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1,020 results on '"Knuutila S"'

53. Loss of Chromosomes 9P and 14Q: Re-Profiling Metastatic Tissue for Re-Targeting Patients with Metastatic Renal Cell Carcinoma

Author

Massari, F., primary, Ciccarese, C., additional, Knuutila, S., additional, Russa, F. La, additional, Bimbatti, D., additional, Modena, A., additional, Zampini, C., additional, Porcaro, A.B., additional, Sava, T., additional, Artibani, W., additional, Martignoni, G., additional, Brunelli, M., additional, and Tortora, G., additional

Published
2014
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55. Targeted Resequencing of 9p in Acute Lymphoblastic Leukemia Yields Concordant Results with Array CGH and Reveals Novel Genomic Alterations

Author

Sarhadi, V.K., Lahti, L.M., Scheinin, I., Tyybäkinoja, A., Savola, S., Usvasalo, A., Räty, R., Elonen, E., Saarinen-Pihkala, U.M., Knuutila, S., Sarhadi, V.K., Lahti, L.M., Scheinin, I., Tyybäkinoja, A., Savola, S., Usvasalo, A., Räty, R., Elonen, E., Saarinen-Pihkala, U.M., and Knuutila, S.

Abstract

Genetic alterations of the short arm of chromosome 9 are frequent in acute lymphoblastic leukemia. We performed targeted sequencing of 9p region in 35 adolescent and adult acute lymphoblastic leukemia patients and sought to investigate the sensitivity of detecting copy number alterations in comparison with array comparative genomic hybridization (aCGH), and besides, to detect novel genetic anomalies. We found a high concordance of copy number variations (CNVs) as detected by next generation sequencing (NGS) and aCGH. By both methodologies, the recurrent deletion at CDKN2A/B locus was identified, whereas NGS revealed additional, small regions of CNVs, seen more frequently in adult patients, while aCGH was better at detecting larger CNVs. Also, by NGS, we detected novel structural variations, novel SNVs and small insertion/deletion variants. Our results show that NGS, in addition to detecting mutations and other genetic aberrations, can be used to study CNVs

Published
2013

56. Impact of TP53 mutation and 17p deletion in mantle cell lymphoma

Author

Halldórsdóttir, Anna Margret, Lundin, A, Murray, Fiona, Mansouri, Larry, Knuutila, S, Sundström, Christer, Laurell, Anna, Ehrencrona, H, Sander, B, Rosenquist, Richard, Halldórsdóttir, Anna Margret, Lundin, A, Murray, Fiona, Mansouri, Larry, Knuutila, S, Sundström, Christer, Laurell, Anna, Ehrencrona, H, Sander, B, and Rosenquist, Richard

Published
2011
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57. CGHpower: exploring sample size calculations for chromosomal copy number experiments

Author

Scheinin, A.I., Ferreira, J.A., Knuutila, S., Meijer, G.A., van de Wiel, M.A., Ylstra, B., Scheinin, A.I., Ferreira, J.A., Knuutila, S., Meijer, G.A., van de Wiel, M.A., and Ylstra, B.

Abstract

Background: Determining a suitable sample size is an important step in the planning of microarray experiments. Increasing the number of arrays gives more statistical power, but adds to the total cost of the experiment. Several approaches for sample size determination have been developed for expression array studies, but so far none has been proposed for array comparative genomic hybridization (aCGH).Results: Here we explore power calculations for aCGH experiments comparing two groups. In a pilot experiment CGHpower estimates the biological diversity between groups and provides a statistical framework for estimating average power as a function of sample size. As the method requires pilot data, it can be used either in the planning stage of larger studies or in estimating the power achieved in past experiments.Conclusions: The proposed method relies on certain assumptions. According to our evaluation with public and simulated data sets, they do not always hold true. Violation of the assumptions typically leads to unreliable sample size estimates. Despite its limitations, this method is, at least to our knowledge, the only one currently available for performing sample size calculations in the context of aCGH. Moreover, the implementation of the method provides diagnostic plots that allow critical assessment of the assumptions on which it is based and hence on the feasibility and reliability of the sample size calculations in each case.The CGHpower web application and the program outputs from evaluation data sets can be freely accessed at http://www.cangem.org/cghpower/. © 2010 Scheinin et al; licensee BioMed Central Ltd.

Published
2010
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58. DNA copy number amplifications in human neoplasms: review of comparative genomic hybridization studies

Author

Knuutila, S., Björkqvist, A. M., Autio, K., Tarkkanen, M., Wolf, M., Monni, O., Szymanska, J., Larramendy, M. L., Tapper, J., Pere, H., El-Rifai, W., Hemmer, S., Wasenius, V. M., Vidgren, V., and Zhu, Y.

Subjects
Research Article
Abstract

This review summarizes reports of recurrent DNA sequence copy number amplifications in human neoplasms detected by comparative genomic hybridization. Some of the chromosomal areas with recurrent DNA copy number amplifications (amplicons) of 1p22-p31, 1p32-p36, 1q, 2p13-p16, 2p23-p25, 2q31-q33, 3q, 5p, 6p12-pter, 7p12-p13, 7q11.2, 7q21-q22, 8p11-p12, 8q, 11q13-q14, 12p, 12q13-q21, 13q14, 13q22-qter, 14q13-q21, 15q24-qter, 17p11.2-p12, 17q12-q21, 17q22-qter, 18q, 19p13.2-pter, 19cen-q13.3, 20p11.2-p12, 20q, Xp11.2-p21, and Xp11-q13 and genes therein are presented in more detail. The paper with more than 150 references and two tables can be accessed from our web site http://www.helsinki.fi/lglvwww/CMG.html. The data will be updated biannually until the year 2001.

