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This event was held at the Halifax Hall venue in Sheffield on 11th & 12th November 2014 and was organised in partnership with Sheffield Children’s NHS Foundation Trust and the University of Sheffield.
Our characteristic genomics events have traditionally taken research based Next Generation Sequencing applications and brought them into a clinical diagnostics theme so that groups from both backgrounds can discuss new areas of collaborations and network together. At this second winter conference, we brought together groups from both of these backgrounds to discuss not just the usual bottlenecks in NGS but also the cutting edge discoveries in the popular application areas such as whole genome, exome, and RNA sequencing. An emphasis was also placed on data quality with presentations showing the quality aspects across laboratories. Data analysis also was addressed with some unique and novel insights.
The recurring positive feedback from attendees to our previous NGS events has highlighted the networking opportunities which have resulted in productive collaborations. The intimate atmosphere of our Sheffield NGS conference provided a relaxed setting for informal networking to take place. This hopefully enabled research, diagnostics & commercial organizations to discuss and exchange ideas, expertise and set up collaborations to improve their current research, products and services.
08.30 – 09.15: Registration, Coffee and Networking
09.15 – 09.30: OPENING by Prof Richard Jones, Pro-Vice Chancellor for Research and Innovation, University of Sheffield
09.30 – 09.45: MINI NETWORKING WORKSHOP
09.45 – 10.15: Dr Ann Dalton, Consultant Clinical Director, Sheffield Children’s NHS Foundation Trust
Realising the clinical potential of Next Generation sequencing
10.15– 10.50: TECHNOLOGY WORKSHOP – Standardising your clinical dry lab by Dr Zhenyu Xu, Sophia Genetics
10.50 – 11.20: Refreshments, Exhibitions and Networking
11.20 – 11.50: Dr Simon Patton, Director at European Molecular Genetics Quality Network
Good or bad sequencing data? Setting a benchmark for the quality of diagnostic NGS in the lab
11.50 – 12.20: Prof Magnus Rattray, Computational & Systems Biology, University of Manchester
Uncovering the mechanisms of transcription by integrating RNA-Seq and ChIP-Seq time course data
12.20 – 13.00: TECHNOLOGY WORKSHOP – NGS Sample to Insight: Intuitive and comprehensive end-to-end preparation, analysis, and biological interpretation of NGS Data by Dr Tim Bonnert, Qiagen
13.00 – 14.00: Lunch, Exhibitions and Networking
14.00 – 14.30: Prof Jacqui Shaw, Professor of Translational Cancer Genetics, University of Leicester
NGS analysis of circulating tumour DNA in patients with breast cancer
14.30 – 15.00: Dr Mike Quail, Sequencing R&D, Wellcome Trust Sanger Institute
Sequencing at Sanger in the year 2014
15.00 – 15.40: TECHNOLOGY WORKSHOP – The Use of Standards in NGS: How Do You Manage Variability in Next Generation Sequencing? by Dr Sarah Leigh Brown, Cambridge Institute Genomics Core, Cancer Research. Sponsored by Horizon Diagnostics
15.40 – 16.10: Refreshments, Exhibitions and Networking
16.10 – 16.40: Dr Mick Watson, Director of ARK-Genomics, The Roslin Institute, University of Edinburgh
Studying the microbiome: technologies, applications and pitfalls
16.40 – 17.10: Dr Bhupinder Bhullar, Lab Head, Developmental Molecular Pathways, Novartis
Clinical genomics for next generation drug discovery
17.10 – 17.40: Dr Sterghios Moschos, Director, Westminster Genomic Services, University of Westminster
Storing the Terrabytes; A case-study how-to
19.00: Networking Dinner (by prior booking only)
9.00 – 9.30: Dr Anneke Seller, Scientific Advisor, Health Education England Lead Consultant Clinical Scientist, Oxford Molecular Diagnostics Centre, Oxford University Hospitals NHS Trust
Genomic Medicine and workforce transformation; a strategy for building bioinformatic capacity and capability in the NHS
9.30 – 10.00: Prof Mark Blaxter, Evolutionary Genomics, University of Edinburgh
NGS and NTD: using high throughput sequencing for neglected tropical disease
10.00 – 10.30: Refreshments, Exhibitions and Networking
10.30 – 11.05: TECHNOLOGY WORKSHOP – Enriching nucleic acids for NGS analysis of gene expression, SNPs, CNVs, alternative splicing, gene fusions and more by Dr Joe Don Heath, NuGEN
11.05 – 11.35: Dr Steve Abbs, Director, East Anglian Medical Genetics Service, Addenbrooke’s Hospital, Cambridge
GEMINI – Clinical Exome sequencing in a Clinical Diagnostic Lab
