SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Single nucleotide polymorphism (SNP) discovery in polyploid ramouz87 Bioinformatics 1 07-09-2010 07:25 AM

Reply
 
Thread Tools
Old 03-06-2017, 03:32 AM   #1
nhaus
Junior Member
 
Location: germany

Join Date: Mar 2017
Posts: 4
Default 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!
nhaus is offline   Reply With Quote
Old 03-06-2017, 11:59 AM   #2
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

The probability that the SNP is associated with a particular disease.
mastal is offline   Reply With Quote
Old 03-06-2017, 12:06 PM   #3
nhaus
Junior Member
 
Location: germany

Join Date: Mar 2017
Posts: 4
Default

and the lower the p value the more likely it is that this es true?
and how do you calculate such a thing?
nhaus is offline   Reply With Quote
Old 03-08-2017, 01:40 AM   #4
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 836
Default

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).
gringer is offline   Reply With Quote
Old 03-08-2017, 02:14 AM   #5
nhaus
Junior Member
 
Location: germany

Join Date: Mar 2017
Posts: 4
Default

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?
nhaus is offline   Reply With Quote
Old 03-08-2017, 03:40 AM   #6
mastal
Senior Member
 
Location: uk

Join Date: Mar 2009
Posts: 667
Default

See the wikipedia definition of Odds Ratio.

https://en.wikipedia.org/wiki/Odds_ratio
mastal is offline   Reply With Quote
Reply

Tags
gwas, p-value, snp

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:53 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO