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PubMed1994

Dominant optic atrophy (OPA1) mapped to chromosome 3q region. I. Linkage analysis.

Dominant optic atrophy, type Kjer (McKusick no. 165500) is an autosomal dominant eye disease. The disease is characterized by moderate to severe visual impairment with an insidious onset during the first decade of life, blue-yellow dyschromatopsia and centrocecal scotoma of varying density. We examined three extended Danish pedigrees using highly informative short tandem repeat polymorphisms and found linkage of the disease gene (OPA1) to a (CA)n dinucleotide repeat polymorphism at locus D3S1314 (Zmax = 10.34 at theta M = F = 0.075). Using two additional chromosome 3 markers we were able to map the OPA1 gene in the region between D3S1314 and D3S1265 (3q28-qter).

Chromosome Mapping↗
PubMed1997

The human Achaete-Scute homologue 2 (ASCL2,HASH2) maps to chromosome 11p15.5, close to IGF2 and is expressed in extravillus trophoblasts.

Here we describe the cloning of the human Achaete Scute Homologue 2 (HASH2) gene, officially designated ASCL2 (Achaete Scute complex like 2), a homologue of the Drosophila Achaete and Scute genes. In mouse, this gene is imprinted and maps to chromosome 7. We mapped the human homologue close to IGF2 and H19 at 11p15.5, the human region syntenic with mouse chromosome 7, indicating that this imprinted region is highly conserved in mouse and man. HASH2 is expressed in the extravillus trophoblasts of the developing placenta only. The lack of HASH2 expression in non-malignant hydatidiform (androgenetic) moles indicates that HASH2 is also imprinted in man.

Amino Acid Sequence↗
PubMed2006

A validated gene expression model of high-risk multiple myeloma is defined by deregulated expression of genes mapping to chromosome 1.

To molecularly define high-risk disease, we performed microarray analysis on tumor cells from 532 newly diagnosed patients with multiple myeloma (MM) treated on 2 separate protocols. Using log-rank tests of expression quartiles, 70 genes, 30% mapping to chromosome 1 (P < .001), were linked to early disease-related death. Importantly, most up-regulated genes mapped to chromosome 1q, and down-regulated genes mapped to chromosome 1p. The ratio of mean expression levels of up-regulated to down-regulated genes defined a high-risk score present in 13% of patients with shorter durations of complete remission, event-free survival, and overall survival (training set: hazard ratio [HR], 5.16; P < .001; test cohort: HR, 4.75; P < .001). The high-risk score also was an independent predictor of outcome endpoints in multivariate analysis (P < .001) that included the International Staging System and high-risk translocations. In a comparison of paired baseline and relapse samples, the high-risk score frequency rose to 76% at relapse and predicted short postrelapse survival (P < .05). Multivariate discriminant analysis revealed that a 17-gene subset could predict outcome as well as the 70-gene model. Our data suggest that altered transcriptional regulation of genes mapping to chromosome 1 may contribute to disease progression, and that expression profiling can be used to identify high-risk disease and guide therapeutic interventions.

Aged↗
PubMed1996

The porcine TTR locus maps to chromosome 6q.

The sequence of a cDNA clone encoding porcine transthyretin (prealbumin) was used to develop polymorphic markers for the TTR locus. The single-strand conformation polymorphism (SSCP) detected is caused by a silent A/T mutation in the penultimate coding codon and can also be revealed as a SacI restriction fragment length polymorphism (RFLP). The TTR locus was mapped to chromosome 6q by segregation and linkage analysis with these polymorphisms. This assignment confirms the predictions of homology between human chromosome 18 and pig chromosome 6q2.5-q2.6.

Animals↗
PubMed1995

The physical map of the chromosome of a serogroup A strain of Neisseria meningitidis shows complex rearrangements relative to the chromosomes of the two mapped strains of the closely related species N. gonorrhoeae.

