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NGS 2015 Milan
March 10, 2015 @ 8:00 am - March 11, 2015 @ 5:00 pm
THIS EVENT TOOK PLACE ON 10th & 11th MARCH
FROM THE CLINIC TO SINGLE CELL ANALYSIS
Our Next Generation Sequencing conferences 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.
This Next Generation Sequencing highlighted the developments of NGS applications in the clinic and in research and covered the following topics:
- Clinical Diagnostics (NGS of Rare Disease & Oncology)
- Establishment of NGS workflows in a clinical lab
- Quality parameters of NGS analysis in a diagnostic lab
- Exome and Genome analysis
- RNASeq (Transcriptome) and Epigenomics work
- Limiting amount of input DNA & RNA eg. Single Cell Analysis
Next Generation Sequencing is a very powerful genomic tool that is opening up new possibilities when it comes to tackling human health issues. Whether it is the effect of the environment on the DNA (Epigenetics) or the expression of individual genes in single cells (single cell transcriptomics) or the meaning and significance of data from NGS Panels, Exomes or Genomes, researchers are driving the applicability of NGS to its limits.
Biotexcel is partnering with leading genomics institutes in Europe to help push the boundries by facilitating dialogue and dissemination of knowledge in a way that enables researchers to come together, network and initiate the next generation of collaborations using NGS.
In line with this philosophy Biotexcel worked in partnership with Dr Sergio Abrignani CSO of the National Institute of Molecular Genetics (INGM) in Italy to hold NGS 2015 Milan.
A G E N D A*
|08.30 – 9.30:||Registration, Coffee & Networking|
|9.30 – 9.45:||Opening by Dr Raffaele de Francesco, Principal Investigator INGM, Milan, Italy|
|9.45 – 10.10:||Dr Ed Quazi – Networking and Collaborations|
|10.10 – 10.40:||Dr Massimiliano Pagani, PI, Integrative Biology, INGM, Italy Long non-coding RNAs identification in human lymphocytes by next generation sequencing|
|10.40 – 11.10:||Coffee, Exhibition & Networking|
|11.10 – 11.30:||Dr Alicja Gruszka , Istituto Europeo di Oncologia (IEO) Tumors generated in mice from circulating cancer cells do not always recapitulate the genotype of the human tumor|
|11.30 – 12.00:||TECHNOLOGY PRESENTATION – Accelerating routine clinical diagnostics using highly accurate, CE-IVD marked NGS solutions by Dr Adam Novak, Sophia Genetics|
|12.00 – 12.30:||Dr Heiko Muller, Center for Genomic Science of IIT@SEMM, Milan Clout in the cloud: Tackling integration of big NGS data with Genometric Query Language|
|12.30 – 13.30:||Lunch, Exhibition & Networking|
|13.30 – 14.00:||Dr Pamela Pinzani, Clinical, Esperimental and Biomedical Sciences, University of Florence Feasibility of a workflow for the molecular characterization of single Circulating Tumor Cells by Next Generation Sequencing|
|14.00 – 14.30:||Prof Raffaele Calogero, Bioinformatics and Genomics Unit, University of Torino Exosome transcriptome analysis might provide novel tools for CLL patient stratification|
|14.30 – 15.00:||TECHNOLOGY PRESENTATION – Genome in a Bottle comes to Europe by Dr Jonathan Frampton, Horizon Diagnostics|
|15.00 – 15.30:||Dr Oliver Stegle, EMBL-EBI, Cambridge, UK Modeling gene expression heterogeneity between individuals and single cells|
|15.30 – 16.00:||Coffee, Exhibition & Networking|
|16.00 – 16.30:||Dr Stephan Ossowski, Centre for Genomic Regulation, Barcelona, Spain Signatures of tumor evolution reveal cancer driving genes and networks|
|16.30 – 17.00:||Dr Arianna Sabò, Center for Genomic Science, IIT, Milan & European Institute of Oncology (IEO), Milan Transcriptional regulation by Myc in growth control and tumorigenesis|
|17.00 – 17.30:||Dr Kevin Blighe, Imperial College London, UK Combining the best of DNA-, RNA-, and ChIP-seq|
