Exome Sequencing

This 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.

The programme will include lecture and laboratory-based practical
sessions covering the following topics:

• 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 of exome sequencing 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.

Course instructors
Peter Ellis Wellcome Trust Sanger Institute, UK
Robert Andrews Cardiff University, UK
Matthew Breen North Carolina State University, USA
Audrey Hendricks University of Colorado, USA

Prerequisites
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

Cost
UK: The
course is subsidised by the Wellcome Genome
Campus Advanced Courses and Scientific Conferences Programme. This is a
residential
course and there is a fee of £1045 towards board and lodging
for non-commercial applicants. Please contact us for the commercial fee.

Applications
Applications for this course can now be completed online. If you have any
problems with the online application process, please contact us.

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. 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. Applications without a supporting
statement cannot be considered.

Deadlines
This course is now closed. Please contact the course organiser to be
added to our mailing list.

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Limited bursaries are
available
(up to 50% of the course fee) and are awarded on merit. If you would like
to apply for a
bursary, please complete the bursary section of the
online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% of the course fee, though in exceptional
circumstances an application for the total course fee may be considered.
Where there are many bursary applications, the selection committee may
issue smaller amounts. We cannot assist with travel costs to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.