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647 results on '"Pinkel D"'

1. A large field CCD system for quantitative imaging of microarrays.

Author

Hamilton, G, Brown, N, Oseroff, V, Huey, B, Segraves, R, Sudar, D, Kumler, J, Albertson, D, and Pinkel, D

Subjects
Humans, DNA, Microscopy, Fluorescence, Oligonucleotide Array Sequence Analysis, Image Processing, Computer-Assisted, Female, Male, Microscopy, Fluorescence, Image Processing, Computer-Assisted, Environmental Sciences, Biological Sciences, Information and Computing Sciences, Developmental Biology
Abstract

We describe a charge-coupled device (CCD) imaging system for microarrays capable of acquiring quantitative, high dynamic range images of very large fields. Illumination is supplied by an arc lamp, and filters are used to define excitation and emission bands. The system is linear down to fluorochrome densities <1000. Resolution referred to the sample is 10 microm, sufficient for obtaining quantitative multicolor images from >30,000 array elements in an 18 mm x 18 mm square.

Published
2006

2. The use of fluorescence in situ hybridisation combined with premature chromosome condensation for the identification of chromosome damage.

Author

Evans, JW, Chang, JA, Giaccia, AJ, Pinkel, D, and Brown, JM

Subjects
Cell Line, Chromosomes, Humans, Chromosome Aberrations, Genetic Techniques, Nucleic Acid Hybridization, Fluorescence, Genetics, Oncology & Carcinogenesis, Oncology and Carcinogenesis, Public Health and Health Services
Abstract

The technique of fusing mitotic cells to interphase cells, thereby producing condensation of the chromosomes of the interphase cell (so-called 'premature chromosome condensation' or PCC), has allowed detection of the initial number of chromosome breaks and their repair following ionising radiation. However, the difficulty and tedium of scoring all the chromosome fragments, as well as the inability to readily detect exchange aberrations, has limited the use of PCC. We describe here the use of the recently developed technique of fluorescence in situ hybridisation with whole chromosome libraries to stain individual human chromosomes (also called 'chromosome painting') with the PCC's and show that this overcomes most of the limitations with the analysis of PCC's. First, by focusing on a single chromosome, scoring of breaks in the target chromosome is easy and rapid and greatly expands the radiation dose range over which the PCC technique can be used. Second, it allows the easy recognition of exchange type aberrations. A number of new applications of this technology, such as predicting the radiosensitivity of human tumours in situ, are feasible.

Published
1991

3. X-Ray Holography at Lawrence Livermore National Laboratory

Author

Trebes, J., Annese, C., Birdsall, D., Brase, J., Gray, J., Lane, S., London, R., Matthews, D., Peters, D., Pinkel, D., Stone, G., Rapp, D., Rosen, M., Weier, U., Yorkey, T., Lotsch, Helmut K. V., editor, Michette, Alan G., editor, Morrison, Graeme R., editor, and Buckley, Chistopher J., editor

Published
1992
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11. Integration of cytogenetic landmarks into the draft sequence of the human genome

Author

BAC Resource Consortium, The, Cheung, V. G., Nowak, N., Jang, W., Kirsch, I. R., Zhao, S., Chen, X.-N., Furey, T. S., Kim, U.-J., Kuo, W.-L., Olivier, M., Conroy, J., Kasprzyk, A., Massa, H., Yonescu, R., Sait, S., Thoreen, C., Snijders, A., Lemyre, E., Bailey, J. A., Bruzel, A., Burrill, W. D., Clegg, S. M., Collins, S., Dhami, P., Friedman, C., Han, C. S., Herrick, S., Lee, J., Ligon, A. H., Lowry, S., Morley, M., Narasimhan, S., Osoegawa, K., Peng, Z., Plajzer-Frick, I., Quade, B. J., Scott, D., Sirotkin, K., Thorpe, A. A., Gray, J. W., Hudson, J., Pinkel, D., Ried, T., Rowen, L., Shen-Ong, G. L., Strausberg, R. L., Birney, E., Callen, D. F., Cheng, J.-F., Cox, D. R., Doggett, N. A., Carter, N. P., Eichler, E. E., Haussler, D., Korenberg, J. R., Morton, C. C., Albertson, D., Schuler, G., de Jong, P. J., and Trask, B. J.

