Path: utzoo!utgpu!watserv1!watmath!uunet!samsung!caen!uwm.edu!bionet!MCCLB0.MED.NYU.EDU!DEUSTACHIO From: DEUSTACHIO@MCCLB0.MED.NYU.EDU Newsgroups: bionet.molbio.genome-program Subject: (none) Message-ID: <0260208560007C85@MCCLB0.MED.NYU.EDU> Date: 12 Mar 91 19:52:00 GMT Sender: daemon@genbank.bio.net Lines: 178 4th International Workshop on Mouse Genome Mapping (Historic Inns of Annapolis, MD - November 4-8, 1990) BACKGROUND This was the fourth in a series of meetings that has taken place annually within the international community of scientists who have a specific interest in mapping the mouse genome. Previous workshops had brought the community together to review the status of the known linkages and current progress in the development of genetic maps. These efforts were very helpful and at the close of the 3rd Workshop, held in Oxford, August, 1989, there was a broad interest in formalizing committees from the research community to review the existing genome information. The initial efforts to establish chromosome specific committees was accomplished before the 1990 workshop and the work of the committees was successfully initiated in Annapolis. Reports on the current status of the map of each chromosome are being prepared for publication as a separate issue of Mammalian Genome in 1991. In addition, the workshop was able to articulate a set of common research goals for mapping the mouse genome that reflect the unique strengths and value of the mouse as an experimental system for genetic studies. These goals include saturated genetic maps based on well-spaced reference loci, physical maps of selected chromosome segments, and the development and dissemination of mouse genomics databases. Progress can be assessed by comparing the consensus statement of research goals that emerged from the meeting with the results that were actually presented. GENETIC MAPPING Goals Establishment of reference loci spaced 5 - 10 cM apart on each chromosome (about 160 - 320 total loci). These should be inexpensive to type; highly polymorphic, so as to identify variation among laboratory strains as well as in interspecific crosses; expressed genes; universally available and, where possible, typeable by PCR assays as well as Southern blotting; and conserved between humans and mice. Ideal reference loci would have all of these properties; for real loci, the properties are listed in decreasing order of urgency. Such sets of reference loci will provide universal cross-reference points for mapping specific genes of interest, and a framework for high-resolution mapping of specific chromosomal regions. Results There are now unambiguously ordered multilocus maps of extended linkage groups on all chromosomes, with adjacent markers spaced no more than 20 cM apart. The maps are composed largely of named genes identified by recombinant DNA probes in Southern blotting assays. Placement of additional genes in these maps is proceeding at a rate of hundreds per year (e.g., Jenkins; Seldin, and many presentations of dense maps of particular chromosomal regions of interest). An initial group of reference loci has been identified for each chromosome. Saturated maps now exist for several parts of the mouse genome. For example, the X chromosome, estimated to be 80 cM in length, now has over 50 DNA markers ordered on it with no more than 5 cM between markers in any case, and extended regions of Chromosomes 1, 2, 3, 16, and 17 are similarly well-mapped. Physical mapping studies have already confirmed the accuracy of some of these maps. Several crucial gaps remaining in these maps are now being addressed. General strategies for the identification of centomeres and telomeres are being developed, and new approaches to the identification of polymorphic anonymous DNA segments should yield large numbers of widely distributed new markers. Strategies devised by Hasties and Jenkins and by Elliott have defined DNA variants associated with several telomeres. The use of a satellite probe specific for the centromeres of laboratory strain mouse chromosomes seems likely to provide a general tag for centromeres as genetic loci in interspecies backcrosses (Matsuda and Chapman). Novel uses of oligonucleotides, whether as probes or as PCR primers, have drastically increased the number of polymorphic loci available for testing while reducing the cost in time and genomic DNA consumed of doing the assays. An array of strategies of this kind were discussed (Avner, Lander, Nadeau, Todd), and some combination of these seems likely to provide the markers needed to fill the remaining gaps in the genetic map. Two strategies exploiting PCR assays for length polymorphisms associated with simple sequence repeats were described. One focussed on anonymous clones screened to identify ones in which the repeat was flanked by unique sequences especially suitable for PCR analysis; the other searched for simple sequence repeats adjacent to genes of interest. Both strategies are yielding prodigious numbers of polymorphic loci. Strategies exploiting adventitious