A physical map of the chromosome of N. meningitidis Z2491 (serogroup A, subgroup IV-1) has been constructed. Z2491 DNA was digested with NheI, SpeI, SgfI, PacI, BglII, or PmeI, resulting in a limited number of fragments that were resolved by contour-clamped homogeneous electric field (CHEF) electrophoresis. The estimated genome size for this strain was 2,226 kb. To construct the map, probes corresponding to single-copy genes or sequences were used on Southern blots of chromosomal DNA digested with the different mapping enzymes and subjected to CHEF electrophoresis. By determining which fragments from different digests hybridized to each specific probe, it was possible to walk back and forth between digests to form a circular macrorestriction map. The intervals between mapped restriction sites range from 10 to 143 kb in size. A total of 117 markers have been placed on the map; 75 represent identified genes, with the remaining markers defined by anonymous cloned fragments of neisserial DNA. Comparison of the arrangement of genetic loci in Z2491 with that in gonococcal strain FA1090, for which a physical map was previously constructed, revealed complex genomic rearrangements between the two strains. Although gene order is generally conserved over much of the chromosome, a region of approximately 500 kb shows translocation and/or inversion of multiple blocks of markers between the two strains. Even within the relatively conserved portions of the maps, several genetic markers are in different positions in Z2491 and FA1090.

Base Sequence↗
PubMed1992

Mapping human chromosomes by walking with sequence-tagged sites from end fragments of yeast artificial chromosome inserts.

Sequence-tagged sites (STSs) derived from end fragments of chromosome-specific yeast artificial chromosomes (YACs) can facilitate the assembly of an overlapping YAC/STS map. Contigs form rapidly by iteratively screening YAC collections with end-fragment STSs from YACs that have not yet been detected by any previous STS. The map is rendered rapidly useful during its assembly by incorporating supplementary STSs from genes and genetic linkage probes with known locations. Methods for the systematic development and testing of the end-fragments STSs are given here, and a group of 100 STSs is presented for the X chromosome. The mapping strategy is shown to be successful in simulations with portions of the X chromosome already largely mapped into overlapping YACs by other means.

Base Sequence↗
PubMed2005

Deletion mapping of chromosome 17 in benign and malignant adrenocortical tumors associated with the Arg337His mutation of the p53 tumor suppressor protein.

The human p53 tumor suppressor gene is located at the short arm of chromosome 17. A germinative mutation (Arg337His) in the tetramerization domain of p53 has been frequently identified in Brazilian children with sporadic adrenocortical tumors. Loss of heterozygosity at this region was demonstrated in the majority of the cases. In the present study, we performed deletion mapping of chromosome 17 in 30 adrenocortical tumors from 29 Brazilian patients (15 children and 14 adults). One boy had bilateral adrenocortical tumor. Sixteen patients had the germinative Arg337His mutation. Loss of heterozygosity analysis using six polymorphic microsatellite markers disclosed loss of the entire chromosome 17 in 18 tumors (10 adenomas and eight carcinomas) from 17 patients. The Arg337His mutation was present in 13 of them. Chromosomal instability involving chromosomes 2, 9, and 11 was also found in 47, 47, and 70% of the 17 patients who exhibited chromosome 17 losses, respectively. The concomitant loss of chromosomes 2, 9, 11, and 17 was evidenced exclusively in malignant tumors. Therefore, chromosomal instability involving three or more chromosomes may contribute to define the malignant adrenocortical lesions. In conclusion, we demonstrated a high frequency of biallelic inactivation of p53 derived from two distinct events, the germinative Arg337His mutation and the acquired loss of the entire chromosome 17. In addition, the isolated loss of the entire chromosome 17 did not correlate with aggressive tumor behavior in these patients with adrenocortical tumors.

Adolescent↗
PubMed1991

The gene for SP-40,40, human homolog of rat sulfated glycoprotein 2, rat clusterin, and rat testosterone-repressed prostate message 2, maps to chromosome 8.

