Smallest Region Of Overlap Research Articles

A homozygous deletion in a small cell lung cancer cell line involving a 3p21 region with a marked instability in yeast artificial chromosomes: Kok K, Van den Berg A, Veldhuis PMJF, Van der Veen AY, Franke M, Schoenmakers EFPM et al. Department of Medical Genetics, University of Groningen, A. Deusinglaan 4, 9713 AW Groningen. Cancer Res 1994;54:4183–4187

All types of lung carcinoma are characterized by a high frequency of loss of sequences from the short arm of chromosome 3, the smallest region of overlap containing D3F15S2 in band p21. Here we characterize a 440-kilobase segment from this region, which we found homozygously deleted in one of our small cell lung cancer-derived cell lines. The homozygous deletion maps between UBE1L and ZnF16, just centromeric to D3F15S2. Yeast artificial chromosomes with inserts originating from the deleted region are very unstable and readily lose parts of their insert.

Frequent loss of heterozygosity at telomeric loci on 22q in sporadic colorectal cancers.

To date, several tumor-suppressor genes responsible for the tumorigenesis of colorectal cancer have been identified. However, studies of loss of heterozygosity (LOH) have suggested several chromosomal regions which may contain additional tumor-suppressor genes for colorectal cancer. To determine the extent and variation of allelic loss on 22q, on which LOH has been frequently observed, a total of 68 sporadic colorectal cancers was examined for LOH on the chromosome arm by means of 16 polymorphic DNA markers. LOH was observed in 28 tumors (41%), of which 9 showed LOH at all informative loci. The remaining 19 tumors showed variable patterns of partial loss on 22q, delimiting the smallest region of overlap (SRO) between D22S90 and D22S94. Moreover, LOH within the SRO correlated with a progression in terms of Dukes' stages. These results suggest that an additional tumor-suppressor gene for colorectal cancer may exist on 22q distally to the NF2 locus and that inactivation of the gene may possibly play a role in the progression or metastasis of colorectal cancers.

Reciprocal translocation at in a neuroblastoma cell line: Isolation of a YAC clone at the break

Band 1p36.1-1p36.2 is frequently involved in chromosomal aberrations of neuroblastoma cells, and therefore thought to harbour genetic information which may be involved in tumorigenesis. To map this putative neuroblastoma locus, we screened neuroblastoma cell lines for reciprocal translocations at 1p36.1-2 which may signal the site of an affected gene. We identified a reciprocal 1;15 translocation in cell line NGP by fluorescence in situ hybridisation (FISH). As a strategy to clone the translocation breakpoint, we isolated yeast artificial chromosomes (YACs) specific for loci at 1p36. Screening of cell line NGP by FISH identified a YAC, 1050 kbp in size, which hybridised to both derivative 1;15 and 15;1 chromosomes. We conclude that this YAC, which maps to D1S160, covers the break. This chromosomal position is within the smallest region of overlap (SRO) found in neuroblastoma tumours and within the region of a constitutional interstitial deletion of a neuroblastoma patient. The YAC we describe here should serve as a DNA source for gene cloning approaches towards the isolation of candidates for the putative neuroblastoma suppressor gene.

Mapping a putative tumor suppressor gene on chromosome 9 bands p21-p22 with microdissection probes.

Deletions of the short arm of chromosome 9 have been observed in a number of malignant cell lines and primary tumor samples using cytogenetic and molecular techniques. These tumors include acute lymphoblastic leukemias, lymphomas, gliomas, melanomas, mesotheliomas, bladder cancer, and lung cancer. The smallest region of overlap (SRO) of these deletions is thought to contain a tumor suppressor gene. A microdissection library was constructed from bands 9p21-p23 to obtain DNA probes that would be useful in further defining the limits of the deletions. Eight single-copy probes were found to be homozygously deleted in at least 1 of the 10 cell lines examined. The mapping of these 8 clones using a panel of cell lines with deletions revealed that 3 probes mapped telomeric to the SRO and 5 clones mapped centromeric to the SRO.

At least two different regions are involved in allelic imbalance on chromosome arm 16q in breast cancer.

Loss of heterozygosity (LOH) or allelic imbalance, the latter term referring to both loss and gain of an allele, on the long arm of chromosome 16 has been repeatedly found in cancers of, e.g., the breast and prostate. This indicates the presence of one or more tumor suppressor genes on 16q. To locate the gene(s) more precisely, a detailed allelic imbalance map of 20 polymorphic markers on this chromosome arm was made for 79 sporadic breast carcinomas. LOH of one or more markers was found in 63% of the tumors. Some had allelic imbalance on a region of 16q which failed to overlap with the LOH in other tumors. We therefore assigned two separate "smallest regions of overlap" to 16q and suggest that this chromosome arm contains at least two different tumor suppressor genes.