Published
2001
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25. X-Ray Holography at Lawrence Livermore National Laboratory

Author

Trebes, J., primary, Annese, C., additional, Birdsall, D., additional, Brase, J., additional, Gray, J., additional, Lane, S., additional, London, R., additional, Matthews, D., additional, Peters, D., additional, Pinkel, D., additional, Stone, G., additional, Rapp, D., additional, Rosen, M., additional, Weier, U., additional, and Yorkey, T., additional

Published
1992
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28. X-RAY HOLOGRAPHY AND BIOLOGICAL IMAGING

Author

Trebes, J., primary, Peters, D., additional, Brase, J., additional, Yorkey, T., additional, Weier, H-U., additional, Birdsall, D., additional, Pinkel, D., additional, and Gray, J.W., additional

Published
1991
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30. Remission induction and continuation therapy in children with first relapse of acute lymphoid leukemia: a Pediatric Oncology Group study

Author

Culbert, S.J., Shuster, J.J., Land, V.J., Wharam, M.D., Thomas, P.R.M., Nitschke, R., Pinkel, D., and Vietti, T.J.

Subjects
Leukemia in children, Health
Abstract

In a recent study, researchers evaluated the treatment of 98 children who had been treated for acute lymphoid leukemia and who had subsequently relapsed. The patients were then treated with vincristine, doxorubicin, and prednisone. Although this treatment regimen more closely resembles that for acute nonlymphoid leukemia, the regimen was chosen for its dissimilarity to the normal regimen after which the patients have already relapsed. It was found that the site of the relapse was an important determinant of survival. Thirty-nine patients experienced their relapse in the bone marrow, a site traditionally associated with poor survival. Thirty-two of these 39 achieved a complete response to their second regimen of chemotherapy, but this remission could be sustained in only one. In contrast, of 20 patients with relapse occurring in the testes, 19 achieved complete responses; 11 of these response have persisted for over four years and the patients are considered cured. Thirty-six evaluable patients had relapses in the meninges, the membranes surrounding the brain. Thirty-four had a second complete remission upon chemotherapy; the remission could be sustained for over four years in eight patients. The results confirm that the prognosis is bleak for children who relapse with leukemia in the bone marrow, but indicate that cures remain possible for children who relapse in the testes or the central nervous system. (Consumer Summary produced by Reliance Medical Information, Inc.)

Published
1991

34. Clinical and Immunological Recovery of Children with Acute Lymphocytic Leukemia Admitted to 'Total Therapy' Studies

Author

Borella, L., Green, A. A., Aur, R. J. A., Simone, J. V., Pinkel, D., Rentchnick, P., editor, Allfrey, V. G., editor, Allgöwer, M., editor, Bauer, K. H., editor, Berenblum, I., editor, Bergel, F., editor, Bernard, J., editor, Bernhard, W., editor, Blokhin, N. N., editor, Bock, H. E., editor, Braun, W., editor, Bucalossi, P., editor, Chaklin, A. V., editor, Chorazy, M., editor, Cunningham, G. J., editor, Dargent, M., editor, Della Porta, G., editor, Denoix, P., editor, Dulbecco, R., editor, Eagle, H., editor, Eker, R., editor, Good, R. A., editor, Grabar, P., editor, Hamperl, H., editor, Harris, R. J. C., editor, Hecker, H., editor, Herbeuval, R., editor, Higginson, J., editor, Hueper, W. C., editor, Isliker, H., editor, Kieler, J., editor, Klein, G., editor, Koprowski, H., editor, Koss, L. G., editor, Martz, G., editor, Mathé, G., editor, Mühlbock, O., editor, Nakahara, W., editor, Old, L. J., editor, Potter, V. R., editor, Sabin, A. B., editor, Sachs, L., editor, Saxén, E. A., editor, Schmidt, C. G., editor, Spiegelman, S., editor, Szybalski, W., editor, Tagnon, H., editor, Taylor, R. M., editor, Tissières, A., editor, Uehlinger, E., editor, Wissler, R. W., editor, Yoshida, T., editor, Pouillart, P., editor, and Schwarzenberg, L., editor

Published
1973
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35. Association of Cri du Chat Phenotype with DNA copy number abnormalities measured by array CGH

Author

Zhang, X.., Niebuhr, E., Snijders, A., Segraves, R., Hamilton, G., Brown, N., Blackwood, S., Hindle, K., Niebuhr, A., Xiuqing, Z., Gray, J., Yang, H., Albertson, D., Bolund, L., and Pinkel, D.

