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PubMed2004

A chromosome bin map of 2148 expressed sequence tag loci of wheat homoeologous group 7.

The objectives of this study were to develop a high-density chromosome bin map of homoeologous group 7 in hexaploid wheat (Triticum aestivum L.), to identify gene distribution in these chromosomes, and to perform comparative studies of wheat with rice and barley. We mapped 2148 loci from 919 EST clones onto group 7 chromosomes of wheat. In the majority of cases the numbers of loci were significantly lower in the centromeric regions and tended to increase in the distal regions. The level of duplicated loci in this group was 24% with most of these loci being localized toward the distal regions. One hundred nineteen EST probes that hybridized to three fragments and mapped to the three group 7 chromosomes were designated landmark probes and were used to construct a consensus homoeologous group 7 map. An additional 49 probes that mapped to 7AS, 7DS, and the ancestral translocated segment involving 7BS also were designated landmarks. Landmark probe orders and comparative maps of wheat, rice, and barley were produced on the basis of corresponding rice BAC/PAC and genetic markers that mapped on chromosomes 6 and 8 of rice. Identification of landmark ESTs and development of consensus maps may provide a framework of conserved coding regions predating the evolution of wheat genomes.

Chromosome Mapping↗
PubMed1994

The putative glioma tumor suppressor gene on chromosome 19q maps between APOC2 and HRC.

The frequent allelic loss of chromosome 19q in human gliomas suggests that 19q harbors a tumor suppressor gene that is integral to glioma tumorigenesis. Our initial deletion mapping of this gene localized the common region of deletion to the distal long arm, 19q13.2-13.4. To bracket the putative tumor suppressor gene further, we have studied this region in 55 gliomas, using loss of heterozygosity studies for 11 well mapped, highly informative microsatellite polymorphisms that cover this area: D19S178; BCL3; APOC2; ERCC1; DM; D19S112; HRC; D19S246; KLK; D19S180; and D19S254 (from centromeric to telomeric). Twenty astrocytic, oligodendroglial, and mixed gliomas had deletions affecting this region. Of nine partial deletions, two cases maintained heterozygosity at APOC2 while showing allelic loss at the more telomeric markers, ERCC1 and DM, while five cases maintained heterozygosity at HRC but lost the more centromeric markers, D19S112 and DM. Nine cases lost the entire D19S178 to D19S254 region. Three astrocytic gliomas, including one with an interstitial deletion, had terminal deletions of 19q13.4. The minimum area of overlap shared by the interstitial deletions is between APOC2 and HRC, including ERCC1, DM, and D19S112. These findings suggest that the glioma tumor suppressor gene maps to an approximately 8-cM/5-megabase region on 19q13.2-13.3 between the proximal marker APOC2 and the distal marker HRC. Among the DNA repair/DNA metabolism genes on chromosome 19q, ERCC1, LIG1, and perhaps ERCC2 are within the common area of deletion; XRCC1 is centromeric and is therefore excluded as a candidate.

Brain Neoplasms↗
PubMed1998

Human CYP11B2 (aldosterone synthase) maps to chromosome 8q24.3.

Aldosterone synthase (AS) is encoded by the CYP11B2 gene, a candidate for familial hypertension. CYP11B2 was previously mapped to chromosome 8q but its precise localization is necessary for genetic studies of hypertension. The present study reports the genetic mapping of the human CYP11B2 gene by radiation hybrid (RH) analysis, the isolation of a bacterial artificial chromosome (BAC) containing this gene and its physical mapping by fluorescent in situ hybridization (FISH). The CYP11B2 locus is on the most distal segment of the long arm of chromosome 8, proximal to the microsatellite polymorphic marker D8S1704. This location, which was confirmed by FISH, is approximately 60cM telomeric to the currently listed human gene locus (chromosome 8q21-22) and corresponds to cytogenetic band 8q24.3. The BACs containing the gene and a high-resolution map of the CYP11B2 locus are useful for genetic studies of hypertension and other endocrine disorders.

Chromosome Mapping↗
PubMed2001

A second gene for otosclerosis, OTSC2, maps to chromosome 7q34-36.

