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    Archived pages: 9 . Archive date: 2013-11.

  • Title: Queensland Centre for Medical Genomics
    Descriptive info: .. Home.. News.. Contact Us.. Vision Statement.. The Queensland Centre for Medical Genomics is committed to deliver and enable personalized medicine for the state of Queensland and Australia.. Mission.. Statement.. To sequence and characterize pancreas and ovarian cancer to an unprecedented depth enabling a more complete understanding of the mechanisms that lead to genetic instability and ultimately cancer.. To develop and  ...   provide access and training to new technology/tools for the Queensland and Australian scientific communities.. To attract additional resources to characterise other cancers that impact on Queensland and Australia.. >> Home.. >> Overview.. >> Technology.. >> Informatics.. >> QCMG Research Projects.. >> Publications.. >> Personnel.. >> News.. >> Contact Us.. Copyright Queensland Centre for Medical Genomics.. Web Design.. by.. Logoland Australia.. Logo Design..

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  • Title: Queensland Centre for Medical Genomics - News -
    Descriptive info: October 2012:.. First 100 pancreatic cancer.. patient genomes published in Nature.. Click here for the paper.. QCMG receives first HiSEQ 2500 upgrade.. June 2012:.. Dr Shivashankar Nagaraj was successful in obtaining.. a QIMR collaborative seed funding grant.. along with Dr Jason Mulveena (QIMR).. November 2011:.. Dr Nic Waddell was a co-investigator on two.. successful grant applications, including one.. for oesophageal cancer and one for a.. focused brain metastasis project.. October 2011:.. Dr Karin Kassahn was awarded.. an Ian Potter Travel award to attend.. the Cold Spring Harbour Laboratory.. Personal Genomes meeting.. December 2010:.. 4.. th.. ICGC meeting organised by.. QCMG and held at Couran Cove,.. Queensland.. June 2010:.. QCMG is officially opened by the.. Premier  ...   libraries).. March 2010:.. The new QCMG development computing cluster was.. commissioned.. The UQ HPC cluster tender has been finalised which will have dedicated infrastructure for the QCMG greatly increasing our ability to map and analyse data coming from the sequencers.. First Australian Pancreatic Genome Initiative (APGI).. meeting held at the Garvan Institute for Medical Research, Dr Brooke Gardiner and Dr Nic Waddell presented data generated from the QCMG.. December 2009/January 2010:.. The fleet of eleven SOLiD instruments was upgraded to.. version 3 plus allowing the outputs to 60 Gbs of mappable data per instrument per run (2 slides Long Mate Pair libraries).. December 2009:.. First milestone achieved, 750 Gb of mapped DNA/RNA.. cancer data completed..

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  • Title: Queensland Centre for Medical Genomics - Contact -
    Descriptive info: Queensland Centre for Medical Genomics.. Institute for Molecular Bioscience.. University of Queensland.. St Lucia QLD 4072.. Phone: 61-7-3346 2392.. Fax: 61-7-3346 2101.. Email all queries to Ms Deborah Gwynne:.. d.. gwynne@imb.. uq.. edu.. au..

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  • Title: Queensland Centre for Medical Genomics - Overview -
    Descriptive info: About the Queensland Centre for Medical Genomics.. The Queensland Centre for Medical Genomics (QCMG) has been established with funding from the Australian National Health and Medical Research Council (NHMRC), the Queensland State Government and the University of Queensland.. The centre s flagship project is the sequencing of 500 Pancreatic and Ovarian cancer genomes as part the International Cancer Genome Consortium (ICGC).. Australia s commitment to the ICGC has required the formation of this world class sequencing centre within the Institute for Molecular Bioscience (IMB), University of Queensland (UQ) and currently employs 38 bioinformaticians and molecular biology research scientists dedicated to medical genome research.. The QCMG s research efforts are built on collaboration with two commercial parties.. The University of Queensland has a long standing collaboration with Applied Biosystems (AB) and is actively involved in the development and refinement of next generation sequencing technology and its applications.. This  ...   the QCMG s ability to manage and interrogate the massive volumes of sequence data generated during genome sequencing.. About the International Cancer Genome Consortium (ICGC).. The primary goal of the ICGC.. is to create comprehensive genomic, transcriptomic and epigenomic atlases of the molecular changes arising in human tumours.. The ICGC will study up to 50 different tumor types and/or subtypes from across the globe over the next 5 years and is committed to making these data available to the entire research community as rapidly as possible.. The ICGC is also committed to accelerating cancer research by facilitating communication and co-ordination amongst its members.. The projects currently instigated by ICGC include:.. Australia (Pancreas, Ovarian),.. Canada (Pancreas),.. China (Stomach),.. France (Liver, Breast (HER2-positive),.. India (Oral Cavity),.. Japan (Liver).. Spain (Chronic lymphocytic leukemia),.. United Kingdom (Breast (several subtypes), lung Melanoma).. Germany (pediatric brain tumours).. LINK to ICGC:.. http://www.. icgc.. org..

