Rapid subchromosomal localization of cosmids by nonradioactive in situ hybridization

Kievits, Tim; Dauwerse, Johannes G.; Wiegant, J.; Devilee, Peter; Mh, Breuning; Cj, Cornelisse; Gj, van Ommen; Pl, Pearson

doi:10.1159/000132913

Cited by 142 publications

(68 citation statements)

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“…Regionally localised BACs were labelled by nick-translation with biotin-14-dUTP (Gibco BRL) or digoxigenin-16-dUTP (Roche Diagnostics) as described by Kievits et al 15 In situ hybridisation using the labelled BACs as probes was performed according to Dauwerse et al 16 Slides containing Epstein Barr virus-transformed cells were processed for Fiber-FISH as described by Datson et al 17 For Fiber-FISH, pairs of BACs labelled in red and green were used as probes.…”

Section: Fluorescent In Situ Hybridisation (Fish) Analysismentioning

confidence: 99%

A high-resolution integrated map spanning the SDHD gene at 11q23: a 1.1-Mb BAC contig, a partial transcript map and 15 new repeat polymorphisms in a tumour-suppressor region

et al. 2001

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Chromosomal region 11q22-q23 is a frequent target for deletion during the development of many solid tumour types, including breast, ovary, cervix, stomach, bladder carcinomas and melanoma. One of the most commonly deleted subregions contains the SDHD gene, which encodes the small subunit of cytochrome b (cybS) in mitochondrial complex II (succinate-ubiquinone oxidoreductase). Germline mutations in SDHD cause hereditary paraganglioma type 1 (PGL1), and suggest a tumour suppressor role for cybS. We present a high-resolution physical map spanning SDHD, covered by 19 YACs and 20 BACs. An approximate 1.1-Mb gene-rich region around SDHD is spanned by a complete BAC contig. Twenty-six new STSs are developed from the BAC clone ends. In addition to the discovery and characterisation of 15 new simple tandem repeat polymorphisms, we provide integrated positional information for 33 ESTs and known genes, including KIAA1391, POU2AF1 (OBF1), PPP2R1B, CRYAB, HSPB2, DLAT, IL-18, PTPS, KIAA0781 and KAIA4591, which is mapped by NotI site cloning. We describe full-length transcript sequence for PPP2R1B, encoding the protein phosphatase 2A regulatory subunit A beta isoform. We also discover a processed pseudogene for USA-CYP, a cyclophilin associated with U4/U6 snRPNs, and a novel gene, DDP2, encoding a mitochondrial protein similar to the X-linked deafness-dystonia protein, which is juxtaposed 5'-to-5' to SDHD. This map will help assess this gene-rich region in PGL and in other common tumours.

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Section: Fluorescent In Situ Hybridisation (Fish) Analysismentioning

confidence: 99%

A high-resolution integrated map spanning the SDHD gene at 11q23: a 1.1-Mb BAC contig, a partial transcript map and 15 new repeat polymorphisms in a tumour-suppressor region

et al. 2001

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“…All tumors were successfully karyotyped and included lesions with 6p21 (n ϭ 17) or 12q15 alterations (n ϭ 33), karyotypic alterations not involving 6p21 or 12q15 (n ϭ 13), or a normal karyotype (n ϭ 32). FISH was performed after GTG banding of the same metaphase spreads according to previously published procedures (Kievits et al, 1992). Metaphases were hybridized with a pool of different cosmids spanning over the breakpoint region 12q15 and flanking the third intron of HMGI-C Kazmierczak et al, 1996b) and with PAC clones containing the HMGI(Y) gene mapped at 6p21.2 (Kazmierczak et al, 1996c).…”

Section: Cytogenetic and Molecular Cytogenetic Analysismentioning

confidence: 99%

HMGI-C and HMGI(Y) Immunoreactivity Correlates with Cytogenetic Abnormalities in Lipomas, Pulmonary Chondroid Hamartomas, Endometrial Polyps, and Uterine Leiomyomas and is Compatible with Rearrangement of the HMGI-C and HMGI(Y) Genes

