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137 results on '"Baumbusch, Lars O."'

2. From Pediatric to Adult Brain Cancer: Exploring Histone H3 Mutations in Australian Brain Cancer Patients

Author

Grebstad Tune, Benedicte, primary, Sareen, Heena, additional, Powter, Branka, additional, Kahana-Edwin, Smadar, additional, Cooper, Adam, additional, Koh, Eng-Siew, additional, Lee, Cheok S., additional, Po, Joseph W., additional, McCowage, Geoff, additional, Dexter, Mark, additional, Cain, Lucy, additional, O’Neill, Geraldine, additional, Prior, Victoria, additional, Karpelowsky, Jonathan, additional, Tsoli, Maria, additional, Baumbusch, Lars O., additional, Ziegler, David, additional, Roberts, Tara L., additional, DeSouza, Paul, additional, Becker, Therese M., additional, and Ma, Yafeng, additional

Published
2023
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5. The prognostic significance of tumor cell detection in the peripheral blood versus the bone marrow in 733 early-stage breast cancer patients

Author

Molloy, Timothy J, Bosma, Astrid J, Baumbusch, Lars O, Synnestvedt, Marit, Borgen, Elin, Russnes, Hege, Schlichting, Ellen, van't Veer, Laura J, and Naume, Bjørn

Abstract

Abstract Introduction The detection of circulating tumour cells (CTCs) in the peripheral blood and disseminated tumour cells (DTCs) in the bone marrow are promising prognostic tools for risk stratification in early breast cancer. There is, however, a need for further validation of these techniques in larger patient cohorts with adequate follow-up periods. Methods We assayed CTCs and DTCs at primary surgery in 733 stage I or II breast cancer patients with a median follow-up time of 7.6 years. CTCs were detected in samples of peripheral blood mononuclear cells previously stored in liquid-nitrogen using a previously-developed multi-marker quantitative PCR (QPCR)-based assay. DTCs were detected in bone marrow samples by immunocytochemical analysis using anti-cytokeratin antibodies. Results CTCs were detected in 7.9% of patients, while DTCs were found in 11.7%. Both CTC and DTC positivity predicted poor metastasis-free survival (MFS) and breast cancer-specific survival (BCSS); MFS hazard ratio (HR) = 2.4 (P < 0.001)/1.9 (P = 0.006), and BCSS HR = 2.5 (P < 0.001)/2.3 (P = 0.01), for CTC/DTC status, respectively). Multivariate analyses demonstrated that CTC status was an independent prognostic variable for both MFS and BCSS. CTC status also identified a subset of patients with significantly poorer outcome among low-risk node negative patients that did not receive adjuvant systemic therapy (MFS HR 2.3 (P = 0.039), BCSS HR 2.9 (P = 0.017)). Using both tests provided increased prognostic information and indicated different relevance within biologically dissimilar breast cancer subtypes. Conclusions These results support the use of CTC analysis in early breast cancer to generate clinically useful prognostic information.

Published
2011

14. The Norwegian childhood cancer biobank

Author

Hermansen, Johanne U., primary, Wojcik, Dorota M., additional, Robinson, Nina, additional, Pahnke, Jens, additional, Haugland, Hans Kristian, additional, Jamtøy, Ann Helen, additional, Flægstad, Trond, additional, Halvorsen, Hanne, additional, Lund, Bendik, additional, Baumbusch, Lars O., additional, and Munthe‐Kaas, Monica C., additional

Published
2021
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15. The Norwegian childhood cancer biobank.

Author

Hermansen, Johanne U., Wojcik, Dorota M., Robinson, Nina, Pahnke, Jens, Haugland, Hans Kristian, Jamtøy, Ann Helen, Flægstad, Trond, Halvorsen, Hanne, Lund, Bendik, Baumbusch, Lars O., and Munthe‐Kaas, Monica C.

