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PubMed1993

Libraries for each human chromosome, constructed from sorter-enriched chromosomes by using linker-adaptor PCR.

We describe here the production of complex libraries enriched in sequences from each human chromosome type, starting with only a few thousand sorter-purified chromosomes. In this procedure, DNA is extracted from the sorted chromosomes, digested to completion by using the frequently cutting restriction endonuclease Sau3A1, and ligated, on each end, to an adaptor oligonucleotide. These fragments are then amplified using PCR with a sequence homologous to the adaptor oligonucleotide as a primer. We have used this procedure to produce PCR libraries for each of the 24 human chromosomes. These libraries were characterized by gel electrophoresis and found to be composed of a continuum of sequences ranging in size from a few hundred to approximately 1,000 bp. The libraries, when used as probes for fluorescence in situ hybridization, stained the target chromosomes more or less continuously, even after PCR amplification for more than 200 cycles. These libraries are useful as hybridization probes to facilitate molecular cytogenetic studies and as sources of probes either for identification of polymorphic short tandemly repeated sequences or for development of sequence-tagged sites.

Base Sequence↗
PubMed1996

Molecular genetic analysis of chromosome arm 17p and chromosome arm 22q DNA sequences in sporadic pediatric ependymomas.

Ependymomas are glial tumors of the brain and spinal cord occurring both sporadically and in a familial syndrome, neurofibromatosis type 2 (NF2). Previous analyses performed on specimens obtained predominantly from adult patients have shown loss of DNA sequences from chromosome arm 22q, which is the location of the NF2 gene. Previously, we documented the consistent loss of chromosome arm 17p DNA in medulloblastoma and astrocytoma, which are the most common brain tumors in children. Although mutation of the TP53 gene located on 17p is the most frequent genetic mutation in all adult tumor types, such mutations are rare in most childhood brain tumors investigated to date. We studied a series of pediatric ependymoma specimens (16 intracranial and 2 spinal) for loss of 17p and 22q DNA sequences and for mutation of the TP53 and NF2 genes. None of the children had the clinical stigmata of NF2. We detected loss of 17p DNA sequences in 9 of the 18 specimens (50%); in 7 of 9 of these specimens (78%), the 144-D6 marker was deleted. In contrast, only 2 of these same 18 specimens (11%) showed loss of 22q DNA. One TP53 gene mutation was detected in a child from a cancer kindred. No mutations were detected in the NF2 gene. Our results suggest that loss of chromosome arm 17p DNA sequences is common in sporadic pediatric ependymomas and that, in contrast to ependymomas in adults, deletion of chromosome arm 22q sequences is rare. Furthermore, TP53 and NF2 gene mutations do not play an important role in the etiology of sporadic pediatric ependymomas.

Adolescent↗
PubMed1987

Mosaic tetrasomy 12p: four new cases, and confirmation of the chromosomal origin of the supernumerary chromosome in one of the original Pallister-Mosaic syndrome cases.

Four new cases are reported in which mosaicism for a supernumerary chromosome interpreted as an isochromosome for 12p [i(12p)] is present. In 2 cases seen in early childhood the mosaicism was present at a low level in peripheral blood and was documented in one case to be present with a higher frequency in fibroblast cultures from skin. These cases have clinical features compatible with those in previously reported cases of the Teschler-Nicola/Killian syndrome, many of whom have now been found to be mosaic for a similar i(12p) chromosome in fibroblast cultures. One case was diagnosed prenatally from amniotic fluid culture. The fourth case was a neonatal death, in which fibroblast cultures were established from muscle and increased activity of LDH-B was demonstrated, supporting the theory that the origin of the additional chromosome was from 12p. Loss of the cell line with the supernumerary chromosome occurs after long-term fibroblast culture. Previously unpublished studies showing increased LDH-B activity in case 1 of Pallister-Mosaic syndrome originally reported in 1977 are also reported. It is of interest that our 2 cases which did not survive birth and one previously published case diagnosed prenatally had diaphragmatic herniae.

Abnormalities, Multiple↗
PubMed2003

Chromosomes that show partial loss or gain in near-diploid tumors coincide with chromosomes that show whole loss or gain in near-triploid tumors: evidence suggesting the involvement of the same genes in the tumorigenesis of high- and low-risk neuroblastomas.

