Technologies and Applications for Genome Analysis

18-27 April 2010
Wellcome Trust Genome Campus, Hinxton, Cambridge
Application deadline: 27 November 2009

Course summary
The course will provide a comprehensive overview and practical experience of the production and uses of DNA microarrays and related high-throughput methods for a broad range of applications in genome analysis.

Course programme
1. Expression analysis on whole genome oligonucleotide arrays
Students will extract and amplify RNA from a number of biological samples. Amplified material will be hybridised to whole genome expression arrays (one-colour platform) and the data extracted for gene expression profiling. Methods for RNA extraction, RNA amplification, assessment of RNA quality and considerations for single and two-colour assays will be discussed.In addition, the application of next generation sequencing for transcriptome analysis will be presented..

2. MicroRNA expression profiling
Students will prepare labelled material from RNA containing the microRNA fraction. This material will be hybridised to oligonucleotide arrays (two-colour platform) designed to interrogate all currently known vertebrate microRNAs.MicroRNA expression profiles will be generated for a number of biological samples.

3. Measuring genomic variation
Copy number variation in the genomes of test samples will be analysed using array comparative genomics.In addition, a range of applications for measuring genomic variation e.g. SNP genotyping will be covered.

4. Whole Genome DNA-protein Interactions
Chromatin immunoprecipitation of DNA-binding proteins will be performed using a mammalian cell line and the resultant material will be prepared for high-throughput Solexa sequencing. Genomic regions will be identified which interact with proteins including modified histones, chromatin remodelling complexes and transcription factors. Participants will also become familiar with similar approaches using genomic arrays in both practical and informatics sessions.

5. Informatics and data mining
The informatics necessary for the analysis of array and high-throughput sequencing data will be fully discussed in practical sessions. Data analysis will include data pre-processing (normalisation), inferential statistics, and descriptive (exploratory) statistics using public data and data generated on the course. Experimental design will also be discussed. The practical sessions will be complemented by short seminars related to the practicals as well as a series of invited seminars.

The practical sessions will be complemented by short seminars related to the practicals as well as a series of invited seminars.

Course instructors
Dr David Vetrie (University of Glasgow, UK)
Dr Cordelia Langford (Wellcome Trust Sanger institute, Cambridge)
Dr Peter Ellis (Wellcome Trust Sanger institute, Cambridge)
Dr Robert Andrews (Wellcome Trust Sanger Institute, Cambridge)
Guest speakers TBC shortly

Cost
The course tuition fees are subsidised by the Wellcome Trust for scientists based in academic institutions anywhere in the world. This is a residential course, without exception, and there is a registration fee of £975 towards board and lodging for academic applicants. The fee for commercial (non-academic) applicants is £4000.

Bursaries
Limited bursaries are available for academics (50 per cent of fee) and are subject to open competition.

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.

Bursaries for Wellcome Trust Advanced Courses
The Wellcome Trust subsidises all courses and workshops, so there are no tuition fees. The ‘course fee' for the UK courses (held at Hinxton) covers on-site accommodation and food for the duration of the course. Bursaries are available to assist with UK course fees, but not travel costs. We are committed to building scientific capacity in developing countries and are expanding the number of courses and workshops run outside of the UK (‘overseas' courses). There is no fee for these courses and bursaries are available for travel, sustenance and accommodation. Please see below for full details.

UK Courses (held at the Wellcome Trust Genome Campus in Hinxton)
A limited number of bursaries are available for each course. These are awarded by the selection committee according to merit. The bursary usually covers 50 per cent 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. All bursary requests to attend UK courses must be accompanied by a bursary application form. This must be completed and signed by your scientific sponsor (supervisor or head of department) and include justification for the bursary. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. We will reject incomplete applications. Both the application form and sponsor's letter must be received before the application deadline. The decision of the selection committee is final.

Overseas courses (held outside the UK)
A number of bursaries are available for each overseas course. These are awarded by the selection committee according to merit. There is no course fee.The bursary will cover travel, accommodation and sustenance. The maximum award for travel (in economy/second class) will be £750. All likely travel costs must be detailed in the overseas bursary application form, which must accompany all bursary requests for courses held outside of the UK. We will notify you of the chosen hotel and sustenance award if successful. The selection committee may judge that a partial award should be granted. We will reject incomplete applications. Both the application form and sponsor's letter must be received before the application deadline.