Subjects
Human genetics -- Research, Phenotype -- Genetic aspects, DNA -- Research, Cri-du-chat syndrome -- Genetic aspects, Genetic disorders -- Research, Biological sciences
Published
2001

39. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

Author

Scheinin, I., Sie, D., Bengtsson, H., Wiel, M.A. van de, Olshen, A.B., Thuijl, H.F. van, Essen, H.F. van, Eijk, P.P., Rustenburg, F., Meijer, G.A., Reijneveld, J.C., Wesseling, P., Pinkel, D., Albertson, D.G., Ylstra, B., Scheinin, I., Sie, D., Bengtsson, H., Wiel, M.A. van de, Olshen, A.B., Thuijl, H.F. van, Essen, H.F. van, Eijk, P.P., Rustenburg, F., Meijer, G.A., Reijneveld, J.C., Wesseling, P., Pinkel, D., Albertson, D.G., and Ylstra, B.

Abstract

Contains fulltext : 139379.pdf (publisher's version ) (Open Access), Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges, including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with approximately 0.1x genome coverage. We improve on previous methods by first implementing a combined correction for sequence mappability and GC content, and second, by applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions was previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1000 samples, most of which were obtained from the fixed tissue archives of more than 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches and better copy number data than high-resolution microarrays at a substantially lower cost.

Published
2014

42. Mantle-cell lymphoma genotypes identified with CGH to BAC microarrays define a leukemic subgroup of disease and predict patient outcome

Author

Rubio-Moscardo, F. (Fanny), Climent, J. (J.), Siebert, R. (Reiner), Piris, M.A. (Miguel A.), Martin-Subero, J.I. (Jose Ignacio), Nieländer, I. (Inga), Garcia-Conde, J. (J.), Dyer, M.J.S. (Martin J. S.), Terol, M.J. (María José), Pinkel, D. (Daniel), and Martinez-Climent, J.A. (José Ángel)

Subjects
Lymphoma, Mantle-Cell, Gene expression profiling
Abstract

To identify recurrent genomic changes in mantle cell lymphoma (MCL), we used high-resolution comparative genomic hybridization (CGH) to bacterial artificial chromosome (BAC) microarrays in 68 patients and 9 MCL-derived cell lines. Array CGH defined an MCL genomic signature distinct from other B-cell lymphomas, including deletions of 1p21 and 11q22.3-ATM gene with coincident 10p12-BMI1 gene amplification and 10p14 deletion, along with a previously unidentified loss within 9q21-q22. Specific genomic alterations were associated with different subgroups of disease. Notably, 11 patients with leukemic MCL showed a different genomic profile than nodal cases, including 8p21.3 deletion at tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) receptor gene cluster (55% versus 19%; P = .01) and gain of 8q24.1 at MYC locus (46% versus 14%; P = .015). Additionally, leukemic MCL exhibited frequent IGVH mutation (64% versus 21%; P = .009) with preferential VH4-39 use (36% versus 4%; P = .005) and followed a more indolent clinical course. Blastoid variants, increased number of genomic gains, and deletions of P16/INK4a and TP53 genes correlated with poorer outcomes, while 1p21 loss was associated with prolonged survival (P = .02). In multivariate analysis, deletion of 9q21-q22 was the strongest predictor for inferior survival (hazard ratio [HR], 6; confidence interval [CI], 2.3 to 15.7). Our study highlights the genomic profile as a predictor for clinical outcome and suggests that "genome scanning" of chromosomes 1p21, 9q21-q22, 9p21.3-P16/INK4a, and 17p13.1-TP53 may be clinically useful in MCL.

