How To Look For Enrichment Of Gwas Snps In List Of Regions

Question

[Rubal7]

Hi Everyone,

I have a list of genomic regions (mapped to hg18) and want to see if these are enriched for GWAS significant SNPs. Does anyone know of a more standardised compilation of GWAS results than here http://www.genome.gov/gwastudies/ ? As compilations of GWAS results will have been done accross different human genome mappings over time won't this cause problems when trying to combine them, or do SNPs such as rs1342525 somehow reference different locations in different mappings ( seems unlikely ).

Anyway, if anyone has any experience of looking for enrichment of GWAS SNPs in a list of genome regions some advice would be great. I haven't found any software for this so far so am planning to manually check if a list of GWAS snps appears significantly more frequently in my regions compared to lists of randomly selected regions of equal size.

Best

Rubal

Answer 1

[ff.cc.cc]

Try the UCSC GWA table for hg18 here

There is also a useful sql script to import data into a mysql db, if you need it.

[Rubal7]

This looks good, can you provide some information on where this dataset comes from? Many thanks

[ff.cc.cc]

Hi, http://hgdownload.cse.ucsc.edu/goldenpath/ is the site where you can download UCSC public data tracks. Very nice to build a local (even portable) installation of selected features.

Answer 2

[Khader Shameer]

See this manuscript on a method for enrichment analysis using GWAS/SNP data/

I can recommend following tools:

1. HaploReg : tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci.
2. GREAT: assigns biological meaning to a set of non-coding genomic regions by analyzing the annotations of the nearby genes.