Published
2022
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20. Short- and long-term impact of hyperoxia on the blood and retinal cells’ transcriptome in a mouse model of oxygen-induced retinopathy

Author

Zasada, Magdalena, primary, Madetko-Talowska, Anna, additional, Revhaug, Cecilie, additional, Rognlien, Anne Gro W., additional, Baumbusch, Lars O., additional, Książek, Teofila, additional, Szewczyk, Katarzyna, additional, Grabowska, Agnieszka, additional, Bik-Multanowski, Miroslaw, additional, Józef Pietrzyk, Jacek, additional, Kwinta, Przemko, additional, and Saugstad, Ola Didrik, additional

Published
2019
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24. Copynumber: Efficient algorithms for single- and multi-track copy number segmentation

Author

Nilsen Gro, Liestøl Knut, Loo Peter Van, Moen Vollan Hans Kristian, Eide Marianne B, Rueda Oscar M, Chin Suet-Feung, Russell Roslin, Baumbusch Lars O, Caldas Carlos, Børresen-Dale Anne-Lise, and Lingjærde Ole Christian

Subjects
Copy number, aCGH, Segmentation, Allele-specific segmentation, Penalized regression, Least squares, Bioconductor, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Cancer progression is associated with genomic instability and an accumulation of gains and losses of DNA. The growing variety of tools for measuring genomic copy numbers, including various types of array-CGH, SNP arrays and high-throughput sequencing, calls for a coherent framework offering unified and consistent handling of single- and multi-track segmentation problems. In addition, there is a demand for highly computationally efficient segmentation algorithms, due to the emergence of very high density scans of copy number. Results A comprehensive Bioconductor package for copy number analysis is presented. The package offers a unified framework for single sample, multi-sample and multi-track segmentation and is based on statistically sound penalized least squares principles. Conditional on the number of breakpoints, the estimates are optimal in the least squares sense. A novel and computationally highly efficient algorithm is proposed that utilizes vector-based operations in R. Three case studies are presented. Conclusions The R package copynumber is a software suite for segmentation of single- and multi-track copy number data using algorithms based on coherent least squares principles.

Published
2012
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25. Pulmonary vascular disease is evident in gene regulation of experimental bronchopulmonary dysplasia

Author

Revhaug, Cecilie, primary, Zasada, Magdalena, additional, Rognlien, Anne Gro W., additional, Günther, Clara-Cecilie, additional, Grabowska, Agnieszka, additional, Książek, Teofila, additional, Madetko-Talowska, Anna, additional, Szewczyk, Katarzyna, additional, Bik-Multanowski, Mirolaw, additional, Kwinta, Przemko, additional, Pietrzyk, Jacek J., additional, Baumbusch, Lars O., additional, and Saugstad, Ola D., additional

Published
2019
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26. Immune System Regulation Affected by a Murine Experimental Model of Bronchopulmonary Dysplasia: Genomic and Epigenetic Findings

Author

Revhaug, Cecilie, primary, Bik-Multanowski, Miroslaw, additional, Zasada, Magdalena, additional, Rognlien, Anne Gro W., additional, Günther, Clara-Cecilie, additional, Ksiązek, Teofila, additional, Madetko-Talowska, Anna, additional, Szewczyk, Katarzyna, additional, Grabowska, Agnieszka, additional, Kwinta, Przemko, additional, Pietrzyk, Jacek J., additional, Baumbusch, Lars O., additional, and Saugstad, Ola D., additional

Published
2019
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27. An iTRAQ-Based Quantitative Proteomic Analysis of Plasma Proteins in Preterm Newborns With Retinopathy of Prematurity

Author

Zasada, Magdalena, primary, Suski, Maciej, additional, Bokiniec, Renata, additional, Szwarc-Duma, Monika, additional, Borszewska-Kornacka, Maria Katarzyna, additional, Madej, Józef, additional, Bujak-Gizycka, Beata, additional, Madetko-Talowska, Anna, additional, Revhaug, Cecilie, additional, Baumbusch, Lars O., additional, Saugstad, Ola D., additional, Pietrzyk, Jacek Józef, additional, and Kwinta, Przemko, additional

Published
2018
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28. Expression of full-length p53 and its isoform Δp53 in breast carcinomas in relation to mutation status and clinical parameters

