Medical Biology - Research Publications

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Author: Doyle, Maria × Author: Papenfuss, Anthony × Author: Tothill, Richard × Start date: 2014 ×

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    Genomic characterisation of Eμ-Myc mouse lymphomas identifies Bcor as a Myc co-operative tumour-suppressor gene
    Lefebure, M ; Tothill, RW ; Kruse, E ; Hawkins, ED ; Shortt, J ; Matthews, GM ; Gregory, GP ; Martin, BP ; Kelly, MJ ; Todorovski, I ; Doyle, MA ; Lupat, R ; Li, J ; Schroeder, J ; Wall, M ; Craig, S ; Poortinga, G ; Cameron, D ; Bywater, M ; Kats, L ; Gearhart, MD ; Bardwell, VJ ; Dickins, RA ; Hannan, RD ; Papenfuss, AT ; Johnstone, RW (NATURE PUBLISHING GROUP, 2017-03-06)
    The Eμ-Myc mouse is an extensively used model of MYC driven malignancy; however to date there has only been partial characterization of MYC co-operative mutations leading to spontaneous lymphomagenesis. Here we sequence spontaneously arising Eμ-Myc lymphomas to define transgene architecture, somatic mutations, and structural alterations. We identify frequent disruptive mutations in the PRC1-like component and BCL6-corepressor gene Bcor. Moreover, we find unexpected concomitant multigenic lesions involving Cdkn2a loss and other cancer genes including Nras, Kras and Bcor. These findings challenge the assumed two-hit model of Eμ-Myc lymphoma and demonstrate a functional in vivo role for Bcor in suppressing tumorigenesis.
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    Bioinformatics Pipelines for Targeted Resequencing and Whole-Exome Sequencing of Human and Mouse Genomes: A Virtual Appliance Approach for Instant Deployment
    Li, J ; Doyle, MA ; Saeed, I ; Wong, SQ ; Mar, V ; Goode, DL ; Caramia, F ; Doig, K ; Ryland, GL ; Thompson, ER ; Hunter, SM ; Halgamuge, SK ; Ellul, J ; Dobrovic, A ; Campbell, IG ; Papenfuss, AT ; McArthur, GA ; Tothill, RW ; Calogero, RA (PUBLIC LIBRARY SCIENCE, 2014-04-21)
    Targeted resequencing by massively parallel sequencing has become an effective and affordable way to survey small to large portions of the genome for genetic variation. Despite the rapid development in open source software for analysis of such data, the practical implementation of these tools through construction of sequencing analysis pipelines still remains a challenging and laborious activity, and a major hurdle for many small research and clinical laboratories. We developed TREVA (Targeted REsequencing Virtual Appliance), making pre-built pipelines immediately available as a virtual appliance. Based on virtual machine technologies, TREVA is a solution for rapid and efficient deployment of complex bioinformatics pipelines to laboratories of all sizes, enabling reproducible results. The analyses that are supported in TREVA include: somatic and germline single-nucleotide and insertion/deletion variant calling, copy number analysis, and cohort-based analyses such as pathway and significantly mutated genes analyses. TREVA is flexible and easy to use, and can be customised by Linux-based extensions if required. TREVA can also be deployed on the cloud (cloud computing), enabling instant access without investment overheads for additional hardware. TREVA is available at http://bioinformatics.petermac.org/treva/.