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  • Title: Queensland Centre for Medical Genomics - Technology -
    Descriptive info: Illumina HiSeq 2000 introduced.. The current sequencing capacity has now been complimented with the recent installation of three Illumina HiSeq 2000s.. The HiSeq 2000s greatly expands the capacity and capabilities of the sequencing core through increased throughput; automated sample processing and increased read lengths (up to 2 x 101 bps).. This compliment of HiSeq 2000s is scheduled to be upgraded during the fourth quarter of 2012 to the HiSeq2500, allowing for increased throughput, longer reads and faster turn around times.. This upgrade will provide QCMG with the enhanced flexibility with the ability to generate a human genome sequence in a single day per machine.. Furthermore as part of this upgrade longer read lengths (2 x 150bp) will be enabled offering greater insight into many of the current complexities of the human transcriptome.. In addition, QCMG has a MiSEQ instrument which was recently upgraded to run 2x250bp read lengths.. Non Optical Sequencing Instruments.. Independently QCMG received a suite of Ion Torrent Personal Genome Machines (PGM) at the beginning of 2011.. This new non-optical sequencing platform has primarily been used for verification experiments using amplicon based sequencing of candidate genes that have shown somatic variations.. QCMG have also used this instrument for bacterial sequencing and  ...   utilizing the power of the Ion Torrent platform coupled with targeted enrichment solutions from Life Technologies.. The unbiased coverage and read lengths offered with the Ion Torrent data is allowing QCMG to focus on regions previously un-tractable to sequencing using alternative technologies.. Automation.. QCMG have implemented a number of robotic platforms to work in unison with the Next Generation Sequencing technologies, allowing QCMG to scale accordingly with the increased throughput.. This section of the QCMG laboratory houses two Agilent Bravo Liquid Handlers, two Life Technologies Library Builders, two Illumina cBots and suite of 4 Ion Torrent One Touch platforms.. This compliment of robotic platforms is currently allowing QCMG to generate well over 50 Fragment libraries per day, and process greater than 96 Exome samples per week while still maintaining high utilization of the Sequencing Platforms though automated solutions for both bead and cluster generation.. LIMs.. QCMG has chosen and implemented GenoLogics Geneus.. TM.. as its sole LIMs package.. Custom configurations have been developed for the Ion Torrent workflow, strongly leveraging the automation and reporting solutions provided within the package.. QCMG has installed the pre-configured Illumina package from Genologics ensuring that these newest additions to the sequencing fleet are encompassed by the LIMs system..

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  • Title: Queensland Centre for Medical Genomics - Informatics -
    Descriptive info: The informatics team supports QCMG research by providing a robust cyberinfrastructure to archive, manage, and analyze the vast amounts of second- and third-generation sequencing data that we produce.. Because high-throughput sequencing generates data at an unprecedented rate one of the most challenging tasks the team faces is migration of data from the sequencing machines to the research team and to a data storage facility.. We have developed an automated pipeline that checks data integrity, archives data in a redundant, persistent hierarchical storage management system, and prepares raw sequencing data for mapping and alignment.. QCMG informaticians constantly strive to keep pace with the rapidly moving front of sequencing technology by developing new applications  ...   evaluation of the mapped data, and the detection of polymorphisms, insertions, deletions, inversions, translocations and copy number changes in genomic and transcriptomic libraries for both disease and normal samples.. These tools can also be adopted by other groups as they acquire next-generation sequencing capabilities.. In order to ensure QCMG software is of the highest quality to meet the requirements of the research team we use task management software to coordinate team efforts, Subversion revision control software to manage the code repository, and formal coding guidelines for programming languages in use at the QCMG which include standards for requirements collection, code styles, unit testing, internal and external documentation, and distribution and deployment methods..

