Gene counting method, as the name implies, is just counting the number of copies of the gene present in an individual and hence a population/study group. In a diploid organism, like humans, the gene counting is done by first assigning the genotype to every sample. All the gene count in a homozygote is 2 while in a heterozygote is 1 for each gene. So if you have two alleles A and B, then gene count for:

the homozygote AA is 2A and

BB is 2B and

heterozygote AB is 1A+1B. 

If a population/group of 100 individuals (total chromosomes/gene copies = 100x2=200, diploid genome) have 70AA, 10AB and 20BB then the gene count is:

Count of A = 2x70+10 = 150

Count of B  = 2x20+10 = 50

This is an easy way to see if there are any differences in the frequencies of the alleles between groups. In the above example the group had an excess of A compared to B.

Hi Ratna

I do not know of any advantages of the method. However, there is one large disadvantage; i.e., comparisons among populations with different number of genotyped individuals are very difficult to make.

This is because you expect an increase in the number of alleles as you increase your sampling number, but you do know nothing about the rate (how many more individuals do you need to find a new allele?)

Therefore, some other methods than direct counting are used in order to make possible comparisons of allele richness among populations (i.e., rarefaction, as in FSTAT).

Hope this helps

Pablo

You can use direct allele counting in case-control studies to create contingency tables and do association tests. There are many free online tools to do this, such as http://vassarstats.net/newcs.html, and many of these sites provide an explanation of the underlying concepts.

Dear all. Thank you very much. You have helped me a lot. Now, I understand. 

can anyone help me how can i calculate haplotypes?