ORIGINAL ARTICLE The impact of frequent HLA haplotypes in high linkage disequilibrium on donor search and clinical outcome after unrelated haematopoietic SCT MM Jo ¨ ris 1,2 , AC Lankester 3 , PA von dem Borne 4 , J Kuball 5 , M Bierings 6 , JJ Cornelissen 7 , ME Groenendijk-Sijnke 8 , B van der Holt 8 , GW Haasnoot 2 , HGM van der Zanden 1 , SM van Walraven 1 , JJ van Rood 1,2 , FHJ Claas 2 and M Oudshoorn 1,2 The MHC region on chromosome 6 contains a large number of non-HLA genes next to the HLA genes. Matching for HLA in unrelated hematopoietic SCT (HSCT) does not necessarily mean that these non-HLA genes are also matched. We selected 348 Northwest European patients transplanted with an HLA-A-, -B-, -C-, -DRB1-, -DQB1-matched unrelated donor (MUD) between 1987 and 2008. Patients’ haplotypes were identified via descend. We were unable to determine the haplotypes of the donor; therefore we used frequent haplotypes (FH) in high linkage disequilibrium (LD) as a proxy for haplotype matching. Presence of a FH in a patient positively affected the probability and speed of identifying a matched unrelated donor. Competing risk survival analysis showed that patients with one or two FH have a statistically significantly decreased probability of developing Xgrade II acute GVDH (aGVHD) without increased risk of relapse compared to patients without FH (HR (95% CI): 0.53 (0.31–0.91)). This association was strongest for those FH with the highest LD between both HLA-A and -C or –B, and HLA-C or –B and -DRB1 (HR (95% CI): 0.49 (0.26–0.92)). These results extend evidence that non-HLA allele coding regions have a significant impact on development of Xgrade II aGVHD. We conclude that there is more to successful HSCT than matching for HLA genes. Bone Marrow Transplantation advance online publication, 15 October 2012; doi:10.1038/bmt.2012.189 Keywords: HLA haplotypes; linkage disequilibrium; unrelated donor search; unrelated HSCT; non-HLA genes; acute GVHD INTRODUCTION Acute GVHD (aGVHD) is a major cause of mortality following unrelated hematopoietic SCT (HSCT). Even in patients transplanted with a 10/10 allele level typed HLA-matched unrelated donor (UD) the incidence of aGVHD may still be significant. 1 This indicates that not only classical HLA antigen mismatches are responsible for the development of aGVHD. The MHC region on chromosome 6 is one of the most densely gene-packed segments of the human genome and contains a large number of non-HLA genes which spread across the entire class II, class III and class I segments. 2 In 10/10 HLA-matched unrelated donor–patient pairs there is no certainty that these non-HLA genes are also matched, because these matched pairs do not necessarily share the same haplotypes. The biological impact of HLA haplotype matching for HSCT has not been explored as extensively as that of matching for HLA alleles or loci. Matching for the HLA-B, -C and HLA-DR, -DQ haplotype blocks, 3 and more recently, matching for HLA-A, -B, -DR haplotypes 4 within 10/10 HLA-matched unrelated donor–patient pairs is associated with less post transplantation complications. Furthermore, Japanese patients having one of three most frequent haplotypes (FH) were found to have differential risk of developing aGVHD. It appeared that the genetic factor of specific haplotypes is associated with either increased or decreased risk of aGVHD. 5 The role of some of these non-HLA genes have been studied (reviewed 6–10 ): single nucleotide polymorphisms and/or microsatellites within cytokine (-receptor) genes and other non-HLA encoded genes, including those of the innate immune system, may indeed influence HSCT outcome. 11–17 Genes in the TNF block, MICA/MICB and microsatellite markers are of specific interest because they are in linkage disequilibrium (LD) with the classical HLA genes and could be inherited together as one genetic unit. 13–15,18–21 The presence of FH in patients also affects the probability and speed of identifying a matched UD. 22–28 It is essential to know the HLA distribution of each population at an allelic level in order to define whether a patient has a high or low probability of finding a matched donor. 27 Our group has previously shown that 30% of Northwest European patients became medically unfit during the search process and therefore did not receive a HSCT (which was unrelated to donor availability). Search time was identified as the most crucial factor in the UD search. 29 The aim of this study was therefore to identify the most frequent 5 locus allele level typed HLA haplotypes in the Dutch population and to elucidate the effect of frequency and LD of the patients’ HLA haplotypes on donor search and clinical outcome of unrelated HSCT. PATIENTS AND METHODS HLA genotyping, HLA-haplotypes and LD All donors and patients were typed at allele level for HLA-A, -B, -C, -DRB1, -DQB1 using PCR sequence-specific primer and sequence-based typing. Patients transplanted before 1996 and their donors were typed at allele 1 Europdonor Foundation, Leiden, The Netherlands; 2 Department of Immunohematology and Blood transfusion, LUMC, Leiden, The Netherlands; 3 Department of Pediatrics, LUMC, Leiden, The Netherlands; 4 Department of Hematology, LUMC, Leiden, The Netherlands; 5 Department of Hematology and Immunology, UMCU, Utrecht, The Netherlands; 6 Wilhelmina Children’s Hospital, UMCU, Utrecht, The Netherlands; 7 Department of Hematology, Erasmus MC-Daniel den Hoed, Rotterdam, The Netherlands and 8 HOVON Data Center, Erasmus MC-Daniel den Hoed, Rotterdam, The Netherlands. Correspondence: MM Jo ¨ ris, Europdonor Foundation, Plesmanlaan 1b, 2333 BZ Leiden, The Netherlands. E-mail: joris@europdonor.nl Received 12 July 2012; revised 20 August 2012; accepted 23 August 2012 Bone Marrow Transplantation (2012), 1–8 & 2012 Macmillan Publishers Limited All rights reserved 0268-3369/12 www.nature.com/bmt