Distinguished Symposium Faculty
Professor Nazneen Rahman (Keynote Speaker)
Head of the ICR Division of Genetics and Epidemiology and Head of the Cancer Genetics Clinical Unit at The Royal Marsden, UK
Title: Using Next-generation sequencing to deliver large-scale clinical genetic testing – what does it take?
Dr Nava Whiteford
Executive Officier for Informatics, Quantum Biosystems, Osaka, Japan
Title: The direct electrical sequencing of DNA and RNA
Dr Alistair Pagnamenta
The Wellcome Trust Center for Human Genetics, University of Oxford, UK
Title: Identification of novel variants in PIGQ and PGAP3 further implicate the GPI pathway in the pathogenesis of neurodevelopmental abnormalities
Dr Olga V Pettersson
Project coordinator, Uppsala Genome Center, National Genomics Infrastructure, Uppsala, Sweden
Title: High-throughput sequencing and analysis of clinical samples – our experience from Ion Proton, Ion Torrent and Pac Bio technologies
Dr Matthew Addis
Title: How to keep genomics data safe, secure and accessible for the long-term
Professor Chris Ponting
Professor of Genomics at University of Oxford, and Associate Faculty at the Wellcome Trust Sanger Institute, UK
Title: Using NGS approaches to identify lncRNAs and to determine their molecular mechanisms
Dr Mike Gilchrist
Group Leader, MRC National Institure for Medical Research, Mill Hill, London, UK
Title: Using high resolution time series data to detect transcriptional events
Dr Jean-Baptiste Cazier
Bioinformatics Core Group Leader, Department of Oncology, University of Oxford, UK
Title: Issues and bottlenecks of applying NGS to cancer genetics
Dr Adam Ameur
Senior Bioinformatician, SciLifeLab, National Genomics Infrastructure, Dept of Immunology, Genetics and Pathology (IGP), Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
Title: Clinical sequencing applications for infection screening and cancer diagnostics
Professor Neil Hall
Director, Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, UK
Title: Comparative genomic’s and transciptomics of Entamoeba parasites
Dr Nick Loman
Research Fellow, University of Birmingham, UK
Title: Metagenomics in clinical microbiology
Dr David L Hirschberg
Mailman School of Public Health, Columbia University, NY, USA
Title: Multiplexed detection of pathogen sequences by Heterologous Extension Ligation Sequencing Reaction (HELSR)
Dr Nick Downey
Integrated DNA Technologies, UK
Title: Enhanced solution based target enrichment using oligonucleotide probes and modified blocking oligonucleotides
Dr Bas Vroling
Bio-Prodict, The Netherlands
Title: Next-generation variant effect predictions and data integration
Professor Tim Hubbard (Keynote Address)
Professor of Bioinformatics, Director of Bioinformatics King's Health Partners and Head of Department of Medical & Molecular Genetics, King's College London, UK
Title: Genome Medicine and the 100,000 genomes project
Dr Vincent Plagnol
Lecturer, UCL Genetics Institute, University College London, UK
Title: Mining 1000s of exome sequences to identify the genetic basis of rare Mendelian disorders
Dr Thomas Keane
Senior Scientific Manager, Vertebrate Resequencing Informatics, the Wellcome Trust Sanger Institute, UK
Title: 1000 genomes/UK10K and bioinformatics behind variant calling
Dr Aziz Aboobaker
Lecturer, Department of Zoology, University of Oxford, UK
Title: Leveraging NGS to understand the mechanisms of animal regeneration and stem cell biology
Mr Stuart Catchpole and Mr Gawain Bennett
Knowledge Exchange & Commercialisation Manager, TGAC, UK
Title: Academia-Industry relationship development illustrated through sequencing of the wheat genome
Next-generation sequencing (NGS) has become a routine technology in just a few years and bears the promise of making personalised medicine a reality, and changing the pace of diagnostics and research in all fields of biological and medical sciences to the level never seen before. What NGS can achieve in a short span of time NGS has never been possible with the conventional sequencing methods.