11.35 – 12.35: PANEL DISCUSSION on NGS Platforms – Dr Mike Quail, Prof Neil Hall and Dr Mick Watson led by Darren Grafham
12.35 – 13.40: Lunch, Exhibitions and Networking
13.40 – 14.15: TECHNOLOGY WORKSHOP – Addressing Challenges in Microbiome DNA Analysis: A Method for Selective Enrichment of Microbial DNA from Contaminating Vertebrate Host DNA by Dr Adam Peltan, New England BioLabs
14.15 – 14.45: Dr James Bradford, Molecular Oncology, University of Sheffield
Tumour and host transcriptome profiling of patient derived tumour models across multiple cancer types using RNA-Seq
14.45 – 15.20: Refreshments, Exhibitions and Networking
15.20 – 15.50: Prof Neil Hall, Functional and Comparative Genomics, University of Liverpool
Microbial Genomics using Next Generation Sequencing
15.50 – 16.20: Dr Miika Ahdesmaki, Principal Informatics Scientist, AstraZeneca
Scalable and reproducible NGS data analysis using open source pipelines
16.20 – 16.50: Dr Eran Elhaik, Bioinformatics Hub, University of Sheffield
Reaching the Holy Grail of Biogeography– from Genome to Home Village with NGS data
16.50 – 17.00: Closing Remarks
Sophia Genetics, a European leader in Data Driven Medicine, brings together expertise in clinical genetics, bioinformatics, machine learning, and genomic privacy. Based in Switzerland, we are known for our high medical standards and Swiss precision when it comes to accuracy and quality management. Sophia Genetics offers health professionals who perform clinical genetic testing bioinformatics analysis, quality assurance, and secure banking of patient DNA sequence data generated by NGS. Sophia Genetics helps clinical laboratories to reduce the cost, overcome complexity and fulfill quality constraints related to the use of NGS in the clinic. www.sophiagenetics.com
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.
Cambridge Bioscience is a leading distributor of life science products with a passion for bringing new and exciting technologies to researchers. Working with over 50 specialist suppliers around the world, we offer an innovative, extensive and diverse range of high quality products, services and instruments supporting research in the areas of next-generation sequencing, exosomes, molecular biology, epigenetics, cell culture, cell analysis and much more. Cambridge Bioscience – A Great Choice For Life Science Research.
Diagenode Corporation is a global Epigenetic company and Diagnostics assay manufacturer based in Liège, Belgaum 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.
New England Biolabs (NEB) manufactures reagents for molecular biology and is a global market leader in the supply of restriction enzymes, polymerases, modifying enzymes and DNA ladders. The NEB offering includes a range of PCR reagents, E.coli expression systems, competent cells, reagents for epigenetics research and kits and modules for next generation sequencing.
The corner-stones of NEB’s reputation are service excellence and products you can trust.
VH Bio is a leading supply and distribution company for the life sciences industry within the United Kingdom and Republic of Ireland. With novel and innovative products sourced from our global partners, VH Bio is the preferred choice for high-quality solutions and technologies within the fields of Molecular Biology, Next Generation Sequencing, DNA and RNA analysis instrumentation, Immunology and Cell Biology.
VH Bio has recently agreed to an exclusive UK and ROI distribution partnership with Enzymatics, who are a leading producer of reagents, kits and assays for life science research and applied science customers worldwide. Their reagents, which set the standard for high purity, have been an integral part of sequencing since 2006 and as such 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.
With the launch of Archer Targeted Sequencing Technology, Enzymatics are also addressing the growing need for novel NGS-based assays. Archer captures and amplifies only gene targets of interest and offers dramatic enhancements in scalability, mutation detection speed, complex mutation identification and reduced costs.
VH Bio also has an exclusive UK and ROI distribution partnership with Advanced Analytical Technologies, Inc. to supply and market the Fragment Analyzer™ Automated Capillary Electrophoresis system, which offers automated, rapid and accurate analysis of NGS fragment libraries, genomic DNA, total RNA and mRNA.
Go to VHBio.com to learn how Enzymatics reagents and kits together with the Fragment Analyzer™ could benefit your laboratory.
