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  • 1
    Publication Date: 2014-05-22
    Description: 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 genomic segmentation: first, visually inspect the profiles and manually annotate altered regions, then SegAnnDB determines the precise alteration locations using a mathematical model of the data and annotations. SegAnnDB facilitates collaboration between biologists and bioinformaticians, and uses the University of California, Santa Cruz genome browser to visualize copy number alterations alongside known genes. Availability and implementation: The breakpoints project on INRIA GForge hosts the source code, an Amazon Machine Image can be launched and a demonstration Web site is http://bioviz.rocq.inria.fr . Contact: toby@sg.cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2008-10-17
    Description: Neuroblastoma, a tumour derived from the peripheral sympathetic nervous system, is one of the most frequent solid tumours in childhood. It usually occurs sporadically but familial cases are observed, with a subset of cases occurring in association with congenital malformations of the neural crest being linked to germline mutations of the PHOX2B gene. Here we conducted genome-wide comparative genomic hybridization analysis on a large series of neuroblastomas. Copy number increase at the locus encoding the anaplastic lymphoma kinase (ALK) tyrosine kinase receptor was observed recurrently. One particularly informative case presented a high-level gene amplification that was strictly limited to ALK, indicating that this gene may contribute on its own to neuroblastoma development. Through subsequent direct sequencing of cell lines and primary tumour DNAs we identified somatic mutations of the ALK kinase domain that mainly clustered in two hotspots. Germline mutations were observed in two neuroblastoma families, indicating that ALK is a neuroblastoma predisposition gene. Mutated ALK proteins were overexpressed, hyperphosphorylated and showed constitutive kinase activity. The knockdown of ALK expression in ALK-mutated cells, but also in cell lines overexpressing a wild-type ALK, led to a marked decrease of cell proliferation. Altogether, these data identify ALK as a critical player in neuroblastoma development that may hence represent a very attractive therapeutic target in this disease that is still frequently fatal with current treatments.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Janoueix-Lerosey, Isabelle -- Lequin, Delphine -- Brugieres, Laurence -- Ribeiro, Agnes -- de Pontual, Loic -- Combaret, Valerie -- Raynal, Virginie -- Puisieux, Alain -- Schleiermacher, Gudrun -- Pierron, Gaelle -- Valteau-Couanet, Dominique -- Frebourg, Thierry -- Michon, Jean -- Lyonnet, Stanislas -- Amiel, Jeanne -- Delattre, Olivier -- England -- Nature. 2008 Oct 16;455(7215):967-70. doi: 10.1038/nature07398.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut Curie, Centre de Recherche, and Inserm, U830, 26 rue d'Ulm, Paris F-75248, France.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18923523" target="_blank"〉PubMed〈/a〉
    Keywords: Cell Division ; Cell Line ; Cell Line, Tumor ; Child ; Gene Dosage ; Genome, Human/genetics ; Germ-Line Mutation/*genetics ; Humans ; Neuroblastoma/enzymology/*genetics ; Nucleic Acid Hybridization ; Phosphorylation ; Point Mutation/*genetics ; Polymorphism, Single Nucleotide/genetics ; Protein-Tyrosine Kinases/chemistry/deficiency/*genetics/metabolism ; Receptor Protein-Tyrosine Kinases
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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