The NGS technology itself is developing at a rapid pace with the introduction of new concepts, definitions and terminologies, new performance platforms and analytical tools, and workflow plans. All this makes it a considerable challenge for the newcomers. The current training course was designed to unravel the mysteries of this exciting technology for the new entrants provided an introduction to the basic methods, available platforms, applications and future directions.
Workstations were provided for hands-on training.
Trainers: Dr Mark Lindsay (University of Bath, UK); Dr Joerg Mages (Partek) and Dr Ivan Lukic (Partek)
Dr Mark Lindsay introduced various aspects of the NGS technology.
Introduction to RNA sequencing
1. Overview on mRNA and long non-coding RNAs and the application of RNAseq
2. Introduction to RNA databases
3. RNA preparation and quality assessment
4. Overview of next generation sequencing platforms.
Dr Joerg Mages and Dr Ivan Lukic offered hands-on training course in sequence data analysis.
Drs Mages and Lukic will cover a complete start-to-finish data analysis, including, sample information management, raw data quality assessment, alignment and trimming, post-alignment quality control, Principal Components Analysis, Quantification, Differential gene/transcript expression, SNP calling and more. Learn how you can turn your raw data into biology using advanced statistics and powerful visualizations. Hands-on exercises will be integrated throughout the lesson for you to practice the techniques discussed.
1. NGS analysis in Partek®Flow®: From Fastq files to differentially expressed genes. Using state-of the art NGS tools was never that easy (Live demo, 1 hour)
2. NGS in Partek Genomics Suite: BAM file import, visualizations, mRNA quantification and SNV detection (Hands-on training, 1.5 hours)
3. Advanced RNA-seq analysis in Partek Genomics Suite: Detecting and eliminating batch effects, advanced Statistics for differential expression, alternative splicing and Pathway analysis. (Hands-on training, 2 hours)
Technology Workshop Presenters
Dr Misha Kapushesky
CEO, Genestack, UK
Dr Alessandro Riccombeni
Senior Scientist, Genestack, UK
Dr Tim Bonnert
Field Application Scientist, Europe, Qiagen
Dr Malathi Raman
NGS Product Manager, Europe, Takara Bio Europe
Dr Joanne Mason
Lead Scientist at the Oxford Molecular Diagnostics NGS Core, UK
Dr Matthew Addis
CTO, Arkivum, UK
Technology Workshop Summaries
Transformation of genomics big data computing and application engineering:
Our workshop will introduce you to Genestack, showing you how to use our platform to analyse your sequencing data. We will show you how to set up a workflow for differential gene expression analysis, starting with unaligned data. Biologists and bioinformaticians will be shown how to automate standard bioinformatic analyses without having to worry about file formats but focusing on the results. We will also show developers the strengths of our Genomics Operating System, showing how to write a simple bioinformatic app and share it with others on Genestack.
Identifying Causal Variants in NGS Data: An Introduction Workshop for Analysis and Biological Interpretation of Human DNA Resequencing Data:
This workshop is aimed at clinicians, biologists, and researchers who either have, or will soon have human DNA resequencing data and wish to undertake the statistical and biological analysis to identify potential causative variants. The course will consist of an introduction seminar on Ingenuity Variant Analysis (http://www.ingenuity.com/products/variant-analysis) with discussions on Next-Generation Sequencing data generation, analysis and interpretation. Attendees can learn how to use Ingenuity Variant Analysis for the identification of causative variants from whole-Exome and whole-Genome samples.