Author

Deppert Wolfgang, Lønning Per E, Geisler Stephanie B, Bergamaschi Anna, Langerød Anita, Myhre Simen, Baumbusch Lars O, Dornreiter Irene, and Børresen-Dale Anne-Lise

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background The tumor suppressor gene p53 (TP53) controls numerous signaling pathways and is frequently mutated in human cancers. Novel p53 isoforms suggest alternative splicing as a regulatory feature of p53 activity. Results In this study we have analyzed mRNA expression of both wild-type and mutated p53 and its respective Δp53 isoform in 88 tumor samples from breast cancer in relation to clinical parameters and molecular subgroups. Three-dimensional structure differences for the novel internally deleted p53 isoform Δp53 have been predicted. We confirmed the expression of Δp53 mRNA in tumors using quantitative real-time PCR technique. The mRNA expression levels of the two isoforms were strongly correlated in both wild-type and p53-mutated tumors, with the level of the Δp53 isoform being approximately 1/3 of that of the full-length p53 mRNA. Patients expressing mutated full-length p53 and non-mutated (wild-type) Δp53, "mutational hybrids", showed a slightly higher frequency of patients with distant metastasis at time of diagnosis compared to other patients with p53 mutations, but otherwise did not differ significantly in any other clinical parameter. Interestingly, the p53 wild-type tumors showed a wide range of mRNA expression of both p53 isoforms. Tumors with mRNA expression levels in the upper or lower quartile were significantly associated with grade and molecular subtypes. In tumors with missense or in frame mutations the mRNA expression levels of both isoforms were significantly elevated, and in tumors with nonsense, frame shift or splice mutations the mRNA levels were significantly reduced compared to those expressing wild-type p53. Conclusion Expression of p53 is accompanied by the functionally different isoform Δp53 at the mRNA level in cell lines and human breast tumors. Investigations of "mutational hybrid" patients highlighted that wild-type Δp53 does not compensates for mutated p53, but rather may be associated with a worse prognosis. In tumors, both isoforms show strong correlations in different mutation-dependent mRNA expression patterns.

Published
2006
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29. Pulmonary vascular disease is evident in gene regulation of experimental bronchopulmonary dysplasia.

Author

Revhaug, Cecilie, Zasada, Magdalena, Rognlien, Anne Gro W., Günther, Clara-Cecilie, Grabowska, Agnieszka, Książek, Teofila, Madetko-Talowska, Anna, Szewczyk, Katarzyna, Bik-Multanowski, Mirolaw, Kwinta, Przemko, Pietrzyk, Jacek J., Baumbusch, Lars O., and Saugstad, Ola D.

Subjects
BRONCHOPULMONARY dysplasia, GENETIC regulation, LUNG diseases, VASCULAR diseases, PULMONARY blood vessels, ANIMAL populations, ANIMALS, BIOLOGICAL models, GENES, LUNGS, MICE, RNA, STATISTICAL sampling, HYPEROXIA, DISEASE complications
Abstract

Objective: To examine the gene expression regarding pulmonary vascular disease in experimental bronchopulmonary dysplasia in young mice. Premature delivery puts babies at risk of severe complications. Bronchopulmonary dysplasia (BPD) is a common complication of premature birth leading to lifelong affection of pulmonary function. BPD is recognized as a disease of arrested alveolar development. The disease process is not fully described and no complete cure or prevention is known. The focus of interest in the search for treatment and prevention of BPD has traditionally been at airspace level; however, the pulmonary vasculature is increasingly acknowledged in the pathology of BPD. The aim of the investigation was to study the gene expression in lungs with BPD with regards to pulmonary vascular disease (PVD).Methods: We employed a murine model of hyperoxia-induced BPD and gene expression microarray technique to determine the mRNA expression in lung tissue from young mice. We combined gene expression pathway analysis and analyzed the biological function of multiple single gene transcripts from lung homogenate to study the PVD relevant gene expression.Results: There were n = 117 significantly differentially regulated genes related to PVD through down-regulation of contractile elements, up- and down-regulation of factors involved in vascular tone and tissue-specific genes. Several genes also allowed for pinpointing gene expression differences to the pulmonary vasculature. The gene Nppa coding for a natriuretic peptide, a potent vasodilator, was significantly down-regulated and there was a significant up-regulation of Pde1a (phosphodiesterase 1A), Ptger3 (prostaglandin e receptor 3), and Ptgs1 (prostaglandin-endoperoxide synthase one).Conclusion: The pulmonary vasculature is affected by the arrest of secondary alveolarization as seen by differentially regulated genes involved in vascular tone and pulmonary vasculature suggesting BPD is not purely an airspace disease. Clues to prevention and treatment may lie in the pulmonary vascular system. [ABSTRACT FROM AUTHOR]