Molecular genetic investigations of the mechanism of tumourigenesis in von Hippel-Lindau disease: analysis of allele loss in VHL tumours

Von Hippel-Lindau (VHL) disease is a dominantly inherited familial cancer syndrome characterised by the development of retinal and central nervous system haemangioblastomas, renal cell carcinoma (RCC), phaeochromocytoma and pancreatic tumours. The VHL disease gene maps to chromosome 3p25-p26. To investigate the mechanism of tumourigenesis in VHL disease, we analysed 24 paired blood/tumour DNA samples from 20 VHL patients for allele loss on chromosome 3p and in the region of tumour suppressor genes on chromosomes 5, 11, 13, 17 and 22. Nine out of 24 tumours showed loss of heterozygosity (LOH) at at least one locus on chromosome 3p and in each case the LOH included the region to which the VHL gene has been mapped. Chromosome 3p allele loss was found in four tumour types (RCC, haemangioblastoma, phaeochromocytoma and pancreatic tumour) suggesting a common mechanism of tumourigenesis in all types of tumour in VHL disease. The smallest region of overlap was between D3S1038 and D3S18, a region that corresponds to the target region for the VHL gene from genetic linkage studies. The parental origin of the chromosome 3p25-p26 allele loss could be determined in seven tumours from seven familial cases; in each tumour, the allele lost had been inherited from the unaffected parent. Our results suggest that the VHL disease gene functions as a recessive tumour suppressor gene and that inactivation of both alleles of the VHL gene is the critical event in the pathogenesis of VHL neoplasms. Four VHL tumours showed LOH on other chromosomes (5q21, 13q, 17q) indicating that homozygous VHL gene mutations may be required but may not be sufficient for tumourigenesis in VHL disease.

Molecular Cytogenetic Characterization of the DiGeorge Syndrome Region Using Fluorescence in Situ Hybridization

DiGeorge syndrome (DGS) is a developmental defect characterized by cardiac defects, facial dysmorphism, and mental retardation. Several studies have described a critical region for DGS at 22q11, within which the majority of DGS patients have deletions. We have isolated nine cosmid and three YAC clones using previously described and newly isolated probes that have been shown to be deleted in many DGS patients. Using fluorescence in situ hybridization and digital imaging, we have mapped and ordered these clones relative to the breakpoints of two balanced translocations at 22q11 (one in a DGS patient and one in the unaffected parent of a DGS child). Our data indicate that the breakpoint in the unaffected individual distally limits the DGS critical region (defined as the smallest region of overlap), while proximally the region is limited by repeat-rich DNA. The critical region includes the balanced translocation breakpoint of the DGS patient that presumably disrupts the gene causing this syndrome.

Deletion mapping of the long arm of chromosome 10 in glioblastoma multiforme

Cytogenetic and restriction fragment length polymorphism (RFLP) studies have shown that loss of one entire copy of chromosome 10 is a common genetic event in glioblastoma multiforme, the most malignant glial brain tumor in humans. In a search for submicroscopic deletions, we carried out an RFLP analysis using markers that had been mapped accurately on chromosome 10 by genetic linkage analysis. We studied 30 patients of whom 15 had loss of heterozygosity (LOH) at one or more loci. In seven cases, LOH was found at every informative locus, whereas in two cases extensive deletions were observed involving both the short and long arms. In six other patients, LOH was confined to a portion of the long arm. The smallest region of overlap among these latter six deletions was flanked by markers D10S12 proximally and D10S6 distally, a 33.4 centimorgan region that maps physically near the telomere (q25.1-qter). This region will serve as an important target for future mapping experiments designed to identify a tumor suppressor gene implicated in this lethal form of human cancer.