SMARTer® Solutions for Low Input Transcriptome Sequencing:
Next Generation Sequencing (NGS) has increased our understanding of biology by enabling highly sensitive RNA expression analysis throughout the transcriptome, across a wide dynamic range. Two particularly powerful applications, single cell RNA-Seq and stranded RNA-Seq, have been the focus of considerable efforts in protocol innovation. Single cell transcriptome analysis has revealed key properties of individual cells, increasing its importance in fields such as cancer, development, neurobiology, and stem cell research. Strand-specific information is necessary to distinguish closely-related genes and non-coding RNAs (e.g. lincRNA) or to define genes in poorly annotated, coding-rich genomes, such as many bacteria.
By utilizing the template switching activity of reverse transcriptase, Clontech’s patented SMART™ technology has enabled researchers to analyze their most challenging samples. The original, dT-primed SMART-based RNA-Seq protocol, designed to work with high-quality RNA or whole cells, is the gold standard for single cell analysis. SMART’s applicability has recently been extended to non-coding RNA and mRNA from degraded samples, such as FFPE. In addition, the use of modified SMART adapters in combination with random priming makes it possible to generate strand-specific sequencing libraries directly from RNA in under four hours. This approach eliminates the laborious enzymatic steps required by other stranded RNA-Seq methods, while maintaining the sensitivity and reproducibility characteristic of SMART.
In this presentation, we will outline these current SMART methods and detail their ability to provide unrivaled mappability, gene body coverage, strand specificity, and sensitivity.
NGS, Big Data and the Future:
NGS has taken the medical world into new areas and expanded our understanding of human biology by enormous amounts. The ability to rapidly decode or sequence entire exomes or genomes of patient populations offers insights that were not possible before – resulting in large quantities of data. This data can present operational bottlenecks within current research lab infrastructures. Whether in a university or a hospital, the current storage capacity and reliability of servers is an issue for the IT department.
Processing a single exome can produce 10 terrabytes of data per patient. But, a clinical trial of 100 patients would result in huge amounts of data. What happens when that trial ends and another one starts? Where do you store your NGS data so that it is secure, protected and guaranteed for the future?
We’ll hear details of Joanne Mason’s experience and we’ll further explore the issues of storing and maintaining such huge data sets for the future and how an archiving service might provide the answer.
(Presenters in Bold)
Metagenomic Exploration of the Viral Microbiome in Hand Foot and Mouth Disease and Herpangina in Thailand
Piyada Linsuwanon1, LinLin Li2, Yong Poovorawan1, and Eric Delwart2
1Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
2Department of Laboratory Medicine, University of California, San Francisco, CA, USA
Transcriptome Analysis of Pseudorabies Virus Using RNA-Sequencing
Peter Olah, Dóra Tombácz, István Prazsák, Nándor Póka, Zsolt Boldogkői
Department of Medical Biology, University of Szeged, Hungary
Real-time RT-PCR analysis of poly(A)-containing transcripts of pseudorabies virus
István Prazsák, Dóra Tombácz, Oláh Péter, Póka Nándor, Zsolt Boldogköi
University of Szeged, Department of Medical Biology, H-6720, Szeged, Somogyi B. str. 4., Hungary
Sequencing the pseudorabies virus genome using Pacific Biosciences SMRT technology
Dóra Tombácz1, Donald Sharon2, István Prazsák1, Peter Oláh1, Nándor Póka1, Zsolt Csabai1, Zsolt Boldogkői1
1Department of Medical Biology, Faculty of Medicine, University of Szeged, Szeged, Hungary
2 Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
Who Attended NGS 2014 Oxford
The following organisations were represented at NGS 2014 Oxford.