Published
2020
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31. Comparison of whole genome expression profile between preterm and full-term newborns

Author

Kwinta, Przemko, primary, Bokiniec, Renata, additional, Bik-Multanowski, Mirosław, additional, Gunther, Clara-Cecilie, additional, Grabowska, Agnieszka, additional, Książek, Teofila, additional, Madetko-Talowska, Anna, additional, Szewczyk, Katarzyna, additional, Szwarc-Duma, Monika, additional, Borszewska-Kornacka, Maria K., additional, Baumbusch, Lars O., additional, Revhaug, Cecilie, additional, Saugstad, Ola D., additional, and Pietrzyk, Jacek J., additional

Published
2017
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32. Abstract 3049: Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing

Author

Demeulemeester, Jonas, primary, Kumar, Parveen, additional, Møller, Elen K., additional, Nord, Silje, additional, Wedge, David C., additional, Peterson, April, additional, Mathiesen, Randi R., additional, Fjelldal, Renathe, additional, Esteki, Masoud Z., additional, Theunis, Koen, additional, Gallardo, Elia F., additional, Grundstad, Jason, additional, Borgen, Elin, additional, Baumbusch, Lars O., additional, Børresen-Dale, Anne-Lise, additional, White, Kevin P., additional, Kristensen, Vessela N., additional, Loo, Peter Van, additional, Voet, Thierry, additional, and Naume, Bjørn, additional

Published
2017
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34. Tracing the origin of disseminated tumor cells in breast cancer using single-cell sequencing

Author

Demeulemeester, Jonas, primary, Kumar, Parveen, additional, Møller, Elen K., additional, Nord, Silje, additional, Wedge, David C., additional, Peterson, April, additional, Mathiesen, Randi R., additional, Fjelldal, Renathe, additional, Zamani Esteki, Masoud, additional, Theunis, Koen, additional, Fernandez Gallardo, Elia, additional, Grundstad, A. Jason, additional, Borgen, Elin, additional, Baumbusch, Lars O., additional, Børresen-Dale, Anne-Lise, additional, White, Kevin P., additional, Kristensen, Vessela N., additional, Van Loo, Peter, additional, Voet, Thierry, additional, and Naume, Bjørn, additional

Published
2016
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37. Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes

Author

Reiche, Kristin, Kasack, Katharina, Schreiber, Stephan, Lüders, Torben, Due, Eldri U., Naume, Bjørn, Riis, Margit, Kristensen, Vessela N., Horn, Friedemann, Børresen-Dale, Anne-Lise, Hackermüller, Jörg, Baumbusch, Lars O., and Publica

Subjects
Transcription, Genetic, Microarrays, DNA transcription, lcsh:Medicine, Breast Neoplasms, Research and Analysis Methods, Biochemistry, Molecular Genetics, Nucleic Acids, Molecular Cell Biology, Breast Tumors, Breast Cancer, Basic Cancer Research, Genetics, Medicine and Health Sciences, Humans, lcsh:Science, Biology and life sciences, lcsh:R, Computational Biology, Cancers and Neoplasms, Obstetrics and Gynecology, Cell Biology, Genomics, Genome Analysis, Chromatin, Gene regulation, Functional Genomics, Neoplasm Proteins, Bioassays and Physiological Analysis, Oncology, Case-Control Studies, RNA, Women's Health, Female, RNA, Long Noncoding, lcsh:Q, Gene expression, Transcriptome Analysis, Research Article
Abstract

