18 - 20 January, 2010, Grand Connaught Rooms, London, UK
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Although more than a thousand bacterial genomes have been sequenced, our understanding of bacterial transcriptomes has lagged far behind. Transcript structure, operon linkages, and absolute mRNA abundance information all provide valuable insights into gene function and regulation, but these aspects of the prokaryotic transcriptome have only been explored on a large scale in a few instances. Here we report the use of a sequencing-based approach (RNA-Seq) in assembling the first comprehensive, single-nucleotide resolution view of a bacterial transcriptome. We sampled the Bacillus anthracis transcriptome using the ABI SOLiD platform, and mapped transcript start sites and operon structure throughout the genome. Our data also provide estimates of absolute transcript abundance on a global scale, and they suggest there is significant transcriptional heterogeneity within a clonal, synchronised bacterial population. Overall, our results offer an unprecedented view of gene expression and regulation in a bacterial cell.
Dr Nicholas H. Bergman Principal Investigator and Genomics Team Leader National Biodefense Analysis and Countermeasures Center
The study of the viral quasispecies in HIV-1 and HCV-infected patients is important for the understanding of the pathways to resistance and can substantially improve treatment. Genotypic and phenotypic methods are commonly used to detect antiviral resistance in clinical specimens. Whereas standard genotyping provides information on the most abundant sequence variants only, the new massively parallel sequencing technologies allow in-depth characterisation of sequence variation in complex viral populations. We will present several case studies on specific target genes in HIV-1 and HCV, thereby demonstrating the power of deep sequencing in providing a better understanding of viral distribution and evolution in response to antiviral therapy.
Dr Ina Vandenbroucke Senior Scientist, Translational Genomics & Genetics Tibotec-Virco BVBA
In my presentation I will highlight the current research of my group at EMBL, which combines large-scale experimental technologies and computational data mining approaches for studying the genomic extent and the mutational formation mechanisms of genomic structural variants (SVs) in humans. SVs, frequently referred to as copy-number variants, are >1kb deletions, duplications, insertions, and inversions responsible for most genetic variation in the human genome. We recently developed high-resolution and massive paired-end mapping, an approach that involves ultrafast sequencing of the end-stretches of 3kb genomic DNA fragments and mapping them against a reference genome to identify SVs at subkilobase resolution. Applying this approach to two human genomes allowed us to obtain insights into the mutational origins of SVs and into the extent at which SVs affect human genes. This session will also explore one aim of the “1000 Genomes Project”, which is the generation of a global map of rare and common genetic polymorphisms in humans, that EMBL is developing analysis approaches for. Furthermore, these approaches are expected to help facilitate, in the near future, the design of next-generation sequencing-based disease association studies that may, for instance, help elucidate the functional impact of chromosomal aberrations associated with human diseases, including cancer.
Dr Jan Korbel Group Leader, Genome Biology Unit European Molecular Biology Laboratory (EMBL)
Next-generation high-throughput DNA sequencing techniques are opening fascinating opportunities in the life sciences. Novel fields and applications in biology and medicine are becoming a reality, beyond the genomic sequencing which was original development goal and application. Serving as examples are: Personal genomics with detailed analysis of individual genome stretches; precise analysis of RNA transcripts for gene expression, surpassing and replacing in several respects analysis by various microarray platforms, for instance in reliable and precise quantification of transcripts and as a tool for identification and analysis of DNA regions interacting with regulatory proteins in functional regulation of gene expression. The next-generation sequencing technologies offer novel and rapid ways for genome-wide characterisation and profiling of mRNAs, small RNAs, transcription factor regions, structure of chromatin and DNA methylation patterns, microbiology and metagenomics. In this session, Dr Ansorge will discuss the development of commercial sequencing devices. Presently commercially available very high-throughput DNA sequencing platforms, as well as techniques under development, are described and their applications in bio-medical fields discussed.
Dr Wilhelm Ansorge Department Lab Nanostructures and Novel Electrical Materials Ecole Polytechnique Federal Lausanne
Peer Stähler CSO & VP Marketing febit biomed gmbh
DNA Sequencing technology development is moving fast. For many, it’s hard to keep up and know which system is best for their lab. As costs of new systems come down and their ease of use increase, there is greater opportunity for academic and biopharma labs to acquire the systems. This extended lunch period will provide time for participants to compare sequencing systems by visiting exhibitor booths and viewing technology demos.
Next Generation sequencing technologies produce vast amounts of data at a rate that would have been unimaginable a few years ago. The aim of Dr Turner’s research team is to develop high-throughput research methods that can exploit this explosion of data in order to answer a broad range of biological questions. The team uses a wide variety of molecular biological techniques and pre-sequencing technologies to create new front-end sequencing applications and bespoke sequencing assays. This session will focus on the latest research on Next Gen sequencing technology and innovative sequencing applications coming out of Dr Turner’s department at the Wellcome Trust Sanger Institute.
Dr Daniel J. Turner Head of Sequencing Technology Development Wellcome Trust Sanger Institute
This presentation will focus on how Covaris AFA technology empowers many scientific disciplines to develop new processes using isothermal and non-contact processes. Main applications for the AFA technology are DNA shearing, tissue and cell disruption (DNA, RNA, protein and biomarker extractions). KBiosciences will share technical insights in this presentation as a partner and co-developer of the Covaris ultra-sound based instrumentation for DNA-shearing applications in Next-Gen- Sequencing: the Covaris Adaptive Focused Acoustics (AFA) DNA-shearing technology. Final part of the presentation will be about Next-Gen sequencing application solutions for high volume emulsion PCR (ePCR) and a high throughput singleplex SNP/InDel validation technology, based on KASP.
Niels Kruize Sales Director KBiosciences Ltd.
Nanopore-based DNA analysis is a single-molecule technique with revolutionary potential. The concept involves using an applied voltage to drive DNA molecules through a narrow pore that separates chambers of electrolyte solution, rather like thread through the eye of a needle. The amount of current which can pass through the nanopore at any given moment therefore varies depending on whether the nanopore is blocked by an A, a C, a G or a T. The change in the current through the nanopore as the DNA molecule passes through the nanopore represents a direct reading of the DNA sequence. This session will explore the current laboratory tests using this novel approach and will discuss the current obstacles at hand that will need to be overcome before realising the true potential of this unique sequencing approach.
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