Question: How To Look For Enrichment Of Gwas Snps In List Of Regions
1
gravatar for Rubal7
6.6 years ago by
Rubal7760
Rubal7760 wrote:

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

genome gwas enrichment • 3.4k views
ADD COMMENTlink written 6.6 years ago by Rubal7760
1
gravatar for ff.cc.cc
6.6 years ago by
ff.cc.cc1.3k
European Union
ff.cc.cc1.3k wrote:

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.

ADD COMMENTlink written 6.6 years ago by ff.cc.cc1.3k

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

ADD REPLYlink written 6.6 years ago by Rubal7760

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.

ADD REPLYlink written 6.6 years ago by ff.cc.cc1.3k
1
gravatar for Khader Shameer
6.6 years ago by
Manhattan, NY
Khader Shameer18k wrote:

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.

ADD COMMENTlink modified 6.6 years ago • written 6.6 years ago by Khader Shameer18k
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