Sulfated glycoprotein 2 (SGP-2) is a rat glycoprotein that is particularly abundant in seminal fluid, where it is found associated with the acrosome and the tail of mature spermatozoa; for this reason it has been suggested that it has an important role in spermatogenesis. On the basis of nucleotide sequence homology, it has been proposed that the orthologous human gene is that coding for serum protein-40,40 (SP-40,40), a serum protein also called complement lysis inhibitor (CLI), SP-40,40 has been shown to act as a control mechanism of the complement cascade: in fact, it prevents the binding of a C5b-C7 complex to the membrane of the target cell and in this way inhibits complement-mediated cytolysis. SGP-2 and SP-40,40 seem then to be part of different biological systems. Furthermore it has been shown that another protein, testosterone-repressed prostate message 2 (TRPM-2), shares sequence homology with SGP-2 and SP-40,40. TRPM-2 is expressed at high levels and in a temporally precisely defined manner in dying cells, an observation that would suggest its involvement in the cascade of events leading to cell death. We have used a large panel of 24 mouse/human hybrid cell lines and a cDNA for SGP-2, which is also highly homologous to that for rat clusterin, to map the chromosomal location of the orthologous human gene. The mapping data and the Southern analysis presented in this paper, in addition to the data available from the literature, strongly suggest that in the human genome there is a single locus homologous to the probe used and that it codes for the protein which has been called, in different species, SP-40,40, SGP-2, clusterin, and TRPM-2. The chromosomal mapping of the locus for this multiname protein should facilitate its cloning and a better understanding of the apparently many biological functions of its product.

Animals↗
PubMed2006

The gene for a rare autosomal dominant form of pompholyx maps to chromosome 18q22.1-18q22.3.

Pompholyx is a rather common disorder characterized by recurrent crops of vesicles or bullae on the lateral aspects of the fingers, as well as the palms and soles with non-erythematous skin. Until now, very few large families have been reported, so no gene or locus has been identified. Here, we performed a genome-wide search in a large Chinese family to map the chromosome location of the responsible gene. We identified a locus at chromosome 18q22.1-18q22.3 with a maximum two-point LOD score of 3.61 at marker D18S1131 (theta = 0.00). Haplotype analyses indicated that the disease gene is located within 12.07 cM region between markers D18S465 and D18S1362, which corresponds to 8.0 Mb. This is the first locus identified for pompholyx. It will aid future identification of the responsible gene, which will be useful for the understanding of the molecular mechanism of pompholyx.

Adolescent↗
PubMed1992

Deletion mapping of chromosome 3p in female genital tract malignancies using microsatellite polymorphisms.

We have constructed deletion maps of chromosome 3p for cancers of the female genital tract (uterine endometrium, uterine cervix and ovary). The tumours were tested for loss of heterozygosity using CA-repeat polymorphisms. The high degree of informativeness of these markers allowed the construction of detailed deletion maps from a relatively small number of samples. A common region of deletion was identified at chromosome 3p13-21.1 in endometrial cancer and at 3p13-14.3 in cervical cancer; 5 out of 13 (38%) endometrial cancers and six out of eight (75%) cervical cancers showed loss of heterozygosity at these regions. In ovarian cancer a separate common region of deletion was identified at 3p21.1-22; two out of four (50%) ovarian cancers had alleles deleted at this region. These data suggest the presence of a tumour-suppressor gene(s) for endometrial and cervical cancer at 3p13-21.3 and a separate gene at 3p21.1-22 that is involved in the carcinogenesis of ovarian cancer.

Adenocarcinoma↗
PubMed1992

The gene for human erythrocyte protein 4.2 maps to chromosome 15q15.

Protein 4.2 (P4.2), one of the major components of the red-blood-cell membrane, is located on the interior surface, where it binds with high affinity to the cytoplasmic domain of band 3. Individuals whose red blood cells are deficient in P4.2 have osmotically fragile, abnormally shaped cells and moderate hemolytic anemia. cDNA clones from both the 5' and the 3' coding regions of the P4.2 gene were used to map its chromosomal location by fluorescence in situ hybridization. The probes, individually or in combination, gave specific hybridization signals on chromosome 15. The hybridization locus was identified by combining fluorescence images of the probe signals with fluorescence banding patterns generated by Alu-PCR (R-like) probe and by DAPI staining (G-like). Our results demonstrate that the locus of the P4.2 gene is located within 15q15.

Biotin↗
PubMed2004

A chromosome bin map of 16,000 expressed sequence tag loci and distribution of genes among the three genomes of polyploid wheat.

Because of the huge size of the common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) genome of 17,300 Mb, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids and deletion stocks. Each EST detected a mean of 4.8 restriction fragments and 2.8 loci. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.

