DNASeq 

Exome/DNA analysis using next generation sequencing (DNASeq)


Aims:  With the wealth of data being generated by the 100,000 Genomes Project and other databases, it is now becoming increasing important to understand the process by which these results are generated and interpreted.  This one day course is designed for scientists and clinicians with little or no experience in exome/DNA sequencing. The course is based upon the protocol described by the 100,000 genome project and aims to provide the experimental and bioinformatics skills required to prepare samples, undertake exome sequencing and the subsequent identification of single nucleotide variations (SNVs) and short Insertions/Deletions (Indels). The course will provide information on the interpretation of this sequencing data including disease association and pathway/GO analysis. We assume that sequencing will be performed by an external provider and will provide advice in this area. The course is computer based and will involve a combination of presentations/exercises to analyse 'actual' next generation sequencing data using publically available programmes.

Content:

Part 1    Sample Preparation and Exon Sequencing

  • Introduction to 100,000 Genome Project and exome/DNA analysis
  • DNA sample preparation
  • Overview of next generation sequencing platforms
  • Overview of Exone Capture kits (Agilent SureSelect, Illumina TruSeq and Nimblegen SeCan EZ)
Part 2:    Sequencing Data Analysis and Interpretation
  • Overview of file formats (FASTQ, SAM/BAM, BED, GTF and VCF files)
  • Introduction to the Galaxy Bioinformatics platform
  • Quality control of raw sequencing data (FASTQC)
  • Mapping of sequencing data to a reference genome (BWA)
  • Quality control of aligned data (PICARD)
  • Viewing data using genome browsers (IGV)
  • Tools for calling SNV and Indels
  • Variant annotation (location, effect, novelty etc)
  • Analysis of affected genes (pathways, gene ontology and disease association)
Dates and location:

Wednesday 6th July 2016 - Just IT Training Rooms, nr Aldgate Tube, London (TBC)

Cost: £349

For reservations contact mailto:m.a.lindsay@bath.ac.uk

Courses

Course Feedback (Overall 4.3/5.0 from > 200 delegates)

'Very instructive, friendly speakers'

'Excellent. Everything very clearly presented'

'Excellent content and teaching'

'Very clear and covers a lot'

  Course Trainers

 Dr David Sims

David Sims is the Programme Head at the MRC funded Computational Genomics Analysis and Training (CGAT) programme at the University of Oxford. David has a BSc in Biochemistry and an MSc in computer science from Glasgow University. In 2006 he obtained a PhD from UCL working on genome-wide RNA interference screening for cell morphology in Drosophilia. He went on to work in integrative cancer genomics, including shRNA screening, exome sequencing and RNASeq in Alan Ashworths's laboratory at the Institute of Cancer Research in London. He is currently involved in training biologists in computational genomics and works on a wide variety of next generation sequencing projects including RNAseq, ChIPseq, exome sequencing, e4C and methylation sequencing.

Professor Mark A Lindsay 

Mark Lindsay is Professor of Molecular Pharmacology at the University of Bath and Honorary Senior Scientist at the National Heart and Lung Institute, Imperial College London. He obtained a BA in Natural Sciences from Cambridge University and a PhD investigating the mechanism of insulin release from Nottingham in 1991. Following an initial post-doctoral position in renal disease, he moved to the National Heart and Lung Institute, Imperial College London in 1994 where he investigated the mechanisms regulating the inflammatory response in the airways and lung. Between 2001 and 2004 he worked at AstraZeneca Pharmaceuticals, where he headed a project team examining the utility of siRNAs for the validation of novel drug targets and the identification of new approaches for the delivery of biopharmaceutics. Since returning to academia in 2004, he has worked at Imperial College London and the Universities of Manchester and Bath. Work within his group has focused upon the role of miRNAs and long non-coding RNAs in the regulation of the innate immune response and the development of respiratory diseases such as asthma, chronic obstructive pulmonary disease and lung cancer.