Disease/Trait SNPs Enrichment Analysis

Question

[tahseen.abbas]

Hello Biostar Community!

I have got some GWAS SNPs in my sequencing data (exome).Can i do some enrichment analysis against the GWAS database to check whether these SNPs are significantly enriched in my data or not? If yes, then how to do it? Please guide.

[Kevin Blighe]

Please tell us the format of the data that you have (VCF?; PLINK PED format?; something else?). Also, 'significantly enriched' for what? - gene ontology?; KEGG pathways?; ...?

Answer 1

[GouthamAtla]

Hi, for this purpose, you need to use Coloc which tells if your SNPs are enriched within the genomic locations of any GWAS SNPs of particular trait.

I guess your statement I have got some GWAS SNPs in my sequencing data is not correct, because from exome-seq, you might have got SNPs and you wanted to check if they are strongly related to trait of your interests.