Conquer the genomics data deluge by applying informatics tools to go beyond SNPs, CNVs, GWAS, sequencing, and gene expression studies to integrate and comprehend the function of genes from the genotype to phenotype level.
MONDAY, 5 OCTOBER
14:00-17:30 Pre-Conference Workshop * - Sequencing Data Storage
Co-organized by CHI and BioTeam
Matthew Trunnell, Manager, Research Computing, Broad Institute
Chris Dagdigian, Founding Partner and Director of Technology, BioTeam, Inc.
Guy Coates, Ph.D., Group Leader, Informatics System Group, The Wellcome Trust Sanger Institute
Additional Speakers to be Announced
BioTeam has been on the frontlines of next-generation sequencing integration, having helped several organizations with the unique next-gen IT, storage, and data management challenges. This workshop will present real-world customer experiences straight from the trenches. You’ll get practical information about the storage support needed by research organizations in the next-gen world.
*Separate registration required
16:00-18:30 Early Conference Registration
18:30 BIOTECHNICA Opening and European Award Ceremony plus Reception
TUESDAY, 6 OCTOBER
08:30-19:00 Conference Registration
08:50 Chairperson’s Remarks
09:05 Understanding the Complete Picture of Genetic Variation
Herbert Auer, M.Sci., Director, Functional Genomics Core, Institute for Research in Biomedicine, Parc Cientific de Barcelona
Genetic differences between individuals can be divided into various categories, including copy number variations, translocations, inversions and single nucleotide polymorphisms, and all of these categories can be scrutinized now by next-generation sequencing within a single experiment. We obtained sequence information of 6.2 gigabases from two drosophila strains, resulting in 25 fold genomic coverage for each strain. This data set is used to highlight challenges of and solutions for understanding genetic variation from Next-Gen data.
09:35 Whole Genome Profiling: A Novel Approach to Using High-Throughput Sequencing for Whole Genome Physical Mapping
Jan van Oeveren, Ph.D., Biostatistician, Bioinformatics Department, Keygene NV
Whole Genome Profiling (WGP) is a new and cost effective method to construct high quality physical maps. Using the power of next-generation sequencing machines, such maps can be constructed by sequence based fingerprinting of a BAC library. The BAC clones are pooled in a multi-dimensional format, followed by sequencing of restriction fragments. The resulting short sequence tags are spaced 2-3kb across the BAC clones and they serve as anchor points to link and order BAC clones into contigs providing a whole genome physical map. The audience will learn about the genomics principles involved and the bioinformatics approach for analyses.
10:05 Towards Generating a Global Map of Copy-Number Variants in Humans by Next-Generation Sequencing
Jan Korbel, Ph.D., Group Leader, Gene Expression, European Molecular Biology Laboratory
As a member of the “1000 Genomes Project” our group is developing approaches for genotyping genomic structural variants following the sequencing of hundreds of human genomes. These approaches are expected to help facilitate, in the future, the design of next-generation sequencing-based disease association studies that may, for example, help eluciDate the phenotypic impact of chromosomal aberrations associated with disease. I will present a summary and key research results of recent advances in genomics and bioinformatics, i.e. next-gen sequencing and the interpretation of data from personal genomics endeavors. Approaches and technologies presented/discussed during the presentation are presently transforming biology and genetics and thus will be of outstanding interest to the audience.
10:35 Coffee Break
11:00 Genetics of Complex Diseases: From Common to Rare Sequence Variants
Sergey Nejentsev, M.D., Ph.D., Royal Society Research Fellow, Department of Medicine, University of Cambridge
Genome-wide association studies (GWAS) of complex multifactorial diseases have identified multiple regions harboring causal variants and genes. However, disease-associated loci sometimes encompass several genes and multiple tightly associated polymorphisms, making it difficult to pinpoint the causal variant and even the disease gene. We used high-throughput next-generation sequencing to identify rare variants in candiDate genes and to test their association with T1D. I will discuss an example of type 1 diabetes (T1D), a complex disease, for which multiple regions containing common disease-associated variants have been reported.