Tallini

Vanni

Manfioletti

et al. 2000

Laboratory Investigation

134

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SUMMARY:High-mobility group (HMG) proteins are nonhistone nuclear proteins that play an important role in the regulation of chromatin structure and function. HMGI-C and HMGI(Y) are members of the HMGI family of HMG proteins, and their expression in adult tissues generally correlates with malignant tumor phenotypes. However, HMGI-C and HMGI(Y) dysregulation as a result of specific rearrangements involving 12q15 and 6p21, the respective chromosomal sites in which the HMGI-C and HMGI(Y) genes are located, is also identified in a variety of common benign mesenchymal tumors, such as lipomas and uterine leiomyomata. The general prevalence of HMGI-C and HMGI(Y) protein expression and its correlation with chromosomal alterations in these benign tumors are unknown. We analyzed 95 human tumors (20 lipomas, 21 pulmonary chondroid hamartomas, 26 uterine leiomyomata, and 28 endometrial polyps) representing a selection of the benign lesions in which karyotypic alterations involving the chromosomal regions 12q15 and 6p21 are frequently detected. All cases were successfully karyotyped and some of them analyzed by fluorescent in situ hybridization with probes spanning the HMGI-C and HMGI(Y) genes. The results of this study demonstrate that expression of HMGI-C or HMGI(Y) is a common occurrence in lipomas, pulmonary chondroid hamartomas, leiomyomata, and endometrial polyps; that it correlates with 12q15 and 6p21 chromosomal alterations (p Ͻ 0.001); and that it is compatible with rearrangement of the HMGI-C and HMGI(Y) genes. The expression pattern and cellular localization of the immunoreactivity support the view that in biphasic lesions composed of a mixture of both stromal and epithelial cells, such as pulmonary chondroid hamartoma and endometrial polyps, the mesenchymal component is the site of the HMGI genetic alterations. (Lab Invest 2000, 80:359-369).

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“…[30][31][32] FISH results were observed through a Leitz DM-RBE microscope (Leica, Rijswijk, The Netherlands) equipped for fluorescence microscopy and mounted with a Photometric Series 200, KAF1400 charged coupled device camera. Image acquisition and processing was performed on a Power Macintosh 7100, using the IP Lab Spectrum Multiprobe software (Photometrics, Munich, Germany).…”

Section: Fluorescence In Situ Hybridization (Fish)mentioning

confidence: 99%

Detection of CBP rearrangements in acute myelogenous leukemia with t(8;16)

et al. 1997

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The CREB-binding protein (CBP) is a large nuclear protein that regulates many signal transduction pathways and is involved in chromatin-mediated transcription. The translocation t(8;16)(p11;p13.3) consistently disrupts two genes: the CBP gene on chromosome band 16p13.3 and the MOZ gene on chromosome band 8p11. Although a fusion of these two genes as a result of the translocation is expected, attempts at detecting the fusion transcript by reverse transcriptase polymerase chain reaction (RT-PCR) have proven difficult; to date, only one inframe CBP/MOZ fusion transcript has been reported. We therefore sought other reliable means of detecting CBP rearrangements. We applied fluorescence in situ hybridization (FISH) and Southern blot analyses to a series of AML patients with a t(8;16) and detected DNA rearrangements of both the CBP and the MOZ loci in all cases tested. All six cases examined for CBP rearrangements have breakpoints within a 13 kb breakpoint cluster region at the 5′ end of the CBP gene. Additionally, we used a MOZ cDNA probe to construct a surrounding cosmid contig and detect DNA rearrangements in three t(8;16) cases, all of which display rearrangements within a 6 kb genomic fragment of the MOZ gene. We have thus developed a series of cosmid probes that consistently detect the disruption of the CBP gene in t(8;16) patients. These clones could potentially be used to screen other cancer-associated or congenital translocations involving chromosome band 16p13.3 as well.

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Rapid subchromosomal localization of cosmids by nonradioactive in situ hybridization

Cited by 142 publications

References 1 publication

A high-resolution integrated map spanning the SDHD gene at 11q23: a 1.1-Mb BAC contig, a partial transcript map and 15 new repeat polymorphisms in a tumour-suppressor region

A high-resolution integrated map spanning the SDHD gene at 11q23: a 1.1-Mb BAC contig, a partial transcript map and 15 new repeat polymorphisms in a tumour-suppressor region

HMGI-C and HMGI(Y) Immunoreactivity Correlates with Cytogenetic Abnormalities in Lipomas, Pulmonary Chondroid Hamartomas, Endometrial Polyps, and Uterine Leiomyomas and is Compatible with Rearrangement of the HMGI-C and HMGI(Y) Genes

Detection of CBP rearrangements in acute myelogenous leukemia with t(8;16)

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