Loss of heterozygosity on the long arm of human chromosome 7 in sporadic renal cell carcinomas

Cytogenetic and molecular analysis of DNA sequences with highly polymorphic microsatellite markers have implicated allele loss in several chromosomal regions including 3p, 6p, 6q, 8p, 9p, 9q, 11p and 14q in the pathogenesis of sporadic renal cell carcinomas (RCCs). Deletions involving the long arm of chromosome 7 have not been described in RCCs although they have been seen in several other tumor types. However, there have been no detailed analysis of loss of heterozygosity (LOH) of 7q sequences in sporadic RCCs. We therefore studied LOH for DNA sequences on 7q with 10 highly polymorphic markers in 92 matched normal/tumor samples representing sporadic RCCs including papillary, nonpapillary, and oncocytomas in order to determine whether allelic loss could be detected in a tumor type with no visible 7q rearrangements at the cytogenetic level. We found chromosome 7q allele loss in 59 of 92 cases (64%) involving one, two, or more microsatellite markers. The most common allele loss included loci D7S522 (24%) and D7S649 (30%) at 7q31.1-31.2, a region that contains one of the common fragile sites, FRA7G. By comparative multiplex PCR analysis, we detected a homozygous deletion of one marker in the 7q 31.1-31.2 region in one tumor, RC21. These results support the idea that a tumor suppressor gene in 7q31 is involved in the pathogenesis of sporadic renal cell carcinomas.     

Isolation and characterization of three microsatellite markers in the proximal long arm of the human X chromosome

Three microsatellites have been identified in cosmids from the human X chromosome. The cosmids have been assigned locus numbers DXS554, DXS559, and DXS566 and have been localized to Xq12-q13 (DXS554 and DXS559) and Xq13 (DXS566). In addition, they have been genetically mapped in relation to the androgen receptor (AR), phosphoglycerate kinase 1, pseudogene 1 (PGK1P1), and phosphoglycerate kinase (PGK1) loci in the proximal long arm. Genetically, the localization of microsatellites at DXS554 and DXS566 is indistinguishable from PGK1, whereas that at DXS559 maps between AR and PGK1, close to PGK1P1. DXS566 is identical to the independently identified DXS441 marker. These markers should be useful for physical and genetic mapping in this region.     

Localization of the human CXC chemokine subfamily on the long arm of chromosome 4 using radiation hybrids

Rat striatin, a recently discovered calmodulin-binding protein belonging to the WD repeat family, is expressed in neurons, mostly in the striatum and motor and olfactory systems. Striatin is localized in the somato-dendritic compartment of neurons, mainly in the spines. It may play a role in dendritic Ca2+ signaling. Here we report the cloning and sequencing of human striatin cDNA (HGMW-approved symbol STRN), the localization of the gene to chromosome 2p22-p21, and its preferential expression in brain. The human cDNA sequence is predicted to encode a 780-amino-acid protein possessing eight WD repeats. Striatin is highly conserved between rat and human with 96% identity and 98% similarity at the amino acid level. Since the Caenorabditis elegans genome also contains a closely related striatin coding sequence, the function of striatin is likely to be well conserved.     

A linkage map of human chromosome 21:43 PCR markers at average intervals of 2.5 cM

A genetic linkage map of human chromosome 21q (HC21q) containing 43 markers genotyped by the polymerase chain reaction in the CEPH pedigrees is presented. The markers placed on this map are highly polymorphic with an average heterozygosity of 61%. The average interval size of the markers localized at 1000:1 odds is 2.5 cM. The map has a total length of 65.5 cM, with male and female lengths of 47.7 and 83.3 cM, respectively. The genotypes used in the construction of this map were subjected to rigorous error checking, which is reflected in the shorter map length compared to previous maps; the estimated error rate in genotyping is less than 0.04%. As noted in previous linkage maps there is increased recombination in females on proximal HC 21q and in the male in a region near the telomere. This map of HC 21 represents a highly informative and dense meiotic linkage map and will be useful in linking disease phenotypes to loci on this chromosome.     

