Clinical Genomics & Informatics Europe - Program
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Bio-IT World and Cambridge Healthtech Institute's Fifth International Clinical Genomics & Informatics Europe Conference will feature four main tracks on Clinical Exome Sequencing, High-Scale ...

Bio-IT World and Cambridge Healthtech Institute's Fifth International Clinical Genomics & Informatics Europe Conference will feature four main tracks on Clinical Exome Sequencing, High-Scale Computing, RNA Sequencing and Genome Informatics. In addition, two pre-conference Symposia on Clinical Epigenetics and Digital Detection Techniques and Applications will be provided. View the full program and details at http://www.clinicalgenomicsinformatics.com

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Clinical Genomics & Informatics Europe - Program Clinical Genomics & Informatics Europe - Program Document Transcript

  • Organized by Cambridge Healthtech Institute Clinical Exome Sequencing RNA-Seq and Transcriptome Analysis ClinicalGenomicsInformatics.com High-Scale Computing Genome Informatics Sequencing Informatics Europe Clinical Genomics &Informatics Bio-IT World & Cambridge Healthtech Institute’s Fifth International 4-6 December 2013 • Sheraton Hotel & Spa • Lisbon, Portugal Pre-Conference Symposia: Clinical Epigenetics Digital Detection *IBM and the IBM logo are trademarks of International Business Machines Corp., registered in many jurisdictions worldwide. Official Media Partner: Premier Sponsors: Register by 16 August and Save Up to €350!Final Agenda Anne Cambon-Thomsen, M.D., Centre National de la Recherche Scientifique (CNRS) Niklas Blomberg, Ph.D., ELIXIR Timothy Hubbard, Ph.D., Wellcome Trust Sanger Institute Hans-Hilger Ropers, M. D., Humboldt University and Max Planck Institute for Molecular Genetics Keynote Speakers:
  • 2 Tuesday, 3 December Wednesday, 4 December Thursday, 5 December Friday, 6 December AM Clinical Epigenetics Symposium Sequencing Stream: Clinical Exome Sequencing Sequencing Stream: Clinical Exome Sequencing Sequencing Stream: RNA-Seq and Transcriptome Analysis PM Sequencing Stream: Clinical Exome Sequencing Sequencing Stream: RNA-Seq and Transcriptome Analysis Sequencing Stream: RNA-Seq and Transcriptome Analysis AM Quantitative Digital Detection Technologies Symposium Informatics Stream: High-Scale Computing Informatics Stream: High-Scale Computing Informatics Stream: Genome Informatics PM Informatics Stream: High-Scale Computing Informatics Stream: Genome Informatics Informatics Stream: Genome Informatics Conference-at-a-Glance About the Event Bio-IT World and Cambridge Healthtech Institute are proud to announce the Fifth International Clinical Genomics & Informatics Europe conference. This year’s meeting will be held 4-6 December 2013 in Lisbon, Portugal. The conference will feature four main tracks on Clinical Exome Sequencing, High-Scale Computing, Genome Informatics, and RNA-Seq and Transcriptome Analysis. In addition, we will be featuring two pre-conference Symposia on Tuesday, 3 December on Clinical Epigenetics and Quantitative Digital Detection Technologies. The conference will tackle the huge amounts of sequencing data produced by new technologies that have introduced significant challenges for bioinformatics, both in terms of the analysis and interpretation of data and clinical implementation of novel variants. Members of the international community will come together to look at the science and informatics required to utilize next-generation sequencing for the molecular diagnosis of complex diseases. Media Partners Sponsors Official Media Partner: Sponsoring Publications: Lead Sponsoring Publications: Sponsoring Organizations: FierceBiotechTHE BIOTECH INDUSTRY’S DAILY MONITOR Web Partners: Clinical Trials to the Clinic CLINICAL INFORMATICS NEWS Premier Sponsors: *IBM and the IBM logo are trademarks of International Business Machines Corp., registered in many jurisdictions worldwide. Corporate Sponsor:
  • Sponsorship & Exhibit Opportunities CHI offers comprehensive sponsorship packages which include presentation opportunities, exhibit space and branding, as well as the use of the pre and post-show delegate lists. Customizable sponsorship packages allow you to achieve your objectives before, during, and long after the event. Signing on early will allow you to maximize exposure to qualified decision-makers! Agenda Presentations Showcase your solutions to a guaranteed, highly-targeted audience. Package includes a 15 or 30-minute podium presentation within the scientific agenda, exhibit space, on-site branding, and access to cooperative marketing efforts by CHI. Breakfast & Luncheon Presentations Opportunity includes a 30-minute podium presentation over breakfast or lunch in the main session room.A limited number of presentations are available for sponsorship and they will sell out quickly. Sign on early to secure your talk! Invitation-Only VIP Dinner/Hospitality Suite Sponsors will select their top prospects from the conference pre-registration list for an evening of networking at the hotel or at a choice local venue. CHI will extend invitations and deliver prospects. Evening will be customized according to sponsor’s objectives: •  Purely social •  Focus group •  Reception style •  Plated dinner with specific conversation focus Exhibit Exhibitors will enjoy facilitated networking opportunities with highly-targeted delegates making it the perfect opportunity to speak face-to-face with prospective clients and showcase your latest product, service, or solution. Exhibit booth comes pre-fabricated with back and side panels, 1 table, 2 stools, 4 spotlights, and 1 electrical connection. Inquire about additional branding opportunities! Looking for additional ways to drive leads to your sales team? CHI can help! We offer clients numerous options for custom lead generation programs to address their marketing and sales needs, including: Custom Lead Generation Programs: • Targeted campaign promotion to unparalleled database of 800,000+ individuals in the life sciences • Experienced marketing team promotes campaign, increasing awareness and leads • Guaranteed minimum of 100 leads delivered per program Web Symposia: • Assistance in procuring speakers • Experienced moderators • Dedicated operations team to coordinate all efforts Whitepapers: • Industry recognized authors, with vast editorial experience, available to help write your whitepaper; or host one of your existing papers. CHI also offers market surveys, podcasts, and more! For additional information, contact: Companies A-K: Katelin Fitzgerald Business Development Manager 781-972-5458 | kfitzgerald@healthtech.com Companies L-Z: Tim McLucas Business Development Manager 781-972-1342| tmclucas@healthtech.com Hotel & Travel Information Conference Venue & Hotel: Sheraton Lisboa Hotel & Spa Rua Latino Coelho No 1 1069-025 Lisboa, Portugal +351-21-312-0000 Please visit www.ClinicalGenomicsInformatics.com to reserve your sleeping accommodations or call the Hotel directly.You will need to identify yourself as a Cambridge Healthtech conference attendee to receive the discounted room rate with the Host Hotel. Reservations made after the cut-off date or after the group room block has been filled (whichever comes first) will be accepted on a space- and rate-availability basis. Rooms are limited, so please book early. Flights: If you need help booking airfare please contact our dedicated travel agent, Rona Meizler, at +1 617-559-3735 or rona.meizler@protravelinc.com. Discounted Room Rate: €120 Single/€140 Double **Includes Breakfast** Discounted Room Rate Cut-off Date: 5 November 2013 Top Reasons to book at the Sheraton Hotel & Spa • Breakfast is included in the room rate. • No commute! The conference is taking place in the hotel. • Ultra modern Spirito Spa & Fitness Center, outdoor heated pool & Mediterranean spa services. • Located just minutes from the city’s downtown Baxia, where you can admire Augusta Street, Russio and Commercio Square (shopping, galleries & theaters). • 15 minutes from Lisbon’s Portela International Airport. • Minutes from local attractions like Avenida da Liberdade, Praca do Comercio (magnificent Square by the River), Estrelas Basilicia, and Belem Tower to name a few.