11:30 FEATURED SPEAKER
The Role of Systems Biology in Bacterial Pathogenesis and Vaccine Discovery
Antonello Covacci, M.D., Global Head, Systems Biology, Novartis Vaccines and Diagnostics
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Sponsored by
12:00 HP peta-byte Scale Storage Solution for Genomics: Mastering Sequencing Data Challenges
Xavier Delore, Product Manager Massive Scale-Out Storage, EMEA, Hewlett Packard
HP’s innovative solutions for management & storage of peta-byte scale data enables research to focus on what matters to them - science. Learn about HP innovations including massively scalable and affordable HP StorageWorks 9100 Extreme Data Storage system, which provides researchers with the storage volume required for instruments that generate terabytes of data per run.
12:30-13:45 Lunch for purchase in the Exhibit Hall and Exhibit Viewing
14:00 Chairperson’s Remarks
14:05 Towards Quantitative Models of Gene Regulation
Thomas Manke, Ph.D., Researcher, Computational Biology, Max Planck Institute for Molecular Genetics
The increasing amount of functional genomics data provides new challenges and opportunities to understand gene regulation. In this talk, I will focus on our recent efforts to model the binding of transcription factors to DNA quantitatively. As an outlook, I will show how quantitative models may be used to predict the effects of sequence variations on regulatory networks.
14:35 Modeling of the U1 snRNP Assembly Pathway in Alternative Splicing in Human Cells using Petri Nets
Janice Kielbassa, M.Sc., Researcher, Biometry and Evolutionary Biology Laboratory, University Claude Bernard
In the molecular mechanism of alternative splicing, a multi-protein-RNA complex - the spliceosome - plays a crucial role. We propose the first abstract model of the regulatory assembly pathway of the human spliceosomal subunit U1 using Petri nets. Our Petri net model covers binding, transport, signaling, and covalent modification processes. Through the computation of structural and behavioral Petri net properties and their interpretation in biological terms, we analyzed our valiDated model and use it to get a better understanding of the complex processes of the assembly pathway.
15:05 Sponsored Presentation (Opportunity Available)
15:35 Refreshment Break
16:00 Colorectal Cancer-Based Gene Expression Signature for Prognosis of Different Tumor Types
Eike Staub, Ph.D, Research Scientist, Bio- & Chemoinformatics DA, Merck Serono R & D, Merck KGaA
Genome-wide expression analysis has already delivered multiple expression signatures to subtype colorectal cancers. We have recently published the first microarray-based prognostic expression signature that originated from an analysis of colorectal cancer data and could also be successfully translated to other cancer types. Here I will outline our analysis strategy and present the results of our study.
16:30 Global Gene Expression Profiling of Progesterone Receptor Modulators in T47D Cells Provides a New Classification System
Weibke Afhüppe, Ph.D., Therapeutic Research Group, Bayer Schering Pharma AG
The progesterone receptor (PR) is a key regulator of female reproductive functions. Compounds with progesterone receptor modulating effects have found numerous utilities in female reproductive health. Due to the broad range of activities, various studies were conducted to assess progesterone receptor antagonists (PAs) and selective progesterone receptor modulators (SPRMs) with respect to progesterone receptor (PR) agonistic and antagonistic activities in vivo. We utilized mammalian two-hybrid assays and gene expression profiling to compare a divergent set of PR modulators. In summary, the data support the popular concept of PR modulator classification in agonists, selective progesterone receptor modulators, mixed and pure antagonists. It further refines previous classification models and accentuates unique effects for each PR modulator.
17:00 Panel Discussion with Afternoon Speakers “Are we Managing the Data Deluge or is it Managing Us?”
Moderator: Herbert Auer, M.Sci., Director, Functional Genomics Core, Institute for Research in Biomedicine, Parc Cientific de Barcelona
17:30 Move to Breakout Discussion Groups
17:45-19:00 Interactive Breakout Discussion Groups
19:00-21:00 CHI Reception
Sponsored by
WEDNESDAY, 7 OCTOBER
08:50 Chairperson’s Remarks
09:05 Tracing Haplotype Homozygosity for Detecting Putatively Functional Genetic Polymorphisms
Markus Schirmer, M.D., M.Sc., Junior Scientist, Clinical Pharmacology, Georg-August-University
The HapMap database currently contains the most informative data set of genetic polymorphisms determined in the same individuals allowing analysis of linkage disequilibrium and haplotype homozygosity. Traced by these methods, the selection signature of a genetic region could be indicative for functional variants which are then candiDates for validation by experimental assays. By this way, a genetic haplotype in TGFBR1 gene was identified not only potentially impacting disease risks (e.g. cancer) but also the therapeutic outcome. This presentation gives an example from the inter-disciplinary working field of bioinformatics and experimental assays with biological material.
