How to solve it hint: malaria
All, the small data file for the SNP association test is posted. There are 5 SNPs, and the data is in two sheets, cases and controls. From your lecture notes you should be able to remember that you can test for association using a chi-squared test — and this data set is large enough for that to be true.
Background information: How do you set up that test? For the chi-squared test you need expected and observed frequencies for four groups: has malaria and allele 1, has malaria and allele 2, no malaria and allele 1, no malaria and allele 2.
To get the expected frequencies:
- count the number of allele 1 in the entire population under test (100o people = 2000 chromosomes)
- divide by the total chromosome population
- multiply by number of chromosomes in each test group to get expected frequencies — this gives you the values you would expect if the null hypothesis, no significant association, was true.
Note: one of the SNPs is the sickle cell allele (HbS) of hemoglobin. This information may help you recognize when you have a correct outcome.