SEQanswers Meaning of the P-value relating to SNP (single nucleotide polymorphism)
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 03-06-2017, 03:32 AM #1 nhaus Junior Member   Location: germany Join Date: Mar 2017 Posts: 4 Meaning of the P-value relating to SNP (single nucleotide polymorphism) Hey guys, im relatively new to the subject and coundnt find a proper answer to my question in the internet yet... :/ I am currently trying to understand a paper about Genom wide association studies (GWAS) and they constantly talk about p-values of SNP. And i just dont understand what the p value is telling me in that context... I hope you guys can help me!
 03-06-2017, 11:59 AM #2 mastal Senior Member   Location: uk Join Date: Mar 2009 Posts: 667 The probability that the SNP is associated with a particular disease.
 03-06-2017, 12:06 PM #3 nhaus Junior Member   Location: germany Join Date: Mar 2017 Posts: 4 and the lower the p value the more likely it is that this es true? and how do you calculate such a thing?
 03-08-2017, 01:40 AM #4 gringer David Eccles (gringer)   Location: Wellington, New Zealand Join Date: May 2011 Posts: 836 P-values are frequently (and in my opinion incorrectly) used to represent the size (or significance) of the genetic difference between two populations at a particular locus. It's better to use p-values as an initial filter, and rank based on another statistic that better represents the thing of biological importance (e.g. chi^2, odds ratio).
 03-08-2017, 02:14 AM #5 nhaus Junior Member   Location: germany Join Date: Mar 2017 Posts: 4 okay. I got another question in that context regarding the Odds Ratio(OR) and I will try to explain what I mean with an example: There is a common SNP in Parkinson that is associated with a higher risk of getting Parkinson, e.g. G vs A. The odds ratio of G is 1.5 . Does that mean that an individual is 1.5 times as likely to get Parkinson as an individual with the A allel?
 03-08-2017, 03:40 AM #6 mastal Senior Member   Location: uk Join Date: Mar 2009 Posts: 667 See the wikipedia definition of Odds Ratio. https://en.wikipedia.org/wiki/Odds_ratio

 Tags gwas, p-value, snp