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  • Title: Queensland Centre for Medical Genomics - Research Projects -
    Descriptive info: The Australian ICGC Project.. The Australian contingent of the ICGC initiative is based at the QCMG/IMB and will study the underlying changes that result in the development of pancreatic and ovarian cancer.. The Australian Pancreatic Cancer Genome Initiative (APGI), co-led by Professor Sean Grimmond from the Institute of Molecular Bioscience in Brisbane, and Professor Andrew Biankin from The Garvan Institute of Medical Research in Sydney, is the Australian project arm of the pancreatic cancer genome initiative.. It is made up of a range of specialists and researchers in pancreatic cancer across the country.. The initiative also includes significant contributions from centres across the globe including Johns Hopkins University and the University of California in the USA, the Ontario Institute for Cancer Research in Canada and the University of Verona in Italy.. Another component of the QCMG will be the sequencing of a set of ovarian cancer tumours through partnership with Professor David Bowtell from the Peter MacCallum Cancer Centre.. Professor Bowtell is part of the Australian Ovarian Cancer Study (AOCS) which is a collaborative research program between clinicians, scientists, patients and advocacy groups aimed at improving the prevention, diagnosis, and treatment of ovarian cancer.. Initiated in 2001 AOCS now has a uniquely powerful resource for ovarian cancer research comprised of bio-specimens, clinical and epidemiological data, ensuring that the QCMG will have samples meeting the ICGC  ...   gene activity, study alternative splicing events, identify promoter and 3' UTR usage, and capture expressed sequence variation (SNPs and mutations).. The QCMG is actively engaged in RNAseq studies of the following areas:.. Creating a human and mouse tissue transcriptome atlas.. Human Embryonic Stem Cells (hESCs) including Pluripotent (iPS) cells.. Human Cell Cycle synchronized cells.. Human Cancer cell lines.. Projects are currently funded by the Australian Stem Cell Centre, the Australia Research Council and Australian National Health Medical Research Council.. Characterizing mammalian microRNA-mRNA interactions.. MicroRNAs (miRNAs) are crucial components of the regulatory circuitry of cells, modulating target gene activity and controlling key biological processes such as cell proliferation and cell death.. Although the mechanism for miRNA regulation is well understood, the biological role of most miRNAs remains unknown.. The major is identifying their mRNA targets.. in vivo.. Currently, the experimental methods for determining miRNA-mRNA interactions are laborious and expensive and computationally derived predictions are plagued with high false positive rates.. Ideally, one would isolate all RNA sequences to which the miRNA is bound.. , and identify them through sequencing, but until recently this approach has not been technically or economically feasible.. The QCMG will exploit recent advances in molecular biology and next-generation sequencing to elucidate the scale and scope of miRNA-mRNA interactions in mammalian to re-derive the rules of miRNA-mRNA interaction based on large-scale data sets..

