<scp>HLA‐OLI</scp>: A new <scp>MHC</scp> class I pseudogene and <scp>HLA‐Y</scp> are located on a 60 kb indel in the human <scp>MHC</scp> between <scp>HLA‐W</scp> and <scp>HLA‐J</scp>
Nickolai Alexandrov, Ting Wang, Lindley C. Blair, Brian Nadon, D. Sayer
Abstract
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.