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Part 2. A GWAS (Genome Wide Association Study) study is genotyping 1,000 individuals (300 controls...

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Part 2. A GWAS (Genome Wide Association Study) study is genotyping 1,000 individuals (300 controls and 700 cases) for 500,000 different SNPs in search for genes involved in the (non-fictional) disease lupus. At position 45,897,592 of chromosome 2, the measurements are as follows for a C/T SNP: - control individuals: 50 C:550 T - case individuals: 200 C: 1200 T 2.1) is one allele more frequent among the cases compared to the controls? Which one? 2.2) To test if the difference in allele frequencies between case and controls is significant, you will now calculate the corresponding chi-square value. Make sure you give the details of your calculations. 2.3) Based on the chi-square value that you obtained in the previous question, you conclude that there is a significant association between allelic state at this position of the genome and lupus. Using the table below, would you say that the odds of this association being spurious are: - 3.84) 3.84 6 6.64 0.01 .64 10.831 0.001 10.83 0.051 A) Greater than 5% chi-square value B) Between 5% and 1% p-value C) Between 1% and 0.1% D) Less than 0.1% 2.4) After performing the same analysis for all 500,000 SNPs, you find 5,042 SNPs for which the chisquare test gives a p-value

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