c‐MYC, RB‐1, TP53, and centromere 8 and 17 copy number in B‐cell non‐Hodgkin's lymphomas assessed by dual‐color fluorescence in situ hybridization

Galteland, Eivind; Holte, Harald; Stokke, Trond

doi:10.1002/(sici)1097-0320(19990415)38:2<53::aid-cyto2>3.3.co;2-s

Cited by 5 publications

(10 citation statements)

References 25 publications

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“…We compared the GeneCount results of 94 lymphomas with previously published FISH data from the same tumors [ 20 - 25 ]. The FISH probes were located at chromosomal regions with frequent copy number changes (Figure 1 and Additional data file 2), and copy numbers within the range of 0-8 had been measured.…”

Section: Resultsmentioning

confidence: 99%

“…We show that the model enabled automatic and genome-wide calculation of DNA copy numbers from aCGH data of both hematopoietic and solid tumors. The feasibility of GeneCount was demonstrated by analysis of 94 lymphomas, for which the DNA index and tumor cell fraction had been determined by use of flow cytometry and an extensive exploration of DNA copy numbers had been performed by the use of FISH in previous studies [ 20 - 25 ]. The GeneCount results, both based on the pre-determined tumor cell fraction and that determined by the model, were compared with the FISH data of 362 genes with and without gains and losses, showing 97% consistency in both cases.…”

Section: Introductionmentioning

confidence: 99%

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GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

et al. 2008

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Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably estimated in the model. Data consistent with FISH results are achieved. We demonstrate significant improvements over existing methods for exploring gene dosages and intratumor copy number heterogeneity in cancers.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

et al. 2008

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“…We did not find any decreased expression of p16 and pRB in the tumors with 9p21ter and 13q13-21.1 (RB1) deletions, respectively, compared to the others. Case 458/88 was the only case that did not express pRB; this case had high-level amplification of 13q by CGH, but no RB-1 alleles (Galteland et al, 1999). Also, none of 13 cases with 9p21-ter loss by CGH had detectable methylation of the p16INK4 gene.…”

Section: Figurementioning

confidence: 94%

“…peak could be identified in the ungated DNA histograms. DNA tetraploid cases have a DNA index in the region 1.9-2.1. d Data were taken fromGalteland et al (1999) or assessed as described therein.…”

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confidence: 99%

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2001

Br J Cancer

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Comparative genomic hybridization (CGH) was employed to study chromosomal aberrations in relation to cell proliferation, apoptosis, and patient survival in 94 cases of B-cell non-Hodgkin's lymphoma diagnosed between 1983 and 1993. Eighty cases had aberrations by CGH. Chromosomal regions 1p21-31.1 (10%), 6cen-q24 (12%), 8p (11%), 9p21-ter (14%), 11q21-23.1 (11%), 13q13-21.1 (12%), and 17p (15%) were frequently lost. Gains were found at 3q21-ter (22%), 6p (11%), 7p (12%), 8q23-ter (13%), 12cen-q15 (17%), 17q24-ter (13%), and 18q13.3-21 (20%). A high number of aberrations (≥ 4, 33 cases) was associated (P ≤ 0.001) with the mantle cell and diffuse large B-cell lymphoma subtypes, a high fraction of tumour cells in S phase, and short survival (RR (relative risk) = 3.7). Loss of 1p21-31.1, 8p, 9p21-ter, 11q21-23.1, and 13q13-21.1 were associated with mantle cell lymphoma (P ≤ 0.03), while gain of 6p and 12cen-q15 were more frequent in diffuse large B-cell and small lymphocytic lymphoma, respectively (P = 0.04). Loss of 8p and 17p, and gain of 3q21-ter, 6p, 7p, and 8q23-ter were associated with a high S phase fraction (P ≤ 0.03), but none of the aberrations were associated with tumour apoptotic fraction (P ≥ 0.13). The most important prognostic CGH parameters (P < 0.001) were losses of 11q21-23.1 (RR = 3.8) and 17p (RR = 4.4), and gain of 6p (RR = 4.2). The latter parameters and IPI were the only ones with independent prognostic value (RR = 10, 5.0, 6.7, and 3.7, respectively; P < 0.001) when assessed together with lymphoma sub-type, primary versus relapse cases, treatment, B symptoms, S phase fraction, and presence of BCL1 and BCL2 translocations. A combined CGH/IPI binary parameter had high prognostic value for patients receiving different treatments, with various lymphoma sub-types, and for primary as well as relapse cases.

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“…PAC DNA (1 µg) was nick-translated and labelled with Cy3-dUTP (Amersham) with the Bio-nick kit from Gibco BRL (Gaithersburg, MD, U.S.A.) in accordance with the manufac-turer's recommendations ; FISH was performed as described previously [14].…”

Section: Fluorescence In Situ Hybridization (Fish)mentioning

confidence: 99%

Organization, chromosomal localization and promoter analysis of the gene encoding human acidic fibroblast growth factor intracellular binding protein

et al. 2000

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Acidic fibroblast growth factor (aFGF) intracellular binding protein (FIBP) is a protein found mainly in the nucleus that might be involved in the intracellular function of aFGF. Here we present a comparative analysis of the deduced amino acid sequences of human, murine and Drosophila FIBP analogues and demonstrate that FIBP is an evolutionarily conserved protein. The human gene spans more than 5 kb, comprising ten exons and nine introns, and maps to chromosome 11q13.1. Two slightly different splice variants found in different tissues were isolated and characterized. Sequence analysis of the region surrounding the translation start revealed a CpG island, a classical feature of widely expressed genes. Functional studies of the promoter region with a luciferase reporter system suggested a strong transcriptional activity residing within 600 bp of the 5' flanking region.

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c‐MYC, RB‐1, TP53, and centromere 8 and 17 copy number in B‐cell non‐Hodgkin's lymphomas assessed by dual‐color fluorescence in situ hybridization

Cited by 5 publications

References 25 publications

GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

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Organization, chromosomal localization and promoter analysis of the gene encoding human acidic fibroblast growth factor intracellular binding protein

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