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Background Many models have been proposed to detect copy number alterations in chromosomal copy number profiles, but it is usually not obvious to decide which is most effective for a given data set. Furthermore, most methods have a smoothing parameter that determines the number of breakpoints and must be chosen using various heuristics. Results We present three contributions for...
Motivation: DNA copy number profiles characterize regions of chromosome gains, losses and breakpoints in tumor genomes. Although many models have been proposed to detect these alterations, it is not clear which model is appropriate before visual inspection the signal, noise and models for a particular profile. Results: We propose SegAnnDB, a Web-based computer vision system for...
Summary: More and more cancer studies use next-generation sequencing (NGS) data to detect various types of genomic variation. However, even when researchers have such data at hand, single-nucleotide polymorphism arrays have been considered necessary to assess copy number alterations and especially loss of heterozygosity (LOH). Here, we present the tool Control-FREEC that enables...
& Nadine Van Roy 1,2 & Frank Speleman 1,2 & Leen Willems 3 & Tim Lammens 2,3 & Geneviève Laureys 2,3 & Gudrun Schleiermacher 4,5,6 & Godelieve A. M. Tytgat 7 & Kathy Astrahantseff 8 & Hedwig Deubzer 8,9,10
Chromosome 17q gains are almost invariably present in high-risk neuroblastoma cases. Here, we perform an integrative epigenomics search for dosage-sensitive transcription factors on 17q marked by H3K27ac defined super-enhancers and identify TBX2 as top candidate gene. We show that TBX2 is a constituent of the recently established core regulatory circuitry in neuroblastoma with...
In neuroblastoma, the most frequent genetic alterations are unbalanced translocations involving chromosome 17. To gain insights into these rearrangements, we have characterized a previously identified der(1)t(1;17) of the CLB-Bar cell line. The 17q breakpoint was mapped by FISH. Subsequently, a rearranged fragment was identified by Southern analysis, cloned in a lambda vector and...
Deletion of the chromosome 1p36 region is a frequent abnormality in neuroblastoma. To gain further insights into the role of this alteration in oncogenesis, we have constructed a specific cDNA microarray representing most known genes and ESTs from the 1p35–36 region and analysed the expression profiles of 15 neuroblastoma cell lines and 28 neuroblastoma tumours. Hierarchical...
Thomas Blanc Gudrun Schleiermacher 1 Ve ronique Mosseri Pascale Philippe-Chomette Isabelle Janoueix-Lerosey Gaelle Pierron Eve Lapouble 1 Michel Peuchmaur Paul Fre neaux Louise Galmiche Nathalie Algret ... Conceptualization: Herve J. Brisse, Thomas Blanc, Gudrun Schleiermacher, VeÂronique Mosseri, Pascale Philippe-Chomette, Isabelle Janoueix-Lerosey, Gaelle Pierron, Michel Peuchmaur, Jean Michon, Olivier Delattre
Neuroblastoma is a pediatric cancer of the peripheral nervous system in which structural chromosome aberrations are emblematic of aggressive tumors. In this study, we performed an in-depth analysis of somatic rearrangements in two neuroblastoma cell lines and two primary tumors using paired-end sequencing of mate-pair libraries and RNA-seq. The cell lines presented with typical...
Background Somatically acquired genomic alterations with MYCN amplification (MNA) are key features of neuroblastoma (NB), the most common extra-cranial malignant tumour of childhood. Little is known about the frequency, clinical characteristics and outcome of NBs harbouring genomic amplification(s) distinct from MYCN. Methods Genomic profiles of 1100 NBs from French centres...
PurposeIdentifying among nephroblastoma those with a high propensity for distant metastases using cell cycle markers: cyclin E as a regulator of progression through the cell cycle and Ki-67 as a tumor proliferation marker, since both are often deregulated in many human malignancies.Methodology/Principal FindingsA staining index (SI) was obtained by immunohistochemistry using anti...
Gudrun Schleiermacher 6 Katleen De Preter 0 1 Design Type Measurement Type Technology Type Factor Type 0 Center for Medical Genetics, Ghent University , Ghent , Belgium 1 Cancer Research Institute Ghent
