HLA association results

Data

Starting from R9, for each release, the analysis team runs association analyses for classical HLA alleles that have been imputed from the FinnGen genotype data. The imputation pipeline has been developed by Jarmo Ritari from the Finnish Blood Service. More information about the imputation is available in the imputation pipeline repository or in the publication:

Ritari J, Hyvärinen K, Clancy J, FinnGen, Partanen J, Koskela S. Increasing accuracy of HLA imputation by a population-specific reference panel in a Finngen biobank cohort. NAR Genomics and Bioinformatics, Volume 2, Issue 2, June 2020, lqaa030, https://doi.org/10.1093/nargab/lqaa030

QCtools is used to generate a variant-level summary of the genotypes.

Association analysis

Association analysis of the classical HLA alleles is performed using regenie. See the core analysis documentation for more information.

Files

As of R9, the outputs of this analysis include:

• A QCtool variant report

• Association analysis summary statistic files

• A summary of the association analysis.

See the release notes for HLA analysis for more information about the data.

The files are available in the green library: /finngen/library-green/finngen_R12/finngen_R12_analysis_data/hla

Read more about imputation of FinnGen HLA alleles and data file of the imputed HLA alleles.