This second annual NGS 2015 Nordic Conference took place at the Medicon Village in Lund and was organised in partnership with the Lund University Cancer Centre.
The conference focussed on the use of Next Generation Sequencing (NGS) technologies and tools to look at human disease whether in a research or a clinical setting.
This focus took the form of presentations over two days in the following areas: NGS Applications and workflows, Personalized Genomics, the Metagenomics link to health/disease, Non-invasive Prenatal testing, Cancer and Rare Disease genetics as well as Data Analysis and Storage. Indeed the panel debate on day 1 allowed delegates to share their views with panel members on how NGS labs are coping with data analysis and storage.
NETWORKING: in addition to the excellent science, NGS 2015 Nordic was characterized by a collaborative air where all delegates got the chance to interact with each other during networking events such as an introductory networking session, a panel debate and a networking dinner on the evening of 27th October.
… and others interested in the latest developments of:
|09.00 – 10.30:||Registration, Coffee & Networking|
|10.30 – 11.00:||Prof Åke Borg, Head of Canceromics, Oncology & Pathology, Lund University NGS in cancer research and clinical diagnostics at Lund University|
|11.00 – 11.30:||Dr Ed Quazi – Networking and Collaborations Workshop|
|11.30 – 12.00:||Dr Valtteri Wirta, Head of Unit, Clinical Genomics, SciLifeLab, Karolinska Institute Implementing NGS-based diagnostics for rare genetic diseases – collaboration between SciLifeLab and Karolinska university hospital|
|12.00 – 12.30:||TECHNOLOGY PRESENTATION by Dr John Wahlgren, Covaris Advantageous use of Covaris AFA technology for DNA/RNA extraction from FFPE tissues and for chromatin shearing applications|
|12.30 – 13.30:||Lunch, Exhibition & Networking|
|13.30 – 14.00:||Prof Jan Gorodkin, Head, Center for non-coding RNA in Technology and Health, University of Copenhagen From alignment of read profiles from small RNASeq data to detection of differential processing|
|14.00 – 14.30:||Dr Klaus Brusgaard, Odense University Hospital, Denmark Targeted next generation sequencing as a diagnostic tool in 163 patients with epileptic encephalopathies|
|14.30 – 15.00:||TECHNOLOGY PRESENTATION by Dr Steve Glavas, Thermo Fisher Scientific Standardized clinical assays with Oncomine panels for therapy selection|
|15.00 – 15.30:||Coffee, Exhibition & Networking|
|15.30 – 16.00:||Dr Petri Auvinen, Laboratory Director, Institute of Biotechnology, University of Helsinki Our second genome and health|
|16.00 – 16.30:||Dr Johan Rung, Facility Manager, Scilifelab, Uppsala University Clinical NGS in Uppsala: from development to routine testing for cancer and inherited diseases|
|16.30 – 17.30:||DEBATE: NGS data analysis and storage: How do we cope with the ever increasing needs?|
|18.00:||DRINKS RECEPTION sponsored by PARTEK|
|19.00:||NETWORKING DINNER (booking required)|
|09.30 – 10.00:||Prof Ulrik Lassen, Phase 1 Unit, Department of Onology, The Finsen Center, Rigshospitalet, Copenhagen Copenhagen prospective personalized oncology (CoPPO): a personalized genomic screening program at the Phase 1 unit at the Rigshospitalet, Copenhagen|
|10.00 – 10.30:||Prof Anne-Lise Børresen-Dale,Genetics and Institute for Cancer Research, Oslo University Hospital, Norway MetAction n-of-1 trial: Actionable target identification for palliative systemic therapy – paving the way for personalized cancer therapy in Norway|
|10.30 – 11.00:||Coffee, Exhibition & Networking|
|11.00 – 11.30:||Prof Tobias Sjöblom, Immunology, Genetics and Pathology and Program Director for U-CAN, Uppsala University Understanding and Exploiting the mutational landscape of human cancers|
|11.30 – 12.00:||TECHNOLOGY PRESENTATION by Dr Svetlana Nikic, llumina Unraveling Genomics Behind Human Diseases Using Illumina Technology|
|12.00 – 12.30:||Prof Albin Sandelin, Computational and RNA Biology, Department of Biology & Biotech Research and Innovation Centre, Copenhagen University The promoter and enhancer landscape of inflammatory bowel disease|
|12.30 – 13.30:||Lunch, Exhibiton & Networking|
|13.30 – 14.00:||Dr Erik Alm, Bioinformatics Lead, Public Health Agency of Sweden NGS as a routine workflow in microbiology surveillance and diagnostics|
|14.00 – 14.30:||Dr Peter Johansen, Molecular Biologist, Clinical Genetics, Rigshospitalet Implementing non-invasive prenatal testing in a public health laboratory|
|14.30 – 15.00:||TECHNOLOGY PRESENTATION by Dr Tamara Steijger, Sophia Genetics NGS-based Diagnostics: How to achieve top analytical performance and guarantee quality|
|15.00 – 15.30:||Coffee, Exhibition & Networking|
|15.30 – 16.00:||Dr Adam Baker, Human Health & Nutrition Division, Chr. Hansen, Denmark Harnessing next generation microbes for Human Health – Insights from NGS sequencing from commercial fermentations|