  • 4 Pre-Conference Symposium: Clinical Epigenetics 08:30 Registration and Morning Coffee 09:00 Chairperson’s Opening Remarks UNDERLYING MECHANISMS LEADING TO DISEASE 09:10 The Molecular Basis of CpG Island Methylator Phenotype Manon van Engeland, Ph.D., Professor, Department of Pathology, School for Oncology and Developmental Biology, Maastricht University Medical Center, The Netherlands 09:40 DNA Methylation and Demethylation in Health and Disease François Fuks, Ph.D., Director, Laboratory of Cancer Epigenetics, Faculty of Medicine, Free University of Brussels, Belgium A host of new actors and novel cytosine modifications and the ten eleven translocation (TET) enzymes have appeared on the scene, sparking great interest. The challenge is now to uncover the roles they play and how they relate to DNA demethylation. Knowledge is accumulating linking these new players to essential biological processes (e.g. cell pluripotency and development) and also to cancerogenesis. We will present data highlighting new modes of action of TETs and their roles in diseases. 10:10 Long Noncoding RNAs and the Specification of Epigenetic Modifications in Development and Disease Marcel Dinger, Ph.D., Head, Clinical Genomics, Centre for Clinical Genomics, Garvan Institute of Medical Research, Australia Although the mechanisms and protein complexes that enact such epigenetic modifications are known, it remains a mystery how these chromatin- modifying factors, which seldom possess any sequence-specificity per se, are directed with such remarkable specificity to particular sites of the genome. In this presentation, I will present evidence to support the case that long non-coding RNAs may fulfill a fundamental role in directing generic chromatin- modifying machinery to particular sites in the genome. 10:40 Coffee Break UTILIZATION OF EPIGENETIC BIOMARKERS IN CLINICAL MANAGEMENT 11:10 DNA Methylation Biomarkers for Early Detection and Monitoring of Cancer Guro Elisabeth Lind, Ph.D., Head, Epigenetics, Department of Cancer Prevention, Institute for Cancer Research, Oslo University Hospital, Norway A panel of methylated biomarkers suitable for detecting colorectal cancer at an early stage will be presented. In tissue samples, this panel outperforms several previously published epi-markers, including VIM and SEPT9 which are included in current non-invasive colorectal cancer tests. We are also working with urological cancers, lymphomas and cholangiocarcinomas and some of our latest data for early detection and/or monitoring of these diseases will be presented. 11:40 The Epigenetic and Genetic Context of MGMT Promoter Methylation and Its Impact on the Predictive versus Prognostic Value as a Biomarker for Glioma Monika E. Hegi, Ph.D., Head, Laboratory of Tumor Biology & Genetics, Department of Neurosurgery, Centre Hospitalier Universitaire Vaudois (CHUV), Switzerland The presentation will review the predictive value of MGMT promoter methylation in glioblastoma (glioma, WHO grade IV) for benefit from alkylating agent therapy. This is a mechanistically plausible relationship due to the DNA repair function of MGMT that removes the most cytotoxic lesion introduced by alkylating agents. Surprisingly, a strong prognostic effect was observed for MGMT methylation in clinical trials with grade III glioma.The genetic and epigenetic context of this surprising, and clinically relevant difference will be discussed. 12:10 Sponsored Presentation (Sponsorship Opportunity Available) 12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 13:10 Session Break 14:00 Chairperson’s Opening Remarks DISCOVERY OF EPIGENETIC MARKERS FOR DIAGNOSTIC & PROGNOSTIC UTILITY 14:05 Dynamic Changes in 5-Hydroxymethylation (5hmC) Signatures Underpin Early and Late Events in Drug Exposed Liver Richard Meehan, Ph.D., Senior Scientist, Chromosomes and Gene Expression, Medical Research Council, The Human Genetics Unit (HGU), Western General Hospital, United Kingdom Combined epigenomic and transcriptomic approaches can identify sets of potential biomarkers for disease progression, including cancer. Our work demonstrates that 5hmC profiling can be used as a unique indicator of cell states during organ maturation and drug-induced responses. 5hmC profiling provides novel epigenetic signatures for integrated pathway analysis and is the foundation for the epigenetics of identity. 14:35 Genome-Wide Methylation Analysis on Neuroendocrine Tumors Christina Thirwell, Ph.D., Senior Lecturer & Medical Oncologist, University College London, United Kingdom My group has undertaken the first large scale integrated genomic analysis of pancreatic and intestinal NETs including exome sequencing, genome-wide DNA methylation analysis, RNA expression and copy number analysis. DNA methylation biomarkers have been identified which differentiate between normal tissue and NETs and also between histological grade of NET. Most recently we have isolated and sequenced DNA from single NET circulating tumor cells (CTCs). Analysis of this “liquid biopsy” will in the future enable us to truly personalize cancer therapy for NET patients. 15:05 Sponsored Presentation (Sponsorship Opportunity Available) 15:35 Refreshment Break 16:10 DNA Methylation in Childhood Cancer Keith Brown, Ph.D., Reader, Molecular Pathology, School of Cellular & Molecular Medicine, University of Bristol, United Kingdom We have used genome-wide DNA methylation analysis to identify epigenetic alterations in clinically important childhood cancers, specifically Wilms’ tumor of the kidney and neuroblastoma, a cancer of the sympathetic nervous system. We have identified the first example of long-range epigenetic silencing in childhood cancer, as well as novel single genes that are silenced by DNA methylation. Analyzes of clinically annotated patient cohorts are being used to test the diagnostic and prognostic utility of these markers. 16:35 DNA Methylation Signatures for Prediction of Biochemical Recurrence after Radical Prostatectomy of Clinically Localized Prostate Cancer Christa Haldrup, Ph.D., Research Scientist, Department of Molecular Medicine, Aarhus University Hospital, Denmark Through screening of prostate cancer samples and samples of adjacent normal prostate tissue, we here identify six genes (AOX1, C1orf114, GAS6, HAPLN3, KLF8, and MOB3B) which are hypermethylated in prostate cancer. Furthermore, DNA methylation of C1orf114 is significantly associated with time to PSA recurrence in multivariate cox regression analysis encompassing standard histopathological parameters in two international radical prostatectomy cohorts. Additionally we develop a dichotomized three gene DNA methylation signature which also predicts time to PSA recurrence in multivariate analysis significantly in two cohorts. 17:10 Single-Cell Genomics to Study DNA-Mutation, Genetic Heterogeneity and Disease Thierry Voet, Ph.D., Head, Laboratory of Reproductive Genomics, KU Leuven, Belgium; Associate Faculty Member, Wellcome Trust Sanger Institute We have developed various wet-lab and computational methods that allow analyzing a solitary cell. We apply these genome-wide methods to study DNA-mutation, genetic heterogeneity and cancer. Furthermore, we developed novel generic single-cell methods for preimplantation genetic diagnosis (PGD) of human cleavage stage embryos in the clinic. 17:35 Close of Symposium 16:00-18:00 Main Conference Registration 3 December 2013
