18 - 20 January, 2010, Grand Connaught Rooms, London, UK
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The first application of routine sequencing in the clinic will likely be targeted sequencing for diagnostics, for which a robust target enrichment procedure is required. We have developed a protocol for target enrichment using short fragment DNA libraries, which yielded high enrichment specificity of 60-75%, good evenness of coverage with 77-92% and 90-98% of targeted regions covered with more than 25% and 10% of the average coverage, respectively, and high accuracy of SNP/mutation detection with only 4.2% false negative and 0.0005% false positive calls. Adaptations of the array design by normalising the number of array features per probe to the obtained coverage of the targeted regions or using a denser tiling path of probes improved the evenness of coverage over the targeted sequence even further. This session will explore how these improvements are important for developing accurate and reproducible disease-specific targeted sequencing.
Dr Harma Feitsma Research Scientist Molecular Diagnostics Philips Research Labs
Next generation sequencing has tremendous potential for clinical applications. For most diagnostic applications a targeted analysis of known disease genes is preferred at present, as this will reduce the number of sequencing errors, facilitate functional interpretation of sequence variations, and overcome limitations in computational power as well as ethical restrictions. This application is of great value for complex monogenic disorders such as blindness, deafness and mental retardation that can be caused by hundreds of genes. In this presentation I will discuss the validation of an array-based sequence capture method for medical resequencing approaches in these disorders. I will also discuss implementation of this approach in the clinical arena, which will have a profound effect on the diagnosis and genetic counselling of patients with complex monogenic disorders, relevant to all diagnostic genetics laboratories.
Dr Joris Veltman Department of Human Genetics Radboud University Nijmegen Medical Centre
Primary interest in early drug discovery is elucidating the effect of the compound on cells. Identification of the target, or the mechanism of resistance, allows one to predict the effects of the compound for future development. We have used Deep Sequencing, coupled with classical genetic tools, on model organisms to reveal compound – target mechanisms of action. With the current available technologies, the single associated base change is identified rapidly and cost effectively. We have also successfully demonstrated this proof of concept on mutagenised cell lines, which harbour many base changes. As sequence reads information increases and costs decrease, the potential to replace many classical genetic methods with a single run of Deep Sequencing becomes possible.
Dr Bhupinder Bhullar Lab Head, Developmental & Molecular Pathways Novartis Institute for Biomedical Research
Since the completion of the human genome project at the beginning of this century, the scientific community has witnessed the development of a range of disruptive novel DNA (and RNA) sequencing technologies. In a first wave, amplification based massive parallel sequencers from 454 Life Technologies (Roche), Solexa (Illumina) and SOLiD (Life Sciences) have come to market. Currently the first papers describing results from single molecule sequencing (Helicos and Pacific Biosciences) are being published and Proof-of-Principle studies on nanopore- based and other alternative sequencing technologies are performed. Each of these technologies, together with the sequencing strategies they support, come with their specific benefits and shortcomings. In this presentation, we will present some case studies of scientific questions that we want to address with massive parallel sequencing approaches and how our choice for a particular technology and strategy is guided by the nature of the problem (deep versus wide, de novo vs. re-sequencing).
Dr Peter Verhasselt Principal Scientist, Translational Genomics & Genetics Johnson & Johnson Pharmaceutical Research & Development
Panelists:
The European Nucleotide Archive (www.ebi.ac.uk/ena), along with its global partner archives, provides the world’s permanent repository for public domain nucleotide sequence and related information. We have recently established the Sequence Read Archive (SRA) to extend coverage to sequencing data from next generation platforms. To meet the many challenges presented by these new data, we have developed and deployed data models that differ radically those we have maintained traditionally. In the talk, I will outline the mission and status of the SRA and will review the challenges that we have met and our approaches to tackling them. In particular, I will focus on the unprecedented large data volumes, the broadening range of applications for which sequencing is now used and the development of technology to make data easily available to the user.
Guy Cochrane Team Leader, European Nucleotide Archive Team European Bioinformatics Institute
High-throughput sequencing has the potential to be a disruptive technology in microbiology. The cost of sequencing continues to fall dramatically and whole bacterial genomes may now be sequenced for less than £500 per isolate. Data produced by these systems offer a paradigm which can unite the clinical microbiologist, public health doctor and basic scientist to open the door to translational research. In this presentation, the use of high-throughput sequencing applied to the important human pathogens /Acinetobacter baumannii, Streptococcus pneumoniae/, /Pseudomonas aeruginosa /and/ Mycobacterium tuberculosis/ will be described. We show the utility of this data for diagnostics through the development of pathogen profiles and /in silico/ antibiogram prediction. We also show its utility for epidemiological studies by using single nucleotide polymorphism data to help unravel chains of transmission within a hospital. Finally, these data also give clues to the molecular basis of virulence and antibiotic resistance.
Dr Nick Loman Bioinformatics Research Associate, Division of Immunity and Infection University of Birmingham
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Transcribed regions have been long been regarded as a distinguishing characteristic of functional portions of the human genome. Massively parallel sequencing of RNAs through next generation sequencing NGS instruments promises, for the first time, sufficient sequencing depth for full transcriptome characterization, that is for the identification of every transcript species in the cell, and their quantification; in particular, for the accurate estimation of the relative abundances of alternative transcript isoforms from the same gene, and of the expression of novel non-coding RNAs. However, the most cost-effective such technologies typically produce very short sequence reads, which compounds transcript reconstruction and quantification. We will discuss computational approaches being developed to address this issue, and produce accurate estimation of transcript quantities in the cell
Roderic Guigó Senior Group Leader, Genomic Regulations, Biomedical Informatics Institut Municipal d’Investigació Mèdica (IMIM)
Next generation sequencing techniques highlight a number of potential cancer susceptibility genes with consistent risk effects across all published datasets. However more comprehensive experimental approaches are needed to identify novel colon cancer genes, in particular those which contain rare, potentially disease-causing variants. To this end, we have begun “whole exome” sequencing of colon cancer patients using microarraybased sequence capture of ~180,000 coding regions followed by massively parallel sequencing using the Roche/454 FLX Genome Sequencer. Comparison of the sequence to the reference genome identified on average ~70,000 single nucleotide polymorphisms. The main challenge after sequencing is the data analysis and especially the functional annotation and filtering of variants. For this purpose we have developed an automated analysis pipeline for resequencing data. This consists of different functional annotation steps including balance of base specific (phyloP) and multi species conservation. Additionally different project specific filtering steps with theme specific databases are included.
Bernd Timmermann Next Generation Sequencing Service Group Max Planck Institute for Molecular Genetics
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