For a given disorder you genotype 10,000 cases and 10,000 controls ...

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For a given disorder you genotype 10,000 cases and 10,000 controls for a SNP with alleles G and A. You observe 1100 cases and 900 controls have the A allele (all others have G).

Create a 2 x 2 table (Table 1) with columns “cases” and “controls” and rows “A allele” and “G allele”. Populate the fields with the corresponding values.

Calculate the odds ratio for getting the disease if you have the A allele. ___________________

To determine the statistical significance of this odds ratio, perform chi-square analysis. Chi-square simply compares observed values versus expected values if there was no association.

Step 1: Create a 2 x 4 table (Table 2) with columns “observed” and “expected” and rows “case A”, “control A”, “case G”, “control G”.

Step 2: Insert the observed data into Table 2.

Step 3: Calculate the expected frequency of the A and G alleles for cases and controls, assuming NO association. This is done by:
Expected A cases = (A cases + A controls) / (total cases + controls)
Expected A controls = Expected A cases (because assuming no association)
Expected G cases = (G cases + G controls) / (total cases + controls)
Expected G controls = Expected A cases (because assuming no association)

Step 4: Insert the expected values into Table 2.

Step 5: Calculate chi square or enter the data in Table 2 into the chi square table on the “chi-square calculator” graphpad website:

Hit the “calculate now” button.

What is the chi-square value? _______
What is the p value? _________

Is this SNP significantly associated with the disorder?    Yes No
This SNP is located between two genes. Give one interpretation for these data.

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