  • 5 Pre-Conference Symposium: Quantitative Digital Detection Technologies 08:30 Registration and Morning Coffee DIGITAL PCR TECHNOLOGIES AND TECHNIQUES 09:00 Chairperson’s Opening Remarks 09:10 Clinical Implementation of ddPCR in the Diagnosis, and Management of Myeloproliferative Neoplasms (MPNs) Christopher Campbell, West Midlands Regional Genetics Laboratory, Birmingham Women’s Hospital, United Kingdom 09:40 Value Assignment of Certified Reference Material by dPCR Technologies Philippe Corbisier, Ph.D., Scientific and Technical Project Manager, Standards for Innovation and Sustainable Development, European Commission - JRC - IRMM, Belgium dPCR technologies allow us to quantify nucleic acids without the use of standard curve and are therefore particularly suited to characterize nucleic acids standards used as calibrants in quantitative PCR experiments. A number of parameters that affect the accuracy of the measurements will be discussed and results using commercially available microfluidic chamber based PCR and droplet digital PCR will be discussed. 10:10 Global Detection of BRAF V600 Mutations Using a Wild-Type Negative LNA Probe-Based Droplet Digital PCR Assay Curtis Hughesman, Ph.D., Post-Doctoral Research Fellow, Michael Smith Laboratories, University of British Columbia, Canada Here we report a reliable method to collectively detect all known BRAF V600 mutations in a single assay using two LNA probes applied in a droplet digital PCR format. We have used this assay to successful screen cell lines and plasmids bearing 8 unique nucleotide mutations at codon 600 of BRAF with an analytical specificity of <0.05%. 10:40 Coffee Break 11:10 Plasma DNA Digital PCR as a Noninvasive Tool for Detection of Genomic Alterations in Metastatic Breast Cancer Gaia Schiavon, M.D., Ph.D., Cridlan Fellow in Medical Oncology – Breast Unit, The Royal Marsden NHS Foundation Trust, United Kingdom Proof of the concept exists that circulating cell-free DNA (cfDNA) carrying tumor-specific alterations is detectable in plasma of these patients and represents a sensitive biomarker of tumor burden. Performing analysis of cfDNA with digital PCR, we screened for the acquisition of HER2 amplification in metastatic breast cancers and this approach could potentially be adapted to the analysis of any locus amplified in cancer. 11:40 The Use of dPCR to Measure Her-2 in Borderline-Amplified Breast Cancer Research Samples Gabriele Zoppoli, M.D., Ph.D., Internal Medicine Resident, University of Genova & IRCCS AOU San Martino IST, Italy Here, we describe the use of dPCR in a set of ERBB2 “equivocal status” BC patients. We also assess TOP2A copy number, and both TOP2A and ERBB2 gene expression intensity, on the described sample set. We discuss dPCR results compared to those obtained by qRT-PCR, IHC, and aCGH methods. 12:10 Sponsored Presentation (Sponsorship Opportunity Available) 12:40 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 13:10 Session Break IMPROVEMENTS TO TRADITIONAL PCR AND MICROFLUIDICS 14:00 Chairperson’s Opening Remarks N. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and Nanotechnologies, Lawrence Livermore National Laboratory, United States 14:05 Preparative Microarrays & Laser Induced Dehybridization: The Intersection of Microarrays, PCR, and Sequencing N. Reginald Beer, Ph.D., Medical Diagnostics Initiative Leader, Center for Micro and Nanotechnologies, Lawrence Livermore National Laboratory, United States This talk will describe a novel approach using a focused IR laser to dehybridize bound oligos from individual microarray spots. The bound oligos can be 200 bp or longer, providing much more information than just the bases complementary to the short probe sequences. This method has the potential to improve detection and downstream analysis for rare or highly divergent targets in genotyping or microbial discovery applications. 14:35 A Novel Platform for Digital Isothermal Nucleic Acid Amplifications Using BART Guy Kiddle, Ph.D., Senior Molecular Biologist, IVD Technologies, Lumora Ltd., United Kingdom Lumora Ltd. has demonstrated that BART technology (a bioluminescent reporter system for isothermal amplification) in conjunction with loop mediated isothermal amplification (LAMP) represent a novel, highly scalable and low-cost platform for digital amplifications based on CCD camera image capture. The LAMP-BART platform has been demonstrated on two applied challenges. This presentation will highlight the potential of dBART, as a commercial alternative to conventional digital PCR. 15:05 Sponsored Presentation (Sponsorship Opportunity Available) 15:35 Refreshment Break SINGLE-CELL ANALYSIS METHODS 16:10 Cell Heterogeneity and Single Cell Analysis: A New Paradigm for Translational Medicine Ferdinando Mannello, Ph.D., Assistant Professor, Cell Biology, Department of Biomolecular Sciences, Section of Clinical Biochemistry and Cell Biology, University “Carlo Bo” of Urbino, Italy Cellular heterogeneity forms the fundamental principle of cell biology, but the new generation technology of single-cell analysis is able to better characterize cells population, identifying and differentiating outlier cells, and driving beyond the capability of conventional technology. Single-cell analysis is the new frontier in “OMICS”-era, which will become a diffuse and efficient investigational strategy for translational medicine. 16:35 Quantitative High-Resolution Genomic Analysis of Single Cancer Cells Burkhard Brandt, Ph.D., Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Germany We present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyzes by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centered by the therapeutically relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics. 17:10 Single-Cell Genomics to Study DNA-Mutation, Genetic Heterogeneity and Disease Thierry Voet, Ph.D., Head, Laboratory of Reproductive Genomics, KU Leuven, Belgium; Associate Faculty Member, Wellcome Trust Sanger Institute We have developed various wet-lab and computational methods that allow analyzing a solitary cell. We apply these genome-wide methods to study DNA-mutation, genetic heterogeneity and cancer. Furthermore, we developed novel generic single-cell methods for preimplantation genetic diagnosis (PGD) of human cleavage stage embryos in the clinic. 17:35 Close of Symposium 16:00-18:00 Main Conference Registration 3 December 2013
  • 6 WEDNESDAY, 4 DECEMBER 07:30 Registration and Morning Coffee TARGETED SEQUENCING 08:30 Chairperson’s Opening Remarks »» KEYNOTE presentation 08:40 New Sequencing Techniques: Why They are Indispensable for Health Care, and What We Can Do to Speed Up Their Clinical Implementation Hans-Hilger Ropers, M. D., Board Certified Clinical Geneticist, Professor of Human Genetics, Humboldt University and Director, Max Planck Institute for Molecular Genetics, Berlin, Germany 09:10 External Quality Assessment for NGS David E. Barton, Ph.D., Chief Scientist, National Centre for Medical Genetics, Our Lady’s Children’s Hospital, Crumlin, Ireland, United Kingdom The European Molecular Genetics Quality Network (EMQN) provides external quality assessment to genetic testing laboratories world-wide. Experience shows that the introduction of new technologies into clinical diagnostics carries risks. Thorough validation and quality assessment are essential. EMQN, in collaboration with UK NEQAS, ran a pilot EQA for Next-Gen DNA sequencing in 2013. Results of this pilot study will be reported. 09:40 Targeted Next-Generation Sequencing Can Replace Sanger Sequencing in Clinical Diagnostics Jan D. H. Jongbloed, Ph.D., Department of Genetics, University of Groningen, University Medical Centre Groningen, The Netherlands This talk will include results of the manuscript on targeted NGS such as recent results of the use of our method in routine clinical diagnostics; a comparison of results in these patients obtained with both targeted and exome sequencing (we have quite some patients that were analyzed with both methods); a study concerning the effect of over dispersion in both methods. 10:10 Coffee Break in the Exhibit Hall with Poster Viewing COMPARING EXOME AND WHOLE GENOME SEQUENCING 10:45 Comparing Exome vs. Genome Sequencing for Genetic Component of Diseases Han G. Brunner, Ph.D., Medical Geneticist, Radboud University Nijmegen Medical Centre, The Netherlands Given that a considerable proportion of rare diseases are based in genetics, patients with complex clinical presentation may soon be included in a program for undiagnosed diseases where the first step is exome sequencing. Such a strategy would provide many accurate diagnoses, thereby reducing doctor’s delay, unnecessary invasive, costly and burdensome procedures. 