Does anyone know how can i realise an SNP-SNP interaction analysis. we achieved a gene-condidate study analysing 3 SNP of a same gene in relation to cancer. we founded how to achieve the gene-environement interaction and haplotyes analysis but we dont know how to do the SNP-SNP interaction analysis (statistical analyse, program, methodology needed .
thanks
Hi Kacem,
Sorry to ask, but did you check if the three SNPs were in linkage or not?
I will advice you on SNP-SNP interaction (epistasis) once you get back.
Regards,
Venk
Hi Venk ,
Among the three SNPs only two are in linkage disequilibrium (REGION 3-UTR). the last one are functional SNP located in the start codon of the gene, which leads to an alternative translation start site.
Best regards,
Kacem
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