sequences for human and model- shops held over the past 2 years (see also want the working draft to be as box, p. 3). organism genes. Other functional- useful as possible.” genomics goals include studies into Observers have predicted that the NIH and DOE sequencing centers gene expression and control, creation 21th century will be the “biology cen- expect their facilities to generate of mutations that cause loss or tury.” The analytical power arising about 60% to 70% of the human DNA alteration of function in nonhuman from the reference DNA sequences of sequence, which will be made avail- organisms, and development of several entire genomes and other able broadly and rapidly via the Web experimental and computational genomic resources is anticipated to to stimulate further research. methods for protein analyses. help jump start the new millennium. Sequencing Technology Comparative Genomics Human DNA Sequencing Although current sequencing capacity The functions of human genes and The HGP’s continued emphasis is on is far greater than at the inception of other DNA regions often are revealed obtaining a complete and highly accu- the HGP, achieving the new sequencing by studying their parallels in nonhu- rate reference sequence (1 error in goals will require a two- to threefold mans. To enable such comparisons, 10,000 bases) that is largely continu- improvement. Further incremental HGP researchers have obtained com- ous across each human chromosome. advances in sequencing technologies, plete genomic sequences for the bacte- Scientists believe that knowing this efficiency, and cost will be needed. For rium Escherichia coli, the yeast sequence is critically important for future sequencing applications, plan- Saccharomyces cerevisiae, and the understanding human biology and for ners emphasize the importance of sup- roundworm Caenorhabditis elegans. applications to other fields. porting novel technologies that may be Sequencing continues on Drosophila The plan calls for generating a “work- 5 to 10 years in development. melanogaster and the laboratory mouse. The availability of complete ing draft” of the human genome DNA Sequence Variation sequence by 2001. The working draft genome sequences generated both A new goal focuses on identifying indi- will comprise shotgun sequence data inside and outside the HGP is driving vidual variations in the human genome. from mapped clones, with gaps and a major breakthrough in fundamental Although more than 99% of human ambiguities unresolved. If these data biology as scientists compare entire DNA sequences are the same across sets can be merged with those from genomes to gain new insights into the population, variations in DNA the private sector, they may increase evolutionary, biochemical, genetic, sequence can have a major impact on the depth of the mapped draft, which metabolic, and physiological path- how humans respond to disease; envi- scientists expect will contain about ways. HGP planners stress the need ronmental insults such as bacteria, half the genes. Draft sequence will for a sustainable sequencing capacity viruses, toxins, and chemicals; and provide a foundation for obtaining the to facilitate future comparisons. drugs and other therapies. high-quality finished sequence and Ethical, Legal, and Social also will be a valuable tool for Methods are being developed to detect Implications (ELSI) researchers hunting disease genes. different types of variation, particu- Rapid advances in the science of genet- larly the most common type called ics and its applications present new single-nucleotide polymorphisms and complex ethical and policy issues (SNPs), which occur about once every Resource Success Story for individuals and society. ELSI pro- 100 to 300 bases. Scientists believe grams that identify and address these SNP maps will help them identify the implications have been an integral A Critical Resource in Public, multiple genes associated with such part of the U.S. HGP since its incep- Private Sequencing complex diseases as cancer, diabetes, tion. These programs have resulted in For sequencing the human genome, vascular disease, and some forms of a body of work that promotes educa- scientists prefer the larger and mental illness. These associations are tion and helps guide the conduct of more stable BAC clones first devel- difficult to establish with conventional genetic research and the development oped with DOE support. gene-hunting methods because a sin- of related medical and public policies. BACs will be a critical component of gle altered gene may make only a the much-publicized private-sector small contribution to disease risk. A continuing challenge is to safeguard sequencing efforts of such companies the privacy of individuals and groups as Celera Genomics and Incyte [see Functional Genomics who contribute DNA samples for p. 7 and HGN 9(1–2), 1 (www.ornl. Efficient interpretation of the func- large-scale sequence-variation stud- gov/hgmis/publicat/hgn/v9n3/ tions of human genes and other DNA ies.
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