Monomorphic variants in TNFA gene

Question

[goyal.shiwali]

I have studied 34 SNPs in a gene with MAF of 0.0001 to 0.0003. On analysis, these all come out to be monomorphic in our study sample. I want to include all these 34 SNPs in my student's thesis. Which statistical tools can be applied to such kind of data?? Thanks in advance

[lakhujanivijay]

Hi goyal.shiwali

Please re frame your question title. The title "Single Nucleotide Polymorphism" does not provide any relevant information.

Read : How To Ask Good Questions On Technical And Scientific Forums

[WouterDeCoster]

In addition, please elaborate on what you mean with 'monomorphic', and tell us how many individuals you have. Are you doing an association study, comparing patients and controls? What is your biological question?

[goyal.shiwali]

Monomorphic means SNPs which exist in one state (same form or genotype), in our case we have studied 286 patients and 300 controls, and in all cases and controls the observed genotype was wild type. The present study is an association study. What type of statistical analysis we can perform on such kind of data???

[WouterDeCoster]

So all are heterozygous alternative allele? Wildtype is a strange term for human genetics.

If you do an association study, and all patients and controls have the same genotype, then it's not associated with your phenotype.

[goyal.shiwali]

Even I know there is no association of these SNPs with the phenotype, my question was if such kind of data exists then what type of statistical analysis we can perform on such kind of data?

[WouterDeCoster]

I'll just repeat my question because you didn't answer it: So all are heterozygous?

Before we can figure out which statistical analysis to do (if anything) you need to know what your biological question is. We already figured out there is no association. Then what do you want to test?

If you want to prove there is no association, just do a Fisher Exact test like you would do with any variant, and see that the p-value is not indicative of significance (it won't).

[goyal.shiwali]

For an association study, a polymorphism has three genotypes, e.g. rs1800629 has G>A change in which there are three genotypes, GG is wild type, GA is heterozygous and AA is mutant. In our case, all the 34 SNPs showed only wild type genotypes and these were confirmed using Sanger sequencing. So the next task we need to perform is to do statistical analysis if possible? If yes then how we can conclude our finding? Thanks

[WouterDeCoster]

Did you even read what I wrote?

Before we can figure out which statistical analysis to do (if anything) you need to know what your biological question is. We already figured out there is no association. Then what do you want to test?

If you want to prove there is no association, just do a Fisher Exact test like you would do with any variant, and see that the p-value is not indicative of significance (it won't).

[goyal.shiwali]

Anyhow thanks for your time