Lecture 13: GWAS

Question 1

Which kind of diseases are investigated using GWAS?

Answer 1

complex diseases with no DSL

Question 2

What is genotype calling?

Answer 2

Determining which genotype a patient has based on the data.

Question 3

Name the typical GWAS error filters:

Answer 3

1) MAF < 0.05
2) error rate (no definitive geotype) > 2 %
3) HWE if p < 0.00001
4) In family samples: more than 5 errors in mendels laws
5) Subjects with excessive transmission rates (deviates from 0.5) - only done in families.
6) relatedness checks - if related when shouldnt be - remove

Question 4

Why are p-values uniformly distributed?

Answer 4

When testing something that derives from the same distribution we can expect the p-values to be uniform (since that is the definition of p-values)