Breast cancer, the second leading cause of cancer death in women, is a highly heterogeneous disease, characterized by distinct genomic and transcriptomic profiles. Transcriptome analyses prevalently assessed protein-coding genes; however, the majority of the mammalian genome is expressed in numerous non-coding transcripts. Emerging evidence supports that many of these non-coding RNAs are specifically expressed during development, tumorigenesis, and metastasis. The focus of this study was to investigate the expression features and molecular characteristics of long non-coding RNAs (lncRNAs) in breast cancer. We investigated 26 breast tumor and 5 normal tissue samples utilizing a custom expression microarray enclosing probes for mRNAs as well as novel and previously identified lncRNAs. We identified more than 19,000 unique regions significantly differentially expressed between normal versus breast tumor tissue, half of these regions were non-coding without any evidence for functional open reading frames or sequence similarity to known proteins. The identified non-coding regions were primarily located in introns (53%) or in the intergenic space (33%), frequently orientated in antisense-direction of protein-coding genes (14%), and commonly distributed at promoter-, transcription factor binding-, or enhancer-sites. Analyzing the most diverse mRNA breast cancer subtypes Basal-like versus Luminal A and B resulted in 3,025 significantly differentially expressed unique loci, including 682 (23%) for non-coding transcripts. A notable number of differentially expressed protein-coding genes displayed non-synonymous expression changes compared to their nearest differentially expressed lncRNA, including an antisense lncRNA strongly anticorrelated to the mRNA coding for histone deacetylase 3 (HDAC3), which was investigated in more detail. Previously identified chromatin-associated lncRNAs (CARs) were predominantly downregulated in breast tumor samples, including CARs located in the protein-coding genes for CALD1, FTX, and HNRNPH1. In conclusion, a number of differentially expressed lncRNAs have been identified with relation to cancer-related protein-coding genes.

Published
2014

38. N-Acetylcysteine Amide Exerts Possible Neuroprotective Effects in Newborn Pigs after Perinatal Asphyxia

Author

Benterud, Torkil, primary, Ystgaard, Martin B., additional, Manueldas, Sophia, additional, Pankratov, Leonid, additional, Alfaro-Cervello, Clara, additional, Florholmen, Geir, additional, Ahmed, Muhammad Shakil, additional, Sandvik, Leiv, additional, Norgren, Svante, additional, Bjørås, Magnar, additional, Baumbusch, Lars O., additional, Solberg, Ronnaug, additional, and Saugstad, Ola Didrik, additional

Published
2016
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39. Abstract LB-051: Tumor heterogeneity and dissemination in breast cancer: Deep sequencing of single disseminated cells from bone marrow compared to primary tumor and lymph node metastases

Author

Møller, Elen, primary, Kumar, Parveen, additional, Nord, Silje, additional, Wedge, David, additional, van Loo, Peter, additional, Peterson, April, additional, Mathiesen, Randi R., additional, Fjelldal, Renathe, additional, Esteki, Masoud Z., additional, Grundstad, Jason A., additional, Borgen, Elin, additional, Baumbusch, Lars O., additional, Børresen-Dale, Anne-Lise, additional, White, Kevin P., additional, Voet, Thierry, additional, Naume, Bjørn, additional, and Kristensen, Vessela N., additional

Published
2015
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40. Abstract A72: Next-generation sequencing of disseminated tumor cells

Author

Møller, Elen K., primary, Kumar, Parveen, additional, Voet, Thierry, additional, Peterson, April, additional, Loo, Peter Van, additional, Mathiesen, Randi, additional, Fjelldal, Renate, additional, Grundstad, Jason, additional, Borgen, Elin, additional, Baumbusch, Lars O., additional, Naume, Bjørn, additional, Børresen-Dale, Anne-Lise, additional, Nord, Silje, additional, and Kristensen, Vessela N., additional

Published
2015
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41. Temporal Profile of Circulating microRNAs after Global Hypoxia-Ischemia in Newborn Piglets.

