Results obtained from T-ARMS PCR
on what basis we select a genotype to dominant or recessive
Dominant vs. recessive describes the relationship between alleles, not genotypes. You need additional information to know which allele is dominant. Do you know the phenotype to go with each genotype? Or the level of gene expression?
You could always run the analysis more than once and see what results you see if you assign G as dominant to A or A as dominant to G.
i mean statistical model such as
GG vs GA+ AA
or
AA vs GA+ GG
@katie A Burnette
Dear Mushtaq, I agree with Katie. Nevertheless I would like to give you an advice. May be it helps You. Try to find information in NCBI, I mean SNP database. At least You will see allele frequency and moreover can receive usefull links on clinical trials and rewievs. One more way is clinicaltrials.gov. I did it some times. It could help.
Mushtaq Ahmad, one of [GG vs GA+ AA] or [AA vs GA+ GG] will be a recessive model (and the other dominant) - depending on which allele is dominant. You could also try other genetic models e.g. co-dominant and additive. However, this will all depend on whether you know the underlying mode of inheritance a priori. If you don't try the genetic-model free approach ( Article The choice of genetic model in the meta-analysis of molecula...
) or standard pairwise approach.
Hi Mushtaq Ahmad. It will be better if you check your rs in NCBI SNP database (dbSNP). There are lots of information including minor allele frequency and OMIM database informations. You can also check the SNP at 1000 genome database. You will find SHIFT and PolyPhen score at that site for your specific SNP which indicates the pathogenic allele.
Dear Mr. Ahmed,
I agree will opinions presented by all scientists. You should identify the exact mutation of the studied gene(s) and get their information from the Ensemble as well as NCBI, which will give you the sequence of the gene and the SNPs in which base and the dominant and the recessive alleles/genotypes can be extrapolated from that . With statistical analysis you have to study the dominant and the codominance or the genotype that involves the combined dominant and /or recessive alleles in the case in comparison with those of the control group. The following link might help you.
http://asia.ensembl.org/index.html?redirect=no
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