HLA loss at posttransplantation relapse. (A-C) B allele frequency of mismatched SNPs for each matched class 1 HLA gene in pretransplantation (gray) or relapse (red) specimens (left) and copy-number analysis of chromosome 6p (right). (A) The relapse specimen with 20% myeloblast percentage harbors a subtle allelic imbalance of HLA-A (left). Analysis of sorted myeloblasts confirms loss of HLA-A in the relapsed leukemic cells (right). (B) The relapse specimen harbors allelic imbalance of all class 1 HLA genes as a result of copy-neutral loss of heterozygosity across chromosome 6p (right; supplemental Figure 2). (C) The relapse specimen harbors allelic imbalance of HLA-B, which was the result of a 1-Mb deletion spanning HLA-B and HLA-C. (D) Clinical and sample characteristics for cases with relapse-specific HLA loss. cGVHD, chronic graft-versus-host disease; MAC, myeloablative conditioning; RIC, reduced-intensity conditioning; URD, unrelated donor.