HLA region

(20240513)

For post-GWAS analyses, we often exclude HLA region due to its complexity of LD.

In gwaslab, exclude_hla is designed to remove variants in the extended MHC (xMHC) region.

From a practical point of view, by default, exclude_hla will remove variants in chr6:25mb~34mb (for both hg38 and hg19).

xMHC region : HIST1H2AA ~ 7.6mb ~ RPL12P1

reference: Horton, R., Wilming, L., Rand, V., Lovering, R. C., Bruford, E. A., Khodiyar, V. K., ... & Beck, S. (2004). Gene map of the extended human MHC. Nature Reviews Genetics, 5(12), 889-899.
range: start of HIST1H2AA ~ end of RPL12P1
- hg38: 25,726,063 ~ 33,400,644
- hg19 : 25,726,291 ~ 33,368,421
- T2T-CHM13v2.0 : 25,591,841 ~ 33,222,006

reference: Shiina, T., Hosomichi, K., Inoko, H., & Kulski, J. K. (2009). The HLA genomic loci map: expression, interaction, diversity and disease. Journal of human genetics, 54(1), 15-39.
range: start of GABBR1 ~ end of KIFC1
- hg38: 29,602,238 ~ 33,409,896
- hg19: 29,570,015 ~ 33,377,673
- T2T-CHM13v2.0 : 29,476,949 ~ 33,231,258