A microsatellite genetic linkage map of human chromosome 13

We have characterized 21 polymorphic (CA)n microsatellites for the development of a genetic map of chromosome 13. Fifteen markers were isolated from a flow-sorted chromosome 13 library, four CA repeats were derived from NotI-containing cosmid clones, and two polymorphic markers were described previously (J. L. Weber, A. E. Kwitek, and P. E. May, 1990, Nucleic Acids Res. 18: 4638; L. Warnich, I. Groenwald, L. Laubscher, and A. E. Retief, 1991, Am. J. Hum. Genet. 49(Suppl.): 372 (Abstract)). Regional localization for all of the markers was performed by amplification of DNA from five somatic cell hybrids containing different deletions of chromosome 13. Genetic markers were shown to be distributed throughout 6 of the 11 resolvable chromosomal subregions. Using data from nine families provided by the Centre d'Etude du Polymorphisme Humain (CEPH), a framework map of 12 of these 21 markers was developed. Six of the 12 markers form three pairs, with each two members of a pair being tightly linked, such that nine systems of markers can be distinguished. The average heterozygosity of these 12 markers is 0.75. The total length of the sex-averaged map is 65.4 cM (Kosambi), with an average distance of 8.2 cM between systems of markers (eight intervals). Seven remaining markers were placed provisionally into the framework map.     

A somatic cell hybrid map of human chromosome 13

We have constructed a chromosome 13 somatic cell hybrid map using seven cell lines: PGMEA6, a hybrid containing the entire chromosome 13, and six hybrids containing various deletions of chromosome 13 (BARF7, PPF22, KBF11, KSF39, CF25, and CF27). We have mapped 80 markers that define 10 regions of chromosome 13 with respect to 10 breakpoints in the mapping panel; these regions range in size from 4 to 24 Mb, with an average size of 8 Mb. The 80 markers sublocalized on our mapping panel include 10 Alu-PCR clones, 6 of which were converted to sequence-tagged sites; 40 (CA)n repeat-containing clones, 27 of which are microsatellite PCR markers; 8 (AAAG)n repeat-containing PCR markers, 1 two-allele PCR marker, 4 genes or expressed sequences, and 17 anonymous DNA probes. This low-resolution physical map can be used as a backbone map for more refined physical mapping using radiation hybrids or yeast artificial chromosomes.     

A high-resolution metric HAPPY map of human chromosome 14

We have mapped 1001 novel sequence-tagged sites on human chromosome 14. The mean spacing between markers is approximately 90 kb, most markers are mapped with a resolution of better than 100 kb, and physical distances are determined. The map was produced using HAPPY mapping, a simple and widely applicable in vitro approach that is analogous to linkage or to radiation hybrid mapping, but that circumvents many of the difficulties and potential artifacts associated with these methods. We show also that the map serves as a robust scaffold for building physical maps using large-insert clones.     

Evidence for two distinct tumor-suppressor gene loci on the long arm of chromosome 11 in human oral cancer

Loss of heterozygosity (LOH) on human chromosome 11 has been reported in a variety of human cancers. To search for the existence of tumor-suppressor gene(s) associated with oral squamous cell carcinoma (SCC) on chromosome 11, we have performed high-resolution deletion mapping in 31 patients with oral SCC using 22 microsatellite markers for this chromosomal region. LOH was observed in 14 of 25 cases (56.0%) that were informative with at least one locus. Most allelic deletions detected in our study were specific to the long arm of the chromosome. Furthermore, the data presented here show 2 distinct, commonly deleted regions. The first region, with frequent LOH, was restricted between markers DIIS939 and DIIS924 separated by 3 centimorgans (cM) on chromosome 11q23. The second region of common deletion was identified between markers DIIS912 and DIIS910, separated by 7 cM at 11q25. Our results suggest that at least 2 tumor-suppressor genes involved in the development of oral SCC are present on the long arm of chromosome 11.     

Isolation of NotI sites from chromosome 22q11

Chromosome 22q11 contains a large number of interesting loci, including genes associated with cancer and developmental defects. The region is also the site of the lambda immunoglobulin variable and constant regions and the BCR, gamma-glutamyl transpeptidase, and GGT-like activity multigene families. Because of the complexities associated with mapping highly related gene families, we have examined the utility of mapping large areas of DNA using a defined approach. A total of 21 complete NotI sites from band q11 were cloned and ordered into six noncontiguous clusters of sites using a combination of somatic cell hybrid panels, NotI jumping and linking libraries, and fluorescence in situ hybridization. The largest cluster spanned an estimated 2 Mb of NotI fragments, the smallest 115 kb. Approximately 3.5 Mb of band q11 could be examined for rearrangements in NotI restriction enzyme fragments. A number of conserved sequences, two genes, and a minimum of two families of related sequences were identified adjacent to NotI sites.     

