How are the genomic regions related to the HLA region best handled, in terms of their complex LD structure? Often the region is simply excluded, but what if the HLA regions are biologically relevant for the phenotype (e.g. MHC complexes and autoimminity?)
Replying to “How are the genomic regions related to the HLA reg…”:
this is a great question - the answer is badly - if your trait involves HLA or other large complex blocks then you might want to add the region as a separate PRS on top of the GWAS back bone PRS
Replying to “How are the genomic regions related to the HLA reg…”:
Depending on what you want to do with the HLA region. for imputation, there is specific reference/method for this goal. For posterior effect estimates and PRS, SBayesRC can handle the HLA region without excluding them