Author

Garberg, Håvard Tetlie, Huun, Marianne U., Baumbusch, Lars O., Åsegg-atneosen, Monica, Solberg, Rønnaug, and Saugstad, Ola Didrik

Subjects
MICRORNA, BIOMARKERS, ISCHEMIA
Abstract

Background: There is a lack of reliable biomarkers that can identify and grade acute hypoxic-ischemic encephalopathy in newborns. MicroRNAs (miRNA) are short, non-coding strands of RNA that are released into the circulation in response to tissue stress and injury. Some miRNAs are highly tissue specific and thus may potentially be non-invasive biomarkers of neonatal hypoxic-ischemic brain injury. Objective: The aim of this study was to characterize the temporal expression of selected circulating miRNAs in a clinically relevant piglet model of neonatal hypoxia-ischemia (HI). Methods: A total of 13 anesthetized newborn piglets were randomized to either a control group (n = 5) or transient global HI group (n = 8). HI was achieved by ventilation with 8% oxygen until the point of severe acidosis (arterial base excess ≤-20 mmol/l) and/or hypotension (mean arterial blood pressure ≤ 20 mm Hg) was reached. Plasma was sampled at baseline, at the end of HI and 0.5, 3.5 and 9.5 h after HI. MiRNA expression was measured by qRT-PCR. Results: Compared to baseline, miR-374a increased during HI (p = 0.01), remained elevated at 0.5 h after HI (p = 0.02) and was downregulated at 9.5 h after HI (p = 0.02). MiR-210 increased during HI (p = 0.02) and rapidly normalized by 0.5 h after HI. MiR-124 and miR-125b did not exhibit significant alterations. Correlations were observed between miR-374a, arterial pH, base excess and lactate levels, and between miR-210 and pO 2 (p < 0.05). Conclusions: Our data suggest that miR-374a and miR-210 are important regulators in neonatal HI and might have a place as biomarkers in this setting. [ABSTRACT FROM AUTHOR]

Published
2017
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43. Long Non-Coding RNAs Differentially Expressed between Normal versus Primary Breast Tumor Tissues Disclose Converse Changes to Breast Cancer-Related Protein-Coding Genes

Author

Reiche, Kristin, primary, Kasack, Katharina, additional, Schreiber, Stephan, additional, Lüders, Torben, additional, Due, Eldri U., additional, Naume, Bjørn, additional, Riis, Margit, additional, Kristensen, Vessela N., additional, Horn, Friedemann, additional, Børresen-Dale, Anne-Lise, additional, Hackermüller, Jörg, additional, and Baumbusch, Lars O., additional

Published
2014
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44. Genomic copy number imbalances associated with bone and non-bone metastasis of early-stage breast cancer

Author

Liu, Yanhong, primary, Zhou, Renke, additional, Baumbusch, Lars O., additional, Tsavachidis, Spyros, additional, Brewster, Abenaa M., additional, Do, Kim-Anh, additional, Sahin, Aysegul, additional, Hortobagyi, Gabriel N., additional, Taube, Joseph H., additional, Mani, Sendurai A., additional, Aarøe, Jørgen, additional, Wärnberg, Fredrik, additional, Børresen-Dale, Anne-Lise, additional, Mills, Gordon B., additional, Thompson, Patricia A., additional, and Bondy, Melissa L., additional

Published
2013
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45. Next-Generation Sequencing of Disseminated Tumor Cells

Author

Møller, Elen K., primary, Kumar, Parveen, additional, Voet, Thierry, additional, Peterson, April, additional, Van Loo, Peter, additional, Mathiesen, Randi R., additional, Fjelldal, Renathe, additional, Grundstad, Jason, additional, Borgen, Elin, additional, Baumbusch, Lars O., additional, Naume, Bjørn, additional, Børresen-Dale, Anne-Lise, additional, White, Kevin P., additional, Nord, Silje, additional, and Kristensen, Vessela N., additional

