Next Generation Sequencing

8-16 October 2012

Wellcome Trust Genome Campus, Hinxton, Cambridge
Deadline for applications: 22 June 2012

Course summary

Next-generation sequencing has become the premier tool in genetic and genomic analysis. This laboratory-based course is directed at scientists who will be generating and interpreting sequence information in their research and wish to gain a better understanding of the techniques involved and their applications. This course is not meant to replace the manufacturers’ training normally supplied with new instruments, nor is it intended to be a training course for those solely interested in next-generation sequencing bioinformatics.

The course will include theoretical and practical information on all of the next-generation sequencing systems available and those on the near horizon. The laboratory element will cover a mix of technologies that will be determined nearer the time, but will be chosen from platforms like the Ion Torrent, PacBio and Illumina Miseq / HiSeq. One aim of the course is to allow participants to make informed decisions about which technology to apply to solve specific research questions they may face in the future. A variety of applications will be covered as time permits, e.g., RNA-Seq, target enrichment, bacterial sequencing, cancer genomics, human variation analysis, etc. All the basic techniques of post-sequencing analysis will be covered, QC, alignment, assembly, variant calling, etc.

Please note: For the data analysis components of the course, applicants will require a working knowledge of the Linux operating system. This can be obtained by various methods and will be enforced.

Programme

Library Prep
• Making libraries from samples
• Both theory and practical sessions

Sequencing
• Overview: Motivation and fundamental concepts
• Detailed description of prominent sequencing technologies: current and future (3rd generation) platforms
• Hands-on laboratory work: preparing chips for sequencing and performing sequencing runs on various platforms

Data analysis
• Data QC: How to determine if a run has performed well
• Alignment to a reference, de-novo assembly, SNP and structural variant-calling of next generation DNA and RNA data
• IT and the data storage problem

Accompanying the lecture and practical sessions will be a series of seminars by invited speakers, who will highlight their ground-breaking work in applications of next generation sequencing (cancer, human diseases, pathogens, etc).

Course instructors

Harold Swerdlow (Head of Sequencing Technology, The Wellcome Trust Sanger Institute, Cambridge, UK)
Carol Churcher (Head of Sequencing Operations, The Wellcome Trust Sanger Institute, Cambridge, UK)
Tony Cox (Head of Sequencing Informatics, The Wellcome Trust Sanger Institute, Cambridge, UK)

2011 Guest speakers (2012 Guest speakers TBC shortly)

Julian Parkhill (Wellcome Trust Sanger Institute, UK)
Richard Durbin (Wellcome Trust Sanger Institute, UK)
Duncan Odom (Wellcome Trust Sanger Institute, UK)
Nick Thomson (Wellcome Trust Sanger Institute, UK)
Susanna Cooke (Wellcome Trust Sanger Institute, UK)

Feedback from previous courses

“I was very impressed with the course overall, everyone involved was incredibly helpful and generous with their time.”

“Thank you very much for a great course!”

How to apply

Target audience and prerequisites
Applicants should be postdoctoral scientists, senior PhD students or junior faculty members actively engaged in or soon to commence research involving next generation sequencing instrumentation.

Linux experience
This course includes a substantial element of sequence data QC and analysis performed on Linux-based computers. To benefit fully from the course it is essential that successful applicants are comfortable working in a Linux-based environment prior to the course. In particular, applicants will be expected to use the command line terminal interface.

Applicants will need to be familiar with, and able to perform, the following:
creating, copying, moving and deleting text files and directories, modifying file and directory permissions, navigating directory structures, examining the contents of text files, executing programs from the command line using pipes and output redirection, compressing and decompressing files (using zip or gzip)

Cost
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, without exception, and there is a registration fee of £950 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £4000.

Bursaries
Limited bursaries are available for non-commercial applicants (50 per cent of fee) and are awarded on merit. Please see our bursaries page for application information and terms and conditions.

Applications
Applicants will be required to complete an application form containing a 300-word outline of the relevance of the course to their research. Please note that documentation supporting their application will be required from the applicant's supervisor/head of department.

To submit an application, please either:

Applications can be accepted by post or email. Sponsors' supporting letters must be returned, signed, by fax or post under separate cover. Please note: Incomplete applications will be rejected.

Applications and letters of support should be sent to:

Wellcome Trust Advanced Courses
Wellcome Trust Genome Campus
Hinxton
Cambridgeshire CB10 1SA
UK

F +44 (0) 1223 495130
E advancedcourses@hinxton.wellcome.ac.uk

Deadlines
Deadline for applications: 22 June 2012

Wellcome Trust, Gibbs Building, 215 Euston Road, London NW1 2BE, UK T:+44 (0)20 7611 8888