09:35 Genome-Wide Association Studies for Genetic Determinants of Warfarin Dose
Panos Deloukas, Ph.D., Senior Investigator, Human & Medical Genetics, The Wellcome Trust Sanger Institute
The anticoagulant warfarin is the 11th most widely prescribed drug and is administered to protect high-risk patients from stroke, deep vein thrombosis, pulmonary embolism and heart attack. However, patients vary widely in the warfarin dose needed to achieve proper blood thinning, which means that initial doses in some patients are too high or too low (risking serious illness or bleeding). A large-scale genome-wide scan in Swedish patients identified both major, VKORC1 (explaining ~30% of dose variability) and CYP2C9 (~11%), as well as minor (CYP4F2; ~1.5%) genes determining therapeutic warfarin dose. Combining results with other ongoing GWAS through meta-analysis may reveal additional genetic factors for dose forecasting.
10:05 Five Annotated Full Length Personal Genomes
Michael Cariaso, Founder, SNPedia.com
This material cross-references five publicly available full length human genomes against dbSNP, HapMap, PubMed, OMIM and SNPedia. SNPedia is a wiki database of annotated SNPs. As of June 2009 it contains 6500 SNPs with approximately five new ones per day. Each genome is profiled as though it were a direct-to-consumer genome, so it is checked for disease risks, pharmacogenomic drug warnings and recreational genomics topics. Example findings include: James Watson carries two CYP2D6*10 variants which limit his ability to metabolize codeine, while the YH Chinese genome shows significant risk of vision loss with age. These are two of the 15,000+ genotyping tests which are performed on every genome. Important details of the method such as Genosets (boolean combinations of unphased SNPs) and Magnitude (a subjective measure of community interest) will be discussed, as well as the planned approach for annotating CNVs and larger structural variants. All of this
information is RDF encoded, semantic web accessible and queryable via a SPARQL interface. The analysis is performed by Promethease, a cross-platform user friendly desktop app freely available for non-commercial use.
10:35 Coffee Break
11:00 Combining Gene Expression Signatures, miRNA Fingerprints and Autoantibody Profiles in Human Tumors
Andreas Keller, M.Sc., Head, Analytical Service, febit biomed
State-of-the art high-throughput microarray platforms allow for measuring mRNA and miRNA expression fingerprints. These data can be augmented, e.g., by seroreactivity patterns of autologous patients. The combination and computational evaluation of the different profiles helps to deepen our understanding of tumors on the molecular level and may contribute to an improved cancer diagnosis in the near future.
The mechanisms on the molecular level of tumor cells are not understood. Thus, the combination of different high-throughput data and the sophisticated computational evaluation contributes to the grasp of relevant information for immune responses against human tumors.
11:30 SHERPA: A Common, Flexible user Interface for Multiple Genetic Genotyping Technology Platforms
Michal Blazejczyk, M.Sc., Lead Programmer, Bioinformatics, Génome Quebec and Montreal Heart Institute Pharmacogenomics Centre
SHERPA, an analysis tool for genotyping data, was developed to provide the analyst with a single point of entry to data analysis of multiple platforms. It uses flexible tabular data displays and plots. In addition, it supports dynamic linking between the various data containers visible on the screen, provides user-defined aggregation and summarization mechanisms, and allows for extensive annotation mechanisms. Analysts can now gather raw data from any genomic platform and analyze it in a single software package using optimized features. This includes a suite of tools for data reporting. These features combine the strengths of all of the individual platforms, and furthermore include analysis functionality that is currently not available in any commercial package.
12:00 Panel Discussion with Morning Speakers “Successful Data Flow in Translational Research”
12:30-13:45 Lunch for Purchase in the Exhibit Hall and Exhibit Viewingg
13:45 Close of Bioinformatics for Genomics Conference