Otosclerosis due to abnormal bone homeostasis of the otic capsule is a frequent cause of hearing loss in adults. Usually, the hearing loss is conductive, resulting from fixation of the stapedial footplate, which prevents normal ossicular vibration in response to sound. An additional type of sensorineural hearing loss may be caused by otosclerotic damage to the cochlea. The etiology of the disease is unknown, and both environmental and genetic factors have been implicated. Autosomal dominant inheritance with reduced penetrance has been proposed, but large families are extremely rare. To elucidate the pathogenesis of the disease, identification of the responsible genes is essential. In this study, we completed linkage analysis in a Belgian family in which otosclerosis segregates as an autosomal dominant disease. After excluding linkage to a known locus on chromosome 15 (OTSC1), we found linkage on chromosome 7q, with a multipoint LOD score of 3.54. Analysis of key recombinant individuals maps this otosclerosis locus (OTSC2) to a 16-cM interval on chromosome 7q34-36 between markers D7S495 and D7S2426.

Alleles↗
PubMed1999

The human dendritic cell marker CD83 maps to chromosome 6p23.

The chromosomal localization of the human CD83 gene was determined using somatic cell hybrids, a radiation hybrid mapping panel and FISH analysis on human metaphase chromosomes. PCR-based analysis of a single chromosome hybrid panel identified the presence of the CD83 gene on human chromosome 6 and subsequent analysis of the Genebridge4 radiation panel located the gene between AFMa192wg9 and AFMb322wd1 with a lod score of 9.2. Finally, using FISH analysis the CD83 gene was localized to chromosome 6 band p23.

Antigens, CD↗
PubMed1995

Placement and refined mapping of established and new markers on human chromosome 11q using a small panel of somatic cell hybrids.

Constructing detailed chromosome maps relies on the ability to place new markers rapidly and accurately. Here we map two new anonymous DNA markers precisely on chromosome 11q and refine the location of established markers using a panel of just six fragmentation hybrids, with reference to four translocation chromosomes. As several of the hybrids retain multiple segments of chromosome 11, it is possible to quickly assign new markers to subintervals using this modest set of hybrid DNAs.

Base Sequence↗
PubMed1987

Human gastrin-releasing peptide gene maps to chromosome band 18q21.

A complementary DNA clone encoding human pre-pro gastrin-releasing peptide, a 27-amino acid neuropeptide and putative growth factor, was used to determine the chromosomal location of this gene. Southern blot hybridization to genomic DNA isolated from a panel of human-rodent somatic cell hybrids unambiguously maps this gene to human chromosome 18. In situ chromosomal hybridization confirms the hybrid data and further localized the gene to chromosome band 18q21. Karyotypic abnormalities in tumors and inherited disease states which involve chromosome band 18q21 may now be studied for correlated changes in the structure and expression of the human GRP gene.

Animals↗
PubMed1997

A branch-and-cut approach to physical mapping of chromosomes by unique end-probes.

A fundamental problem in computational biology is the construction of physical maps of chromosomes from hybridization experiments between unique probes and clones of chromosome fragments in the presence of error. Alizadeh, Karp, Weisser and Zweig (Algorithmica 13:1/2, 52-76, 1995) first considered a maximum-likelihood model of the problem that is equivalent to finding an ordering of the probes that minimizes a weighted sum of errors and developed several effective heuristics. We show that by exploiting information about the end-probes of clones, this model can be formulated as a Weighted Betweenness Problem. This affords the significant advantage of allowing the well-developed tools of integer linear-programming and branch-and-cut algorithms to be brought to bear on physical mapping, enabling us for the first time to solve small mapping instances to optimality even in the presence of high error. We also show that by combining the optimal solution of many small overlapping Betweenness Problems, one can effectively screen errors from larger instances and solve the edited instance to optimality as a Hamming-Distance Traveling Salesman Problem. This suggests a new approach, a Betweenness-Traveling Salesman hybrid, for constructing physical maps.

Chromosome Mapping↗
PubMed1995

Human protein synthesis initiation factor eIF-4 gamma is encoded by a single gene (EIF4G) that maps to chromosome 3q27-qter.

