Super Cool NGS Things and Funky Clinical Stuff The 7th Oxford Genomics Forum was a 1-day event which took place on the Wednesday 13th July at the University of Oxford’s Old Road Campus.
This Forum was held in partnership between the Oxford Genomics Centre and Biotexcel as a platform to bring together genomic researchers from diverse areas to discuss the latest advances, technologies, tools and directions in Genomics.
The scientific theme of the forum covered the following areas:
The Forum consisted of 3 keynote talks given by opinion leaders who then chaired sessions of short talks by key figures in those areas. There were also plenty of opportunities for delegates to brainstorm ideas and discuss topics that are making the genomic headlines.
… and all those interested in the latest developments of:
|08.30 – 09.30:||Registration, Coffee & Networking|
|09.30 – 09.50:||Network and Collaborations by Dr Ed Quazi, Biotexcel|
Chaired by Dr Dave Ruff Super Cool Technologies: technological advancements in Single Cell and others
|09.50 – 10.15:||Dr Dave Ruff, University of Oxford & Fluidigm Revolutionizing our view of the functional genome, transcriptome and proteome through innovative single-cell workflows|
|10.15 – 10.40:||Prof Thierry Voet, KU Leuven & Sanger Institute Single-cell (multi-omics) sequencing to study the biology of cellular heterogeneity in health and disease|
|10.40 – 11.05:||Dr Alex Shalek, Massachusetts Institute of Technology (MIT) | Broad Institute, USA Immunology from the “Bottom-Up” with Single-Cell Genomics|
|11.05 – 11.25:||TECHNOLOGY PRESENTATION by Rowan Gibson, Covaris DNA and RNA extraction with Covaris AFA technology for NGS analysis|
|11.25 – 11.50:||Clive Brown, CTO, Oxford Nanopore Technologies An overview of Nanopore developments for 2016|
|11.50 – 12.45:||Lunch, Exhibition & Networking|
Chaired by Prof Julian Knight The Regulation Thing: Epigenetics and Gene regulation
|12.45 – 13.10:||Prof Julian Knight, University of Oxford Genetic modulators of the immune response in health and disease|
|13.10 – 13.30:||TECHNOLOGY PRESENTATION by Vipul Patel, Analytik Jena We change the way to prep with SmartExtraction|
|13.30 – 13.55:||Prof Vardhman Rakyan, Centre for Genomic & Child Health, Blizard Institute Gene-environment induced epigenetic dynamics in the mouse|
|13.55 – 14.20:||Dr Elzo de Wit, Netherlands Cancer Institute Gene regulation in the 3D genome|
|14.20 – 14.45:||Dr Daniel Gaffney, Sanger Institute, Cambridge Fine-mapping regulatory variants using ATAC-seq in stimulated immune cells|
|14.45 – 15.05:||TECHNOLOGY PRESENTATION by Carl Jarman, Labcyte Miniaturization of Next Gen Sequencing processes with the Echo Acoustic Dispensing Platform|
|15.05 – 15.35:||Refreshments, Exhibition & Networking|
Chaired by Prof Ian Tomlinson Funky Clinical Stuff: Genomic Medicine & Cancer
|15.35 – 16.00:||Prof Ian Tomlinson, University of Oxford Differential Clonal Evolution In Oesophageal Cancers In Response To Neo-Adjuvant Chemotherapy And The Implications For Clinical Management|
|16.00 – 16.25:||Dr David Wedge, University of Oxford Genomic evolution and heterogeneity in 2,800 cancers|
|16.25 – 16.50:||Prof Krina Zondervan, University of Oxford Understanding endometriosis through genomics: progress and challenges|
|16.50 – 17.15:||Prof Xin Lu, Ludwig Institute for Cancer Research Cellular plasticity, cellular heterogeneity and single cell sequencing|
|17.15 – 18.00:||PANEL DEBATE Is Single Cell Analysis really going to change genomic research? How do we break the translational bottleneck?|
|18.00 – 19.00:||DRINKS RECEPTION sponsored by Cambridge Epigenetix|
Covaris is the recognized industry leader for DNA fragmentation and Adaptive Focused Acoustics (AFA®) has become the gold standard for shearing DNA and RNA in Next-Generation Sequencing applications. Without introducing GC bias or thermal-induced damage, users can precisely and accurately fragment DNA and RNA to the 100-1500bp range with the microTUBE™, 2-5kb range with the miniTUBE™, and 6-20kb range with the g-TUBE™. Building on the superior capabilities of AFA, Covaris has developed truXTRAC™, which efficiently extracts nucleic acids from FFPE tissues. The highly simplified workflow ensures high yield extraction of nucleic acids and allows for the seamless integration into NGS and other molecular applications. By using AFA technology on Covaris instruments, scientists can achieve better amplificability of released nucleic acids in single and multi-sample formats. Additionally, the truChIP™ Chromatin Shearing Kits provide an optimized, flexible, and universal protocol for chromatin shearing on the high performance Focused-ultrasonicators, thus enabling the inclusion of truChIP Chromatin Shearing into any ChIP Protocol. The truXTRAC and truChIP kits bring the advantages of AFA and Focused-ultrasonication directly to the lab with increased sensitivity and reproducibility. With an installed base of more than 3,500 systems worldwide, the Covaris AFA process is extensively cited in peer-reviewed research articles on DNA fragmentation using all available NGS systems and is considered to be the gold standard for DNA shearing. Covaris Focused-ultrasonicators are recommended by all major sequencing platform providers, and are used by leading Genome Centers worldwide including: the Centre National de Génotypage (CNG), the Wellcome Trust Sanger Institute, the Broad Institute, and the Beijing Genomics Institute (BGI). For more information, please visit: www.covarisinc.com
