遺伝統計学集中講義

Genetic Statistics
Lectures
（３）
Handling of single SNP data
Single SNP data analysis
• Create 2x3 contingency table
– Parameters
•
•
•
•
•
Allele frequency of risk allele
Prevalence
Population size
Risk per genotype
No. cases and controls.
– Fx
• ROUND
– Hardy-Weinberg equilibrium
– Excel file “Create2x3.xls”
SNP data analysis（１）
•
•
•
•
•
•
•
No. cases and controls.
No. inds per genotype
No. Total samples
Genotype frequency, allele frequency
Whisch allele is risky
OR
Excel “3-3-41SNPcontrol-case.xls”
SNP data analysis（２）
• Hardy-Weinberg equilibrium test
– Expected numbers
– χ2 ｐ
– HWE exact test
– Cases, Controls, Total
SNP data analysis（３）
• Case control association tests
– Genotype test(２ｘ３ table, df=2)
– ２ｘ２ contingency table
test(allele,dominant,recessive)
– Trend test for allele
– Trend tests for dom. and rec.
– Excel “Trend.xls”
SNP data analysis（４）
• OR～RR
– Compare OR and RR
– Confidence interval and p

Download Report