Next Generation Sequencing

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.

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
including, PacBio, Illumina (Miseq, HiSeq) and Oxford Nanopore MinION.
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 (e.g.,
RNA-Seq, target enrichment, bacterial sequencing, cancer genomics, human
variation analysis) along with all the basic techniques of
post-sequencing analysis (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. This course is not meant to replace the
manufacturers’
training normally supplied with new instruments, nor is
it intended for
applicants interested solely in data analysis (for which we offer a
separate Next Generation Sequencing Bioinformatics course).

Feedback from the 2016 course

• “The course was excellent and I got a huge amount out of it that is directly applicable to what I am doing, as well as useful for my future career. Evening activities were a lot of fun. In general, a very enjoyable and productive experience.”
• “It was really a great opportunity for me to be part of the training. i really gained a lot of knowledge. thanks to the organizers and the instructors, you are all wonderful.”
• “Excellent Course.”
• “Thank you very much for the course. Everything was much better than my most optimistic expectations.”
• “I’m very impressed- the whole course was incredibly well thought out and organised. Thanks to the course organisers.”

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

Library Prep

• Making libraries from samples (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 data storage problems

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.

Course instructors
Tony
Cox Wellcome Trust Sanger Institute, UK
Michael
Quail Wellcome Trust Sanger Institute, UK
Jacqui
Keane Wellcome Trust Sanger Institute, UK

Guest speakers
Daniel
Gaffney
Wellcome Trust Sanger Institute, UK
Elizabeth
Murchison University of Cambridge, UK
Julian
Parkhill Wellcome Trust Sanger Institute, UK

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. Please
note: This course is not meant to replace the
manufacturers’
training normally supplied with new instruments, nor is
it intended for
applicants interested solely in
next-generation sequencing
bioinformatics.

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 is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
residential
course and there is a fee of £1040 towards
board and lodging for non-commercial applicants. Please contact us for
the commercial fee. Additional, limited bursaries are
available (up to
50% of the course fee) and are awarded on merit, please see the
“Bursaries” tab for further information.

Applications
Applications for this course can 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
Deadline for Applications: Closed

Travel visas
Please contact the
event organiser if you require a letter to support a
travel visa
application. Note that letters will be provided to confirmed
attendees.

Non-European Economic Area or Swiss nationals may be required to have a
visa to enter the UK.
Early application is strongly advised, as this process can take 6-8 weeks
or longer.

Please visit the following websites for further information:
UK Border Agency website and information for general visitors and business
visitors.

Cost
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 £1040 towards board and lodging for
non-commercial applicants. Please contact us for the commercial fee.

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, 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.