11:15 Comparing Clinical v. Whole Exome Sequencing for Monogenic Diseases and Undiagnosed Patients Pascal Joset, Ph.D., Research Associate, Institute of Medical Genetics, University of Zurich, Switzerland The advent of NGS techniques is paving the way for novel large scale approaches with an unforeseen diagnostic power. While whole exome sequencing may provide theoretically the highest cost-efficient power, it may miss mutations due to incomplete coverage. We therefore evaluated the power of a “clinical exome” limited to about 2700 genes with currently known monogenic mutations. 11:45 Sponsored Presentation (Sponsorship Opportunity Available) 12:15 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 13:15 Session Break 14:00 Chairperson’s Remarks 14:05 Increasing Accuracy for Exome and Whole Genome Sequencing Gholson J. Lyon, M.D., Ph.D., Assistant Professor of Human Genetics, Cold Spring Harbor Laboratory and Research Scientist, Utah Foundation for Biomedical Research, United States Our recent results suggest that more caution should be exercised in genomic medicine settings when analyzing individual exomes and genomes, including interpreting positive and negative findings with scrutiny, especially for indels. We advocate for renewed collection and sequencing of multi-generational families to increase the overall accuracy of whole genomes. 14:35 Changing the Clinical Genetic Testing Paradigm: Reducing Cost and Increasing Utility Steve Lincoln, Senior Vice President, Scientific Applications, InVitae, United States 15:05 Experiences from our Integrated Genomics Clinic; Rapid Identification and Clinical Reporting of Causative Mutations throughWGS andWES Elizabeth Worthey, Ph.D., Human and Molecular Genetics Center, The Medical College of Wisconsin, United States MCW’s Genomic Medicine Clinic has been operational for more than 18 months. As the first genomics based integrated genetics clinic of its kind its development required definition of appropriate: patient counseling, analysis, interpretation, and reporting. I will discuss how to incorporate genomic data to support diagnosis with a particular focus on the informatics as well as providing discussion of the discoveries, challenges and lessons learned applying NGS in the clinic. 15:35 Sponsored Presentation (Sponsorship Opportunity Available) 16:05 Refreshment Break in the Exhibit Hall with Poster Viewing 16:45 Exome Sequencing in Complex Disease: Data Quality and Clinical Heterogeneity Sarah Ennis, Ph.D., Associate Professor, Head, Genomic Informatics, Genomic Informatics, University of Southampton Human Genetics & Genomic Medicine, United Kingdom This talk will present key aspects in the exome analysis of a cohort of paediatric patients diagnosed with severe inflammatory bowel disease. The talk will outline some key issues with regard to data management and quality and go on to present approaches to pathway analysis in complex disease and present key findings that underpin disease in individual patients. 17:15 Panel Discussion with Day’s Speakers 17:45 Welcome Reception in the Exhibit Hall with Poster Viewing 19:15 Close of Day THURSDAY, 5 DECEMBER 08:00 Morning Coffee DEVELOPING TECHNOLOGIES AND INTERFACE FOR INTERPRETING GENOMES 08:30 Chairperson’s Opening Remarks 08:35 Strategies for Disease-Gene Identification in Exome Sequencing Peter N. Robinson, Institute for Medical Genetics and Human Genetics, Charité- Universitätsmedizin Berlin, Germany Whole exome sequencing (WES) is revolutionizing many areas of diagnostics and research in human genetics, but the sheer number of candidate genes revealed by typical WES studies represents a challenge to medical and biological interpretation. We will present new algorithms for utilizing phenotypic analysis and protein interaction networks to effectively prioritize candidates in exome sequencing studies. Clinical Exome SequencingInaugural Sequencing4-5 December 2013 Changing the Nature of Genetic Diagnosis
  • 7 09:05 The Post-WGS Cancer Genome: Alphabet Soup, Syllabus or Cyclopaedia? German Pihan, M.D., Staff Pathologist and Director, Hematopathology Service, Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, United States Review of how the WGS cancer genome data deluge is changing our views of the pathogenesis and biology of cancer as well as how the new knowledge may be harnessed to combat the “Emperor of all maladies.” 09:35 Sponsored Presentation (Sponsorship Opportunity Available) 10:05 Coffee Break in the Exhibit Hall with Poster Viewing 10:45 Sponsored Presentation (Sponsorship Opportunity Available) 11:15 Integrated Exome Sequencing and Copy Number Analysis of Pancreatic Cancer Reveals a HER2-Amplified Subtype Mark Cowley, Ph.D., Senior Bioinformatics Research Officer, Genome Informatics & Clinical Genomics, The Kinghorn Cancer Centre, Garvan Institute of Medical Research, New Zealand We have recently performed WES and copy number analysis from 99 pancreatic ductal adenocarcinoma tumors within the ICGC. By copy number analysis, and supported by WGS, microarray analysis, IHC and FISH, we identified a case with HER2-amplification. Our results have potentially defined the first targeted therapy for pancreatic cancer, which we are taking to an adaptive clinical trial. »» PLENARY KEYNOTE 11:45 From Genome Annotation to Genome Medicine Timothy Hubbard, Ph.D., Senior Group Leader, Wellcome Trust Sanger Institute, United Kingdom 12:35 Close of Conference thursday, 5 DECEMBER 11:30 Conference Registration »» PLENARY KEYNOTE 11:45 From Genome Annotation to Genome Medicine Timothy Hubbard, Ph.D., Senior Group Leader, Wellcome Trust Sanger Institute, United Kingdom I will describe the status of the human genome sequence and its annotation, in particular the generation of the GENCODE geneset as part of the ENCODE project and the impact of RNA-seq. I’ll also discuss the latest human genome assembly from the Genome Reference Consortium (GRC). As the UK plans to sequence 100,000 human genomes in the National Health Service (NHS), I’ll discuss requirements for integrating genomics into healthcare systems and summarize progress towards genomic medicine in UK. 12:35 Enjoy Lunch on Your Own ADVANCES IN RNA-SEQ DATA ANALYSIS 14:00 Chairperson’s Opening Remarks 14:05 De Novo Full-Length Transcriptome Analysis by a Hybrid Sequencing Analysis by a Hybrid Sequencing Approach Wei Chen, Ph.D., Senior Scientist & Group Leader, Max Delbruck Center for Molecular Medicine, Germany I will present a hybrid sequencing approach based transcriptome analysis pipeline that reports high quality transcripts in their full length independent of reference genome sequences. Using full-length cDNA libraries in conjunction with Single Molecule Read-Time (SMRT) DNA sequencing technology, we can directly capture the full-length transcripts, but with low sequencing accuracy. To report high quality transcriptome, we then developed a novel computational tool, IPEC, which utilizes the high quality Illumina sequencing data to correct random errors generated. 14:35 Detecting Differential Splicing Employing Splicing Compass on RNA Sequencing Data Rainer König, Ph.D., Group Head, Divisions of Theoretical Bioinformatics, Heidelberg University, Germany The emergence of next-generation RNA sequencing (RNA-seq) provides an exciting new technology to analyze alternative splicing on a large scale. We present a new method and software to predict genes that are differentially spliced between two different conditions using RNA-seq data. Our method employs geometric angles between the high dimensional vectors of exon read counts. With this, differential splicing can be detected even if the splicing events comprise of higher complexity and involve previously unknown splicing patterns. 