Published
1998

60. Prognostic value of metaphase-fluorescence in situ hybridization in follow-up of patients with acute myeloid leukemia in remission

Author

El-Rifai W, Ruutu T, Elonen E, Liisa Volin, and Knuutila S

Subjects
Adult, Chromosome Aberrations, Male, Antineoplastic Agents, Middle Aged, Prognosis, Disease-Free Survival, Translocation, Genetic, Leukemia, Myeloid, Acute, Bone Marrow, Karyotyping, Chromosomes, Human, Humans, Female, Chromosome Deletion, In Situ Hybridization, Fluorescence, Metaphase, Aged, Bone Marrow Transplantation, Follow-Up Studies
Abstract

The presence of residual leukemic cells was studied using metaphase-fluorescence in situ hybridization (FISH) in 22 patients with acute myeloid leukemia treated with chemotherapy only or chemotherapy followed by allogeneic bone marrow transplantation. The patients were followed up during their complete remission (CR) for 4 to 108 months (median, 21 months). A total of 88 BM samples was studied. In most of the samples more than 1,000 metaphase cells were analyzed. Residual leukemic cells were detected in 9 of 22 patients (41%). All patients who had an increasing and/or persisting level of abnormal cells in two or more subsequent samples or whose initial samples contained more than 1% of abnormal cells relapsed with one exception, in whom the later subsequent samples showed disappearance of abnormal cells. The time span before the first positive sample seems to be insignificant with regard to the outcome of relapse. Absence or single occurrence of abnormal cells followed by their disappearance was in agreement with CR in all the cases (16 patients). Our results indicate that metaphase-FISH is a reliable tool in the quantitation of residual leukemic cells and provides valuable prognostic information for patients with AML.

Published
1997

63. Potential role of a navigator gene NAV3 in colorectal cancer

Author

Carlsson, E, primary, Ranki, A, additional, Sipilä, L, additional, Karenko, L, additional, Abdel-Rahman, W M, additional, Ovaska, K, additional, Siggberg, L, additional, Aapola, U, additional, Ässämäki, R, additional, Häyry, V, additional, Niiranen, K, additional, Helle, M, additional, Knuutila, S, additional, Hautaniemi, S, additional, Peltomäki, P, additional, and Krohn, K, additional

Published
2011
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64. 1q gain and CDT2 overexpression underlie an aggressive and highly proliferative form of Ewing sarcoma

Author

Mackintosh, C, primary, Ordóñez, J L, additional, García-Domínguez, D J, additional, Sevillano, V, additional, Llombart-Bosch, A, additional, Szuhai, K, additional, Scotlandi, K, additional, Alberghini, M, additional, Sciot, R, additional, Sinnaeve, F, additional, Hogendoorn, P C W, additional, Picci, P, additional, Knuutila, S, additional, Dirksen, U, additional, Debiec-Rychter, M, additional, Schaefer, K-L, additional, and de Álava, E, additional

Published
2011
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74. 376 POSTER NAV3–anovel cancer biomarker

Author

Sipilä, L., primary, Karenko, L., additional, Siggberg, L., additional, Abdel-Rahman, W., additional, Helle, M., additional, Häyry, V., additional, Knuutila, S., additional, Peltomäki, P., additional, Ranki, A., additional, and Krohn, K., additional

Published
2008
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75. Acute lymphoblastic leukemia in adolescents and young adults in Finland

Author

Usvasalo, A., primary, Raty, R., additional, Knuutila, S., additional, Vettenranta, K., additional, Harila-Saari, A., additional, Jantunen, E., additional, Kauppila, M., additional, Koistinen, P., additional, Parto, K., additional, Riikonen, P., additional, Salmi, T. T., additional, Silvennoinen, R., additional, Elonen, E., additional, and Saarinen-Pihkala, U. M., additional

Published
2008
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81. Comparison of bone marrow high mitotic index metaphase fluorescence in situ hybridization to peripheral blood and bone marrow real time quantitative polymerase chain reaction on the International Scale for detecting residual disease in chronic myeloid leukemia

Author

Lundan, T., primary, Juvonen, V., additional, Mueller, M. C., additional, Mustjoki, S., additional, Lakkala, T., additional, Kairisto, V., additional, Hochhaus, A., additional, Knuutila, S., additional, and Porkka, K., additional

Published
2008
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93. 60 Asbestos-associatedmalignancies in the lung and pleura show distinct genetic aberrations

Author

Lindholm, P., primary, Nymark, P., additional, Wikman, H., additional, Salmenkivi, K., additional, Nicholson, A., additional, Korpela, M.V., additional, Kaski, S., additional, Ruosaari, S., additional, Hollmén, J., additional, Vanhala, E., additional, Karjalainen, A., additional, Anttila, S., additional, Kinnula, V., additional, and Knuutila, S., additional

Published
2006
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