|19.30:||Networking Dinner (by Registration Only)|
|09.00 – 9.30:||Dr Giancarlo Russo, Functional Genomics Center UZH Zurich, Switzerland Highly sensitive, non-invasive detection of colorectal cancer mutations using single molecule, third generation sequencing|
|09.30 – 10.00:||Dr Simon Patton, Director at European Molecular Genetics Quality Network (EMQN), Manchester, UK Good or bad sequencing data? Setting a benchmark for the quality of diagnostic NGS in the lab|
|10.00 – 10.30:||TECHNOLOGY PRESENTATION – Combining NGS Sequencing with DEPArray™ Digitalized Samples to resolve heterogeneity on solid tumors by Dr Raimo Tanzi, Silicon Biosystems|
|10.30 – 11.00:||Coffee, Exhibition & Networking|
|11.00 – 11.30:||Dr Tommaso Pippucci, Medical Genetics Unit, University of Bologna Using Exome Sequencing to Solve Rare Disorders|
|11.30 – 12.00:||Prof Alessandra Ferlini, Medical Genetics, University of Ferrara, Italy Biomarker and gene discovery by omics within the FP7 Neuromics Project|
|12.00 – 12.30:||TECHNOLOGY PRESENTATION – SMARTer® Solutions for Next Generation Sequencing by Dr Irit Paz, Takara Clontech|
|12.30 – 13.00:||Prof Alessandra Renieri, Medical Genetics, University of Siena and UOC Genetica Medica Azienda Ospedaliera Univeristaria Senese NGS and medical genetics: towards new frontiers in clinical practice|
|13.00 – 14.00:||Lunch, Exhibition & Networking|
|14.00 – 14.30:||Dr Elisabetta Rossi, Immunologia e Diagnostica Molecolare Oncologia, University of Padova, Italy Circulating Tumour Cells and deep sequencing|
|14.30 – 15.00:||TECHNOLOGY PRESENTATION – Every Cell Has a Story – Igniting a Revolution through single-cell biology by Dr Amy Hamilton, Fluidigm|
|15.00 – 15.30:||Prof Marco Bianchi, Translational Genomics and Bioinformatics, San Raffaele University, Milano Locating and counting nucleosomes|
|15.30 – 16.00:||Dr Barbara Di Camillo, Information Engineering, University of Padova, Italy Measuring differential gene expression with RNA-seq: challenges and strategies for data analysis|
|16.00 – 16.30:||Coffee, Exhibition & Networking|
*PLEASE NOTE: the agenda may be subject to change
Dr Massimiliano Pagani
Dr Oliver Stegle
EMBL-EBI, Cambridge, UK
Dr Christian Beisel
Genomic Facility, ETH Zurich, Switzerland
Prof Raffaele Calogero
Bioinformatics and Genomics Unit, University of Torino
Dr Stephan Ossowski
Centre for Genomic Regulation, Barcelona, Spain
Dr Simon Patton
Director at European Molecular Genetics Quality Network (EMQN), UK
Dr Tommaso Pippucci
Medical Genetics, Policlinico S.Orsola-Malpighi, Bologna
Head of laboratory services, Sheffield Childrens NHS Foundation Trust, UK
Prof Alessandra Ferlini
Medical Genetics, University of Ferrara
Dr Elisabetta Rossi
Immunologia e Diagnostica Molecolare Oncologica, University of Padova
Dr Bruno Amati
Center for Genomic Science, IIT@SEMM, Milan
Prof Alessandra Renieri
Medical Genetics, University of Siena and UOC Genetica Medica Azienda Ospedaliera Univeristaria Senese
Prof Barbara di Camillo
Bioengineering, University of Padova
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
Silicon Biosystems, with offices in Bologna Italy and San Diego CA has developed an instrument platform for cell and molecular biology which can sort, manipulate, and collect individual or groups of rare cells. Using a proprietary electronic chip-based microfluidic cartridge and microscopic image analysis the DEPArray™ system can recover as little as one single cell from a suspension of tens of thousands of cells with 100% purity, allowing downstream molecular analyses such as whole genome amplification and sequencing. The technology has application in the molecular characterization of circulating tumor cells, tumor infiltrating cells, stem cells, FFPE and circulating fetal cells.