|16.00 – 16.30:||Dr Göran Jönsson, Melanoma Genomics Unit, Canceromics, University of Lund Analysis of genetic evolution of melanoma tumors by multi-region whole exome sequencing|
We would like to thank you all the sponsors for their support:
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
Thermo Fisher Scientific is the world leader in serving science. Our mission is to enable our customers to make the world healthier, cleaner and safer. Through our Thermo Scientific, Applied Biosystems and Invitrogen brands, we offer an unmatched combination of innovative technologies, purchasing convenience and support.
Driving innovation: As a startup, Illumina aspired to transform human health. Our initial products enabled researchers to explore DNA at an entirely new scale, helping them create the first map of gene variations associated with health, disease, and drug response. Every breakthrough opened up a new world, and showed us how much further there is to go. Finding answers: While the rate of progress is accelerating exponentially, we are only beginning to understand the clinical significance of the genome. What causes a cancer cell to mutate? What is the origin of a puzzling disease? Is it possible to prevent the next outbreak? Or safeguard the world’s food supply? These are just a few of the challenges that inspire us to push the boundaries of our imagination. Making a difference now: Today we are a global leader in genomics – an industry at the intersection of biology and technology. At the most fundamental level, we enable our customers to read and understand genetic variations. We strive to make our solutions increasingly simple, more accessible, and always reliable. As a result, discoveries that were unimaginable even a few years ago are now becoming routine – and are making their way into patient treatment. Empowering a healthy future: We now have the ability to sequence at an unprecedented scale. Collectively, this will give us a much deeper understanding of genetics than ever before. We will begin to truly unlock the power of the genome. These advances will trigger a fundamental shift in healthcare and beyond. Medicine will continue to become more preventive and more precise. We will be healthier, longer. We have only just begun. For more information visit www.illumina.com
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
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.
Eppendorf is a leading life science company that develops and sells instruments, consumables and services for liquid handling, sample handling and cell handling in laboratories worldwide. Its product range includes pipettes and automated pipetting systems, dispensers, centrifuges, mixers, spectrometers and DNA amplification equipment as well as ultra-low temperature freezers, fermentors, bioreactors, CO2 incubators, shakers and cell manipulation systems. Consumables such as pipette tips, test tubes, microliter plates, and disposable bioreactors complement the range of highest-quality premium products. Eppendorf offers a broad range of high quality, smart consumables and precise instruments to perform all steps upstream of the sequencing itself: from sample generation and storage via sample preparation/purification, library preparation, and quantification to PCR amplification. Eppendorf products are most broadly used in academic and commercial research laboratories, e.g., in companies from the pharmaceutical and biotechnological as well as the chemical and food industries. They are also aimed at clinical and environmental analysis laboratories, forensics and at industrial laboratories performing process analysis, production and quality assurance. Eppendorf was founded in Hamburg, Germany in 1945 and has about 2,930 employees worldwide. The company has subsidiaries in 25 countries and is represented in all other markets by distributors. www.eppendorf.com
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
Nordic Biolabs AB. One of the leading distributors within Life Science in Scandinavia. We have a broad range of products for most of the applications within Cell culture, Proteomics, Biobanking and Molecular biology research. If you work on gene regulation, Epigenetics, NGS, PCR, DNA/RNA purification Cell culture, ….. and more! Don´t hesitate to contact our experienced Product Support Team backed up with the R&D from our suppliers for best technical support and advices in your daily research. We carefully select our suppliers and are proud to announce we carry products from well established suppliers as Active Motif, BD/Difco, Biocision, Biolegio, Biosan, Enzymatics, GE healthcare/Hyclone, Lexogen, Lucigen, Micronic, MP Biological, Ritter, Rubicon, Sartorius, Shield, Stratec Molecular, Thermo Fisher scientific/Pierce, TPP and Zymo.
