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A/B blood groups and malaria

From the earlier data it certainly looked like O blood group is associated with severe malaria outcomes. But what about A/B blood group?

Including the variants as seperate predictors​

The second variant in this data, rs8176746, encodes A/B blood type, with the 'T' allele encoding 'B' blood type and the 'G' allele (which the reference sequence carries) encoding 'A' blood type. For the most part, the O blood group mutation only occurs an A blood type background.

Note

Satisfy yourself of this by tabling the two variants in the data.

To test for association with A/B status, we could of course just put the A/B SNP in the model instead. For a simple approach I suggest encode as an additive model for simplicity:

data$rs8176746_dosage = NA
data$rs8176746_dosage[ data$rs8176746 == 'G/G' ] = 0
data$rs8176746_dosage[ data$rs8176746 == 'G/T' ] = 1
data$rs8176746_dosage[ data$rs8176746 == 'T/T' ] = 2
Challenge question

Use logistic regression to test for association between A/B blood type and severe malaria status. Are they associated? What is the estimated relative risk and confidence interval?

Warning

The A/B and O blood group variants are linked - could O blood type be a confounding factor?

Note. For extra marks, find a way to encode A/B/O blood group directly. Approximately this is done using the following table which lists genotypes for rs8176719 and rs8176746:

combined genotype  blood group phenotype
-----------------  ---------------------
    C/C  G/G               A
    C/C  G/T               AB
    C/C  T/T               B
    -/C  G/G               A
    -/C  G/T            B or A? (*)
    -/C  T/T               B
    -/-  G/G               O
    -/-  G/T               O
    -/-  T/T               O

Note. There is a worked solution in case you get stuck.