Published
2013
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46. Low-grade and high-grade mammary carcinomas in WAP-T transgenic mice are independent entities distinguished by Met expression

Author

Otto, Benjamin, primary, Gruner, Katharina, additional, Heinlein, Christina, additional, Wegwitz, Florian, additional, Nollau, Peter, additional, Ylstra, Bauke, additional, Pantel, Klaus, additional, Schumacher, Udo, additional, Baumbusch, Lars O., additional, Martin-Subero, José Ignacio, additional, Siebert, Reiner, additional, Wagener, Christoph, additional, Streichert, Thomas, additional, Deppert, Wolfgang, additional, and Tolstonog, Genrich V., additional

Published
2012
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47. High-resolution analyses of copy number changes in disseminated tumor cells of patients with breast cancer

Author

Mathiesen, Randi R., primary, Fjelldal, Renathe, additional, Liestøl, Knut, additional, Due, Eldri U., additional, Geigl, Jochen B., additional, Riethdorf, Sabine, additional, Borgen, Elin, additional, Rye, Inga H., additional, Schneider, Ida J., additional, Obenauf, Anna C., additional, Mauermann, Oliver, additional, Nilsen, Gro, additional, Christian Lingjaerde, Ole, additional, Børresen-Dale, Anne-Lise, additional, Pantel, Klaus, additional, Speicher, Michael R., additional, Naume, Bjørn, additional, and Baumbusch, Lars O., additional

Published
2011
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48. Genomic Architecture Characterizes Tumor Progression Paths and Fate in Breast Cancer Patients

Author

Russnes, Hege G., primary, Vollan, Hans Kristian Moen, additional, Lingjærde, Ole Christian, additional, Krasnitz, Alexander, additional, Lundin, Pär, additional, Naume, Bjørn, additional, Sørlie, Therese, additional, Borgen, Elin, additional, Rye, Inga H., additional, Langerød, Anita, additional, Chin, Suet-Feung, additional, Teschendorff, Andrew E., additional, Stephens, Philip J., additional, Månér, Susanne, additional, Schlichting, Ellen, additional, Baumbusch, Lars O., additional, Kåresen, Rolf, additional, Stratton, Michael P., additional, Wigler, Michael, additional, Caldas, Carlos, additional, Zetterberg, Anders, additional, Hicks, James, additional, and Børresen-Dale, Anne-Lise, additional

Published
2010
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50. Framework for Identifying Common Aberrations in DNA Copy Number Data.

Author

Istrail, Sorin, Pevzner, Pavel, Waterman, Michael S., Speed, Terry, Huang, Haiyan, Ben-Dor, Amir, Lipson, Doron, Tsalenko, Anya, Reimers, Mark, Baumbusch, Lars O., Barrett, Michael T., Weinstein, John N., Børresen-Dale, Anne-Lise, and Yakhini, Zohar

Abstract

High-resolution array comparative genomic hybridization(aCGH) provides exon-level mapping of DNA aberrations in cells or tissues. Such aberrations are central to carcinogenesis and, in many cases, central to targeted therapy of the cancers. Some of the aberrations are sporadic, one-of-a-kind changes in particular tumor samples; others occur frequently and reflect common themes in cancer biology that have interpretable, causal ramifications. Hence, the difficult task of identifying and mapping common, overlapping genomic aberrations (including amplifications and deletions) across a sample set is an important one; it can provide insight for the discovery of oncogenes, tumor suppressors, and the mechanisms by which they drive cancer development. In this paper we present an efficient computational framework for identification and statistical characterization of genomic aberrations that are common to multiple cancer samples in a CGH data set. We present and compare three different algorithmic approaches within the context of that framework. Finally, we apply our methods to two datasets - a collection of 20 breast cancer samples and a panel of 60 diverse human tumor cell lines (the NCI-60). Those analyses identified both known and novel common aberrations containing cancer-related genes. The potential impact of the analytical methods is well demonstrated by new insights into the patterns of deletion of CDKN2A (p16), a tumor suppressor gene crucial for the genesis of many types of cancer. [ABSTRACT FROM AUTHOR]

Published
2007
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