Entering edit mode
9.4 years ago
attiafatima
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0
How important is genotype frequency in SNP study? I our study design there are 2 groups progress and non-progress. We identified significant SNPs in progress group on basis of p-value using plink software and based on micro array study. In our results genotype frequencies are significant while allele frequencies are not significant and similarly haplotypes on haploview are also not significant.
Our SNPs are in strong LD and test for Hardy-Weinberg equilibrium suggested that the genotypes for both the SNPs were in Hardy-Weinberg proportions and there was no deviation from Hardy-Weinberg equilibrium.
Can anybody comment on the role of genotype frequency being significant in this case?
I think it's odd that the genotype frequency is significant but it's not in HW equil. If there is an enrichment for one genotype over the other then it might be selected for various evolutionary reasons (or enriched in disease if that's your game)