Messenger RNA binding to the ribosome, the rate-limiting step in eukaryotic protein synthesis, is catalyzed by the eIF-4 group of initiation factors. These factors collectively bind to the m7GTP-containing cap of mRNA and unwind mRNA secondary structure at the expense of ATP. One member of the group, eIF-4 gamma, is the target for proteolytic cleavage during picornavirus infection, an event that is thought to be responsible for the inhibition of host cellular mRNA translation. Human eIF-4 gamma migrates as a cluster of polypeptides in the range of 200-220 kDa during SDS-PAGE, raising the possibility that it is a family of proteins encoded by separate genes. In this study, we present genomic Southern blotting results which indicate that there is only a single gene, here designated EIF4G. Furthermore, we have employed a PCR approach to map EIF4G to chromosome 3q27-qter.

Animals↗
PubMed2003

A gene locus for steroid-resistant nephrotic syndrome with deafness maps to chromosome 14q24.2.

Steroid-resistant nephrotic syndrome (SRNS) leads to end-stage renal disease (ESRD) in childhood or young adulthood. Positional cloning for genes causing SRNS has opened the first insights into the understanding of its pathogenesis. This study reports a genome-wide search for linkage in a consanguineous Palestinian kindred with SRNS and deafness and detection of a region of homozygosity on chromosome 14q24.2. Multipoint analysis of 12 markers used for further fine mapping resulted in a LOD score Z(max) of 4.12 (theta = 0) for marker D14S1025 and a two-point LOD score of Z(max) = 3.46 (theta = 0) for marker D14S77. Lack of homozygosity defined D14S1065 and D14S273 as flanking markers to a 10.7 cM interval. The identification of the responsible gene will provide new insights into the molecular basis of nephrotic syndrome and sensorineural deafness.

Alleles↗
PubMed2000

Molecular cloning and expression analysis of the human DA41 gene and its mapping to chromosome 9q21.2-q21.3.

DA41 was previously identified as one of the DAN-binding proteins, via a yeast-based two-hybrid screening strategy. In the present study, we cloned a human homolog of DA41 cDNA. Structural analysis revealed that human DA41 cDNA consisted of 2,861 nucleotides in length and encoded a protein of 589 amino acids, with a predicted molecular mass of 62.4kDa. Human DA41 exhibited an 86% amino acid sequence identity to rat DA41, indicating the evolutionarily conserved structure and function of DA41. A database search for DA41-related protein(s) identified mouse PLIC-1, PLIC-2, frog XDRP1, and yeast DSK2. DA41 and each DA41-related protein contain a ubiquitin-like domain in their amino-terminal regions. DA41 was expressed ubiquitously in adult human tissues, with relatively higher levels in pituitary gland, adrenal gland, kidney, thymus, and placenta. Fluorescence in situ hybridization (FISH) revealed that DA41 was mapped to human chromosome 9q21.2-q21.3, a position overlapping the candidate tumor suppressor locus for bladder cancer.

Adaptor Proteins, Signal Transducing↗
PubMed1999

A novel locus for Usher syndrome type II, USH2B, maps to chromosome 3 at p23-24.2.

Usher type II syndrome is defined by the association of retinitis pigmentosa, appearing in the late second to early third decade of life, with congenital moderate to severe non-progressive hearing loss. This double sensory impairment is not accompanied by vestibular dysfunction. To date, only one Usher type II locus, USH2A, at chromosome band 1q41, has been defined. Here, we demonstrate by linkage analysis, that the gene responsible for Usher type II syndrome in a Tunisian consanguineous family maps to chromosome 3 at position p23-24.2, thus providing definitive evidence for the genetic heterogeneity of the syndrome. A maximum lod score of 4.3 was obtained with the polymorphic microsatellite markers corresponding to loci D3S1578, D3S3647 and D3S3658. This maps the gene underlying USH2B to a chromosomal region which overlaps the interval defined for the non-syndromic sensorineural recessive deafness DFNB6, raising the possibility that a single gene underlies both defects. However, the audiometric features in the patients affected by USH2B and DFNB6 are very different.