Fine mapping and cloning of the breakpoint associated with menkes syndrome in a female patient

The gene responsible for Menkes syndrome has been assigned to Xq13 by a combination of comparative mapping and linkage analysis. A previous report has mapped the translocation breakpoint associated with the disease in a female patient to an interval delimited by PGK1 and a group of six more proximal Xq13 markers, including DXS56. We have characterized a number of PGK1- or DXS56-positive YACs, from which we have generated six new markers. One of them identifies a small overlap region between a PGK1-positive YAC and three DXS56-positive YACs, distal to the Menkes breakpoint. A 560-kb region covered by a DXS56-positive YAC has been restriction-mapped and subcloned, disclosing a 187-kb MluI fragment astride the breakpoint. A probe mapping distal to the rearrangement in the same interval reveals altered PGFE fragments in a hybrid constructed from the translocation patient's DNA. We describe the development of a cosmid contig extending 150 kb from a nearby CpG island across the breakpoint. This contig includes four adjacent clones displaying cross-specific hybridization.

Refined localization of human connexin32 gene locus, GJB1, to Xq13.1

Connexins are the peptide subunits of gap junctions that interconnect cells to allow the direct, intercellular transfer of small molecules. Recently, the human connexin32 gene (locus designation GJB1) has been regionally mapped by three other laboratories to Xp11–q13, Xcen-q22, and Xp11–q22. The smallest region of overlap from these studies is Xcen-q13. By using a series of somatic cell hybrid mapping panels and a rat connexin32 cDNA probe, we have localized the human GJB1 locus to a much smaller region in proximal Xq13.1, in interval 8, as described by Lafrenière et al. (8).

Segregated thalamocortical pathways to inferior parietal and inferotemporal cortex in macaque monkey.

Inferior parietal and inferotemporal cortex, which process different aspects of visual information through largely segregated pathways from the visual cortex, both receive thalamic afferents from the pulvinar complex. We examined the topography of pulvinar projections to these two cortical regions by placing multiple injections of different tracers (fluorescent dyes, horseradish peroxidase) in the inferotemporal and inferior parietal cortex of macaque monkeys. The patterns of label observed after injections in inferotemporal gyrus indicate that area TEO and the ventral part of area V4 receive a major input from the ventral part of the lateral pulvinar (PuLv) while area TE has strong connections with the caudal pole of the medial pulvinar (PuM) and only minor connections with PuLv. In contrast, injections in the caudal inferior parietal cortex demonstrate that area PGc, on the lateral surface of the inferior parietal gyrus, and area POa, in the ventral bank of intraparietal sulcus, receive strong projections from PuM and the adjacent fringe of the dorsal part of the lateral pulvinar (PuLd). Paired injections of two different tracers in the inferotemporal and inferior parietal cortex of the same hemisphere revealed a nearly complete segregation of the two populations of labeled neurons in the pulvinar, with only a small region of overlap in PuM, close to the PuM/PuLd border. These results demonstrate a clear separation of the thalamic afferents to the inferior parietal and inferotemporal cortex which parallels the separation of prestriate afferents to these two cortical territories (Morel & Bullier, 1990).

Positional cloning and characterization of a paired box- and homeobox-containing gene from the aniridia region

Based on the map location of the aniridia (AN) locus in human chromosomal band 11p13, we have cloned a candidate AN cDNA (D11S812E) that is completely or partially deleted in two patients with AN. The <70 kb smallest region of overlap between the two deletions encompasses the 3′ coding region of the cDNA. This cDNA, which spans over 50 kb of genomic DNA, detects a 2.7 kb message specifically within all tissues affected in AN. The predicted polypeptide product possesses a paired domain, a homeodomain, and a serine/threonine-rich carboxy-terminal domain, structural motifs characteristic of certain transcription factors. The concordance between expression and pathology, map location, structure, and predicted function argues that the cDNA corresponds to the AN gene.

Smallest region of overlap in Wilms tumor deletions uniquely implicates an 11p13 zinc finger gene as the disease locus

The development of Wilms tumor (WT) has been associated with the inactivation of a “tumor suppressor” locus in human chromosome 11 band p13. Several WTs that exhibit homozygous deletions of an 11p13 candidate WT gene in its entirety have been reported. We report here a partial deletion of the candidate gene which, upon comparison with other documented homozygous deletions, permitted a precise definition of the critical genomic target in Wilms tumor. The smallest region of overlap between these deletions is a 16-kb segment of DNA encompassing the 5′ exon(s) of an 11p13 gene coding for a zinc finger protein, together with an associated CpG island. This finding supports the notion that the candidate gene in question corresponds to the 11p13 WT1 Wilms tumor locus.