15:05 A Hybrid Approach to Comprehensive Transcriptome Reconstruction Using Genome-Guided and de novo RNA-Seq Assembly Leveraging Trinity and PASA2 Brian Haas, Manager, Genome Annotation, Outreach, Bioinformatics and Analysis, The Broad Institute, United States Existing reference genomes or draft genome assemblies may yield a limited view of the transcript content of a sample due genome misassembly, sequencing gaps, or genuine sequence variation between sequenced samples and available reference genomes. Here we present a hybrid approach that combines genome-guided and de novo RNA-Seq assembly to annotate gene structures and capture those transcripts missing or otherwise insufficiently represented by genome assemblies. We demonstrate our approach to be highly effective across diverse eukaryotes and to the restructured genomes of human breast cancer cell lines. 15:35 Sponsored Presentation (Sponsorship Opportunity Available) 16:05 Refreshment Break in the Exhibit Hall with Poster Viewing 16:50 Sponsored Presentation (Sponsorship Opportunity Available) EXPLORING THE COMPLEXITY OF THE TRANSCRIPTOME 17:20 Profiling microRNAs and Circular RNAs in Brain – Implication for Disease and Development Jørgen Kjems, Ph.D., Professor & Director, Department of Molecular Biology and Genetics, Aarhus University, Denmark Circular RNA (circRNA) has recently been established as significant regulator of miRNA activity and evidence suggest that differential expression of circRNA may play a role in tissue development end progression of disease. In particular microRNA-7 appear to be tightly controlled by a circular RNA sponge for miR-7 (ciRS-7) in a dynamic fashion in brains from placental animals. We have profiled mRNA, miRNA and ciRS expression in fetal pig brains and uncovered novel non-coding RNA controlled pathways involved in brain development. RNA-Seq and Transcriptome AnalysisInaugural Sequencing5-6 December 2013 Unraveling Layers of Expression
  • 8 17:50 Regulation of Transcriptional Heterogeneity by Chromatin and Transcription Machinery Vicente Jose Pelechano, Ph.D., Senior Scientist, Steinmetz Group, Genome Biology, EMBL, Germany We have recently revealed an extensive layer of isoform diversity previously hidden among overlapping RNA molecules. Given the existence of overlapping, variable transcript isoforms, determining the functional impact of the transcriptome requires identification of full-length transcripts, rather than just the genomic regions that are transcribed. By systematically applying TIF-Seq, we will present new insights in how this extensive transcript diversity can be generated by a relatively simple eukaryotic genome with limited splicing, and within a genetically homogeneous population of cells. 18:35 Close of Day FRIDAY, 6 DECEMBER 08:00 Morning Coffee CLINICAL APPLICATIONS OF RNA-SEQ 08:30 Chairperson’s Opening Remarks 08:35 Lighting Up the Dark Matter: Targeted RNA Sequencing Reveals Novel Non-coding RNAs Transcribed from Intergenic Disease-Associated Regions Marcel Dinger, Ph.D., Head, Clinical Genomics, Garvan Institute of Medical Research, Australia The relatively recent discovery of widespread transcription of potentially functional long noncoding RNAs (lncRNAs) from the mammalian genome led us to investigate whether or not GWAS hits in noncoding regions could be reconciled by the transcription of regulatory RNAs from these loci.To detect such specifically expressed transcripts, we used capture arrays targeting 350 noncoding regions of the genome associated with disease and sequenced the captured RNA transcribed from these regions. We have identified >1,500 new lncRNAs whose expression appears to be specifically associated with disease. 09:05 The Identification of Long Stress-Induced Non-Coding Transcripts David I. Smith, Ph.D., Professor, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States In an attempt to identify important regulatory transcripts we previously utilized whole genome tiling arrays to examine the entire genomes response to the cellular stress of the tobacco carcinogen NNK. I will describe some of the work that we have done to characterize these interesting transcripts. A number of transcripts identified from the RNA- seq head and neck data correspond to the LSINCTs that were identified from the original tiling array experiment. 09:35 Sponsored Presentation (Sponsorship Opportunity Available) 10:05 Coffee Break in the Exhibit Hall with Poster Viewing 10:45 Alternative Protein-Coding Transcripts in Prostate Cancer Melanie Lehman, Ph.D., Research Fellow, Australian Prostate Cancer Research Centre, Queensland University of Technology, Australia We have applied de novo transcriptome assembly methods to RNA-seq data to profile RNA expression in prostate cancer cells. We have identified alternative protein-coding RNAs that are missing canonical functional domains as well as long coding RNAs (lncRNAs) that are overlapping—and often mistaken for—protein-coding RNAs. I will present the implications of these alternative transcripts to pathway and functional analysis in the context of our research in late stage prostate cancer. 11:15 RNA-Seq to Identify and Characterize Cancer-Specific Transcript Variants Rolf I. Skotheim, Ph.D., Group Leader, Genome Biology, Department of Cancer Prevention, Oslo University Hospital, Norway 11:45 Deciphering the Neuroblastoma Transcriptome by RNA-Seq, qPCR and Exon-Level Resolution Array Analyzes Alexander Schramm, Ph.D., Lab Head, Oncology Research, Children’s Hospital, University Hospital Essen, Germany During my presentation, I will report on integration of technologies required to understand which coding and non-coding RNAs are transcribed in a cancer cell. Results from array-based technologies, qPCR and next-generation RNA seq will be compared using the embryonal tumor, neuroblastoma, as a model system. An automated workflow for the analyzes of RNA-seq data will be presented. Finally, I will discuss some ideas for integrating NGS data into clinical decision making. 12:15 Sponsored Presentation (Sponsorship Opportunity Available) 12:45 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 13:15 Session Break REFINING EXPRESSION ANALYSIS 14:00 Chairperson’s Opening Remarks 14:05 Standards in RNA-Seq Data Analysis Stuart Brown, Ph.D., Associate Professor, Cell Biology; Director, Sequencing Informatics Group of Center for Health Informatics & Bioinformatics, NYU School of Medicine, United States 14:35 RNA-Seq and Microarray Gene Expression Vie for Superiority within a Comprehensive Study Design Weida Tong, Ph.D., Division Director, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, United States The 3rd phase of the FDA-led community wide Microarray Quality Control (MAQC-III) project investigated the reliability and utility of RNA-Seq. All the samples in this project were profiled by both RNA-Seq and microarrays, which produced unprecedented opportunity to comprehensively compare RNA-seq with microarrays. RNA-Seq seems to provide comparable or better transcriptomic profiling as compared with the standard microarray technology for the elucidation of biological responses.This project involves ~200 participants from >80 organizations with comprehensive results that will impact FDA policy. 15:05 Multi-Platform and Cross-Methodological Reproducibility of Transcriptome Profiling by RNA-Seq in the ABRF Next-Generation Sequencing Study (ABRF-NGS) Christopher Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell Medical College, United States We use standard reference samples to evaluate RNA-Seq across a range of sample quality levels, sample preparation methods and bioinformatics analysis approaches, with results that have the potential to improve the utility and comparability of these various methods and five NGS platforms (Illumina, PacBio, 454, PGM, Proton). Importantly, we demonstrate that even severely degraded RNA, when prepared and analyzed with appropriate methods, can be as useful as intact RNA for sequencing-based quantitative profiling. 15:35 Functional Dysregulation in Inflammatory Diseases Carsten O. Daub, Ph.D., Assistant Professor, Biosciences and Nutrition & Science for Life Laboratory, Karolinska Institutet, Sweden Employing genome-wide expression profiling for contrasting disease and control patients allows not only identification of differentially regulated protein or non-coding transcripts but also inference of the underlying regulatory events. 16:05 Close of Conference Inaugural Sequencing5-6 December 2013 RNA-Seq and Transcriptome Analysis Unraveling Layers of Expression
