We have undertaken a study to identify the potential SNP’s associated with PCOS in Indian Population. We selected few previously known SNPs and carried out PCR-RFLP method to identify the gene polymorphism. We need to check whether the polymorphisms show any deviations from Hardy-Weinberg Equilibrium (HWE). When we read the literature, we came to know that the deviations from the Hardy-Weinberg Equilibrium (HWE) or the Linkage disequilibrium (LD) can be estimated with the help of χ2 test. But we don’t know how to prepare or what all things to be considered while preparing the data sheet for the analysis and how to interpret the results? If anybody is willing to help us, we will be very grateful to them.
pls see this link on the FINETTI program where you can visualize the HWE deviations.
http://ihg.gsf.de/cgi-bin/hw/hwa1.pl
you may also follow this question
https://www.researchgate.net/post/Is_there_a_threshold_for_the_hardy-Weinberg_equilibrium/1
Its very simple. There are plenty of hardy Weinberg online calculators available. All you need to input is the genotype counts in the cells. Ideally you should calculate separately for your controls and then cases. If the p value is less than 0.05 then it implies there is a deviation and you should look in to the causes of it. If it is >0.05 then no issues and you can report the p value and chi-squared values in the article.
You can do it by hand.
Assuming a biallelic marker (A and B) with allele frequencies p and q, the expected proportions under HWE is the binomial expansion p2 + 2pq+q2. From your allele counts, you can estimate p and q, and hence the expected genotypic proportions: p2, 2pq and q2 for e.g., AA, AB, BB, respectively. For each cell, subtract the the observed genotype count from the expected count and square the result. The sum of the squared differences across the (in this case three) cells is chi-square distributed with 1df.
Note: You should calculate HWE in the control group only. HWE is theoretically a test of random mating within a population, although in practice it is used as a genotyping quality control check. One would not necessarily expect HWE among cases at an associated locus.
All previous answers are suitable, but be careful to test HWE equilibrium on controls only. Do not test on patients as a variant strongly associated with the disease would sometimes show deviance from HWE in patients sample. Deviance from HWE in control subjects may result from genotyping errors, from stratification of the control sample...
You can also use the Haploview software to test for HWE in your control population (http://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview).
Regarding HWE deviance you have some papers about it:
Am J Hum Genet 2005 76:887-883 A note on exact tests of Hardy-Weinberg equilibrium.
Am J Hum Genet. 2005 Jun;76(6):967-86. Epub 2005 Apr 15.
Rational inferences about departures from Hardy-Weinberg equilibrium.
Eur J Hum Genet. 2005 Jul;13(7):840-8.
Hardy-Weinberg equilibrium in genetic association studies: an empirical evaluation of reporting, deviations, and power.
Ann Hum Genet. 2007 Sep;71(Pt 5):701-3; author reply 704. Epub 2007 Mar 27.
On the usage of HWE for identifying genotyping errors.
As suggested by others HW equilibrium calculation is very easy to do. U can also follow this link also, www.tufts.edu/~mcourt01/.../Court%20lab%20-%20HW%20calculator.x...
Download this excel file and have to put respective numbers of genotypes for a particular SNP. Rest follow advice by others to interpret the results.
See also, Waples, R.S. (2015) Testing for Hardy-Weinberg proportions: Have we lost the plot? Journal of heredity 106 (1): 1-19.
I am sure that until now you have done your analysis. This is a useful aricle for new readers.
Article New alterations at potentially regulated regions of the Glia...
hello Veera Manikandan R can you suggest me should we check HWE in gender wise stratified controls? and what if the controls are not in HWE in one the genser population.
Deviations from Hardy-Weinberg equilibrium for a genetic variant can be calculated using the Chi-square test. An online calculator for this, which can handle variants with up to 10 alleles can be found here: https://www.genecalculators.net/pq-chwe-check.html.
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