Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, May 1993; 5(1)
Because of limited space, HGN is unable to print full reports of six meetings held since July 1992. Citations for the proceedings of two meetings and excerpts from four reports are shown below. For more information, contact HGMIS or the report's author.
Second International Workshop on Open Problems in Computational Molecular Biology
July 19-August 2, 1992, Telluride, Colorado
ORGANIZERS: Andrzej Konopka [National Cancer Institute (NCI)] and Peter Salamon [San Diego State University (SDSU)].
COORDINATOR: Danielle Konings (University of Colorado at Boulder).
SPONSOR: DOE Human Genome Program.
COSPONSORS: CONVEX, SUN, GCG, IntelliGenetics, MasPar, and SiliconGraphics.
FOCUS: Computational experiments in molecular biology and computational methods to classify large amounts of sequence data.
SELECTED PRESENTATIONS AND DISCUSSIONS
New Research Results: Computational analysis of the evolution of G-proteins; possible roles of tandem repeats polymorphism in recombination; neighbor-dependent mutation rates and their relationship to the bias toward low-complexity sequences in eukaryotic genomes; and maximum entropy relationships in nucleotide and protein sequences.
Research Approaches to Molecular Biology Software Development: Methods for automated sequence annotation and database organization; segmenting nucleotide and protein sequences; determining biological (as opposed to statistical) significance of oligopeptide and oligonucleotide matches from comparisons of "all-against-all" database entries; computational techniques to determine genome organization; protein motif representation that takes into account conservation of structure and/or function; formalization of heuristic protocols for genome map assembly; and progress in predicting protein structure from sequence data.
Methodology of Computational Molecular Biology: Machine metaphors and the methodological consequences for sequence research; logical aspects of inductive inference from incomplete, inexact, and inaccurate data; language metaphors that take into account three-dimensional conformations of meaningful texts; paradoxes resulting from simultaneous use of language and mechanism metaphors for DNA sequences; specification of database properties leading to maximum data integrity; and factors contributing to the paradigm of computational molecular biology.
The Third International Workshop on Open Problems in Computational Molecular Biology will be held July 12-26, 1993 [Contact: A. Konopka, 301/846-5396].
Peer-reviewed papers from the 1992 workshop will appear in a special issue of Computers and Chemistry (Vol. 17, 1993); papers from the first (1991) workshop were published in the journal's April 1992 [16(2)] issue.
[Reported by Andrzej K. Konopka (NCI) and Peter Salamon (SDSU)]
Genome Sequencing and Analysis Conference IV
September 26-30, 1992, Hilton Head, South Carolina
ORGANIZERS: J. Craig Venter [The Institute for Genomic Research (TIGR)] and C. Thomas Caskey (Baylor College of Medicine).
SPONSORS: NIH National Center for Human Genome Research, DOE Office of Health and Environmental Research, and TIGR.
FOCUS: Sequencing results and technology development.
SELECTED MEETING TOPICS
Sequencing and Mapping Results: Data obtained by multiplex sequencing of Escherichia coli, Mycoplasma leprae, and human sources; new genomic sequences from E. coli, Caenorhabditis elegans, and Drosophila melanogaster; sequencing of a 90-kb P1 insert from the bithorax region of the Drosophila genome; update on whole-genome physical mapping using megaþyeast artificial chromosomes; identification of many of the 13,000 available human expressed sequence tags (ESTs) by sequence similarity to genes identified in bacteria, yeast and C. elegans; demonstrations that sequencing and analysis of large regions of anonymous human DNA are now reasonably straightforward.
Technology Development: New or improved mapping, sequencing, and functional characterization methods; use of single-band-resolution fluorescence in situ hybridization to map cDNA fragments less than 1 kb long; use of tandem hexamers as primers for chromosome walking without ligation; sequencing by hybridization as a fast and inexpensive method for fingerprinting cDNAs and genomic fragments; collection of transposon-insertion mutants that facilitate positional cloning strategies for many genes in C. elegans; new sequencing technologies, including multiplexing and hybridization using high-density filters; database designs for tracking sequencing and mapping information from genomic and EST projects.
