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Fernando Rivadeneira Genetic Laboratory Association testing - - PowerPoint PPT Presentation
Fernando Rivadeneira Genetic Laboratory Association testing - - PowerPoint PPT Presentation
Fernando Rivadeneira Genetic Laboratory Association testing Compare the allele distribution between cases and controls Only the markers that are close to a true risk increasing allele will be overrepresented in patients Only the
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Association testing
- Compare the allele distribution between cases
and controls
- Only the markers that are close to a true risk
increasing allele will be overrepresented in patients
- Only the markers that are close to a protective
risk increasing allele will be underrepresented in patients
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Research True relationship Finding yes no + (association) type 1 error
- (no association)
type 2 error
Error rate
Alpha/p-value Power = 1- beta beta
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True risk allele Marker Allele Proportion carriers 0.2 0.35 Odds ratio heterozygote 2 1.49 Odds ratio homozygote 4 2.27 Proportion carriers 0.2 0.35 Odds ratio heterozygote 1.5 1.24 Odds ratio homozygote 1.5 1.36
Comparing odds ratios for true risk allele and marker (r2=0.80)
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Adjustment for Multiple Testing
Test1 Test2
- k
- k
0.95 * 0.95=0.90 wrong
- k
- k
wrong wrong wrong 1-0.90=0.10 instead of 0.05 Bonferroni adjustment p = 0.05/2, the joint probability of at least 1 false + is 1- (0.975 2) = 1 – 0.95 = 0.05 If you test 125 variants, then the joint probability of at least 1 false + is 1- (0.95 125) = 1 – 0.00 = 1 Bonferroni adjustment p = 0.05/125 = 4.0 x 10-4
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