The wild allele of the SNP has higher frequency than variant risk allele in both control and case population, So how I can interpret this?
It could be that the sampled organisms in both your case population and control population were mostly mutants since the wild allele is the allele you would typically expect to find most often in the population. The wild type allele would typically not be the minor allele. Other reasons such as sequencing errors and incorrect prior assumptions about allele frequencies could also be the reason why the results were unexpected. One option is to repeat the experiment using different biological repeats and doing more technical repeats of the same biological sample.
Other studies and also meta-analysis also demonstrated this fact about this polymorphism.
If the phenomena is widely observed, the lower wild type allele frequency might be have been caused by genetic drift:
https://en.wikipedia.org/wiki/Genetic_drift
It means there is more than one SNP causing risk for the disease in your cases, and you haven't yet discovered or tested the other one(s). Is the frequency of the risk allele higher in cases than controls? That is the only metric that matters for this analysis.
Thank you Simon, could you please explain more, or tell me some key words to search about this topic.
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