Detailed deletion mapping of the long arm of chromosome 6 in adult T-cell leukemia

Previously, we have found that the loss of heterozygosity (LOH) was frequently observed on chromosome 6q in acute/lymphoma-type adult T-cell leukemia (ATL), suggesting a putative tumor-suppressor gene for ATL may be present on chromosome 6q. To further define a region containing this gene, we performed fine-scale deletional mapping of chromosome 6q in 22 acute/lymphomatous ATL samples using 24 highly informative microsatellite markers. LOH was found in 9 samples (40. 9%) at 1 or more of the loci examined. Of the 9 samples, 8 shared the same smallest commonly deleted region flanked by D6S1652 and D6S1644 (6q15-21). The genetic distance between these two loci is approximately 4 cM. These results suggest that a putative tumor-suppressor gene on chromosome 6q15-21 probably plays a very important role in the evolution of acute/lymphomatous ATL. Our map provides key information toward cloning the gene.     

Linkage analysis between manic-depressive illness and markers on the long arm of chromosome 11

The effect of two cyclic enkephalin analogs (IVS-43 and IVS-46) on the group and individual behavior of rhesus macaques and hamadryas baboons has been studied. A pronounced influence of IVS-46 on competitive and operant goal-directed behavior of the monkeys was identified.     

Independent amplification and frequent co-amplification of three nonsyntenic regions on the long arm of chromosome 20 in human breast cancer

DNA amplification at 20q13.2 is common in breast cancer, correlates with poor prognosis, and may reflect location of an important oncogene. Recently, other regions along 20q were also found to undergo amplification. Here, amplification levels and patterns of co-amplification were analyzed by interphase fluorescence in situ hybridization at 14 loci along 20q in 146 uncultured breast carcinomas and 14 cell lines. Three regions were independently amplified in uncultured tumors: RMC20C001 region at 20q13.2 (highly amplified in 9.6% of the cases), PTPN1 region 3 Mb proximal (6.2%), and AIB3 region at 20q11 (6.2%). Co-amplifications involving two or three of these regions were seen in 11 of the 19 highly amplified tumors. The results suggest that three distinct nonsyntenic regions along 20q may be important and that complex chromosomal rearrangements underlie their frequent co-amplification in breast cancer.     

Seven genes from human chromosome 18 map to chromosome 24 in the bovine

Bovine sequence tagged sites (STSs) were developed for seven genes and used for synteny mapping with a hybrid bovine x rodent cell line panel. The genes were thymidylate synthase (TYMS), pituitary adenylate cyclase activating peptide (ADCYAP1), and melanocortin-2 receptor (MC2R) from the short arm of human chromosome (HSA) 18 and N-cadherin (CDH2), transthyretin (TTR), gastrin-releasing peptide (GRP), and plasminogen activator inhibitor 2 (PAI2) from the long arm of HSA 18. Primers for these genes were designed with human, ovine, or bovine sequences aligned with a sequence from a second species. The bovine PCR product was cloned, and the fragment was sequenced to verify that the homologous gene was indeed amplified. A second set of bovine-specific PCR primers were developed for each gene from these sequences. These STSs were used for synteny mapping, and all seven genes were syntenic with markers of bovine chromosome (BTA) 24. The concordance with BTA 24 was at least 96.5% for all genes.     

The gene encoding human glutathione synthetase (GSS) maps to the long arm of chromosome 20 at band 11.2

Two forms of glutathione synthetase deficiency have been described. While one form is mild, causing hemolytic anemia, the other more severe form causes 5-oxo-prolinuria with secondary neurological involvement. Despite the existence of two deficiency phenotypes, Southern blots hybridized with a glutathione synthetase cDNA suggest that there is a single glutathione synthetase gene in the human genome. Analysis of somatic cell hybrids showed the human glutathione synthetase gene (GSS) to be located on chromosome 20, and this assignment has been refined to subband 20q11.2 using in situ hybridization.     

