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SNP FAQ Archive [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2005-.
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I am having trouble understanding how the Hardy-Weinburg Probability (HWP) value is calculated for SNP records. I’m no statistician, so it would be helpful if you could include an example.
A good explanation of HWP and how it is calculated can be found in an online Wikipedia article.
Currently, we use the chi-square and p-value in our HWP calculations. Here is an example of how we calculate the HWP for ss221 in a population (population id as 506) following the HWP equation.
_
GtyFreq subsnp_id pop_id gty_str cnt 0.411 221 506 A/G 37.000000 0.144 221 506 A/A 13.000000 0.444 221 506 G/G 40.000000 _
cnt AlleleFreq subsnp_id pop_id allele 117.000000 0.650 221 506 G 63.000000 0.350 221 506 A _
subsnp_id pop_id ind_cnt 221 506 90.000000 _
subsnp_id pop_id chr_cnt 221 506 180.000000 _
subsnp_id pop_id Degree of Freedom 221 506 1 _
exp_gtyFreq subsnp_id pop_id exp_gtyCnt allele_1 allele_2 gty_str 0.422 221 506 38.025 G G G/G 0.455 221 506 40.950 G A A/G 0.122 221 506 11.025 A A A/A _
subsnp_id pop_id gty_str observed_gtyCnt 221 506 G/G 40.00 221 506 A/G 37.00 221 506 A/A 13.00 _
subsnp_id pop_id Chi-square 221 506 0.837 After obtaining the chi-square value, calculate the p-value using the degrees of freedom via the gamma function, or many websites offer p-value calculators. (9/11/07)
How is HWP (Hardy Weinberg Probability) found in the Population Diversity section of the refSNP report determined, and how does it relate to genotype data?
A good explanation of HWP and how it is calculated can be found online. The next question in this section also contains information you should find useful. (6/4/07)
Your Hardy Weinberg probabilities are calculated using 2 df—an incorrect calculation. Because only one independent parameter is being used to estimate (p=1-q), = there should only be 1 df.
Thanks for pointing out the inclusion of failed assays in the Hardy Weinberg estimates for refSNP (rs) clusters appearing on rs cluster reports as well as in the genotype and allele frequency reports. We will exclude such genotypes in the Hardy Weinberg equilibrium calculations for the release of dbSNP build 120.
Many of the assumptions of the Hardy Weinberg equilibrium are not necessarily met in the submissions to the dbSNP, but we do believe that there is utility (although limited) in calculation of Hardy Weinberg equilibrium over rs clusters. Please see the Hardy Weinberg equilibrium performed over submitted SNPs (ss) by population. These are listed in the submitted SNP details page as well as in the genotype and allele frequency report. Please be aware, however, that the population in the context of dbSNP may (or may not) differ from a population as defined in a population genetics context.
The displayed value for HWP on your web page is different than the FAQ which calculates it. Am I using the correct calculation method?
To speed up database update, we have used a lookup table which is binned. This is a contributory factor as to why the P value is not exact but should be close. To calculate the P value (chi-square distribution), we used the Gamma Function. I think we got the C algorithm from Numeric Recipe book.
If you are interested in HWE, have you looked at Fisher Exact test? From what biologists have told us, the Fisher Exact test is a better way to estimate HWP especially when sample size is small. When time allows, we hope to switch our HWE calculations from the Chi-square test to the Fisher Exact test.(08/01/08)
- Hardy Weinberg Equilibrium Data - SNP FAQ ArchiveHardy Weinberg Equilibrium Data - SNP FAQ Archive
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