- 4titude, UK
- AgroEcology, UK
- Arkivum, UK
- Bio-Prodict,, The Netherlands
- British Columbia Inst Technology, Canada
- Cartagenia N.V., Belgium
- Centrum Badań DNA, Poland
- Chulalongkorn University, Bangkok, Thailand
- Columbia University, USA
- Enzymatics, USA
- Exiqon, Denmark
- Food Standards Agency, UK
- Genestack, UK
- Hospital Israelita Albert Einstein, Brazil
- ICR Chester Beatty Labs (London), UK
- Ingenuity, USA
- Integrated DNA Technologies, UK
- ISRA/CERAAS, Senegal
- Israel Inst Biol Research, Israel
- Jagiellonian University Medical College, Poland
- King Faisal Specialist Hospital, Saudi Arabia
- KU-Leuven, Belgium
- Masaryk University, Czech Republic
- Medical Univ Innsbruck, Austria
- MGZ Bayerstrabe, Czech Republic
- MRC National Institure for Medical Research, UK
- Nanopore Technologies Ltd, UK
- NIHR Biomedical Research Centre, UK
- Oxford Biomedical Research Centre, UK
- Pacific Biosciences, UK
- Partek, UK
- PerkinElmer, UK
- Procrea Lab, Switzerland
- Qiagen, UK
- Quantum Biosystems, Japan
- Rio de Janeiro Federal University, Brazil
- Rouen Hospital, France
- Royal Children’s Hospital, Australia
- Royal Institute of Technology, Sweden
- Sartorius Stedim Lab Ltd, UK
- Scientific Institute of Public Health, Belgium
- SciLifeLab, National Genomics Infrastructure, Sweden
- Sophia Genetics, Switzerland
- SynLab Suisse, Switzerland
- Takara Bio Europe, France
- The Cyprus Institute of Neurology and Genetics, Cyprus
- The Genome Analysis Centre, UK
- The Royal Marsden, UK
- The Scripps Research Institute, USA
- The Wellcome Trust Sanger Institute, UK
- Universidad de Santiago de Compostela, Spain
- Universidade Federal do Rio de Janeiro, Brazil
- University College London, UK
- University Hospital Geneva, Switzerland
- University of Bath, UK
- University of Birmingham, UK
- University of Liverpool, UK
- University of Oxford, UK
- University of South Bohemia in Ceske Budejovice, Czech Republic
- University of Szeged, Hungary
- University Stavanger, Norway
- Uppsala Genome Center, Sweden
- Uppsala University, Sweden
- VHBio, UK
- VitalnSilica, Poland
- Yonsei University, Korea
- Zurich University, Switzerland
NGS 2014 Sponsors and Exhibitors
QIAGEN Redwood City, the company’s Center of Excellence in Biological Analysis and Interpretation, is a leading provider of biomedical information and analysis solutions for the exploration, interpretation and analysis of complex biological systems. Marketed under the Ingenuity brand, these innovative solutions are used by tens of thousands of researchers and clinicians at hundreds of leading institutions worldwide. Further information can be found at www.qiagen.com/ingenuity.
Quantum Biosystems was formed in January of 2013 and is developing 4th Generation DNA and RNA sequencing systems for the low cost and high throughput analysis of whole genomes. While present systems require complicated sample preparation, and costly instruments, the QB platform has no such barriers to entry and is well positioned to bring about what some have called “the Democratization of DNA sequencing”.
The platform allows the direct sequencing of single stranded DNA and RNA without labelling or modification, on silicon devices which can be produced on the same production lines as consumer grade integrated circuits. As the system uses no proteins or other reagents it is potentially ultra-low cost, enabling consumer level genome sequencing.
Based on basic research at the University of Osaka, the QB platform uses sub-nanometer gaps and picoamp level currents to directly detect the conductance of single DNA and RNA molecules. This breakthrough in molecular sensing promises to bring to about a fundamentally new class of sensors.
Arkivum provides a large scale, long term, cost effective data archiving service with a unique 100% data integrity guarantee.
Managed Service means more to us than just ensuring that the service is available. Arkivum’s service constantly monitors the health of the archive, upgrading and migrating as technology advances, to ensure that data held within our service is always current and accessible. This means that:
o For every bit of data that you put in we will return it to you bit perfect in one year or 50 years or more;
o Arkivum provides the only digital archiving service underwritten by a 100% data integrity guarantee.
