H0: no causal variant
H1: causal variant for trait 1 only
H2: causal variant for trait 2 only
H3: two distinct causal variants
H4: one common causal variant
What I have in mind for trait 1 is "expression level of gene A", for trait 2 is "breast cancer".
H0 is easy to understand: the genomic region interrogated has nothing to do with trait 1 or trait 2.
H1 is a little harder. First I thought I understand it, but now I am not sure. Does it really mean there is a variant in the underlying genomic region that is causing (NOT being associated with) the changes in expression level of gene A? First I thought it merely suggests association instead of causality here, but the "causal" in "causal variant" puts me to rethink.
H2 similar to H1.
H3 & H4 are quite confusing. To make my questions clearer, please take a look at the figure below (Verena Zuber 2022)
Guess my questions could be simplified to:
which plot in the above figure corresponds to H3 and which plot to H4?
May I guess B corresponds to H4? A to H3?
How about plot C, D, and E? Are they tested as well?
Which hypothesis is equivalent to "The change of gene A expression level causes the change of risk of breast cancer"?
Which plot describes the scenario of "The change of gene A expression level causes the change of risk of breast cancer"? C & E?
For coloc, we have 5 competing hypotheses:
H0: no causal variant H1: causal variant for trait 1 only H2: causal variant for trait 2 only H3: two distinct causal variants H4: one common causal variant
What I have in mind for trait 1 is "expression level of gene A", for trait 2 is "breast cancer".
H0 is easy to understand: the genomic region interrogated has nothing to do with trait 1 or trait 2.
H1 is a little harder. First I thought I understand it, but now I am not sure. Does it really mean there is a variant in the underlying genomic region that is causing (NOT being associated with) the changes in expression level of gene A? First I thought it merely suggests association instead of causality here, but the "causal" in "causal variant" puts me to rethink.
H2 similar to H1.
H3 & H4 are quite confusing. To make my questions clearer, please take a look at the figure below (Verena Zuber 2022)
Guess my questions could be simplified to:
Thanks so much in advance!