  • 9 4-5 December 2013 Informatics High-Scale Computing Turning Big Genomics Data into Smart DataFifth Annual Wednesday, 4 DECEMBER 07:30 Registration and Morning Coffee SUPPORTING GENOMICS WITH IT INFRASTRUCTURE 08:30 Chairperson’s Opening Remarks »» KEYNOTE PRESENTATION 08:40 ELIXIR: The European Research Infrastructure for Life Science Data Niklas Blomberg, Ph.D., Founding Director, ELIXIR, United Kingdom The mission of ELIXIR is to construct and operate a sustainable infrastructure for the sharing of biological information throughout Europe, to support life science research and drive its translation to medicine and the environment, the bio industries and society.The challenges in storing, integrating and analyzing the data from modern biological experiments are real; ELIXIR meets this challenge through a distributed e-infrastructure of bioinformatics services built around established European centres of excellence. 09:10 Scalability, Reproducibility and Traceability in Large-Scale NGS Facilities Gianmauro Cuccuru, Ph.D., Researcher, CRS4 Bioinformatics Laboratory, Italy As the rate of samples to process increases, manually performing and tracking operations becomes increasingly difficult, costly and error- prone, while processing the massive amounts of data poses significant computational challenges. We will present how combining scientific workflow applications (Galaxy) with state-of-the-art processing technologies like Hadoop, OMERO and iRODS can help address these challenges, thus, empowering more complex life science studies while providing scalability, full reproducibility and traceability. 09:40 Providing the Clinical Genomics Platform: A How-To Guide for Flexible and Extensible Services for Clinical Big Data Brent Richter, Executive Director, Enterprise Research Infrastructure & Services, Information Systems & Academic Programs, Partners HealthCare & Massachusetts General Hospital/ Brigham & Women’s Hospital, United States Managing NGS data and reporting results require secure but extensible infrastructures. Continuing to adopt these platforms to additional clinical areas such as pathology and microbiotics is the current challenge, but the future brings the promise of network medicine that incorporates all information about a patient, from genomics to real-time imaging. What will be the information technology architectures required that places storage, networks and analytics together in a secure and available environment? What services need to be developed? 10:10 Coffee Break in the Exhibit Hall with Poster Viewing 10:45 1000 Genomes/UK10K Projects: Data Management and Data Sharing Thomas Keane, Ph.D., Senior Scientific Manager, Vertebrate Resequencing Informatics, Wellcome Trust Sanger Institute, United Kingdom We have now reached the point where large-scale human disease association studies are carried out primarily using next-generation sequencing technologies. These studies can generate many hundreds of terabases of sequencing data. One of the key challenges is to devise scalable and robust data management and data sharing solutions. In this talk, I will cover how we have addressed these challenges at the Wellcome Trust Sanger Institute. 11:15 Implementation of the CDC Translational Informatics Platform: From Genetic Variants to the National Swedish Rheumatology Quality Register Jesper Tegnér, Ph.D., Professor, Strategic Chair, Computational Medicine and Head, Unit for Computational Medicine, Center for Molecular Medicine, Medicine, Karolinska Institutet and Karolinska University Hospital, Sweden 11:45 Sponsored Presentation Sponsored by Speaker to be Announced 12:15 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 13:15 Session Break CLOUD AS A COMPUTING RESOURCE 14:00 Chairperson’s Opening Remarks 14:05 Cloud4Science: Using Public Clouds in NGS Pipelines Ignacio Blanquer, Ph.D., Associate Professor/Researcher, Computer Systems/Institute of Instrumentation for Molecular Imaging, Universitat Politècnica de València, Spain Cloud4Science is an initiative funded by Microsoft to boost the use of clouds in science. The first prototype focuses on genomics on the cloud (www. cloud4science.eu) and integrates a complete pipeline for mutation detection analysis running on Windows Azure cloud, which users can easily deploy and run using their Azure credentials. Cloud4Science has focused on the issues in data transfer, provenance and massive processing from a user-friendly portal that transparently deploys the needed resources. 14:35 Cost-Effective GPU-Grid for Genome-Wide Epistasis Calculations Benno Pütz, Ph.D., Statistical Genetics, Max Planck Institute of Psychiatry, Germany With local restrictions on handing out clinical data to external computer centers, the cloud, we were forced to establish appropriate computing resources in-house as an alternative solution. From a price/performance point of view, low-cost systems based on consumer graphics cards turned out to be our best option. The system setup as well as some of the work performed on epistasis will be presented. 15:05 CloudMC: A Cloud Computing Platform for Radiation Calculations Hector Miras, Medical Physicist, Department of Medical Physics, Virgen Macarena University Hospital, Spain Rubén Jiménez, Chief Software Architect, R&D Division, Icinetic, Spain Monte Carlo (MC) algorithms are considered the gold standard for radiation calculations, but they are computationally expensive. That is why they are not used in routine clinical practice. CloudMC is a platform developed on Windows Azure intended for parallelization of radiation calculations using MC algorithms. This platform allows any user to have access to a big computing power to perform MC simulations paying only for the resources used. 15:35 Sponsored Presentation Sponsored by Speaker to be announced 16:05 Refreshment Break in the Exhibit Hall with Poster Viewing 16:45 Bioinformatics Use Cases for Cloud Computing Mohamed M. El-Kalioby, Research Scientist, Bioinformatics Group, Center for Informatics Science, Nile University, Egypt Bioinformatics data is getting larger and larger every day, especially after NGS. Computation infrastructure required to handle this is getting harder and is expensive to build. How can we utilize the scalability and availability of cloud computing for such activities? 17:15 The EUDAT Project and Cloud Storage Wolfgang Gentzsch, Ph.D., Co-Founder, The UberCloud HPC Experiment; Executive Consultant, HPC, Grid and Cloud; Advisor, EUDAT; Chairman, ISC Cloud Conferences, Germany EUDAT aims to develop and support a Collaborative Data Infrastructure allowing researchers to share data across communities and carry out research effectively. EUDAT’s data services, like persistent storage, identification, authenticity, workflow execution and mining, can leverage cloud storage. But copyright or national law might not allow the data to leave the country or even the data centre in which they are curated. EUDAT takes a long-term view of the data it holds and is considering “trust marks” for digital archiving. 17:45 Welcome Reception in the Exhibit Hall with Poster Viewing 19:15 Close of Day *IBM and the IBM logo are trademarks of International Business Machines Corp., registered in many jurisdictions worldwide.