Chromosome Mapping↗
PubMed1987

Human c-fos proto-oncogene mapped to chromosome 14, band q24.3-q31. Possibilities for oncogene activation by chromosomal rearrangements in human neoplasms.

The human c-fos proto-oncogene was mapped by in situ hybridization to chromosome 14, band q24.3-q31. As a probe we used 3H-labelled mouse c-fos RNA transcribed in vitro by SP6-RNA-polymerase. Of a total of 40 grains on chromosome 14, 19 (47.5%) were located within the 14q24.3-q31 region (p much less than 0.001). Mechanisms for c-fos to gain transforming ability by a break in a critical part of the gene have recently been described. Thus there are several possibilities for chromosomal aberrations within the 14q24.3-q31 region to be responsible for c-fos deregulation and which may result in neoplastic growth. Such specific aberrations are found in a variety of human neoplasms.

Animals↗
PubMed1997

Exclusion of CAG/CTG trinucleotide repeat loci which map to chromosome 4 in bipolar disorder and schizophrenia.

The hypothesis that expanded trinucleotide repeats contribute to the pathogenesis of schizophrenia and bipolar disorder has been recently supported by three independent studies which have shown that patients with either disorder tend to have larger CAG/CTG repeat expansion detection products than controls. In an attempt to identify the specific expanded CAG/CTG locus or loci which are associated with schizophrenia and bipolar disorder, we determined the repeat size at CAG/CTG loci mapping to candidate regions for psychosis. In this study we report our findings from eight loci which map to chromosome 4. We conclude that these loci are unlikely candidates for CAG/CTG repeat expansion in schizophrenia and bipolar disorder.

Bipolar Disorder↗
PubMed2000

A fifth locus for primary autosomal recessive microcephaly maps to chromosome 1q31.

Primary microcephaly is a genetic disorder in which an affected individual has a head circumference >3 SDs below the age- and sex-related mean. A small but apparently normally formed brain is the reason for the reduced head circumference, and, probably because of this, all affected individuals are mentally retarded. The condition is genetically heterogeneous, and four loci have already been identified. We now report a fifth locus, MCPH5, which is an 8-cM region mapping to chromosome 1q31, defined by the markers GATA135F02 and D1S1678.

Adult↗
PubMed1987

The human placental alkaline phosphatase gene and related sequences map to chromosome 2 band q37.

A human placental alkaline phosphatase (PLAP) cDNA was isolated from a lambda gt 10 library of the cell line HEp-2. Southern blots probed with a fragment of the cDNA clone showed that the human genome may contain more than one PLAP-related sequence. The PLAP probe showed person-to-person variation in banding pattern with a number of enzymes. Using a panel of human/rodent somatic cell hybrids the PLAP sequences were mapped to chromosome 2. In situ hybridization confirmed this assignment and localized the gene(s) to chromosome 2 band q37.

Alkaline Phosphatase↗
PubMed1999

Genomic structure, alternative transcripts and chromosome location of the human LIM domain binding protein 1 gene LDB1.

By protein interaction screening using a radioactive LMO2 protein probe we have isolated a LIM domain binding protein. The gene shows high homology to independently isolated genes from mouse, Xenopus and Drosophila called Ldb1/Nli/Clim-2, Xldb1 and Chip, respectively. The human and mouse genes differ by only two amino acids, suggesting that the gene that we have isolated is the human homologue. Here we describe the genomic organization, alternative transcript forms and the chromosome mapping of the human gene LDB1 (alias NLI). The gene is spread over at least 12 kb and has 11 exons. Preceding the described ATG initiation site in the mouse a highly conserved region between mouse, chicken and human was detected with a second possible in frame initiation site coding for further 36 amino acids. An alternative splice site adding six nucleotides corresponding to the addition of two amino acids at the end of exon 10 was found. The gene was mapped to chromosome 10q24-->q25 by in situ hybridization, a region frequently deleted in many types of cancer. Fine mapping with a radiation hybrid panel localized the gene in the interval between the markers D10S603 and D10S540.

Adaptor Proteins, Signal Transducing↗