Y-chromosome variants associate with acute GVHD. (A) Acute GVHD in sex-matched and sex-mismatched donor–recipient pairs, including a statistically significant association (star) in female-to-male (F>M) allogeneic stem cell transplant. Variants were identified in 4 genes (PCDH11Y, USP9Y, UTY, and NLGN4Y), which are displayed with approximate locations on the Y chromosome (B). Precise genomic coordinates and nucleotide and amino acid positions are tabulated, with variant residues shown in red. In some cases, alternative proteasomal cleavage prediction resulted in multiple peptides. (C-E) HLA-restricted affinity prediction for each color-coded peptide is shown for acute GVHD and non-GVHD patients (C) and summarized (D), with application of the recommended threshold for strong binders per male recipient (E). WT, wild-type.