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  • Title: Queensland Centre for Medical Genomics - Publications -
    Descriptive info: Sleeping Beauty Mutagenesis Reveals Cooperating Mutations and Pathways in Pancreatic Adenocarcinoma.. Karen M.. Mann, Jerrold M.. Ward, Christopher Chin Kuan Yew, Anne Kovochich, David W.. Dawson, Michael A.. Black, Benjamin T.. Brett, Todd E.. Sheets, Adam J Dupuy, David K.. Chang, Andrew V.. Biankin, Nic Waddell, Karin S.. Kassahn, Sean M Grimmond, Alistair G.. Rust, David J.. Adams, Nancy A.. Jenkins, and Neal G.. Copeland (2012) Proc Natl Acad Science USA 2012 Mar 15.. 109(16):5934-41.. Limited extragenic transcription suggests that most conserved non-coding sequences are regulatory factor binding sites.. M Hemberg, JM Gray, N Cloonan, T Kim, SM Grimmond, ME Greenberg, and G Kreiman (2012) NAR.. 2012 Jun 8.. [Epub ahead of print].. Qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles.. Sarah Song*, Katia Nones, David Miller, Ivon Harliwong, Karin Kassahn, Mark Pinese, Marina Pajic, Anthony J.. Gill, Amber L.. Johns, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Christina Xu, Felicity Newell, Australian Pancreatic Cancer Genome Initiative, Peter Wilson, Lynn Fink, Andrew V.. Biankin, Nic Waddell, Sean M.. Grimmond*, John V.. Pearson 2012.. PLoS One, 7(9): e45835.. RON is not a prognostic marker for resectable pancreatic cancer.. Carole M.. Tactacan, David K.. Chang, Emily S.. Humphrey, Mark J.. Cowley, Jianmin Wu, Anthony J.. Gill, Angela Chou, Sean M.. Grimmond, Katia Nones, Robert L.. Sutherland, Andrew V.. Biankin and Roger J.. Daly.. (2012) Cancer Epidemiology, Biomarkers & Prevention In press July 16th 2012.. Encyclopedia of Molecular Cell Biology and Molecular Medicine Tag Sequencing.. K Krishnan, S Wani, SM Grimmond, N Cloonan (2012).. (Chapter) Wiley & Sons.. The deubiquitinase USPX suppresses pancreatic ductal adenocarcinoma.. Pedro A.. Pérez-Mancera, Alistair G.. Rust, Louise van der Weyden, Glen Kristiansen, Allen Li, Aaron L.. Sarver, Kevin A.. T..  ...   T, Grimmond, SM, Little, MH, and McMahon, AP (2012).. Development.. Accepted for publication 1.. st.. March, 2012.. Carriage of an ACME II Variant has Contributed to MRSA ST239-like Strain Replacement in Liverpool Hospital, Sydney, Australia.. , Espedido, BA, Steen, JA, Barbagiannakos, T, Mercer, J, Paterson, DL, Grimmond, SM, Cooper, MA, Gosbell ,IB, van Hal, S, and Jensen, SO (2012).. Antimicrobial Agents and Chemotherapy.. Accepted for publication 29.. Feb 2012.. Expression Divergence of Innate Immune Genes is driven by Highly Constrained Promoters Hypersensitive to Multiple Regulatory Inputs.. Schroder, K, Irvine, KM, Taylor, MS, Semple, CA, Akalin, A Cao, K, Le Labzin, L, Bokil, NJ, Faulkner, GJ, Baillie, JK, Gongora, M, Daub, CO, McLachlan, J, Goldman, N, Grimmond, SM, Carninci, P, Suzuki, H, Hayashizaki, Y, Lenhard, B, Hume, DA, and Sweet, MJ (2012).. Proc Natl Acad Science USA.. Accepted 23.. rd.. Feb, 2012.. Next generation sequencing technology and its applications.. Encyclopedia of Molecular Cell Biology and Molecular Medicine (Chapter- in press).. Krishnan, K, Wani, S, Grimmond, SM, and Cloonan, N (2012).. MicroRNAs and their isomiRs function cooperatively to target common biological pathways.. Cloonan*, N, Wani, S, Xu, Q, Gu, J, Lea, K, Heater, S, Barbacioru, C, Steptoe, A, Martin, HC, Nourbakhsh, E, Krishnan, K, Gardiner, B, Wang, X, Nones, K, Steen, J, Matigan, N, Wood, D, Kassahn, K, Waddell, N, Shepherd, J, Lee, C, Ichikawa, J, McKernan, K, Bramlett, K, Kuersten, S, and SM Grimmond*.. (*corresponding author) (2012).. Genome Biology.. Dec 30;12(12):R126.. [Epub ahead of print].. PINA v2.. 0: Mining Interactome modules.. Wu J, Cowley M, Pinese M, Kassahn K, Waddell N, Pearson J, Grimmond SM, Biankin, A, Hautaniemi S 2012.. Nucleic Acid Research Jan;40(1):D862-5.. Epub 2011 Nov 8.. QCMG Publications for 2009.. QCMG Publications for 2010.. QCMG Publications for 2011..

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  • Title: Queensland Centre for Medical Genomics - Personnel -
    Descriptive info: PERSONNEL.. CEO.. Professor Sean M.. Grimmond.. Executive Officer.. Dr Peter J.. Wilson.. Executive Secretary.. Ms Deborah L.. Gwynne.. "Wet" Laboratory.. Sequencing Manager.. Mr David K.. Miller.. Sequencing Specialist.. Dr Tim J.. Bruxner.. Sequencing Specialist.. Dr Craig R.. Nourse.. Research Assistant.. Ms Suzanne K.. Manning.. Mr Ehsan Nourbakhsh.. Ms Senel Idrisoglu.. Ms Ivon Harliwong.. Ms Angelika N.. Christ.. Ms Shivangi Wani.. "Dry" Laboratory.. Senior Bioinformatics Manager.. Mr John V.. Pearson.. Deputy Bioinformatics Manager.. Dr  ...   Systems Administrator.. Mr E.. Scott Wood.. Senior Research Officer.. Dr Nicola Waddell.. Dr Nicole Cloonan.. Dr Karin S.. Kassahn.. Dr Ann-Marie Patch.. Bailey.. iSEnior Research Officer.. Dr Michael C.. J.. Quinn.. Research Officer.. Dr Shivashankar H.. Nagaraj.. Dr Katia Nones.. Dr Felicity S.. Newell.. Dr Stephen H.. Kazakoff.. Mr Nick M.. Waddell.. Ms Qinying (Christina) Xu.. Mr Oliver J.. Holmes.. Mr Matthew J.. Anderson.. Students.. PhD Student.. Ms Kelly Quek.. Mr David Wood..

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  • Archived pages: 9