Informatics: The Data Fair, a new conference feature, allowed comparison and on-site analysis of unpublished sequence data, using computers ranging from PCs to supercomputers. Participants analyzed about 20,000 unpublished EST sequences (6,200,000 nucleotides) from human brain, lymphocyte, and liver cells; mouse testes; C. elegans; and Plasmodium falciparum; as well as 438 kb of new genomic sequences from D. melanogaster, C. elegans, M. leprae, and E. coli. Several new genes were identified during comparison of ESTs and genomic sequences, especially in E. coli, providing further evidence of the complementary nature of genome projects in all organisms. Several groups demonstrated software packages for sequence analysis and project support.
[Reported by Alison Hay Tinsley (TIGR)]
Human Genome Project International Conference: Human Genome '92
October 14-17, 1992, Nice, France
ORGANIZERS AND COSPONSORS: Human Genome Organization and Science.
FOCUS: Highlights of the latest technologies, progress, and social issues of the genome project for the research community and the general public.
SELECTED MEETING TOPICS
Whole-Genome Mapping: The microsatellite mapping approach at Genethon is expected to produce a 2-cM-resolution map by 1994. Aimed toward assembling the genome as yeast artificial chromosome (YAC) contigs, roughly half the genome has already been covered in contigs with a mean length of 1.5 Mb. The potential of large-scale cDNA sequencing for generating maps based on gene function was explored.
Technologies for Visualizing DNA: Combining fluorescence in situ hybridization with fluorescence-activated cell sorting or atomic force microscopy with light microscopy may make possible the improved resolution of YAC or cosmid separations to the 10- to 200-kb range.
Human Diversity and Variation: Although populations show large variations, the homogeneity of Europeans when compared to the global population is surprising.
Mapping Model Organisms: The impact of the Drosophila genome project on genome analysis of the malaria-causing parasite was discussed. Mouse maps are used to dissect multifactorial traits whose genetics would be inaccessible in humans.
Patenting cDNA Fragments: A spirited debate took place on the ethics and practicality of patenting cDNA fragments. Attendees felt that the real challenge is to encourage industry to translate the products of human genome research most effectively into powerful tools that will aid in improving the quality of human health throughout the world.
[Reported by Barbara R. Jasny (Science) and Robin Yeaton Woo (American Association for the Advancement of Science)]
First International Workshop on Chromosome 18
July 21-22, 1992, Chicago
SPONSORS: NIH, DOE, the European Community through the Human Genome Organization, and the Dutch Research Organization.
FOCUS: Preparation of consensus genetic linkage and physical maps of chromosome 18, assessment of available mapping resources, and facilitation of entry into the Genome Data Base.
SELECTED MEETING TOPICS
Mapping Information Presented
New Genes: GOLF (G olfactory protein, 18p11.3-11.2); PACAP (pituitary adenylate cyclase activating protein, 18p11.32); and two desmogleins (DSGII, DSGIII, 18). The pMCT108.2 (D18S24) probe appears to contain DNA sequences derived from both chromosomes 9 and 18.
Genetic Mapping Data: Over 50 polymorphic markers; a framework map including 21 markers [4 restriction fragment length polymorphisms (RFLPs) and 13/17 microsatellite markers having PIC values > 70%; the markers were tested on 19 families, and 13 were also mapped physically using a panel of somatic cell hybrids]. A Centre d'Etude du Polymorphisme Humain (CEPH) framework map of 33 markers (1000:1 odds; 7/33 with PIC values > 70%). Three markers are common to both framework maps.