NuGEN Technologies has revolutionized NGS sample preparation with novel approaches that allow life science researchers to mine genomic information from a broad range of sample types with the flexibility of varying input amounts down to a single cell. NuGEN’s methods encompass a breadth of NGS applications including strand-specific RNA-Seq, target enrichment of DNA and RNA, Methyl-Seq, ChIP-Seq and more, all employed in rapid and simple workflows.
Novel core technologies from NuGEN include: Single Primer Enrichment Technology (SPET) for generation of targeted sequencing libraries to enable analysis of SNPs, CNVs, alternative splicing and gene fusions from as little as 10 ng genomic DNA or total RNA; Selective Priming Technology forgeneration of strand-specific RNA-Seq libraries for transcriptome studies from as little as 10 pg total RNA or true single cell lysates; Insert Dependent Adaptor Cleavage (InDA-C) for targeted depletion of uninformative transcripts, such as ribosomal RNA, globin, and other uninformative high-abundance transcript species, in strand-specific RNA-Seq libraries generated from as little as 10 ng total RNA.
QIAGEN Bioinformatics provides industry-leading, powerful analytics solutions and intelligent interpretation of genomics data, leading to faster time to insight.
Analyzing raw data is one of the most significant challenges in next-generation sequencing, and the QIAGEN CLC bio product line for instance enables user-friendly and comprehensive analysis, comparison, and visualization of sequencing data, as well as enterprise-level handling, curating, and analysis of NGS data. Furthermore, QIAGEN Bioinformatics facilitates the understanding of raw data, including examination within the context of complex biological processes, and rapidly increasing throughput that makes analyses time and labor intensive. The QIAGEN Ingenuity product line includes interpretation of upstream/downstream effects of gene expression changes, along with identification of disease-causing variants from human NGS data, and also modeling and understanding of complex ‘omics data.
Horizon Diagnostics (HDx), a business unit of Horizon Discovery Ltd, is a leading provider of genetically defined, human genomic reference standards, including FFPE cell line sections and purified gDNA. These standards offer a sustainable source of reference material to laboratories, proficiency schemes and manufacturers, providing an unprecedented level of control.
Genotypic tumor profiling is becoming increasingly routine in the battle against cancer, and next generation sequencing (NGS) is offering a way to quickly and affordably establish baseline tumor genetics. Platforms such as MiSeq™ and Ion Torrent™ are increasingly used to interrogate tumors using pre-defined cancer panels such as Ampliseq™ or Truseq™. The range of steps involved in a NGS workflow, combined with the sheer number of biomarkers being screened, has the potential to create unprecedented levels of variability. In order to generate results with confidence, it is therefore important to manage potential workflow variability from sample extraction and sample selection through to sequencing and variant calling.
In response to the growing number of scientists using NGS instruments to study tumor genetics, Horizon Diagnostics has developed a range of Quantitative Multiplex Reference Standards for general use. These highly defined reference standard contain engineered endogenous mutations, each calibrated by digital PCR to a chosen allelic frequency ranging between 0.5% and 25%.
Source BioScience is one of Europe’s leading providers of commercial sequencing offering services on the most prominent next generation sequencing platforms including the Illumina MiSeq and HiSeq.
The Illumina platforms are the most effective technologies and deliver a wide range of read lengths, enabling the broadest range of applications including genome sequencing, transcriptome sequencing, ChIP sequencing, metagenomics and targeted resequencing.
Our service is Illumina CSPro accredited and certified from Agilent for target enrichment, and operates through a robust quality management system. With state of the art facilities in the UK, Germany, Ireland and the USA, and GLP, GCP and CPA accreditations, we ensure that our clients enjoy the highest quality of data and service as well as quick turnaround times.
We also offer bespoke advanced bioinformatic solutions to assist researchers in the analysis of the vast amounts of data produced by the Illumina sequencing systems.
Our contract research services feature a broad range of microarray, genotyping and gene expression applications on Affymetrix, Agilent, Illumina and Fluidigm platforms.
Find out more – visit lifesciences.sourcebioscience.com
NanoString Technologies provides life science tools for translational research and molecular diagnostic products. The company’s nCounter® Analysis System, which has been employed in basic and translational research and cited in 500 peer review publications, has also now been applied to diagnostic use with the nCounter Dx Analysis System. The nCounter-based Prosigna™ Breast Cancer Prognostic Gene Signature Assay is marketed for use on the nCounter Dx Analysis System which is FDA 510(k) cleared.