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  • 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!

  • #2
    The probability that the SNP is associated with a particular disease.

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    • #3
      and the lower the p value the more likely it is that this es true?
      and how do you calculate such a thing?

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      • #4
        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).

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        • #5
          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?

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          • #6
            See the wikipedia definition of Odds Ratio.

            https://en.wikipedia.org/wiki/Odds_ratio

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