Analytik Jena offers products for manual and fully automated nucleic acid extraction, homogenization, liquid handling, bio-imaging, standard and quantitative PCR. The unique SmartExtraction is revolutionizing the way we do extraction. No centrifugation, No Magnetic beads, No Silica. Just an intelligent pipette tip. qTOWER range is defining higher standards for qPCR machines. These highly specified German manufactured qPCR thermal cyclers provide the reliability, performance, integration and flexibility required by labs today. Analytik Jena’s broad portfolio of products meet the demands of the life science laboratory and provide a modern look. www.bio.analytik-jena.com
For laboratories using next-generation sequencing, Echo® liquid handlers have lowered the costs and effort required for library preparation to an unprecedented level. Labcyte, a global biotechnology tools company headquartered in Sunnyvale, California, is revolutionizing liquid handling. Echo liquid handling systems use sound to precisely transfer liquids without contact, eliminating the use of pipettes. Labcyte instruments are used worldwide throughout the pharmaceutical industry, diagnostic companies, genome centers, genomic service companies, biotechnology firms, contract research organizations, and academic institutions. Our customers work across a wide spectrum of scientific research, including drug discovery, genomics, proteomics, diagnostics, precision medicine, and imaging mass spectrometry. Labcyte has 53 U.S. patents and others internationally. For more information, visit www.labcyte.com.
At Illumina, our mission is to improve human health by unlocking the power of the genome. We supply innovative technologies and revolutionary assays for the analysis of genetic variation and function, making studies possible that were not even imaginable just a few years ago. With such rapid advances in technology taking place, it is mission critical to have solutions that are not only innovative, but flexible, scalable, and complete with industry-leading support and service. As a global company that places high value on collaborative interactions, rapid delivery of solutions, and prioritizing the needs of its customers, we strive to meet this challenge.
Lexogen is a transcriptomics and Next Generation Sequencing (NGS) company, focusing on the development of technologies for complete transcriptome sequencing. Our portfolio includes innovative molecular biology kits and services for RNA-Seq. We offer library preparation kits for total RNA, mRNA, custom sequencing, and 3’ mRNA sequencing suitable for low quality RNA or FFPE samples for whole transcriptome sequencing and accurate gene expression profiling. The library preparation protocols are based on Lexogen’s proprietary technologies which eliminate the need for RNA or cDNA fragmentation, allowing to preserve superior strand-specificity (>99.9%) and enabling rapid (under 5 hours) turnaround times. The products are compatible with the Illumina, Ion Torrent, and SOLiD platforms, and are also available as automated versions. Other products include the SPLIT RNA Extraction Kit, the TeloPrime Full-Length cDNA Amplification Kit, and SQUARE, a service enabling hypothesis-free identification and quantification of known and unknown full-length transcripts. The TeloPrime kit generates full-length cDNA from total RNA. It is highly selective for full-length RNA molecules that are both capped and polyadenylated and therefore no cDNA from degraded RNA is being amplified. The Mix2 RNA-Seq Data Analysis Software yields highly accurate concentration estimates for gene isoforms by adapting to the positional coverage bias in RNA-Seq data. Lexogen is based in Vienna, Austria, and has a subsidiary in New Hampshire, US
BMG LABTECH is an international manufacturing and distribution company specialising in microplate instrumentation for over twenty five years. During this time BMG has earned the reputation of being a technology leader in the field with a history of firsts – the first fluorescence polarisation reader, the first laser-based nephelometer, the first spectrometer based reader and the first and only reader to use the Linear Variable Filter monochromator system. BMG’s readers are multi-mode readers designed for the measurement of fluorescence, fluorescence polarisation, time-resolved fluorescence, absorbance and luminescence. They provide the highest sensitivity, flexibility and reliability and all instruments are designed to be easily integrated into automated systems for higher throughput assays. All BMG LABTECH microplate readers are “Made in Germany” , they are conceived, developed, assembled, and tested entirely at our headquarters in Germany. All instruments are supported by a fully qualified team of, scientists engineers, and technicians dedicated to bringing you high-quality products of exceptional value and performance.