A bacterial artificial chromosome-based framework contig map of human chromosome 22q

We have constructed a physical map of human chromosome 22q using bacterial artificial chromosome (BAC) clones. The map consists of 613 chromosome 22-specific BAC clones that have been localized and assembled into contigs using 452 landmarks, 346 of which were previously ordered and mapped to specific regions of the q arm of the chromosome by means of chromosome 22-specific yeast artificial chromosome clones. The BAC-based map provides immediate access to clones that are stable and convenient for direct genome analysis. The approach to rapidly developing marker-specific BAC contigs is relatively straightforward and can be extended to generate scaffold BAC contig maps of the rest of the chromosomes. These contigs will provide substrates for sequencing the entire human genome. We discuss how to efficiently close contig gaps using the end sequences of BAC clone inserts.     

The prognostic significance of deletion of the long arm of chromosome 20 in myeloid disorders

OBJECTIVE: The effect of cigarette smoking on gallbladder (GB) emptying and refilling after a fatty meal was examined in 10 healthy volunteers (four women and six men, mean age 27.6 yr). METHODS: On three different days, the subjects underwent in randomized order: a control test without smoking (C), or they smoked two cigarettes during the early (0-20 min; S0-20), or late (20-40 min; S20-40) phase of the meal-induced GB emptying. GB volumes were measured ultrasonographically before the meal and at 10, 20, 30, 40, 60, 90, 120, 150, and 180 min postprandially. Two-way ANOVA was applied for statistical assessment of the results. RESULTS: The fasted GB volumes amounted to 15.7 +/- 1.8 cm3 (C), 15.0 +/- 1.7 cm3 (S0-20), and 18.4 +/- 2.3 cm3 (S20-40), F2;18 = 1.524, NS. Maximum GB emptying was observed until 60 min after the meal, with a nadir of the GB volume amounting to 7.3 +/- 1.3 cm3 (C), 6.6 +/- 1.2 cm3 (S0-20), and 7.1 +/- 1.1 cm3 (S20-40). No significant difference was found between the stimuli tested when absolute GB volumes were considered: F2;180 = 2.725, NS. Analysis of the GB emptying-refilling curves normalized for the fasted GB volume revealed that a significant inhibitory effect was produced by smoking two cigarettes during the late phase of GB emptying on the subsequent GB refilling: F2;162 = 11.066, p < 0.001 for the whole curve, and F2;72 = 7.126, p < 0.005 for the refilling phase. A significant contrast was found next between S20-40 and the control day (p < 0.001 whole curve; p < 0.005 refilling phase only), as well as between S20-40 and S0-20 (p < 0.001 whole curve; p < 0.025 refilling phase only). CONCLUSION: We conclude that smoking two cigarettes does not disturb the fatty meal-induced GB contraction in healthy humans. Subsequent GB refilling is delayed if smoking takes place during the late phase of the postprandial GB contraction.     

Ophthalmic findings with partial trisomy (duplication) of the long arm of chromosome 7

BACKGROUND: The sensitivity of diagnostic imaging of processes in the parotid gland has been increased by improved spatial resolution, yet specificity remains unchanged. The purpose of this study was to determine whether the low-flow color duplex technique alters the specificity of B-mode ultrasonography. PATIENTS AND METHODS: Forty-one patients with tumors of the parotid gland were examined by color duplex echography as well as histologically. Twenty-eight of the 41 patients had benign tumors and 13 had malignant disease. In 17 of 41 patients, color duplex ultrasonography failed to detect any vascularization within the tumor. Histopathological examination showed that 3 of these 17 tumors were malignant and 14 of 17 were benign. Intranodal vascularization was detected in 24 cases. Ten of these patients were found to have malignant tumors of the parotid gland; 14 had benign parotid tumors. RESULTS: Our present findings show that marked intratumoral vascularization especially appears in malignant tumors. In contrast to lymph nodes, the location and texture of intranodal blood vessels do not provide information about the nature of the neoplasm. CONCLUSIONS: Low flow duplex ultrasonography does not increase the specificity of preoperative examination in tumors of the parotid gland.