Technology Workshop by Genestack:
02 April 2014, 14.00-16.00: Transformation of genomics big data computing and application engineering
Summary: 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.
Presenters: Dr Misha Kapushesky (CEO) and Dr Alessandro Riccombeni (Senior Scientist) Genestack, UK
M Kapushesky: Most recently team leader in functional genomics at the European Bioinformatics Institute, where his team developed bioinformatics data systems for academia and industry, such as Gene Expression Atlas, Misha Kapushesky has first-hand experience in dealing with big data in genomics and has participated in and led international consortia applying bioinformatics to medical research. Before joining the EBI in 2001, he worked at several high-tech start-ups in the area of large-scale data search and processing around Boston, USA. He was educated at Cambridge (Ph.D., Genetics), Oxford and Cornell Universities (B.S., Mathematics).
A Riccombeni: Before doing research on regulatory genomics at UCL Cancer Institute, Alessandro Riccombeni studied comparative genomics of pathogenic yeasts in Dublin, Ireland. During this time he collaborated with Illumina in Cambridge, UK on local assembly of large structural variants. Prior to that he studied de novo originated oncogenes at the IFOM-IEO campus in Milan, Italy, and worked in the Carbohydrate Chemistry group at the University of Lisbon, Portugal. He was educated in Ireland at University College Dublin (Ph.D., Bioinformatics) and in Italy at the University of Milan-Bicocca (B.S., Biotechnologies).
Technology Workshop by Qiagen/Ingenuity Systems
02 April 2014, 16.30-18.30: Identifying Causal Variants in NGS Data: An Introduction Workshop for Analysis and Biological Interpretation of Human DNA Resequencing Data
Summary: 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/
Presenter: Dr Tim Bonnert
Field Application Scientist, Europe, Qiagen
Technology Workshop by TaKaRa/Clontech
Summary: 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.
Presenter: Dr Malathi Raman
NGS Product Manager, Europe, Takara Bio Europe
Technology Workshop by Arkivum
Join our workshop to hear Joanne Mason, Lead Scientist from Oxford Molecular, share her experiences working with NGS data on a daily basis.
Summary: 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.
Presenter: Dr Joanne Mason, Lead Scientist at the Oxford Molecular Diagnostics NGS Core, UK, & Dr Matthew Addis, CTO, Arkivum, UK
J Mason: Joanne is funded by the BRC to carry out translational science modernising clinical diagnostics and bring NGS technologies into clinical practice in the NHS. Joanne works alongside clinicians, clinical scientist and research scientist in multidisciplinary teams. Oxford Molecular Diagnostics NGS Core run an Ion Torrent PGM, Illumina MiSeq and Illumina HiSeq and run disease specific amplicon panels to whole human exome and genome sequencing.
M Addis: Matthew is CTO of Arkivum and previously worked at the University of Southampton IT Innovation Centre. Over the last decade, Matthew has worked with a wide range of organisations on solving the challenges of long-term data retention and access, including in the lifesciences, aerospace, broadcasting and scientific sectors. By working with national archives and industry leaders across the UK and Europe, Matthew has investigated the issues of long-term data archiving, including preservation strategies, system architectures, total cost of ownership and how to mitigate the risk of loss of critical data assets. This resulted in IT Innovation spinning-out Arkivum ltd, which provides data archiving as a service. Matthew currently works on risk-based approaches to digital preservation and data retention including how to meet regulatory compliance as well as keep data accessible.