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Human Genome News, July 1992; 4(2)
The Second International Workshop on Human Chromosome 16 was held in Adelaide, South Australia, February 26-28 and was attended by 40 participants, including 23 from 7 overseas countries. The meeting was sponsored by NIH, DOE, and the National Health and Medical Research Council of Australia and organized by Ed Hildebrand [Los Alamos National Laboratory (LANL)] and Grant Sutherland [Adelaide Children's Hospital (ACH), Australia].
The use of an extensive, recently developed mouse-human somatic cell hybrid panel having an average distance of 1.6 Mb between adjacent breakpoints has greatly increased the resolution of the human chromosome 16 cytogenetic-based physical map. The map includes many Centre d'Etude du Polymorphisme Humain DNA markers, as well as cosmids fingerprinted with repetitive sequences and assembled into contigs by the Los Alamos genome center. Radiation hybrid panels for chromosome 16 have been constructed by Isabella Ceccherini (Instituto G. Gaslini, Genova, Italy) and Michael Siciliano (M. D. Anderson Cancer Center) for mapping and cloning particular regions.
Raymond Stallings and Norman Doggett (LANL) presented data showing that contigs representing 15% of chromosome 16 have now been physically mapped using either the hybrid cell panel or fluorescence in situ hybridization (FISH) techniques [David Ward (Yale University)]. This percentage will increase rapidly as sequence tagged sites are constructed from the contig ends, facilitating somatic cell hybrid panel mapping. Contig gaps will be closed by using yeast artificial chromosomes (YACs) from both total genomic and flow-sorted chromosome 16-specific YAC libraries. The construction of YAC contigs on chromosome 16 is progressing, especially in such areas of biological interest as the genes for polycystic kidney disease (PKD1) and Batten disease (CLN3) and in the vicinity of two fragile sites (FRA16A and FRA16B). Combined use of the somatic cell hybrid panel, cosmid contigs, and YACs provides a powerful approach for cloning or mapping specific chromosomal regions.
Peter Harris (Medical Research Council, Oxford) has now cloned both telomeres of chromosome 16, enabling the extent of the physical maps to be defined.
Helen Kozman (ACH) presented a chromosome 16 genetic map that consists of 62 polymorphic markers, including most of the previously published restriction fragment length polymorphism markers. The sex-averaged map is 162 cM long (131 cM in males, 198 cM in females) and shows excess male recombination at the telomeres and excess female recombination on each side of the centromere.
A number of polymerase chain reaction (PCR)-based (AC)n microsatellite markers are being incorporated into this genetic map. Marker isolation and high-resolution multipoint mapping are progressing in the vicinity of PKD1 and CLN3, efforts that should allow refined localization and positional cloning of these two disease genes.
John Mulley (ACH) compiled a list of 19 index markers for chromosome 16, including 10 PCR-formatted markers and 10 markers with a heterozygosity greater than 0.7.
A total of 82 genes have now been located on chromosome 16, with 8 new assignments since HGM 11. Three new disease-gene localizations were reported at the workshop.
Two patients with Rubinstein-Taybi syndrome (dysmorphic facies, broad thumbs, big toes, and mental retardation) were reported to have a reciprocal translocation involving the short arm of chromosome 16. Martijn Breuning (Leiden University, Netherlands) reported that 6 of 24 patients with this syndrome were found by FISH to have submicroscopic deletions.
The second disease localization was reported by Dan Kastner (NIH, Bethesda). Familial Mediterranean Fever, an autosomal recessive disorder characterized by acute attacks of fever with sterile peritonitis, pleurisy, or synovitis, was genetically mapped to the chromosome 16 short arm. Linkage disequilibrium between different ethnic groups strongly suggests the presence of at least two mutant alleles with different clinical manifestations.
The third new disease assignment was a gene for late-onset familial breast cancer presented by Rachel Giles (University of California, Berkeley). A number of families that do not demonstrate linkage to the assigned chromosome 17 gene showed tentative linkage to DNA markers on the chromosome 16 long arm.
Anne-Marie Cleton-Jansen (Leiden University) and Hitoshi Tsuda (National Cancer Institute, Tokyo) showed that loss of heterozygosity in breast tumors involved at least two and probably three regions of the chromosome 16 long arm. Of particular interest was the revelation that the region of heterozygosity loss on the distal tip of the chromosome 16 long arm coincides with the probable location of the late-onset familial breast cancer gene.
Stephen Reeders (Yale University) presented an update on cloning the autosomal dominant polycystic kidney disease (PKD1), which was mapped to a 700-kb CpG island-rich segment on the tip of the chromosome 16 short arm. Progress has been difficult because the region is extremely gene rich, with at least 23 identified genes now being analyzed.
Batten disease (juvenile-onset neuronal ceroid lipfuscinosis CLN3) has been mapped to 16p12. A high-resolution linkage map has been constructed within this region, and the genetic location of CLN3 is being refined. An informal consortium was established to facilitate the exchange of materials and the identification of additional microsatellite repeats in the Batten disease region.
Gerd Scherer (University of Freiburg, Federal Republic of Germany) and Jenny Marshall Graves (La Trobe University, Australia) compiled comparative data on mapping loci in the mouse and human genomes. While human serum albumin (HSA) 16q markers are all syntenic on MNU8, the locations of HSA 16p markers have been found to be distributed among four mouse chromosome 16s; this is in contrast to cattle where all HSA 16p markers are syntenic. Participants agreed to make a concerted effort to obtain gene probes on human chromosome 16; Breuning will distribute the probes to groups interested in comparative mapping.
As maps have become more complex, the need has grown for new software to aid in mapping, data management, and the map assembly process at the laboratory and committee levels. Two prototype systems were described: (1) CHROMINFO, designed in Reeders' laboratory, and (2) SIGMA, developed by Michael Cinkosky and James Fickett (LANL).
All new data are being entered into Genome Data Base. Summary tables listing reference markers, genes, and disease loci are available by sending e-mail to "firstname.lastname@example.org" with the single word "chromosome-16" in the text field.
Extensive discussions took place on resource availability and sharing among laboratories; participants proposed that all reagents be made available to the research community when the manuscript characterizing the reagents is accepted for publication. Many reagents are available on request from their originators, although sharing is limited by the cost and logistics of preparation and distribution. Where possible, reagents will be made available through such existing repositories as the American Type Culture Collection in Rockville, Maryland.
To further mapping objectives and to support and expedite studies of human biology and biomedical technology applications, future workshops will continue to facilitate cooperation and collaborations by providing a forum for introducing new information and reagents. The next workshop on chromosome 16 will be held in the United States in the fall of 1993.
A complete report of the Chromosome 16 meeting, in addition to abstracts of poster presentations, will be published in Cytogenetics and Cell Genetics.
Chromosome 16 Meeting Contact:
Reported by David F. Callen, Adelaide Children's Hospital and Ed Hildebrand, Los Alamos National Laboratory
The electronic form of the newsletter may be cited in the following style:
Human Genome Program, U.S. Department of Energy, Human Genome News (v4n2).
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.