Kem-En-Tec was founded in 1987 by a team of Danish scientists from the Protein Laboratory at the University of Copenhagen. Kem-En-Tec Nordic is a strong and reliable partner and our success is based on reliability, high service level, flexibility and a high technological knowledge and support. We consider ourselves your service partner more than an “over the desk” supplier. Kem-En-Tec’s fundamental concept is to apply, offer and support the ideas and results of research & development by representing new and better quality products, ensuring improved results and more efficient use of resources for our customers. Our trained scientific staff isn’t hidden behind a call center, and we take pride in the fact that you will quickly receive a qualified reply – also if you choose to contact us by E-mail. Our services include extensive pre- as well as post selling support. Currently Kem-En-Tec repressent a platform of products from more than 100 companies in the field of Protein Technology, Molecular Biology, Cellularbiology, Diagnostics and Environmental studies.
Triolab is a professional sales company founded in 1986. Triolab sells in vitro diagnostic equipment to the healthcare sector and we provide products and services for POC coagulation, hematology, microbiology, molecular diagnostics, clinical biochemistry, disease-specific analyzes, transfusion medical analyzes and for the preanalytical phase. Triolab represents many of the most successful European and American manufacturers of in vitro diagnostic. Most of our suppliers are ISO certified, and they deliver all products of recognized quality. In the field of molecular diagnostics, Triolab can offer both reagents, controls and instruments for diagnostic use and research. From different suppliers we can offer PCR kits and real-time PCR kits for the diagnostics of infectious and respiratory diseases, both as multiplex panels and singleplex. We have both low and high throughput instruments for real-time PCR and automated DNA purification. From leading suppliers Triolab offers different mutation analysis kits (B-RAF, K-Ras, BCR-ABL, ALK), as well as ELISA kits for the monitoring of anti-TNF-α. In the field of Next Generation Sequencing we offer kit for oncogenetics, humangenetics and kit for gene translocation analyses and gene clonality analyses for the detection of leukaemia and lymphoma for the most common NGS platforms.
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.
Exiqon is a leading supplier of solutions for RNA research used by academia, biotech and pharmaceutical companies world-wide. Exiqon Services offer a range of RNA analysis services using Next Generation Sequencing (microRNA, small RNA, mRNA and whole transcriptome RNA-seq) and qPCR, from profiling and biomarker discovery to validation. Exiqon combines RNA expertise with flexible and comprehensive sample-to-answer services, tailored to your requirements. Exiqon also offers a unique online data analysis service for RNA NGS, called XploreRNA. Researchers around the world use Exiqon’s products and services to make groundbreaking discoveries about the correlation between gene activity and the development of disease. By taking advantage of our proprietary LNA™ technology, we have developed the most sensitive and specific technologies for analysis of RNA. Our miRCURY LNA™ microRNA qPCR platform has enabled us to pioneer the field of microRNA biomarker discovery in biofluids (serum, plasma and urine). Exiqon is experienced in collaborating with pharmaceutical companies in their effort to develop new medicines based on non-coding and coding RNA as biological markers.