We performed two-color fluorescence in situ hybridization analysis to detect the numbers of chromosomes 1 and 17, 1p deletion, and 17q gain in 177 neuroblastomas, including 101 tumors that were found by a mass-screening program for infants. Sixty-eight tumors with disomy 1 or tetrasomy 1 were classified as the Dis1 group, and 109 tumors with trisomy 1, pentasomy 1, or a mixed population of cells with trisomy 1 and cells with tetrasomy 1 were classified as the Tris1 group. 17q gain was the most frequent genetic event, followed by 1p deletion, and MYCN amplification in both Dis1 and Tris1 tumors. However, the incidence of all the genetic events was higher in Dis1 tumors than in Tris1 tumors. These findings suggest that Tris1 tumors are more resistant to acquiring the genetic events than are Dis1 tumors. In addition, there was an accumulation of genetic events in more advanced stages, with the exception of a high incidence of 17q gain in the stage IVS Tris1 tumors. Comparative genomic hybridization analysis, which was performed in 59 of the 177 tumors, showed that chromosomes partially lost or gained in Dis1 tumors coincided with chromosomes totally lost or gained in Tris1 tumors. Dis1 and Tris1 tumors were considered to have near-diploid/tetraploid and near-triploid/pentaploid chromosome numbers, respectively. These findings suggest that the same tumor-suppressor genes or oncogenes may be involved in the development and progression of both high- and low-risk neuroblastomas, and that the ploidy state of the tumor plays a fundamental role in the heterogeneous behavior.

Allelic Imbalance↗
PubMed2006

Chromosome transfer experiments link regions on chromosome 7 to radiation resistance in human glioblastoma multiforme.

Glioblastoma multiforme (GM) is the most lethal form of brain tumor, with a median survival of approximately 1 year. Treatment options are limited. Radiation therapy is a common form of treatment, but many tumors are resistant. In earlier studies, we found that gain of chromosome 7 is associated with radiation resistance in human primary GM. In this study, we extend that result to a model system in which we transferred chromosome 7 to recipient cells and confirmed radiation resistance as a function of chromosome 7 gain. We identified three candidate regions on chromosome 7 that conferred radiation resistance in our model system.

Brain Neoplasms↗
PubMed1993

Linkage of Alzheimer's disease to chromosome 21 and chromosome 19 markers: effect of age of onset assumptions.

Age of onset heterogeneity in Alzheimer's disease families was modelled by allowing for different liability classes for affected individuals according to their age of onset when calculating lod scores to chromosome 21 and chromosome 19 markers. Linkage to chromosome 21 was supported in the Boston data set, and the method of age correction did not greatly change the lod scores when only affected individuals were analyzed. The location of a gene on chromosome 19 for late age of onset illness was affected by the assumptions about early onset individuals.

Adult↗
PubMed1988

Loss of alleles on chromosome 18 and on the short arm of chromosome 17 in polyploid colorectal carcinomas.

The zygosity of 19 colorectal carcinomas (either near-diploid or polyploid) from patients known to be heterozygous for RFLPs located on chromosome 18 or on the short arm of chromosome 17 has been examined. In most cases, at least one allele was significantly under-represented. The reason for the absence of complete loss of heterozygosity was investigated for 5 polyploid tumors. It was shown that the diploid component which, in these tumors, is essentially composed of non-neoplastic cells, remains heterozygous as the polyploid component invariably loses heterozygosity. The results strongly suggest that many colorectal carcinomas originate from a single cell which had lost at least part of either chromosome 18 or of one short arm of chromosome 17, or both.

Adult↗
PubMed1993

Mammalian homologues of the Drosophila Son of sevenless gene map to murine chromosomes 17 and 12 and to human chromosomes 2 and 14, respectively.

Activating mutations in the ras genes are commonly found in a wide range of human tumors. We recently cloned two mammalian genes, Son of sevenless 1 (mSos1) and Son of sevenless 2 (mSos2), whose protein products appear to be important positive regulators of ras proteins. Given the proposed role of Sos proteins in ras regulation, and the frequent occurrence of activated ras alleles in tumor cells, we were interested in determining whether the Sos genes may also be activated inappropriately by DNA rearrangement in tumor cells. To investigate this possibility, we have determined the chromosomal locations of both the mouse and the human Sos1 and Sos2 genes, using a combination of genetic linkage analysis and in situ hybridization to chromosomal spreads. We find that the murine Sos1 and Sos2 genes map to chromosomes 17E and 12C3.3-D and their human counterparts to chromosomes 2p21-2p2 and 14q21, respectively. Neither the human nor the mouse Sos loci map close to known mutations or to regions showing consistent karyotypic abnormalities in tumor cells.

