DNASeq

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:

Friday 10th December - On-line course (Maximum 8 people)

Cost: £249

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

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

Professor Mark A Lindsay 

Mark Lindsay is Professor of Molecular and Computational Pharmacology at the University of Bath  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 2005 he worked at AstraZeneca Pharmaceuticals, where he headed a project team examining the utility of siRNAs and antisense for target discovery and as novel therapeutics.  Since returning to academia in 2005, he has worked at Imperial College London and the Universities of Manchester and Bath. Work within his group has focused upon examining the role of the transcriptome in the inflammation associated with multiple diseases. Professor Lindsay has recently undertaken a 12 month secondment as the acting Head of Biology at the MRC Nucleic Acid Therapy Accelerator at the Harwell Science Campus (near Oxford). The nucleic acid therapy accelerator (NATA) is a new UK research initiative with a mission to accelerate the development of nucleic acid therapeutics, building partnerships with industry and academia from around the world.