If in a studies population the observed genotype frequency and the allele frequency of the studies gene is different from the expected genotype frequency calculated according to HardyWeinberg equation (p2x 2pqxq2 =1). what does that mean? and why this happen ?
firstly a detail...the HW equilibrium is p2 +2pq +q2 =1 and refers to 2 alleles in a population that are in equilibrium. When this equation is not true then it means that some factor is acting in favour ( or against) one allele . Some factors that will cause this equation to not work are mating choices , genetic bottlenecking, genetic disorders, founder effects and inbreeding ( there are more) any of which can favour or discriminate against one allele so that the other is not in equilibrium with it
Thank you very much for your reply. what I mean is that for example for my specific studied SNP the observed genotype frequency was for eg:
AA= 0.42
Aa= 0.54
aa=0.03
and the allele frequency was :
A=0.69
a=0.31
While when calculation the expected genotype frequency predicted by the HW equilibrium, the result was:
AA= p2= 0.69 x 0.69=0.48
Aa= 2pq =2 x 0.69 x 0.31=0.43
aa=q2= 0.31x 0.31= 0.09
so the observed and the expected genotype are not exactly the same. Does that mean the genotype distribution is not in HW equilibrium ? or just what matter is that the sum of the 3 genotype should equal to 1?
HW says that the frequencies of alleles and genotypes will stay the same through the generations as long as there are no evolutionary influences. For HW to be accurate the following rules must apply
Mating must be random
Population size must be large, so a few individuals are not accounting for a significant portion of the gene pool
No migration, meaning individuals cannot be entering or leaving the population
No random mutations are occurring in the genes being studied
No natural selection applies related to the genes being studied
I expect that your allele frequencies do not add up to 1.0 ( 0.99 is very close) could be due to a small sample size and if,for instance each of your allele frequencies was 0.003 higher it would be rounded down to the figures given at 2 decimal places but, in reality, using the third decimal place the sum would be very close to 1.0
Concerning the exact ratios small sample size will give different figures from the ideal as will non random mating due to health, wealth or biological fitness (survival) and can you be reasonably sure that people are not entering or leaving the studied population. HW does not indicate a reason for disequilibrium it just calculates that there is a disequilibrium and leaves the user to study the research group to determine the most likely cause of the disequilibrium
Thanks again. So I understand that most probably my study group is not in HW equilibrium due to the small sample size ( my sample size is only 59 cases) and really I cant be sure of the other factors like random mating, migration, natural selection etc....
most probably yes. If you want to look at the results ( .42AA, .54 Aa and .03aa) in a different context let us apply it to sickle cell disease SCD and let A be normal and a be sickle then aa will be low due to homozygous sicklers dying early in the population and AA could be low due to normal in the populations dying early due to malaria but Aa heterozygotes can be over represented as the heterozygotes are protected partly from malaria but do not suffer from SCD.
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