Animals↗
PubMed1996

The gene encoding LERK-7 (EPLG7, Epl7), a ligand for the Eph-related receptor tyrosine kinases, maps to human chromosome 5 at band q21 and to mouse chromosome 17.

The eph-related receptors are the largest subfamily of receptor tyrosine kinases. Recently, we and others have identified seven different, but related, cDNAs encoding membrane-bound ligands for this family of receptors. One member, LERK-7, is attached to the cell membrane via glycosyl-phosphatidylinositol linkage and has been found to be a ligand for the eph-family receptors hek, elk, eck, and rek. Using PCR-based screening of human x rodent somatic cell hybrid DNAs, we have assigned the gene that encodes LERK-7 (EPLG7) to human chromosome 5. Fluorescence in situ hybridization to metaphase chromosome preparations using a genomic clone from the locus refined this localization to chromosome 5, band q21. In addition, Southern blot analysis of DNAs from interspecific backcross mice indicated that the mouse homologue Epl7 maps to a homologous region on chromosome 17.

Animals↗
PubMed1996

Genetic analysis of the epidermal differentiation complex (EDC) on human chromosome 1q21: chromosomal orientation, new markers, and a 6-Mb YAC contig.

The epidermal differentiation complex (EDC) unites a remarkable number of structurally, functionally, and evolutionarily related genes that play an important role in terminal differentiation of the human epidermis. It is localized within 2.05 Mb of region q21 on human chromosome 1. We have identified and characterized 24 yeast artificial chromosome (YAC) clones by mapping individual EDC genes, sequence-tagged site (STS) markers (D1S305, D1S442, D1S498, D1S1664), and 10 new region-specific probes (D1S3619-D1S3628). Here we present a contig that covers about 6 Mb of 1q21 including the entire EDC. Fluorescence in situ hybridization on metaphase chromosomes with two YACs flanking the EDC determined its chromosomal orientation and established, in conjunction with physical mapping results, the following order of genes and STSs: 1cen-D1S442-D1S498-S100A10-THH-FLG- D1S1664-IVL-SPRR3-SPRR1-SPRR2-LOR- S100A9-S100A8-S100A7-S100A6-S100A5-S100 A4- S100A3-S100A2-S100A1-D1S305-1qtel. These integrated physical, cytogenetic, and genetic mapping data will be useful for linkage analyses of diseases associated with region 1q21 and for the identification of novel genes and regulatory elements in the EDC.

Cell Differentiation↗
PubMed1999

The murine Bin1 gene functions early in myogenesis and defines a new region of synteny between mouse chromosome 18 and human chromosome 2.

We cloned and functionally characterized the murine Bin1 gene as a first step to investigate its physiological roles in differentiation, apoptosis, and tumorigenesis. The exon-intron organization of the >/=55-kb gene is similar to that of the human gene. Consistent with a role for Bin1 in apoptosis, the promoter included a functional consensus motif for activation by NF-kappaB, an important regulator of cell death. A muscle regulatory module defined in the human promoter that includes a consensus recognition site for myoD family proteins was not conserved in the mouse promoter. However, Bin1 is upregulated in embryonic development by E10.5 in myotomes, the progenitors of skeletal muscle, supporting a role in myogenesis and suggesting that the mouse and human genes may be controlled somewhat differently during development. In C2C12 myoblasts antisense Bin1 prevents induction of the cell cycle kinase inhibitor p21WAF1, suggesting that it acts at an early time during the muscle differentiation program. Interspecific mouse backcross mapping located the Bin1 locus between Mep1b and Apc on chromosome 18. Since the human gene was mapped previously to chromosome 2q14, the location of Bin1 defines a previously unrecognized region of synteny between human chromosome 2 and mouse chromosome 18.

Adaptor Proteins, Signal Transducing↗
PubMed1992

The recombination activating genes, RAG 1 and RAG 2, are on chromosome 11p in humans and chromosome 2p in mice.