  • 10 THURSDAY, 5 DECEMBER 08:00 Morning Coffee NGS DATA MANAGEMENT AND ANALYTICS 08:30 Chairperson’s Opening Remarks 08:35 Preprocessing of High-Throughput Sequencing Data Speeds Up Targeted Research Tomasz Konopka, Ph.D., Research Scientist, Sebastian Nijman Laboratory, Informatics and Synthetic Biology, CeMM, Research Center for Molecular Medicine, Austrian Academy of Sciences, Austria Information encoded in high-throughput sequencing reads can be valuable for targeted hypothesis-driven research questions. It is thus worthwhile to access relevant portions of large datasets in fastq format without costly processing of the remainder. The TriageTools suite available on SourceForge provides fast utilities for preprocessing fastq data. It includes a method for extracting reads likely to map onto predefined regions of interest and extracting data on a few DNA- or RNA-seq samples’ target genes with speedup factors up to ~90. 09:05 Compression Models for DNA Sequences Armando J. Pinho, Ph.D., Director, Instituto de Engenharia Electrónica e Telemática de Aveiro (IEETA) and Associate Professor, Departamento de Electrónica, Telecomunicações e Informática (DETI), Universidade de Aveiro, Portugal Research in the genomic sciences is confronted with the volume of sequencing and resequencing data increasing at a higher pace than that of data storage and communication resources, shifting a significant part of research budgets from the sequencing component of a project to the computational one. Hence, being able to efficiently store sequencing and resequencing data is a problem of paramount importance. In this talk, we will present and discuss DNA sequence compression models that we have been developing during the past years. 09:35 An Integrated High Performance Computing Sponsored by Platform for Genomics and Translational Research Janis E. Landry-Lane, Program Director, World Wide High Performance Technical Computing, Life Sciences/Higher Education Segments, IBM Tzy-Hwa (Kathy) Tzeng, Ph.D., Senior Technical Staff Member, IBM Life Science and NGS Solution High-performance computing and storage are required to efficiently process data generated by NGS.The applications used to map reads and detect variants are typically CPU and I/O intensive. IBM has characterized this workload and developed optimal genomics platform to address the demand.The goal of any sequencing project is to gain insight into diverse range of biological processes by integrating genome data with corresponding phenotypes. Large computational capacity and sophisticate algorithms are mandatory in the translational platform.We will illustrate how IBM seamlessly integrates genomics and translational platforms. 10:05 Coffee Break in the Exhibit Hall with Poster Viewing 10:45 Sponsored Presentation (Sponsorship Opportunity Available) 11:15 Management of Genomic Big Data in a Country-Wide Collaborative Initiative for Rare Disease Gene Finding Joaquin Dopazo, Ph.D., Head, Computational Genomics, Centro de Investigacion Principe Felipe, Spain About 1000 exomes were analyzed in a nationwide initiative to find disease genes in many inherited diseases.This flood of DNA and RNA-seq data led to pipeline optimization for NGS data analysis, including accelerating runtimes and increasing sensitivity in mapping and variant calling processes, the development of new visualization tools and the development of new systems-biology-based candidate gene prioritization methods.The Medical Genome Project and the Spanish network for Rare Diseases constitute an example of a collaborative nationwide genome project. »» PLENARY KEYNOTE 11:45 From Genome Annotation to Genome Medicine Timothy Hubbard, Ph.D., Senior Group Leader, Wellcome Trust Sanger Institute, United Kingdom 12:35 Close of Conference THURSDAY, 5 DECEMBER 11:30 Conference Registration »» PLENARY KEYNOTE 11:45 From Genome Annotation to Genome Medicine Timothy Hubbard, Ph.D., Senior Group Leader, Wellcome Trust Sanger Institute, United Kingdom 12:35 Enjoy Lunch on Your Own ANALYTICAL TOOLS 14:00 Chairperson’s Opening Remarks 14:05 Annotate-it and eXtasy: Interpretation and Prioritization of Single-Nucleotide Variation in Clinical Genomics Alejandro Sifrim, Ph.D., Research Scientist, Yves Moreau Laboratory, Bioinformatics, Electrical Engineering, Katholieke Universiteit Leuven, Belgium The human genome harbors a plethora of neutral, common and rare variations. In order to find the cause of genetic disease, one must be able to distinguish these neutral variants from the disease-causing variants. Here we present Annotate-it and eXtasy, two software tools which aid the clinical geneticist in discovering disease-causing SNVs. 14:35 TAG (Tumor Analysis in Galaxy): A Web Server Application for the Detection of Somatic Mutations in the Absence of Associated Healthy Control Andrew Stubbs, Ph.D., Assistant Professor, Bioinformatics, Erasmus University Medical Center, The Netherlands The first step in tumor analysis is typically a correction with a normal sample, taken from the individual’s healthy tissue for which 80%-95% of variations in a tumor sample present in the healthy tissue. We have developed a web-based, control-free tumor analysis and reporting application with a “virtual normal” as reference to determine somatic mutations. It removed up to 97% of the variants detected by the standard tumor/normal approach. We will present our analysis, available in a public Galaxy/CLOUD. 15:05 Harnessing e-Science Central for NGS Simon Woodman, Ph.D., Senior Research Associate, Systems Research Group, Newcastle University, United Kingdom The talk will be about how we use e-Science Central for analyzing NGS data within the Cloud4Science project. This will include the pipelines we have implemented and challenges faced by storing and analyzing very large data sets. I will also examine the importance of provenance capture and analysis in this environment. 4-5 December 2013 5-6 December 2013 Informatics Informatics High-Scale Computing Genome Informatics Turning Big Genomics Data into Smart Data Deciphering Disease through Sequencing Data Fifth Annual Second Annual *IBM and the IBM logo are trademarks of International Business Machines Corp., registered in many jurisdictions worldwide.