Abnormalities, Multiple↗
PubMed1995

New phenotype of the cerebral autosomal dominant arteriopathy mapped to chromosome 19: migraine as the prominent clinical feature.

A survey was carried out on a large family presenting the symptoms of familial arteriopathy (CADASIL) recently mapped to chromosome 19. This is characterised clinically by recurrent subcortical infarcts developing into pseudobulbar palsy and subcortical dementia, and radiologically by early MRI abnormalities. To characterise this familial condition, 43 members older than 20 years and spreading over four generations were studied clinically (31 living, 12 deceased), genetically, and radiologically by MRI (n = 31). Twenty out of 43 were found to be clinically symptomatic and of these 13 out of 31 had MRI abnormalities. Genetic studies mapped this condition to the locus of CADASIL (lod score > 3). The natural history suggests a chronological clinicoradiological staging of this phenotype of CADASIL: stage I between 20 and 40 years with frequent migraine-like episodes and well delineated lesions of the white matter; stage II between 40 and 60 years with stroke-like episodes, bipolar or monopolar-like psychotic disorders, coalescent lesions of the white matter, and well delineated lesions of the basal ganglia; and stage III over 60 years with subcortical dementia, pseudobulbar palsy, diffuse leukoencephalopathy, and multiple well delineated lesions of the basal ganglia. This phenotype differs from the other two previously described by high frequency of migraine, frequency of psychotic disorders, and early neurological manifestations. The new acronym "cerebral autosomal dominant arteriopathy with subcortical infarcts, leukoencephalopathy, and migraine" (CADASILM) is proposed to better describe this particular subvariety of CADASIL.

Adult↗
PubMed2005

A novel autosomal recessive non-syndromic hearing impairment locus (DFNB47) maps to chromosome 2p25.1-p24.3.

Hereditary hearing impairment (HI) displays extensive genetic heterogeneity. Autosomal recessive (AR) forms of prelingual HI account for approximately 75% of cases with a genetic etiology. A novel AR non-syndromic HI locus (DFNB47) was mapped to chromosome 2p25.1-p24.3, in two distantly related Pakistani kindreds. Genome scan and fine mapping were carried out using microsatellite markers. Multipoint linkage analysis resulted in a maximum LOD score of 4.7 at markers D2S1400 and D2S262. The three-unit support interval was bounded by D2S330 and D2S131. The region of homozygosity was found within the three-unit support interval and flanked by markers D2S2952 and D2S131, which corresponds to 13.2 cM according to the Rutgers combined linkage-physical map. This region contains 5.3 Mb according to the sequence-based physical map. Three candidate genes, KCNF1, ID2 and ATP6V1C2 were sequenced, and were found to be negative for functional sequence variants.

Chromosome Mapping↗
PubMed1999

Cloning and characterization of a novel beta integrin-related cDNA coding for the protein TIED ("ten beta integrin EGF-like repeat domains") that maps to chromosome band 13q33: A divergent stand-alone integrin stalk structure.

Herein we describe the cDNA sequence of a novel human gene, ITGBL1, encoding a beta integrin-related protein termed TIED [for ten beta integrin epidermal growth factor (EGF)-like repeat domains]. Overlapping cDNA clones from fetal lung, HUVEC, and osteoblast cDNA libraries encode a sequence comprising a typical signal peptide, followed by a hydrophilic 471-amino-acid domain containing 10 tandem EGF-like repeats strikingly similar to those found in the cysteine-rich "stalk-like" structure of integrin beta subunits. The EGF-like repeats of TIED and beta integrins are unique in that they alternate in homology and possess two additional cysteines (eight in total) whose positions differ from those in the other eight-cysteine EGF-like domains of laminin, fibrillin, and the latent TGF-beta binding proteins. TIED mRNA transcripts of 2.8 kb were detected in aorta, thymus, and osteogenic sarcoma cells. The ITGBL1 gene was mapped to human chromosome 13, band 13q33. We suggest that ITGBL1 may be linked in some way with the evolution of the integrin beta subunits.

3' Untranslated Regions↗