Interpretation of Risk Loci From Genome-wide Association Studies

Assignment Task

Details of GWAS Loci

To complete this assessment, you must select ONE of the three loci listed in this folder (( I selected number 1 rs10791824_chr11_GWAS))

• The files are named with the sentinel SNP and the chromosome, with each file having the following columns: rsID, chromosome, position, p_value (this information is required for analysis in LDLink)
• All loci are taken from the paper "Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis", Nature Genetics, 47, pages 1449-1456. This paper is attached with the assessment.

The analysis of these files must include:

• A figure using LDLink to define the range of linkage disequilibrium and the boundaries of the region likely to include the causal SNP (or SNPs) [ USE GRCh37 and European populations, insert the sentinel SNP in the file name as “Variant”, select a region + 200,000bp ]
• A figure from the UCSC Genome Browser [ GRCh37 ] that shows annotation of the locus, including DnaseI hypersensitivity site, H3K4me3, H3K4me1, H3K27ac, , and gene [removed]eQTL, RNAseq – to be covered in the Week 7 tutorial)
• The overall rationale of the assessment is to provide a summary of the regulation of genes in the human genome, and to then to use results from GWAS to apply a systematic strategy to identify possible causal SNPs within the locus your have chosen, with a focus on regulatory DNA

1. You will be provided with a choice of GWAS results that identify a locus that illustrates an aspect of the genetic basis of gene regulation and common disease. You will select one result to describe and analyse in your review

2. The review will begin with a clear description of the problem you are investigating, and will include the aims of the review

3. Using current research papers and review articles, you will describe the theory of gene regulation and place this in the context of findings from GWAS. This is also called an argument - the use of evidence (what you provide from published papers and figures) and reasoning (your ability to synthesize information and develop your points in a logical manner) that is used to solve a problem and reach a conclusion.

4. To do this, your review must include ONE figure from the University of California at Santa Cruz (UCSC) Genome Browser (covered in the online practical classes). The figure must be described in an accompanying figure legend, with the source of the images provided in the figure legend and correctly cited in the reference list .

5. Your analysis of data from the UCSC Genome Browser must also incorporate considerations of linkage disequilibrium by incorporating ONE figure from the LDLink set of tools that will be covered in the online practical classes. 

6. You will be limited to a maximum of 10 references, with references correctly formatted in the Vancouver style

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