Partek® Incorporated develops intuitive NGS & Microarray data analysis software built on a foundation of superior statistics and advanced visualizations. For decades, scientists have leveraged Partek software to publish thousands of successful scientific papers. It’s the most complete start-to-finish solution available and the fastest way from raw data to biology. – Workflows for all NGS and Microarray applications including RNA-Seq, miRNA, WGS, Exome Seq, SNV, CNV, ChIP-Seq and Methylation. – Import raw data, perform alignment, scaling, statistics, visualization, and annotation, identify pathways and functional genomics, and achieve qPCR validation – With Complimentary and unlimited scientific support and training, we’re here to help at every step. Request a free trial of our software at www.partek.com Questions? Please contact: Mikaela Gabrielli ~ Manager Marketing and Business Development email@example.com, mobile: +33 (0) 630 214 643
Amplexa Genetics A/S was founded in 2006 and is an expert in efficient molecular genetic testing. The company consists of experienced researchers equipped with the latest technologies who provide their expertise to the genetic health care sector. Klaus Brusgaard, Co-Director and Co-Founder of Amplexa Genetics, has a PhD in Molecular Genetics and since 1997 he has worked as a Clinical Geneticist at Odense University Hospital and Odense University where he is now Professor of Bioinformatics & Clinical Genetics. Since the beginning Amplexa Genetics has provided a wide range of traditional molecular genetic tests using Sanger sequencing. For the last three years this service has been expanded to also include Next Generation Sequencing panels to physicians in the public health care sector and private clinics. A genetic counseling service is offered if required. The service is reliable and cost effective with the highest standards of quality. Amplexa Genetics is participating in the European Molecular Genetics Quality Network (EMQN) 2008 – 2012 quality assessment schemes for mutation scanning and sequencing (External Quality Assessment – EQA). Amplexa is the National Danish NGS Screening Centre for molecular genetic analysis in Epilepsy”.
The Medicon Village is conveniently located close to Lund city centre and can be easily reached by bus from the central station. Bus route 1 and 6 run regularly (every 10 minutes) and the journey takes only 8 minutes. The closest stop to the Medicon Village is Lund Sparta which is only 200 m away from the entrance. More detailed information on buses and timetables can be found on this website: www.reseplanerare.resrobot.se
Alternatively the Medicon Village can also be reached by a short taxi ride from Lund Central Station (around 4 Km).
Whether you are traveling from the south or the north you’ll probably approach Lund from the E22 motorway. Take exit 22 (Lund Nord) into the E6 motorway and leave at the first exit. Turn left at the first roundabout and follow Scheelevägen for 1 km until you find the Medicon Village (n. 2) on your right hand side.
COPENHAGEN AIRPORT is located around 50 Km from Lund. It’s directly connected to many international destinations and offers scheduled flights operated by most airlines including many low cost airlines. Copenhagen Airport is connected to Lund Central Station by regular direct trains: journey time is around 35 minutes and the price of a second class ticket is 137 SEK. The ticket office is located in Terminal 3 above the railway station. You can visit www.oresundstag.se to plan your journey.
MALMO AIRPORT: Malmö Airport is located 30 km from Malmö, and offers scheduled flights as well as charter flights to a number of destinations including various Eastern European cities. Flygbussarna Airport Coaches operates buses between the airport and Lund Central Station. The buses depart directly outside the airport terminal and travel time is around 40-50 minutes depending on the traffic. A return ticket costs around 200 SEK. More information can be found on the Flygbussarna website: www.flygbussarna.se
Lund has been on the main railway line between Malmö and Stockholm since 1857. Today there are direct connections to Copenhagen and Elsinore via the Oresund Bridge. This connections are mainly served by the Öresundståg. There are regular direct trains from:
Copenhagen Airport – 35 minutes journey
Copenhagen – 50 minutes journey
Malmo – 10 minutes journey
Gothenburg – 3 hours journey
Stockholm – just over 4 hours Odense – there are no direct trains from Odense to Lund, but you can change in Copenhagen and total journey time will be less than 3 hours
You can visit www.oresundstag.se to plan your journey.
Lund can be easily reached by car and below you can find an indication of some of the distances:
Malmo – 20 Km
Copenhagen – 65 Km (road has toll)
Odense – 215 Km (road has toll)
Gothenburg – 260 Km
Aarhus – 240 Km (via ferry)