Measurement of kaons in the Helios experiment

We have measured kaons and pions in the rapidity interval 0.8--1.3 and p{sub T} interval 100--600 MeV/c. We have observed an excess in the ratio of positive kaons to pions over what is expected from p-p for transverse momenta above 300 MeV/c. No such excess is seen for negatives. This excess of K/{pi} increasing with p{sub T} has been observed in 14.5 GeV/A Si + Au collisions by E802 at the AGS. Though their data are concentrated at high p{sub T}, there is a small region of overlap between the coverage of HELIOS and E802 for p{sub T} = 0.4--0.5 GeV/c. In this region the K/{pi} ratios for both positive and negative particles are very similar even though the bombarding energies differ by more than an order of magnitude. We find no strong indication that the rise in K/{pi} above values expected from p-p collisions is higher for high-E{sub T} events than for low-E{sub T} events.

Bihemispheric Axonal Bifurcation of the Afferents to the Visual Cortical Areas during Postnatal Development in the Rat.

Numerous cortical neurons in the juvenile and adult rat project to visual areas of both hemispheres whereas the vast majority of subcortical structures projecting to the visual cortex send strictly ipsilateral projections (Dreher et al., 1990). In the present study, the authors have sought to determine whether this pattern of axonal bifurcation in the connectivity of the visual areas undergoes a change during postnatal development. Two retrograde fluorescent dyes were used, fast blue (FB) and diamidino yellow (DY). Large multiple injections of one of the dyes were placed in all visual areas of one hemisphere and a small injection of the other dye was placed in area 17 of the opposite hemisphere. Labelled neurons were observed in subcortical and cortical structures on the side of the small injection. The experiments were performed on ten neonatal albino rat pups aged between 3 and 12 postnatal days (p.n.d.) at the time of injection and the results were compared with those obtained in the juvenile and adult animals, as reported in the preceding paper. In the thalamus of newborn animals, neurons belonging to nuclei located away from the midline send strictly ipsilateral cortical projections. However, in the midline nuclei of the intralaminar thalamic complex, a small region of overlap was observed between neurons projecting ipsilaterally and neurons projecting contralaterally in animals aged less than 9 postnatal days. In addition, in these neonatal animals a small number of bilaterally projecting neurons was detected in this region of overlap. In all other subcortical structures examined (ventral tegmental area, diagonal band of Broca, claustrum), the laterality of the projection was the same in the newborn and the adult animals. In particular, in the claustrum of neonatal animals, as in adult animals, there was a large contingent of contralaterally projecting neurons and only a very small number of bilaterally projecting neurons. The results in the cortex contrast with those observed in subcortical structures. Whereas ipsilaterally projecting neurons were distributed in a broadly similar way in newborn and adult animals, the laminar and areal distribution of contralaterally projecting neurons in newborn animals clearly differed from those observed in the adult animals. Furthermore, double labelled neurons were more numerous in animals aged less than 12 days than in adults. The proportions of such bilaterally projecting neurons were computed with respect to the numbers of neurons sending ipsilateral projections to area 17. These proportions are constant at all ages in the claustrum and cortical area 8. In areas 18a, 29 and 35 on the other hand, the proportions of bilaterally projecting neurons increase after 5 days and reach a peak in the period extending from 9 to 11 days of age when more than half of the neurons projecting ipsilaterally also send an axonal branch to the contralateral cortex. In cortical areas 29 and 35, this peak is followed by a sudden drop to the adult level at 12 postnatal days, whereas the return to the adult level is gradual in area 18a. These results demonstrate that, in subcortical structures and in cortical area 8, the laterality of the afferent connections to the visual cortex does not change during postnatal development. By contrast, cortical areas 18a, 29 and 35 go through a stage when numerous cells send bifurcating connections to both hemispheres. The timing of the decrease in proportions of bilaterally projecting neurons in these areas suggests that numerous neurons retract their callosal axonal branch when the adult pattern of callosal connectivity is established at 9 - 11 days of age.

Binocularity in the Little Owl, &lt;i&gt;Athene noctua&lt;/i&gt;

The efferent projections from the visual thalamus to the Wulst were studied in the little owl, Athene noctua. Cells of origin were identified by retrograde labeling after injections of wheat-germ-agglutinin-conjugated horseradish peroxidase into the Wulst. The labeled-cell distribution was correlated with the distribution of anterogradely labeled retinal terminals as revealed by intraocular injections of horseradish peroxidase. The results demonstrated a bilateral thalamofugal visual pathway ascending from the nucleus dorsolateralis anterior thalami (DLA). Projections from the visual thalamus to the Wulst showed a specific and orderly pattern, and retrogradely labeled cells of DLA were distributed equally, in a complementary fashion, on both sides of the brain, with a small region of overlap. Retinal termination fields in DLA largely overlapped relay neurons projecting to either Wulst, although the overlap was not complete. Despite differences in the organization of avian and mammalian visual pathways, which reflect their separate evolutionary origins, similarities between the DLA in the little owl and the lateral geniculate nucleus in mammals suggest that, during evolution similar selective pressures for binocularity led to a similar morphological organization.

