Bio-IT World and Cambridge Healthtech Institute’s Second Annual
Deciphering Disease through Sequencing Data
5-6 December 2013 | Sheraton Lisbon Hotel & Spa | Lisbon, Portugal
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FRIDAY, 6 DECEMBER
08:00 Morning Coffee
08:30 Chairperson’s Opening Remarks
John Gurnett, Healthcare Field Director, EMEA, EMC
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 Using NGS and in vitro Models to Understand Structural and Regulatory Variation in Gastric Cancer
Carla Oliveira, Ph.D., Head, Expression Regulation, Cancer Group, IPATIMUP, Portugal
Gastric carcinoma (GC) is the second leading cause of cancer death worldwide with over 700,000 deaths per year. A systematic approach to identify subgroups of gastric cancer based on clinico-pathologic features, cancer-specific molecular profiles and patients’ survival is missing. We followed a strategy of gastric cancer stratification based on rigorous histo-pathology characterization and molecular profiling according to three important prognostic factors in gastric cancer (E-cadherin LOH, MSI and HER2). A collaborative team from IPATIMUP, Coimbra Genomics and BGI is currently performing WGRS, RRBS and RNA-seq of 50 pairs of stratified gastric cancers and paired normal tissue. Adequate bioinformatics pipelines and in vitro models, to validate candidate pathways emerging from our NGS approach, are in place at IPATIMUP. We hope to shed light onto GC-specific molecular signatures crucial for the identification of therapy targets and for the development of new therapeutic options.
10:05 Coffee Break in the Exhibit Hall with Poster Viewing
10:45 The Ethical Introduction of Genome-Based Information and Technologies into Public Health
Heidi Carmen Howard, Ph.D., Assistant Professor, Biomedical Ethics, IQ Healthcare, Radboud University Medical Centre, Netherlands and Senior Research Fellow, Département d’épidémiologie et de Santé Publique, INSERM, Faculté de Médecine, Université Toulouse, France
Public health genomics, wherein genomics would be integrated in all aspects of healthcare and public health, is gradually being proposed as a future reality. And, although laudable, these advances also bring with them a slew of ethical and social issues that challenge the normative frameworks used in clinical genetics until now. With this in mind, we highlight herein five principles that are used as a primer to discuss the ethical and responsible introduction of genome-based information and genome-based technologies into public health.
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.
11:45 How the Electronic Healthcare Record Can Facilitate Translational and Integrative Medicine
Amnon Shabo, Ph.D., Project Leader, IBM Healthcare & Life Sciences Standards Program, IBM Haifa Research Lab
Health records could include various types of information generated along the translational continuum from discovery to policy and thus could facilitate the translational processes and enable meaningful reasoning by clinical decision support applications. To harmonize the various types of information, it is important to develop a universal health information language that is based on several languages/formats to represent data and knowledge. New effort in Clinical Genomics standardization will be presented.
12:15 pm The 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
The policies of data sharing are strongly re-affirmed by numerous research institutions and funders. This movement in the context of the availability of large-scale sequencing technologies for studying human genomic variation is confronted with the legal and ethical aspects regarding privacy, confidentiality, clinically useful information and the duties attached. Issues related to identifiability, consent process and regulation of access especially challenge the existing framework. Current developments will be discussed.
12:45 Luncheon Presentation (Sponsorship Opportunity Available) or Lunch on Your Own
13:15 Session Break
14:00 Chairperson’s Opening Remarks
Mary Ann Brown, Executive Director, Conferences, Cambridge Healthtech Insitute (CHI), United States
14:05 Selected Poster Presentation: Identifying Fusion Genes in Cancer Samples
Liliana Greger, Ph.D., Research Scientist, Brazma Group, Functional Genomics, The European Bioinformatics Institute, EMBL
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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