9:00 – 9:45 Registration
9:45 – 10:00 Introduction by the Chair
Professor Eric F.P.M. Schoenmakers, Radboud University Nijmegen Medical Centre (RUNMC)
& Nijmegen Centre for Molecular Life Sciences (NCMLS), Nijmegen, The Netherlands.
10:00 – 10:30 Identification of novel biomarkers by high-resolution copy number profiling and homozygosity mapping in hematologic 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 Netherlands
Recent progress in genomics technology has made detailed characterization of the cancer genome feasible. One example involves the development of high-resolution SNP-based genotyping arrays for detecting regions of genomic amplifications, deletions, and copy-neutral homozygosity. Application of these arrays has revealed major new insights into the field of cancer genomics, particularly in hematologic malignancies, which has led to the discovery of several new biomarkers. In this presentation, examples will be presented for childhood acute lymphoblastic leukemia and myelodisplastic syndrome.
10:30 – 11:00 Comparison of MicroRNA detection platforms
Dr. Ioannis Ragoussis, Wellcome Trust Centre for Human Genetics, University of Oxford, UK
11:00 - 11:15 Speakers photo
11:15 – 11:45 Mid-morning break
11:45 – 12:15 Methylome analysis using array and sequencing based approaches
Professor Stephan Beck, Cancer Institute, University College London, UK
DNA methylation plays an essential role in biology with wide-ranging implications for human health and disease. To understand the rules governing DNA methylation and the consequences if DNA methylation is perturbed requires genome-wide analysis of its temporal and spatial plasticity. Almost 60 years after the discovery of 5-methyl cytosine and about 25 years since the discovery that altered DNA methylation plays a role in disease aetiology, particularly in cancer, technologies have finally become available for whole-genome DNA methylation profiling (methylome analysis) with ever increasing resolution. I will present data from our efforts using array- and sequencing-based platforms for high-throughput DNA methylation analysis, discuss some of the lessons learnt and give an outlook on how the data may be used in an integrated approach – termed ‘reverse phenotyping’ – to analyse and better understand the (epi)genomics of phenotypic plasticity in health and disease.
12:15 – 12:45 Selected Abstracts
12:45 – 13:00 Brief introduction to the Biopark
13:00 – 14:00 Lunch and Poster Viewing
14:00 – 14:30 Talk to be confirmed
14:30 – 15:00 A comparison of expression profiling by deep sequencing and microarrays
Dr. Peter A.C. ‘t Hoen, Center for Human and Clinical Genetics, Leiden University Medical Center (LUMC),
Leiden, The Netherlands
15:00 – 15:30 Afternoon Tea/Coffee and Last Poster Viewing
15:30 - 16:00 Use of new sequencing technologies for the annotation of cancer genomes
Dr. Peter J. Campbell, Sanger Institute, Cambridge, UK
We are now 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 less than 1 cent per kilobase (kb). Techniques have been developed which allow the detection of genomic rearrangements, copy number changes, point mutations and small insertions and deletions as well as epigenetic alterations 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 other 98% of the human genome including, for example, promoters, enhancers and non-coding RNAs. At the Cancer Genome Project, we have developed protocols for mapping acquired rearrangements to the base-pair level, providing insights into the diversity of aberrant processes sculpting the genome which underlie the evolution and development of cancer.
16:00 – 16:30 Talk to be confirmed Professor Henk Stunnenberg, Radboud University, The Netherlands
16:30 – 17:00 Chairman’s summing up.
18:00 Soiree at *The Best Western Homestead Court Hotel* for all the participants