CpG islands surround a DNA segment located between translocation breakpoints associated with genitourinary dysplasia and aniridia

We have isolated a DNA segment absent from all the constitutionally deleted chromosomes 11 of our patients with Wilms tumor. This marker separates two balanced translocations that break in band 11p13: the distal one associated with aniridia (AN2), and the proximal one with genitourinary dysplasia (GUD). The GUD breakpoint maps within the smallest region of overlap (SRO) for the Wilms tumor (WT) gene locus, thus strengthening the previous suggestion of an association between Wilms tumor and other abnormalities of the genitourinary system. The 11p13 translocation breakpoint associated with T-cell acute lymphatic leukemia (T-ALL) is centromeric to the SRO and separated from the WT locus by at least one known gene. This region of the human genome (11p13) is rich in CpG islands that potentially identify genes, some of which may be involved in the various phenotypes associated with the WAGR syndrome. This is consistent with the proposition that the majority of human genes are in G-negative bands.

Chromosomal jumping from the DXS165 locus allows molecular characterization of four microdeletions and a de novo chromosome X/13 translocation associated with choroideremia.

Choroideremia (tapeto-choroidal dystrophy, TCD), an X chromosome-linked disorder of retina and choroid, causes progressive nightblindness and central blindness in affected males by the third to fourth decade of life. Recently, we have been able to map the TCD gene to a small region of overlap between five different, male-viable Xq21 deletions that were found in patients with TCD and other clinical features. Two families were identified in which classical, nonsyndromic TCD is associated with small interstitial deletions that are only detectable with probe p1bD5 (DXS165). To characterize these and two other deletions that were identified more recently, we have used the chromosome walking and jumping techniques to generate a set of five chromosomal-jumping clones flanking the DXS165 locus at various distances. With these clones, we could localize four of the eight deletion endpoints and the breakpoint on the X chromosome of a female with a de novo X/13 translocation and choroideremia. These studies assign the TCD gene, or part of it, to a DNA segment of only 15-20 kilobases.

The separation of Carex disticha and Carex sartwellii and the status of Carex disticha in North America

To clarify the relationship between the Eurasian Carex disticha and the North American Carex sartwellii, 38 morphological characters were measured in 30 specimens of each. Various qualitative features were also scored. Through analysis of variance (ANOVA), a reduced number of 10 important continuous characters was obtained and the sample of each taxon was increased to 50. ANOVA of these 10 characters revealed that perigynium length and perigynium beak length were the most important discriminating characters, but in a scatter diagram of these two, 15% of the sample occupied a region of overlap. Principal-component analysis and discriminant analysis using the 10 characters resulted in a separation of the two groups, but a small region of overlap existed in both cases. The two taxa are distinct by virtue of accumulation of small morphological and other differences in a number of characters, rather than by sharp differentiation in a few characters. Carex disticha has larger perigynia with beaks (0.8–)1–1.5(–2.3) mm long, whereas C. sartwellii has smaller perigynia with beaks 0.4–1(–1.2) mm long. All distinguishing features are discussed and a key is provided. Immature vouchers for the occurrence of C. disticha in southwestern Quebec are confirmed on the basis of features of the inflorescence. The only other North American station of C. disticha, discovered in Simcoe Co., Ontario, in 1972 and extant in 1986, is also confirmed in the numerical analyses.

The poliovirus sensitivity (PVS) gene is on chromosome 19q12→q13.2

Sensitivity to nonmodified poliovirus infection is an autosomal dominant trait, specific to primates. The gene for poliovirus sensitivity (PVS) is encoded on human chromosome 19. In order to sublocalize the PVS gene, we infected rodent-human hybrid cell lines that divide human chromosome 19 into four regions with poliovirus 1 and/or 3. When infected, these hybrid cell lines showed the typical cytopathic effect of poliovirus infection only if they contained 19q12→q13.2 as the smallest region of overlap. Appropriate negative and positive controls were used. PVS may be of relevance to myotonic dystrophy (DM) and the inherited motor neuron diseases: to DM because it localizes to the same region of chromosome 19 and to the inherited motor neuron diseases because it encodes a cell-surface receptor expressed on motor neurons.