HLA‐OLI: A new MHC class I pseudogene and HLA‐Y are located on a 60 kb indel in the human MHC between HLA‐W and HLA‐J

Analysis of publicly available whole‐genome sequence data from the Human Pangenome Project and the 1000 Genomes Project has identified a DNA segment of approximately 60 kb in the major histocompatibility complex (MHC) between HLA‐W and HLA‐J that is present in some MHC haplotypes but not others. This DNA segment is largely repeat element‐rich but includes the pseudogene HLA‐Y, thus pinpointing the location of this pseudogene, and a new HLA class I sequence we have called HLA‐OLI. HLA‐OLI clusters phylogenetically with the HLA class I pseudogenes, HLA‐P and HLA‐W, and appears to have a similar genetic structure. The availability of whole‐genome sequence data from diverse populations enables a detailed characterization of the MHC at the population level and will have implications for understanding MHC disease associations and the non‐HLA MHC factors that impact unrelated hematopoietic cell transplant outcomes.