Diagenode Corporation is a global Epigenetic company and Diagnostics assay manufacturer based in Liège, Belgium and Denville, NJ, USA. Diagenode offers the most comprehensive range of Epigenetic products in the world, amongst its product portfolio are the famous Bioruptor® Shearing devices, Premium® and Blueprint® antibodies, IP-Star® automated workstations and many reagents. From Diagenode’s founding in 2003 in Liège as a local Biotechnology startup, the company has expanded rapidly. Diagenode has opened its US branch in 2006 and developed a distribution and partnering network across the entire world with strong anchorages in Japan and other Asia-Pacific countries. Diagenode has been profitable since its creation. The company planned to develop extensively its range of innovative products in both the Epigenetics and Infectious diseases markets. In October 2013, Diagenode’s headquarters have moved into a brand new facility near to the Univeristy of Liège’s campus.
As pioneers in sequencing with a rich heritage in diagnostics, Roche Sequencing Solutions is committed to a future that fosters innovation to provide solutions that enable scientific discovery and deliver clinical value. Roche’s portfolio of proven target enrichment solutions is advancing research in human health, agriculture, evolutionary biology, and more. Incorporated in our Sequencing Solutions team is Kapa Biosystems, a provider of genomic tools in the life sciences sector that employs proprietary technologies to optimize enzymes for next-generation sequencing (NGS) sample prep, as well as polymerase chain reaction (PCR) and real-time PCR applications.
Eurofins Genomics, with major offices and production sites in Europe, Japan and the USA, is an international provider of genomic services established around the core business lines DNA sequencing, oligonucleotides, siRNA and gene synthesis. The company’s main mission is focussed on providing customer convenience and high quality services in industrial scale for the life science industries and academic research institutions around the world. Eurofins Genomics competence in the synthesis of Oligo’s has made the company a European market leader and a strong global player. For further information about Eurofins Genomics, please visit www.eurofinsgenomics.com
We strive to partner with our customers to pursue truth in the complex biological world. Our contribution is the application of microfluidics and mass cytometry technologies to provide simplified and elegant workflows for life scientists making research breakthroughs and businesses providing quality services. Partner with us, whether the quest is to understand the profile and function of individual cells or to meet the high-throughput and data quality demands of a production-scale laboratory. Engage with us at fluidigm.com.
Oxford Nanopore Technologies™ is developing a new generation of nanopore-based electronic systems for analysis of single molecules, including DNA, RNA and proteins. The MinION™ device, the PromethION™ and GridION™ systems are designed to provide novel qualities in molecular sensing such as real-time data streaming, improved simplicity, efficiency and scalability of workflows and direct analysis of the molecule of interest. The devices may be used in scientific research, personalised medicine, crop science, security and defence and environmental applications. Products and services are priced for low total-cost-of-ownership DNA sequencing (or other analyses). www.nanoporetech.com
Our mission at LGC is ‘science for a safer world’. We are a leading international life sciences measurement and testing company providing a range of measurement products and services which underpin the safety, health and security of the public, including reference materials and proficiency testing, genomics reagents and instrumentation, and expert sample analysis and interpretation. LGC works with customers in Pharmaceuticals, Diagnostics, Agricultural Biotechnology, Food, Environment, Government and Academic research markets.LGC is a global leader in genomics technologies and services and is a key partner for customers’ projects from early stage research, to routine applications. We deliver high-quality, flexible genomic solutions that enable breakthrough cost savings to life science professionals across a wide range of industries including human research and health, academia and agricultural biotechnology. We provide a full range of products and services for high-throughput DNA extraction, sequencing and genotyping, and work with some of the largest and most prestigious universities, consortia and cohort studies around the world.Our portfolio includes KASPTM genotyping chemistry which can be run on the SNPline™ for rapid, high throughput economical SNP analysis, and the IntelliQube® a fully automated, integrated, medium to high-throughput platform for quantitative and end point PCR, and Nexar® PCR /qPCR automation platforms. LGC provides high quality probes for use in qPCR and end-point PCR. We are a global leader in custom oligo design and manufacturing with the ability to manufacture at GMP level. DNA extraction, sequencing, and genotyping services are also available.