  • 11 15:35 Sponsored Presentation Sponsored by 15:50 Sponsored Presentation (Opportunity Available) 16:05 Refreshment Break in the Exhibit Hall with Poster Viewing EXOME SEQUENCING 16:50 Sponsored Presentation (Sponsorship Opportunity Available) 17:20 Sequenza – A Bayesian Analytical Framework to Provide Comprehensive Characterization of Tumor Samples Based on Exome Sequencing Zoltan Szallasi, M.D., Senior Research Scientist, Children’s Hospital Informatics Program, Harvard Medical School, United States and Professor, Systems Biology, Danish Technical University, Denmark We are presenting here a powerful bayesian statistics-based analytical framework to analyze exome sequence data from tumor biopsies. Sequenze produces accurate estimates on normal tissue contamination and ploidy levels. It produces highly accurate mutational calls and also enables to extract loss of heterozygosity and copy number variations as accurately as SNP array profiles. We will also present several clinical case studies where Sequenza-based analysis of tumor exome sequences produced valuable clinical information. 17:50 EVA-Suite (Exome Variation Analyzer): A User-Friendly Web Solution for Annotating, Filtering and Prioritizing Candidate Variants in Medical Genomics Hélène Dauchel, Ph.D., Assistant Professor, Genomics and Applied Bioinformatics, University of Rouen, France To provide clinicians and human geneticists with user-friendly assistant software to help them deal with variation analysis in medical NGS projects, we have partnered with medical geneticists and developed EVA-Suite (Exome Variation Analyzer), a user-friendly web interface and free solution. It allows non-programming biomedical experts to manage variation data by themselves, from annotation to functional effect analysis of candidate variants through efficient versatile filtering strategies. Demonstrative examples for germline mutations in genetic disorders and somatic cancer mutations will be exposed. 18:20 Close of Day FRIDAY, 6 DECEMBER 08:00 Morning Coffee THERAPEUTIC TARGETS 08:30 Chairperson’s Opening Remarks 08:35 Clinical Genome Architecture Circuitry and Next-Generation Cancer Drug Targets Dimitrios H. Roukos, M.D., Ph.D., Founding Director, Centre for BioSystems & Genomic Network Medicine, CBS.GenNetMed and Department of Surgery, Ioannina University School of Medicine, Greece The ENCODE data change the “central dogma” of one-gene/protein- one phenotype which continues to represent the foundation of all drugs developed and currently used in clinical practice. Latest advances in clinical genomics and dynamic signaling networks are presented revealing the exciting perspectives and challenges in targeting individual cancer patient and discovering the next-generation transcriptional circuitry-based drugs. Challenges and perspectives of genomic network medicine are discussed. 09:05 Big Data in Drug Discovery – Challenges and Perspectives Philip Groth, Ph.D., IT Business Partner, CoE Research, Bayer HealthCare Pharmaceuticals, Germany After the discovery that mutations influence cancer initiation and development, targeted drugs like Crizotinib or Imatinib have shown dramatic effects on treatment of some cancers. To deepen understanding of the role of mutations in cancer, NGS has been employed to generate large-scale genomic mutation data. These “Big Data” must be stored, processed and analyzed to develop innovative cancer treatments. We present perspectives on cancer sequencing efforts, insights into the manifold technical, ethical, legal and scientific challenges and some solutions. 09:35 Sponsored Presentation (Sponsorship Opportunity Available) 10:05 Coffee Break in the Exhibit Hall with Poster Viewing TRANSLATION INTO THE CLINIC 10:45 The Ethical Introduction of Genome-Based Information and Technologies into Public Health Heidi Howard, Ph.D., Senior Research Fellow, Département d’épidémiologie et de Santé Publique, Faculté de Médecine, Université Toulouse, France 11:15 Challenges of Translation of Next-Generation Sequencing to Clinical Practice Ángel Carracedo, Ph.D., Director, Fundación Galega de Medicine Xenómica (FPGMX), Hospital Clínico Universitario, Spain We will discuss some of challenges of the use of NGS for the diagnosis of Mendelian diseases and pharmacogenomics. Some of the main problems need advanced bioinformatics tools and are related to the amount of the data generated and the interpretation of variants of uncertain significance. We will show our approaches to face these problems. »» KEYNOTE PRESENTATION 11:45The Ethical Dimensions of Data Sharing and the Maze of Identifiability Anne Cambon-Thomsen, M.D., Director, Research, Centre National de la Recherche Scientifique (CNRS), France 12:15 Sponsored Presentation (Sponsorship Opportunity Available) 12:45 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own 13:15 Session Break RNA-Seq 14:00 Chairperson’s Opening Remarks 14:05 Standards in RNA-Seq Data Analysis Stuart Brown, Ph.D., Associate Professor, Cell Biology; Director, Sequencing Informatics Group of Center for Health Informatics & Bioinformatics, NYU School of Medicine, United States 14:35 RNA-Seq and Microarray Gene Expression Vie for Superiority within a Comprehensive Study Design Weida Tong, Ph.D., Division Director, Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, FDA, United States The 3rd phase of the FDA-led community-wide Microarray Quality Control (MAQC-III) project investigated the reliability and utility of RNA-Seq. All the samples in this project were profiled by both RNA-Seq and microarrays, which produced unprecedented opportunity to comprehensively compare RNA-seq with microarrays. RNA-Seq seems to provide comparable or better transcriptomic profiling as compared with the standard microarray technology for the elucidation of biological responses.This project involves ~200 participants from >80 organizations with comprehensive results that will impact FDA policy. 15:05 Multi-Platform and Cross-Methodological Reproducibility of Transcriptome Profiling by RNA-Seq in the ABRF Next-Generation Sequencing Study (ABRF-NGS) Christopher Mason, Ph.D., Assistant Professor, Computational Biomedicine, Weill Cornell Medical College, United States We use standard reference samples to evaluate RNA-Seq across a range of sample quality levels, sample preparation methods and bioinformatics analysis approaches, with results that have the potential to improve the utility and comparability of these various methods and five NGS platforms (Illumina, PacBio, 454, PGM, Proton). Importantly, we demonstrate that even severely degraded RNA, when prepared and analyzed with appropriate methods, can be as useful as intact RNA for sequencing-based quantitative profiling. 15:35 Functional Dysregulation in Inflammatory Diseases Carsten O. Daub, Ph.D., Assistant Professor, Biosciences and Nutrition & Science for Life Laboratory, Karolinska Institutet, Sweden Employing genome-wide expression profiling for contrasting disease and control patients allows not only identification of differentially regulated protein or non-coding transcripts but also inference of the underlying regulatory events. 16:05 Close of Conference
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