Rubicon Genomics is a provider of ThruPLEX® and PicoPLEX™ kits for pre-analytical amplification of nucleic acids for research and clinical applications. Our technologies’ simple protocols, fast time to results and unique ability to amplify nucleic acid from “difficult” samples such as single cells or cell free DNA differentiate our products and enable researchers and healthcare providers to more easily and cost-effectively realize the benefits of the genomic revolution. For more information, visit www.rubicongenomics.com
Genome Diagnostics Nijmegen is an ISO 15189:2012 certified laboratory, which provides high quality and up to date diagnostics of genetic disorders for patients and their families. The laboratory is equipped with the latest technologies to perform various types of diagnostic services. In all the diagnostic services offered, a full diagnostic interpretation of clinically relevant variants is included. The laboratory has over 130 coworkers and performs >25.000 tests and >4000 diagnostic exomes each year. Genome Diagnostics Nijmegen is part of the Department of Human Genetics of the Radboud university medical center and is based in the Netherlands. For information; www.genomediagnosticsnijmegen.nl
GATC Biotech is Europe’s leading service provider of DNA and RNA sequencing with more than 10.000 academic and industrial customers worldwide. Since more than two decades GATC Biotech offers sequencing and bioinformatics solutions for every customer request, from single samples up to large scale projects, from Sanger to next and third generation sequencing. The areas of interest of our innovative products are as versatile as life itself covering human diagnostics, translational research, biomarker verification as well as plant and animal breeding. As a renowned brand, we are not only mastering a broad range of technologies and related downstream data analysis, but also processing millions of customer samples in professional quality and ready for diagnostic purposes. Having Agilent and Illumina Certified Service Provider status, GATC Biotech offers true multiplatform sequencing using all leading sequencing technologies in its own labs: Sanger Sequencing with a fleet of ABI 3730xl, next and third generation sequencing on several Illumina HiSeq 2500, Illumina MiSeq and Pacific Biosciences’ PacBio RS II. Headquartered in Constance, Germany, GATC Biotech houses its ISO 17025 certified Genome and Diagnostic Centre with a focus on next and third generation sequencing. The European Custom Sequencing Centre located in Cologne focuses on Sanger sequencing. This advantageous location ensures fast delivery of samples and resulting in an optimal service experience. All laboratories have highly integrated and fully automated processing pipelines and enable full compliance with latest state-of-the-art quality standards.
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%.
Advanced Analytical Technologies Inc. (AATI) develops, manufactures and markets high-throughput, fully-automated nucleic acid and genetic analysis systems. The company’s products have both commercial and research applications and are designed to improve processes within the molecular diagnostics, pharmaceutical, life science, agricultural and biofuels industries. The company’s product portfolio includes instruments for the parallel analysis of biomolecules, DNA, RNA, genomic DNA, double-stranded DNA, pharmaceutical compounds and proteins using capillary electrophoresis (CE) with fluorescence detection or UV absorbance. The company’s flagship product, the Fragment Analyzer, is recognized as the best-in-class, multi-channel, automated fluorescence-based CE detection system for the simultaneous analysis of the quantity and quality of nucleic acids, including: dsDNA fragments, gDNA, NGS fragments and RNA (total and messenger) and microsatellites (SSR). Advanced Analytical Technologies, Inc. (AATI) simplifies complex genomics workflows to accelerate research and discovery in pharmaceuticals, life science, biofuels, biotechnology and healthcare. The company has facilities in Ames, Iowa, USA and Heidelberg, Germany. We support customers through a global network of distributors and support centers.
WaferGen Biosystems is an innovative life science company offering genomic tools for whole-genome, targeted resequencing, genotyping and expression genetic analysis. The Apollo 324T is our fully-automated walk-away library preparation solution for whole-genome and transcriptome Next-Generation Sequencing (NGS) applications. The Seq-ReadyT TE workflow, powered by the SmartChipT massively-parallel singleplex PCR technology, is an affordable and simple one-step target enrichment and library prep workflow that delivers excellent sequencing coverage for easy implementation in clinical labs benefiting clinical customers from improved accuracy and precision. Our SmartChipT Real-Time PCR System is a next-generation genetic analysis platform for profiling and validating molecular biomarkers. It provides a range of high-throughput capabilities including microRNA and mRNA (gene expression) profiling as well as single nucleotide polymorphism (SNP) genotyping. In the heart of our qPCR and TE system is a SmartChip with 72×72 nanoscale-wells (each of 100 nL), allowing the completion of 5184 qPCR reactions per chip. We also can provide service on our systems.
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.
