HLAassoc

[jhylwq123]

Thank u for creating this amazing tool! I have two questions.

1. How does HLA-TAPAS deal with the multiallele situation in logistic regression model(HLA alleles，two field)?
2. If I impute HLA region in Michigen web server, Can i also do the omnibus test based on the results? As my understanding, perform omnibus test need the bim file of reference panel, which is not available now.

[yluo86]

Thank you @jhylwq123 for using HLA-TAPAS.

1. For HLAassoc module - that is to perform linear/logistic regression using PLINK, treats individual HLA alleles/variants independently. In other words, if an individual has HLA-A01:01 and HLA-A01 at two different resolutions, HLAassoc will test each one independently.
2. For omnibus test, you can find the bim file here: https://github.com/immunogenomics/HLA-TAPAS/blob/master/resources/wgsMHC.bglv4.bim (G-group) and https://github.com/immunogenomics/HLA-TAPAS/blob/master/resources/wgsMHC.4digit.bglv4.bim (4-digit)

[jhylwq123]

Thank you so much. Your comments really helped me. May I ask two more questions about omnibus?

1. When I perform Omnibus, it generate two files. One is for each amino acid position ,the other is for each amino acid haplo. But I can't interpret these two files properly. For example, the AA_DRB1_31_32552069 position has 4 amino acid which are AA_DRB1_31_32552069_exon2_F, AA_DRB1_31_32552069_exon2_FL, AA_DRB1_31_32552069_exon2_FV, AA_DRB1_31_32552069_exon2_I and 2 haplo. Does that mean AA "F,FL,FV" is one haplo, and AA "I" is the another haplo. In the amino acid haplo file, it gives the p value of "AA_DRB1_31_32552069_exon2_I", Does the P mean the difference between "AA_DRB1_31_32552069_exon2_I" and "AA F,FL,FV " ? And why sometimes the haplo is NA in the file?
2. I have two GWAS cohorts tested by two microarray for the same trait. If I want to meta the results of omnibus, which file you recommend me to use, the one for each amino acid position or the one for each amino acid haplotype?

[asangphukieo]

@jhylwq123 Did you find the answer? I also have this ambiguous amino acid issue.

@yluo86 Could you please provide the meaning of AA e.g. "F,FL,FV"?