6-14 October 2015
Wellcome Trust Genome Campus, Hinxton, Cambridge
This popular laboratory- and computer-based training course provides a comprehensive overview of the latest principles and techniques for exome sequencing, also known as pulldown, sequence capture and targeted sequencing.
Participants will gain practical laboratory experience as well as training in variant calling, quality control, and association analysis.
Solution hybrid capture is used to enrich for all known exon sequences (the exome) or for customised regions from genomic DNA, for the purpose of sequencing the regions of interest. The enriched targets are sequenced using next generation technology to a high coverage and analysed for variants. For comparison, the concepts for array CGH (aCGH) will be covered as an approach for analysing somatic DNA copy number variation, along with a broader overview of comparative genomics approaches. Preliminary analysis will take the form of mapping sequence to the reference and calculating quality metrics informing on sequence and mapping quality.Variants (SNPs, INDELs) will be called from the mapped data
With increased use of analytical methods using DNA isolated from formalin fixed clinical samples, attention will be paid to the consequences of sample processing, including duration of exposure to formalin fixation.
Material to be covered will include:
- Sample quality assessment and logistics
- DNA fragmentation and quantification
- DNA library preparation
- Sequence capture
- Bait design
- Overview of Illumina sequencing
- Sequence mapping
- QC metrics
- SNP/insertion/deletion calling
- SNP consequence analysis
- Protein impact analysis
- Variant annotation
- Case-only analysis
- Case/control analysis
- Rare SNP discovery
- Impact of formalin fixation on data quality ofexome seqeuncing and CGH analysis
- Overview of comparative genomics approaches
Teaching will be complemented by opportunities to interact with academic and technical experts working at the cutting-edge of the field.
Dr Peter Ellis (Wellcome Trust Sanger Institute, Hinxton, UK)
Dr Robert Andrews (Cardiff University, UK)
Dr Matthew Breen (North Carolina State University, USA)
Dr Audrey Hendricks (University of Colorado, USA)
Feedback from the 2014 course
“The course was brilliant, and the teaching was of really high quality for both the lab aspects and the bioinformatics.”
“I personally enjoyed every aspect of the course and feel like I gained all the skills I was aiming to from my time at the Wellcome trust. Thank you for such a well run, enjoyable, informative course.”
“I think all the instructors, presenters and organizers of the course did a good job, Kudos. I will try not to let them down and pass on this knowledge and information to others.”
How to apply
Applicants should be post-doctoral scientists or third-year PhD students undertaking their own research, core-lab service providers are also encouraged to apply. Applicants must be familiar with standard molecular biology lab techniques. Basic UNIX skills and the ability to confidently use Excel are also required.
The course tuition fees are subsidised by The Wellcome Trust for scientists based in non-commercial institutions anywhere in the world. This is a residential course and there is a fee of £1045 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £4200.
Limited bursaries are available for non-commercial applicants (up to 50 per cent of fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).
Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor or head of department. A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline.
Deadline for applications: 5 June 2015