Expedeon has developed a primer-free whole genome amplification for single cell technology called TruePrime™ in collaboration with Professor Luis Blanco and Professor Margarita Salas, the scientists who discovered the phi29 DNA polymerase(used in Multiple Displacement Amplification) and more recently the TthPrimPol primase. TthPrimPol has the unique property of binding randomly to denatured ssDNA and primes using dNTPs. TruePrime™ technology combines the phi29 DNA polymerase and the TthPrimPol primase which eliminate the need for random primers. It shows unprecedented homogenous genome amplification and coverage. The nature of the TthPrimPol primase, as opposed to random primers, does not generate chimeras and other amplification artefacts, and does not amplify external DNA contaminations. This results in exquisite sensitivity (1-10fg), very low allelic dropout rate (ADO), and both high SNVs call rate and high CNVs detection, which was not possible so far with existing method (MDA, DOP-PCR, MALBAC). TruePrime™ technology is especially suited for single cell work and any other situation where DNA is scarce (low sample availability, FFPE, forensics and palaeontology…). It is optimised for analysis by NGS, arrays or PCR. Expedeon is exploring the amplification of cell-free DNA with TruePrime™, and has also developed VersaWave; a non-destructive DNA and RNA absolute quantification instrument.
CEGX, a spin-out life sciences company spun out from the University of Cambridge, was co-founded in 2012 by Professor Shankar Balasubramanian FRS and Dr. Bobby Yerramilli-Rao. The company’s founding technology, ox-BS sequencing, allows end-users to discriminate between 5-hydroxymethylcytosine (5hmC) & 5-methylcytosine (5mC) at a single-base resolution, which was previously impossible with traditional bisulfite sequencing methods. It has since developed a number of complementary technologies and seeks to capitalize on a wide set of applications in life sciences, as well as continue to develop breakthrough epigenetics tools. For more information, visit www.cambridge-epigenetix.com.
Headquartered in Tucson, Arizona, HTG’s mission is to empower precision medicine at the local level. In 2013 the company commercialized its HTG Edge instrument platform and a portfolio of RNA assays that leverage HTG’s proprietary nuclease protection chemistry. HTG’s product offerings have since expanded to include its HTG EdgeSeq product line, which automates sample and targeted library preparation for next-generation sequencing. Additional information is available at www.htgmolecular.com.
The Oxford Genomics Centre is based at the Wellcome Trust Centre for Human Genetics (WTCHG), a research institute of the Nuffield Department of Medicine at the University of Oxford funded by the Wellcome Trust and numerous other sponsors. Genomic technologies, and in particular high-throughput sequencing, are revolutionising modern biomedical genetics. Research discoveries are accelerating, and many have been translated into clinical applications. Sustaining capability and high-level expertise in these technologies is a key strategic priority of the WTCHG in maintaining its position as one of the leading international research institutes in the field. The central objective of the Oxford Genomics Centre is to bring together genomics and analysis services to support scientists from Oxford and elsewhere wanting to exploit the latest in high-throughput genomics techniques in their research. We collaborate with the WTCHG’s multidisciplinary research teams in human genetics, functional genomics, epidemiology and structural biology, and with researchers across the world.
Richard Doll Building
Old Road Campus
University of Oxford
Oxford, OX3 7LF
If coming by car from the east, M40 Junction 8 or 8a, take the A40 then A420 to Headington Centre and follow signs for Churchill Hospital which will bring you to the Old Road Campus. From the north, M40 Junction 9, take A34 then A40 Northern ring road, turning off at Marston (B4150), then B4495 towards Headington and follow signs to Churchill Hospital. From the south and west, approach from the A4142 Eastern ring road and B 4495.
The Campus can be found by following signs to the Churchill Hospital. The Richard Doll is a big, white, modern building, and adjacent to Old Road Campus Research Building. The entrance to the Doll building is exactly opposite the entrance to the Wellcome Trust Centre for Human Genetics.
Please note that the campus car park is reserved to University staff and permit holders only. The Churchill Hospital parking nearby is intended for hospital visitors only.
PARK & RIDE
It may be advisable to park at Thornhill Park & Ride, one mile east of Headington, Oxford, on the A40. At Thornhill there is a bus no. 600 going to the “Churchill Drive” stop or it is possible to pre-order a taxi and drive to the campus (10 mins).
The Campus is three miles from the mainline station at Oxford (allow 15 mins by taxi from the station forecourt).
001 Taxis: 01865 240000
Radio Taxis: 01865 242424
Royal Cars: 01865 777333