Arkivum’s service is targeted at organisations that have a defined responsibility to archive electronic data for long periods of time, where:
o there is a compliance requirement is driven either by cost savings, legalisation or by industry good practice;
o easy access to archived data is required.
With large volumes of data – which are growing at increasing rates year on year – which need to be retained, such organisations face ever increasing storage costs as they retain this archive data on expensive media such as disk.
Arkivum provides a low cost, highly secure and easy to use solution to these challenges.
The benefits of the Arkivum approach include increased levels of compliance whilst at the same time reducing the IT spend on storage and administrative overhead.
Pacific Biosciences offers the PacBio® RS II Sequencing System to help scientists solve genetically complex problems. Based on our novel Single Molecule, Real-Time (SMRT®) technology, our products enable: de novo genome assembly to finish genomes in order to fully identify, annotate and decipher genomic structures; targeted sequencing to more comprehensively characterize genetic variations; and DNA base modification identification to help characterize epigenetic regulation and DNA damage. Our technology provides the industry’s highest consensus accuracy and longest read lengths along with the ability to detect real-time kinetic information. The PacBio RS II System, including consumables and software, provides a simple, fast, end-to-end workflow for SMRT Sequencing.
Our customers and our scientific collaborators have published a number of peer-reviewed articles in journals including Nature, Genome Research and The New England Journal of Medicine highlighting the power and applications of the SMRT platform in projects such as finishing genomes, rare mutation discovery and the identification of chemical modifications of DNA related to virulence and pathogenicity. Our R&D efforts are focused on expanding the performance of our platform by exploiting the unique capabilities of our Zero-Mode Waveguide (ZMW)-based technology and by expanding the application space.
By providing access to genetic information that was previously inaccessible, Pacific Biosciences enables scientists to increase their understanding of biological systems.
VH Bio is a leading supply and distribution company for the life sciences industry dedicated to consistently delivering quality products and services that will meet and anticipate the needs of the United Kingdom and Republic of Ireland scientific communities.
VH Bio has recently won exclusive UK and ROI distribution rights from Enzymatics, who are a leading producer of reagents, kits, assays and software for life science research and applied science customers worldwide. Enzymatics reagents, which set the standard for high purity, have been an integral part of sequencing since 2006. The hallmarks of Enzymatics’ products and manufacturing services are quality, rapid turnaround, and flexibility. These attributes have positioned Enzymatics as the premier consumable partner across the sequencing industry – from the major platform manufacturers to the end users of these revolutionary technologies. As a result, today Enzymatics products underpin the majority of sequencing reactions that are run across the globe.
VH Bio has an exclusive UK and ROI distribution partnership with Advanced Analytical Technologies, Inc. (AATI) to market the Fragment Analyzer™ Automated Capillary Electrophoresis System which offers automated, rapid and accurate analysis of NGS fragment libraries, as well as intact genomic DNA, total RNA and mRNA. The system also offers multiple gel formulas for SSR/microsatellites and mutation detection (TILLiNG).
Please visit our stand to learn how Enzymatics reagents and kits, together with the Fragment Analyzer™, could benefit your laboratory.
Integrated DNA Technologies (IDT) is a leader in the manufacture and development of products for the research and diagnostic life science market. The largest supplier of custom nucleic acids in the world, IDT serves academic research, biotechnology, and pharmaceutical development communities.
IDT products support a wide variety of applications, including next generation sequencing (NGS), DNA amplification, SNP detection, microarray analysis, expression profiling, gene quantification, and synthetic biology. Platform-independent NGS products and services are available in addition to DNA and RNA oligonucleotides, qPCR assays, siRNA duplexes, and custom gene synthesis. Individually-synthesized xGen™ Lockdown™ Probes enable improved target capture. IDT also manufactures custom adaptors, fusion primers, Molecular Identifier tags (MIDs), and other workflow oligonucleotides for NGS. A TruGrade™ processing service is also available to reduce oligonucleotide crosstalk during multiplex NGS.