cross-reaction of mouse genomic DNA with human VNTR probes and with randomly chosen oligomer sequences appear likely to define numerous useful polymorphisms as well. Elegant in situ hybridization experiments suggest that many of the classes of sequences used to define these new anonymous probes, although widely distributed over the genome, may tend to concentrate in regions corresponding to Giemsa bands (Boyle and Ward). This biased distribution raises the intriguing possibility that in the course of simply pushing genetic maps to closure, we're going to learn a considerable amount about the long range physical organization of mammalian chromosomes, and perhaps about the evolution of this organization as well. Committees were established at the meeting to initiate a systematic review of the maps of each chromosome. These reviews are being prepared for publication as a separate issue of Mammalian Genome early in 1991. PHYSICAL MAPPING Goals An ordered set of recombinant clones spanning the whole genome, mapped at low resolution everywhere and mapped at high resolution in regions of particular genetic interest. Results Physical maps spanning megabase regions near loci of interest were described by several groups (Chr 1, near gld - Seldin; the X inactivation center - Avner, Brown; Chr 17, near Fu - Rossi and Tilghman). The first two maps were constructed by restriction mapping analysis of large DNA fragments; the last is an assembled YAC contig. The first two maps span loci previously identified and resolved by genetic analysis. These data, together with the growing stream of YAC clones centered on genes of interest emanating from the libraries maintained at Princeton (Tilghman) and ICRF (Lehrach) suggest that resources for large-scale cloning and mapping that are already available may be sufficient to assemble large parts of the desired long-range DNA map of the mouse genome, and their use to attack genomic regions of special interest is rapidly becoming routine. At the same time, significant development of the technology itself is taking place in these same labs. The developments reviewed at the meeting included improved methods for screening high-density filters of YAC libraries (Lehrach) and for generating and interpreting fingerprinting data for YAC clones (Shin and Lander). A particular strength of the mouse as an experimental system is the existence of series of deletion mutations centered on several genes known to play crucial roles in early development and in neural function. The application of physical mapping to these mutant animals, now underway, will provide direct access to a series of fascinating genes, as well as providing a powerful model system in which to assess the reliability of various long-range mapping strategies (Rinchik; Holdener and Magnuson). INFORMATICS Goals The collection, integration, analysis, display, and dissemination of mouse genomics information. Results An impressive collection of databases record gene mapping results (Davisson, Peters), molecular clones and probes (Eppig), and physical mapping data (Zehtner). Specific modifications of each database to assure that it can continue to accomodate the flow of data and that it can, increasingly, store raw data (e.g., recombination fractions and haplotypes) as well as derived interpretations (e.g., linkage maps) were described. At a more general level, work is underway to create methods for integrating and displaying these data in interactive systems that can draw simultaneously on the multiple available data sources (Eppig, Mobraaten, and Nadeau). Work is likewise underway in conjunction with the GDB project (Pearson) to provide users ready access to integrated mouse and human genomic information. CONCLUSION The elaboration of a map of the mouse genome based on DNA markers is well underway. Numerous points of cross-reference have been established to the classical map based on the visible mutations and biochemical markers that are unique strengths of the mouse as a system for experimental mammalian genetics. The use of several mouse species and genetically defined inbred strains has yielded highly informative mapping resources, both for global mapping and for detailed analysis of specific chromosomal regions. As the map continues to grow and to incorporate classical mutant loci, it can only increase in importance as a resource for the comparative mapping of the human genome, including the identification of experimental models of human hereditary disease. Even in its present, incomplete form, the map is supporting both an array of physical mapping and cloning experiments directed at specific mutant genes or chromosomal regions of interest, and providing a powerful test system for the development of new technology. --------- * The program of the meeting and abstracts of presentations are available from Verne Chapman (Department of Molecular Biology, Roswell Park Memorial Institute, Elm and Carleton Streets, Buffalo, NY 14263 USA). (Report prepared by Peter D'Eustachio, Joe Nadeau, and Verne Chapman)