Sponsored by the U.S. Department of Energy Human Genome Program
Human Genome News Archive Edition
Human Genome News, March 1992; 3(6)
The growing focus on use of the mouse as an important tool for characterizing and mapping human disease genes was emphasized strongly at the Fifth Mouse Genome Mapping Workshop at Lunteren, Netherlands, in October 1991. Decades of genetic mapping in the mouse, allied with more-recent advances in molecular mapping, have provided a dense genetic map of the mouse genome, and concomitant expansion of the human genetic map has made possible the characterization of most linkage groups conserved between mouse and human genomes.
Human geneticists have unparalleled opportunities for identifying mouse mutants and candidate genes that may be homologous to human disease genes and for relating the mapping of candidate human gene sequences to mutant loci in the mouse. Identifying such homologies in the mouse provides an excellent vehicle for further studies of the genetics, pathophysiology, and potential therapy of human diseases with genetic components.
New mutations at mouse loci can be generated by several techniques-radiation, chemical mutagenesis, or gene targeting. Identification of deletion mutations is an aid to understanding the structure- function relationships at a particular locus and also to mapping in the region.
The development of interspecific backcrosses as a genetic mapping tool was an important turning point in mapping the mouse genome. Interspecific backcrosses use two different mouse species as the parents: laboratory strains are crossed to the wild mouse species Mus spretus, and the F1 progeny are usually backcrossed to the laboratory strains. The divergence between parental strains in interspecific backcrosses allows every DNA marker to be mapped; gene order is determined by a simple haplotype analysis because the crosses are multipoint. (Multipoint means that individual progeny from the backcross are each analyzed with many DNA markers; the genetic analysis thus involves many points along the chromosome.) A number of genome-wide genetic maps developed using largely classical probe technology were presented at the meeting, demonstrating that the density of mapped probes is rapidly approaching the target of 1 marker/cM. (See related article, Mouse Working Group.)
Mouse and human geneticists are now using new tools for rapid production of genetic maps. In mouse, the most common dinucleotide repeat (CA)n is spaced on average every 18 kb. Markers such as microsatellites are highly variant (90%) in interspecific crosses and even in intraspecific crosses, where about half the markers vary between two different parental inbred strains.
Random amplified polymorphic DNA (RAPD), a new class of markers generated by polymerase chain reaction with short random ten-nucleotide oligomers, has been shown to be highly variable between species and laboratory strains and represents an additional large source of markers for genome mapping.
Cross Referencing the Maps
The full value of the detailed probe and microsatellite maps under construction will be realized only if the maps are cross referenced. For each chromosome, committees have already determined a number of reference loci (spaced at 10- to 20-cM intervals) to act as common anchor points for the various backcross mapping programs. Cross referencing will enable the better use of raw data in newly developed database software for compilation of mouse genetic maps.
Genome-Wide Mapping Efforts
The power of dense genetic maps of the mouse genome has been demonstrated recently by the localization of a number of new loci involved with disease, developments that have been accelerated by use of genome-wide maps of rapidly usable microsatellite loci. Analyzing backcross progeny from a cross using the nonobese diabetic (NOD) strain of mouse with microsatellite loci covering most of the mouse genome has identified new susceptibility loci on mouse chromosomes 1, 3, and 11 and defined the likely location of homologous loci in the human genome. This NOD strain has a disease that is similar to Type I diabetes in humans. Interestingly, the susceptibility gene on mouse chromosome 1 is linked to the Lsh locus, which is involved with susceptibility to bacterial and parasitic infections and, like Type I diabetes, could have a macrophage involvement. Similar genetic analyses in a rat cross segregating for hypertension have identified a major blood pressure gene on chromosome 10 close to the angiotensin-converting enzyme (ACE) gene.
High Regional Marker Density
Interspecific backcrosses have been used in several major studies to provide very detailed genetic maps in a number of defined regions of the mouse genome, in particular those harboring interesting mutations. In many cases, the backcross has included the mutation of interest to identify closely linked startpoints for physically mapping and characterizing the mutant gene.
These detailed regional maps often have a marker spacing of 1 cM or less (corresponding to 2 Mb or less) and allow linkup of adjacent markers through pulsed-field gel electrophoresis to provide physical maps of substantial megabase regions of the mouse genome. Each physical map provides a framework for establishing overlapping maps of yeast artificial chromosome (YAC) contigs that will supply access to all the underlying sequences. Whereas genome-wide approaches to YAC contig mapping probably have room for further development, the first major efforts are likely to be in regions already saturated with markers and where rudimentary physical maps are in place.
Mouse YAC Libraries
Access to mouse YAC libraries is a key issue for the development of the mouse and human genome programs. Isolating mouse YAC clones homologous to human disease genes is an important step in beginning the genetic and possible transgenic analysis in the mouse. Princeton University, Imperial Cancer Research Fund, and St. Mary's Hospital (London) have constructed partial EcoR I YAC libraries with the pYAC4 vector.
Embryonic YAC contigs have been constructed in several regions of the mouse genome, a process that will be greatly improved by techniques for rapidly identifying overlapping clones.
The mouse genome informatics program at Jackson Laboratory is developing a fundamental mouse genome database [Encyclopedia of the Mouse Genome] and software tools for the analysis and display of mouse map information. At present the Mouse Genome Database includes the Genomic Database of the Mouse (GBASE), Homology Database (HMDP), and the Mouse Cytogenetic Database (MCD); GENEVIEW, a software package for a wide variety of map presentations, has been developed at the U.K. Medical Research Council Radiobiology Unit at Harwell. A proposed mouse gene mapping consortium including all the major centers working on genome-wide mapping would have a pivotal role in maintaining the Mouse Genome Database and integrating genome-wide map information.
Lunteren was the site of the inauguration of the International Mammalian Genome Society (IMGS) and the first meeting of its elected secretariat. IMGS will organize annual mapping workshops through a central office presently located in Buffalo, New York (Contact: Verne Chapman, Roswell Park Memorial Institute, 716/845-5840, Fax: 716/845-8169); help coordinate the activities of chromosome committees; advise on database developments; and foster relationships with the Human Genome Organization (HUGO) through the HUGO Mouse Genome Committee.
A full report from each mouse chromosome committee was recently published in a special issue of Mammalian Genome [Volume 1: S1-534 (1991)]. The report included a chromosome map, locus list, and reference loci assigned for each chromosome.
Version 1.0 of the database has been released and is available on disk from Jackson Laboratory. Contact:
Submitted by Steve Brown
St. Mary's Hospital Medical School, London
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v3n6).
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.