Serving over 80,000 life sciences researchers, IDT is widely recognized as the industry leader in custom oligonucleotide manufacture due to its unique capabilities. IDT pioneered the use of high throughput quality control (QC) methods and is the only oligonucleotide manufacturer to offer purity guarantees and 100% QC. Every oligonucleotide is analyzed by mass spectrometry and purified oligonucleotides receive further analysis by CE and HPLC. The company maintains an engineering division dedicated to advancing synthesis, processing technology, and automation. An in-house machine shop provides rapid prototyping and custom part design/control. Additionally, IDT offers unrivalled customer support, receiving approximately 100,000 calls annually with an average wait time of only 8 seconds.
A dedicated GMP manufacturing facility for molecular diagnostics provides oligonucleotides for In Vitro Diagnostic Devices (IVDs) or Analyte Specific Reagents (ASRs) for Laboratory-Developed Tests (LDTs). This manufacturing process is customer-defined and controlled, and facilitates progression from research to commercialization.
PerkinElmer is a global leader focused on improving human and environmental health. Our solutions range from enabling the discovery of more effective diagnostics and therapies, to making sure that the food we eat, the water we drink, and our environment are safe from contaminants. PerkinElmer’s Next Generation Sequencing (NGS) sample preparation solutions eliminate the processing bottlenecks presented by today’s NGS technologies and enable more efficient use of the sequencer capacity. Sample preparation is the key to high quality data for next generation sequencing. Protocols are complex multi-step methods requiring precise execution. In addition to being labour intensive and not scalable, manual methods introduce run-to-run and operator-to-operator variability. PerkinElmer’s automation, microfluidics and bioinformatics platforms enable scientists to process samples from start to finish in a user-friendly, easy-to-implement manner. Standardized hardware configurations with verified protocols tested with real samples by sequencing and instrumentation to measure the fundamental characteristics of nucleic acids provide the needed flexibility and quality control for dynamically changing applications. With PerkinElmer NGS liquid handling automation and microfluidic solutions, the quality of NGS libraries is increased reducing failure rate in the preparation process and eliminating tedious, labour-intensive repetitive procedures. Our solutions will enable NGS users to keep pace with the short development cycles in the very dynamic NGS market.
PerkinElmer, Chalfont Road, Seer Green, Beaconsfield, HP9 2 FX, UK
4titude® specialises in the design, manufacture & marketing of consumables and bench top instrumentation for the life sciences industry. Since its foundation in 2005, 4titude® continues to grow a range of innovative products focussed on:
o PCR & sequencing
o Assay screening
o Microplate sealing
o Liquid handling
o NGS sample processing consumables
The launch of the 4titude® FrameStar® range of two-component PCR plates in 2006 marked the beginning of the ongoing success story that is 4titude®. FrameStar® is now the most comprehensive range of two-component (polycarbonate frame) consumables in the life sciences market with the recent additions of Framestrips™ and dividable Break-A-Way plate.
Another area of special expertise is plate sealing solutions. 4titude® offers the widest range of sealing films and foils to meet the highest customer expectations and continues to develop innovative sealing solutions for sealing applications in the life sciences market.
4titude® also provides expert, innovative help for customers with specific needs, either under the 4titude® brand or as an OEM agreement, offering everything from custom toolmaking, design and injection moulding services to barcoding and labware calibration.
Strong, steady growth in sales has allowed 4titude® to invest in the highest quality manufacturing facilities with ISO 9001 certified processes and UK ISO7 and ISO8 clean room production according to ISO14644-1. To ensure the best results for customers, products are tested at every manufacturing step and strict quality guidelines are adhered to at all times.
4titude® is a member of the SiLA (Standardization in Lab Automation) consortium, working towards SILA compliance of our instruments and consumables. The 4titude® Automated-4-Sealer (A4S) and the 4LAB automated high-precision pipetting system are two new products that show our ongoing commitment to new technologies and innovations for life sciences.