Published
2005

43. Statement by members of the Ponte di Legno group on the right of children with leukemia to have full access to essential treatment for acute lymphoblastic leukemia

Author

Arico, M, Basso, Giuseppe, Biondi, A, Conter, V, Masera, G, Rognoni, G, Valsecchi, Mg, Cario, G, Gadner, H, Haas, O, Harbott, J, Panzer, R, Riehm, H, Shrappe, M, Stackelberg, A, Stanulla, M, Zimmermann, M, Camita, B, Caroll, W, Gaynon, P, Hunger, S, Nachman, J, Schultz, K, Winick, N, Horstmann, M, JANKA SCHAUB, G, Stary, J, Trka, J, Sallan, S, Silverman, L, Pieters, R, Veerman, A, Bertrand, Y, Suciu, S, Leverger, G, Horibe, K, Eden, Ob, Harrison, C, Gibson, B, Forestier, E, Schmiegelow, K, Vettenranta, K, Campana, D, COUSTON SMITH, E, Evans, We, Handgretinger, R, Pui, Ch, Relling, Mv, Lang, Dc, Manabe, A, Tsuchida, M, Pinkel, D., Tognoni, G, Masera, G, Pui, C, Eden, T, Nachman, J, Gadner, H, Gaynon, P, Evans, W, and Schrappe, M

Subjects
Pediatrics, medicine.medical_specialty, Clinical Trials as Topic, Statement (logic), business.industry, Lymphoblastic Leukemia, Health Policy, International Cooperation, Child Welfare, Hematology, Patient Advocacy, Precursor Cell Lymphoblastic Leukemia-Lymphoma, medicine.disease, Health Services Accessibility, Precursor Cell Lymphoblastic Leukemia Lymphoma, Leukemia, Oncology, Acute lymphocytic leukemia, medicine, Humans, business, Child
Published
2004

47. Array-based comparative genomic hybridization for genome-wide screening of DNA copy number in bladder tumors

Author

Joris Veltman, Fridlyand J, Pejavar S, Ab, Olshen, Je, Korkola, DeVries S, Carroll P, Wl, Kuo, Pinkel D, Albertson D, Cordon-Cardo C, An, Jain, and Fm, Waldman

Subjects
neoplasms, Molecular diagnosis, prognosis and monitoring [UMCN 1.2]
Abstract

Item does not contain fulltext Genome-wide copy number profiles were characterized in 41 primary bladder tumors using array-based comparative genomic hybridization (array CGH). In addition to previously identified alterations in large chromosomal regions, alterations were identified in many small genomic regions, some with high-level amplifications or homozygous deletions. High-level amplifications were detected for 192 genomic clones, most frequently at 6p22.3 (E2F3), 8p12 (FGFR1), 8q22.2 (CMYC), 11q13 (CCND1, EMS1, INT2), and 19q13.1 (CCNE). Homozygous deletions were detected in 51 genomic clones, with four showing deletions in more than one case: two clones mapping to 9p21.3 (CDKN2A/p16, in nine cases), one at 8p23.1 (three cases), and one at 11p13 (two cases). Significant correlations were observed between copy number gain of clones containing CCNE1 and gain of ERBB2, and between gain of CCND1 and deletion of TP53. In addition, there was a significant complementary association between gain of CCND1 and gain of E2F3. Although there was no significant relationship between copy number changes and tumor stage or grade, the linked behavior among genomic loci suggests that array CGH will be increasingly important in understanding pathways critical to bladder tumor biology.

Published
2003

48. Cyclin D1 is a candidate oncogene in cutaneous melanoma

Author

Sauter, E, Yeo, U, von Stemm, A, Zhu, W, Litwin, S, Tichansky, D, Pistritto, G, Nesbit, M, Pinkel, D, Herlyn, M, and Bastian, B

Subjects
Skin Neoplasms, Cultured, Gene Amplification, Gene Dosage, Settore BIO/14, Apoptosis, Oncogenes, Fluorescence, Tumor Cells, Transduction, Genetic, Humans, Melanoma, Tumor Cells, Cultured, Transduction, Genetic, In Situ Hybridization, Fluorescence, Cell Division, Cyclin D1, In Situ Hybridization
Published
2002

50. Recurrent reciprocal genomic Rearrangements of 17q12 are associated with renal disease, diabetes, and epilepsy

Author

Mefford, H.C., Clauin, S., Sharp, A.J., Møller, R.S., Ullmann, R., Kapur, R., Pinkel, D., Cooper, G.M., Ventura, M., Ropers, H.H., Tommerup, Niels, Eichler, E.E., Bellanne-Chantelot, C., Mefford, H.C., Clauin, S., Sharp, A.J., Møller, R.S., Ullmann, R., Kapur, R., Pinkel, D., Cooper, G.M., Ventura, M., Ropers, H.H., Tommerup, Niels, Eichler, E.E., and Bellanne-Chantelot, C.

Abstract

Udgivelsesdato: 2007/11

Published
2007

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