AB ANALITICA was established in 1990 and is located in Padua, in the north-eastern part of Italy. It is specialized in the development and the sale of diagnostic systems for professional use. Highly qualified researchers and a constant collaboration with Research Institutes, Universities, and Hospitals, has allowed AB ANALITICA to consolidate over the years scientific knowledge and experience to develop diagnostic systems in line with the most recent medical guide lines, with the objective to provide quality, innovation, and security. AB ANALITICA is an UNI EN ISO 9001:2008 certified company for the design, development, production and trade of breath test, in-vitro diagnostic medical devices and in the year 2006 the certification UNI EN ISO 13485:2012 was obtained for the design, development, production and trade of in vitro medical-diagnostic devices (IVD). AB ANALITICA is particularly aware of emerging technologies and the requirements of the diagnostic market. As a result, it has invested in its own research and development department, which is involved in advanced molecular biology diagnostics in the following sectors: microbiology, virology, onco-hematology, and genetics. The competences of the company are related to diagnostics with molecular biology technologies for both the qualitative and quantitative determination of nucleic acids, the development of biobanking management systems, and in vivo/in vitro diagnostics with breath test technology and the use of stable isotopes. AB ANALITICA has a sales agent network that covers the entire Italian territory and local distributors in many export countries.
Takara Bio Europe and Clontech Laboratories are members of the Takara Bio Group, a leading supplier of tools for life scientists worldwide. Through our brand names TAKARA® and CLONTECH® we develop innovative technologies in the fields of Cell Biology, Molecular Biology and Proteomics, including PCR and qPCR reagents, RT enzymes, library construction kits, the In-Fusion Cloning system and SMARTer™ cDNA synthesis kits. Learn more about our market-leading product family for NGS: www.clontech.com/NGS
Diatech Pharmacogenetics is the only company in Italy focusing research efforts into pharmacogenetics, intended as the study of genetic variation that affect response to drugs. Support to Diatech’s research efforts derives from selling pharmacogenetic tests for personalized and predictive medicine with priority focused to the most invasive therapies: antitumoral treatments. Pharmacogenetic kits (CE IVD) developed by Diatech aim to personalize chemotherapy and radiotherapy, leading to higher efficacy, and to reduced side effects.
Diatech LabLine is a new company that distributes products for biomedical research, and much more. The instruments and reagents that we distribute are currently used in our laboratories for research and development, where we are developing molecular diagnostic kits, mainly dedicated to pharmacogenetics cancer. Lab Line Diatech offers the best products for a forward look and to innovate the Italian market.
Founded in 1983 with the original name of CELBIO, EuroClone is committed in distributing and developing innovative products for the life sciences industry. The company is since 30 years a recognized provider of safety cabinets, isolators, cytogenetics reagents and high-technology molecular and cell biology products.
Biosense is a distributing company focusing on high technology solutions for genomics, including systems and reagents for genotyping, gene expression, preparation of NGS sequencing, epigenetic and methylation studies, preparation and analysis of DNA and protein microarrays.
Fluidigm provides advanced tools for single cell genomics and proteomics research, inspiring this rapidly growing field of single cell analysis.
Istituto Nazionale di Genetica Molecolare (INGM) is a no-profit research foundation aimed at the discovery and initial development of new therapies and new diagnostics in the fields of tumors and autoimmune diseases. INGM is located inside the campus of the IRCCS Ospedale Maggiore Policlinico in Milan, in the new Padiglione Enrica Pessina e Romeo Invernizzi, that has been built thanks to the generous donation from Enrica Pessina e Romeo Invernizzi. INGM comes to life to be a “translational” medical Research Institute that creates scientific knowledge capable of generating value on the basis of the intellectual property that ensues from its research activities. To achieve these objectives, INGM will develop scientific research strongly connected with clinics, drawing benefit from being located inside one of the most important European hospitals. Research activities are coordinated by a Chief Scientific Officier with scientific and managerial expertise who is supported by a Scientific Advisory Board composed by researchers having a high international profile. The INGM Foundation was established by the Italian Ministry of Health, the Ministry of Foreign Affairs, the IRCCS Ospedale Maggiore of Milan and the Lombardy Region.
FONDAZIONE ISTITUTO NAZIONALE GENETICA MOLECOLARE
INGM “Romeo ed Enrica Invernizzi”
Via Francesco Sforza, 35
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