LP_HLA

Analysis scripts and summary statistics data for HLA fine-mapping for oral and non-oral lichen planus (LP) in FinnGen.

J Ritari, MP Reeve, FinnGen, M Siponen, M Vehviläinen, T Salo, K Osoegawa, M Fernandez Viña, B Goudey, J Partanen, E Mignot. Fine mapping of HLA effects in Oral and non-Oral lichen planus. https://www.medrxiv.org/content/10.1101/2025.11.17.25340396v1

Scripts in src/:

• LP_HLA_data.R Data preparation steps prior to analysis. Conversion of imputed HLA genotype data to dosages. Preparation of basic covariate and LP phenotype matrices for use with Regenie.

• LP_HLA_functions.R Helper functions for analyses. Loading R libraries, functions for converting dosage information to plink format for input to Regenie. Functions for processing association output files produced by Regenie.

• LP_HLA_homozygotes.R Definition and extraction of DQA1-DQB1 homozygotes from imputed HLA allele data. HLA allele association analayses on DQ homozygotic samples using Regenie. Plotting the results.

• LP_HLA_allele_combinations.R Analysis of known combinations of HLA-DQA1 and HLA-DQB1 alleles as they occur in imputed FinnGen HLA data. Definition of DQ allele pairs and their dosages. DQ combination genotype association analysis using Regenie. Plotting the results.

• LP_HLA_allele_conditional.R Conditional association analysis of HLA alleles using Regenie. Specific HLA allele dosages are included as additional model covariates. Plotting the results.

• LP_HLA_SNPs.R Association analyses on MHC region SNP genotypes conditioned on specific HLA allele dosages using Regenie. Plotting the results.

Association summary statistics data in supplementary_data/:

Excel tables of all conditional association analysis results.

• LP_HLA_alleles_conditional Conditional association analysis of HLA alleles. Each conditioning step is in its own sheet, with the additional HLA allele covariates given in the last column.

• LP_HLA_DQ_homozygotes_conditional Conditional association analysis of HLA alleles limited to HLA DQA1-DQB1 homozygous samples. Each conditioning step is in its own sheet, with the additional HLA allele covariates given in the last column.

• LP_HLA_DQA1-DQB1_diploid_haplo_conditional Conditional association analysis of diploid DQA1-DQB1 haplotypes. The first column gives the analysed genotype defining the haplotypes. Each conditioning step is in its own sheet, with the additional HLA allele covariates given in the last column.

• LP_HLA_DQA1-DQB1_haplo Conditional association analysis of DQA1-DQB1 haplotypes. The first column gives the analysed genotype defining the haplotypes. Each conditioning step is in its own sheet, with the additional HLA allele covariates given in the last column.

• LP_HLA_DQB1_heterozygotes Association analysis of heterozygous combinations of HLA-DQB1 alleles. The first column gives the analysed genotype defining the DQB1 allele combinations.