The recombination activating genes RAG-1 and RAG-2 are adjacent genes that act synergistically to activate variable-diversity-joining (V(D)J) recombination. Southern analysis of hybrid cell lines derived from patients with the Wilms tumor-aniridia-genitourinary defects-mental retardation (WAGR) syndrome and from mutagenized cell hybrids selected for deletions in chromosome 11 has allowed us to map the chromosomal location of the human RAG locus. The RAG locus defines a new interval of human chromosome 11p, but is not associated with any genetically mapped human disease. Guided by the chromosomal localization of the human recombination activating genes, we have also mapped the location of the mouse Rag locus.

Animals↗
PubMed1991

Duplications of the X chromosome in males: evidence that most parts of the X chromosome can be active in two copies.

We have analysed two duplications of the X chromosome in male patients using chromosome replication and DNA methylation patterns as determinants of the functional status of the duplicated segments. In both cases, the large duplicated regions, Xq12-q22 and Xq26.3-qter, were not inactivated. A review of previously reported male cases revealed that these duplications were also not subject to inactivation. Taken together, the examined duplications cover almost the entire X chromosome except the pericentromeric region and Xq25-26. Thus, most regions of the X chromosome can be present in two functional copies without lethal consequences.

Blotting, Southern↗
PubMed1989

Increased bleomycin-induced chromosome damage in lymphocytes of patients with common variable immunodeficiency indicates an involvement of chromosomal instability in their cancer predisposition.

To study mutagen-induced chromosome instability in cancer disposition, late S and G2 lymphocytes of 15 patients with common variable immunodeficiency and 14 healthy controls were exposed to bleomycin in vitro. The groups did not differ in the frequency of spontaneous chromosome aberrations. In bleomycin-treated samples we found higher numbers of break events per cell and increased frequency of cells with aberrations compared to the control group. A slightly reduced breakage of chromosome group D was noted in patients. These results support the hypothesis that a higher incidence of cancer in patients with genetically determined immunodeficiencies may be explained by an increased mutagen-induced chromosome instability in at least some of them.

Bleomycin↗
PubMed1995

Assignment of a human autoimmune antigen, p80-coilin gene to chromosome 17q21-q23 and of its possible pseudogene to chromosome 14.

In order to determine the chromosomal locations of an autoimmune antigen, the coilin gene and its pseudogene, we amplified the segments of the two genes by the polymerase chain reaction (PCR) and screened a panel of somatic cell hybrids for the presence of the gene products. The results indicate that the human coilin gene and its pseudogene can be assigned to chromosome 17 and chromosome 14, respectively. Further analysis of cell hybrids bearing chromosome 17 with various deletions localized the coilin gene to the region q21-q23.

Animals↗
PubMed1989

The aniridia-Wilms' tumour association: molecular and genetic analysis of chromosome deletions on the short arm of chromosome 11.

We have analysed karyotypes and DNA from three patients with aniridia (congenital absence of irises) and Wilms' tumour. All three had constitutional deletions from the short arm of chromosome 11. The minimum region of overlap of the deletion involves a small region of band 11p13 presumed to contain the genetic loci responsible for both phenotypic abnormalities. Using cells from these patients, somatic cell hybrids with transformed mouse cells have been prepared. Individual subclones retaining either the deletion-11 chromosome or the normal chromosome 11, in addition to a variety of other human chromosomes, have been identified. The relative position of these breakpoints have been determined and the panel of hybrids has been used to map randomly-isolated 11p13 DNA sequences. The characterisation of these deletions has provided a useful panel of hybrids for random mapping strategies designed to identify the Wilms' and aniridia genes.

Cell Line↗
PubMed1992

Meiotic chromosome condensation and pairing in Saccharomyces cerevisiae studied by chromosome painting.

Non-isotopic high resolution in situ hybridization was applied to cytological preparations of sporulating yeast cells. Ribosomal DNA (rDNA) and chromosome V-specific recombinant lambda clones were used to tag individual chromosomes and chromosome subregions. This allowed the study of chromosome behaviour during early meiotic prophase. It was found that chromatin becomes condensed and homologous DNA sequences then appear to become aligned prior to synaptonemal complex formation.

Chromosome Banding↗