BEGIN:VCALENDAR VERSION:2.0 PRODID:-//Talks.cam//talks.cam.ac.uk// X-WR-CALNAME:Talks.cam BEGIN:VEVENT SUMMARY:Microarray- and deep sequencing-based profiling approaches: the te chnological evolution continues… - Professor Eric F.P.M. Schoenmakers\,. Dr Roland P. Kuiper\, Dr. Ioannis Ragoussis\,. Professor Stephan Beck\,P rofessor Johan den\,Dr. Peter J. Campbell\, DTSTART:20090709T080000Z DTEND:20090709T160000Z UID:TALK18852@talks.cam.ac.uk CONTACT:Dr Astrid Englezou DESCRIPTION:\nThis one-day meeting aims at providing the audience with a c omprehensive overview and in-depth comparison of currently available resea rch tools\, including array-\, bead- or massive parallel sequencing-based platforms as well as experimental considerations in relation to expression -\, genomic-\,and epigenetic-profiling. Illustrated by real-life examples\ , various internationally acknowledged speakers will provide the attendee with critical experimental design parameters. Pitfalls associated with spe cific technologies as well as their solution will be discussed extensively .\n This meeting has CPD approval .\n\n\nThe Chair will be Professor Eric F.P.M. Schoenmakers\, Radboud University Nijmegen Medical Centre (RUNMC) & Nijmegen Centre for Molecular Life Sciences (NCMLS)\, Nijmegen\, The Neth erlands. \n\nThe Agenda includes: \n\nIdentification of novel biomarkers by high-resolution copy number profiling and homozygosity mapping in hemat ologic malignancies. Dr Roland P. Kuiper\, Microarray Facility Nijmegen\, Oncology Research\, Radboud University Nijmegen Medical Centre (RUNMC) & Nijmegen Centre for Molecular Life Sciences (NCMLS)\, Nijmegen\, The Nethe rlands.\nRecent progress in genomics technology has made detailed characte rization of the cancer genome feasible. One example involves the developme nt of high-resolution SNP-based genotyping arrays for detecting regions of genomic amplifications\, deletions\, and copy-neutral homozygosity. Appli cation of these arrays has revealed major new insights into the field of c ancer genomics\, particularly in hematologic malignancies\, which has led to the discovery of several new biomarkers. In this presentation\, example s will be presented for childhood acute lymphoblastic leukemia and myelodi splastic syndrome.\n\nDeciphering the role of miRNAs in hypoxia by Digital Gene Expression profiling\n Dr. Ioannis Ragoussis\, Wellcome Trust Centre for Human Genetics\, University of Oxford\, UK \nHypoxia in tumours may c onfer resistance to conventional therapies and is associated with a poorer prognosis. MicroRNA expression alterations have been described in cancer and certain microRNAs have shown regulation by hypoxia. \n\nWe performed a time course exposition to hypoxia (1% oxygen for 16h\, 32h and 48h) using MCF7 cancer cell cultures. We also investigated the effect of VHL suppres sion in RCC4 renal cancer cells by comparing to RCC4 cells transfected wit h VHL. The microRNA fraction was isolated from total RNA and sequenced usi ng the GA II analyser. Gene expression profiles were determined using Ill umina WG-6 v3 arrays and ImicroRNA arrays v.1. This led to the identificat ion of 376 different microRNAs and microRNA variants in MCF7 samples and 2 83 in RCC4 and RCC4+VHL cells. Relative microRNA expression analysis showe d a set of 36 microRNAs disregulated in all 3 hypoxia times compared to no rmoxia. A second set of 62 microRNAs appeared to be disregulated from 32h of hypoxia onwards\, suggesting a more severe reaction to hypoxia. Concern ing RCC4 cells\, 102 microRNAs showed differential levels of expression co mpared to RCC4+VHL cell. New microRNAs were identified using a novel machi ne learning algorithm and are being validated. MicroRNA target sequences w ere identified among genes differentially expressed in hypoxia and correla ted with microRNA expression. All this information will enhance our unders tanding of hypoxia mediated regulation of gene expression.\n\n\nMethylome analysis using array and sequencing based approaches . Professor Stephan B eck\, Cancer Institute\, University College London\, UK \nDNA methylation plays an essential role in biology with wide-ranging implications for huma n health and disease. To understand the rules governing DNA methylation an d the consequences if DNA methylation is perturbed requires genome-wide an alysis of its temporal and spatial plasticity. Almost 60 years after the d iscovery of 5-methyl cytosine and about 25 years since the discovery that altered DNA methylation plays a role in disease aetiology\, particularly i n cancer\, technologies have finally become available for whole-genome DNA methylation profiling (methylome analysis) with ever increasing resolutio n. I will present data from our efforts using array- and sequencing-based platforms for high-throughput DNA methylation analysis\, discuss some of t he lessons learnt and give an outlook on how the data may be used in an in tegrated approach – termed ‘reverse phenotyping’ – to analyse and better understand the (epi)genomics of phenotypic plasticity in health and disease. \n \n\nA comparison of expression profiling by deep sequencing a nd microarrays \nProfessor Johan den. Dunnen Center for Human and Clinical Genetics\, Leiden University Medical Center (LUMC)\, Leiden\, The Netherl ands\n\nWe have done the first large-scale comparison between deep sequenc ing and microarray-based expression profiling. With the Illumina digital g ene expression assay\, we obtained ~2.4 million sequence tags per sample\, their abundance spanning four orders of magnitude. Results were highly re producible\, even across laboratories. The correlation with five different microarray platforms was modest and most significant for Affymetrix. The changes in expression observed by deep sequencing were larger than observe d by microarrays or quantitative PCR. While undetectable by microarrays\, antisense transcription was found for 51% of all genes and alternative pol yadenylation for 47%. Deep sequencing provides a major advance in robustne ss\, comparability and richness of expression profiling data and is expect ed to boost collaborative\, comparative\, and integrative genomics studies . \n\nUse of new sequencing technologies for the annotation of cancer geno mes. Dr. Peter J. Campbell\, Sanger Institute\, Cambridge\, UK \nWe are n ow entering an era in which it will be feasible to catalogue every genetic event in a cancer. Next generation sequencing platforms already offer the capacity to generate gigabases (Gb) of sequence each week at a cost of le ss than 1 cent per kilobase (kb). Techniques have been developed which all ow the detection of genomic rearrangements\, copy number changes\, point m utations and small insertions and deletions as well as epigenetic alterati ons on a single instrument. This will be a significant advance on existing approaches to cancer genomics. The analysis will be genuinely genome-wide \, cataloguing genetic changes not only in coding sequence but also the ot her 98% of the human genome including\, for example\, promoters\, enhancer s and non-coding RNAs. At the Cancer Genome Project\, we have developed pr otocols for mapping acquired rearrangements to the base-pair level\, provi ding insights into the diversity of aberrant processes sculpting the genom e which underlie the evolution and development of cancer. \n \n Abstracts for poster presentation only can be submitted up to two weeks before the e vent. Please note that there will be a best poster prize. All accepted ab stracts will be published in the meeting proceedings \n\n\n\nIf you would like to book a place at the meeting\, please visit :\n www.regonline.co.uk /microarrays09\n\n\n LOCATION:The BioPark\, Hertfordshire\,AL7 3AX UK END:VEVENT END:VCALENDAR