Physical Mapping: A somatic cell hybrid panel was developed using human cells with various structural rearrangements of chromosome 18 [includes 1 hybrid retaining only chromosome 18 (HHW324) and 26 additional hybrids that distinguish 24 intervals of chromosome 18]. A lambda phage library was prepared from HHW324 (205 clones selected and sublocalized to chromosome 18 by Southern blot analysis); sequence tagged sites (STSs) were prepared for a number of genes and D segments and localized to this panel of hybrids. A 7-hybrid panel was developed dividing chromosome 18 into 8 regions (used to map 22 genes and D segments); a number of probes refined by using DNA with chromosome 18 deletions were localized.
New RFLP Probes, YAC Library: A hybrid panel is being used to determine the allele frequencies and cytogenetic location of RFLP probes. A yeast artificial chromosome (YAC) library prepared from a hybrid cell line retaining 2 copies of chromosome 18 as the only human chromosome material has yielded 84 human-specific YACs. These were characterized, fingerprinted, and screened for STS content; initial contigs were established. Fluorescence in situ hybridization was used to localize 60 of these YACs to chromosome 18.
Radiation Hybrids: Radiation-reduced hybrids were generated from a hybrid cell line retaining a single copy of chromosome 18 as the only human material; a set of 92 radiation hybrids were tested for 50 markers; a radiation hybrid map is under construction.
Disease Studies:Trisomy 18 parental origin studies showed the additional chromosome to be maternal in most cases (85 to 95%); two panels of somatic cell hybrids prepared from cells containing deletions of 18q or partial duplications of chromosome 18 enabled construction of a preliminary phenotypic map (molecular analyses performed with probes from the lambda phage library described below); probes were ordered cytogenetically by loss-of-heterozygosity analysis of colon carcinomas; YAC technology was used to clone the synovial sarcomaþassociated translocation breakpoint of the t(X;18) (p11.2;q11.2) regions.
Somatic Cell Hybrids: Panel of six somatic cell hybrids defining seven intervals on chromosome 18; hybrids selected to form a reference panel for mapping chromosome 18 (both deposited in the Human Genetic Mutant Cell Repository at the Coriell Institute in Camden, New Jersey).
STSs: 156 STSs available in a compendium from Gary Silverman (Harvard University), including 75 from 20 cloned genes and 81 from 76 anonymous DNA markers (44 of these are CA repeats or other highly polymorphic loci).
YACs and Cosmids: A YAC library prepared from the HHW324 hybrid (average insert size of about 300 kb) and other YAC clones; CEPH YAC library for screening chromosome 18þspecific sequences [Eric Lander (Whitehead Institute)]; a flow-sorted chromosome 18 cosmid library prepared by Dean Nizetic and Hans Lehrach (Imperial Cancer Research Fund), of which about 20,000 clones have been gridded (this fraction of about 5 to 6 chromosome equivalents will be stamped onto high-density filters for hybridization screening with low-copy probes).
Phage Clones and Libraries: A lambda phage library prepared from the HHW324 hybrid is available from Joan Overhauser (Thomas Jefferson University); a 24X genomic-equivalent lambda library (average insert of about 15 kb) was deposited with the American Type Culture Collection by Pieter de Jong (Lawrence Livermore National Laboratory).
Needed Resources: New markers, particularly new microsatellite markers; telomeric YAC clones; a gridded and arrayed chromosome 18 cosmid library; and reference markers converted to those based on the polymerase chain reaction.
A complete chromosome 18 meeting report is in Cytogenetics and Cell Genetics [63, 77-96 (1993)].
The second chromosome 18 workshop is scheduled for July 19-20 in Nijmegen, Netherlands [Organizers: Ad Geurts van Kessel (Int. 31-80/61-41-07, Fax:/54-21-51) and Joan Overhauser 215/955-5188, Fax: -5393).]
[Reported by Michelle M. Le Beau (University of Chicago), Ad Geurts van Kessel (University of Nijmegen), and Joan Overhauser (Thomas Jefferson University)]
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v5n1).
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.