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immunogenomics / HLA-TAPAS

HLA-TAPAS pipeline for HLA association and fine-mapping studies
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HLAassoc #15

Open jhylwq123 opened 2 years ago

jhylwq123 commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 commented 5 months ago

@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"?