Microsatellite scanning of the immunogenome for associations with graft-versus-host disease following haematopoietic stem cell transplantation

Abstract

Non-HLA gene polymorphisms contribute to the immune response, leading to complications of haematopoietic stem cell transplantation (HSCT). A systematic approach using 4,321 microsatellite (MS) markers typing for 2,909 immune response genes (‘immunogenome’) on pooled DNA of 922 Japanese donors and recipients of HSCT was used to identify recipient and donor risk loci for graft-versus-host disease (GVHD). Splitting the population into discovery and confirmation cohorts (460/462 pairs), DNA pools were created for a 2-step pooled DNA screening. Fisher’s exact test for 2x2 (each MS allele) and 2xm Chi Square tests were performed, comparing allele frequencies of recipient/donor pools with GVHD grade 0-1 with those of GVHD grade 2-4. The independent, 2-step pooled DNA screening process has effectively reduced false-positive associations. In the final pooled DNA analysis, 17 (recipient) and 31 (donor) MS loci remained associated with risk or protection from GVHD and were further investigated by individual genotyping in the combined cohorts. Ten of these loci were confirmed to have consistent associations with GVHD; of these, two associations remained when applying multiple testing correction and multivariate statistics: D6S0035i (MAPK14, p=0.00035, OR=0.68) and D1S0818i (ELTD1, p=0.000078, OR=1.52). These findings implicate important new immunoregulatory genes with the process of moderate to severe acute GVHD. These data show that genetic susceptibility to GVHD following HSCT is complex and depends on multiple recipient and donor risk loci. Large-scale genomic screening with microsatellites on pooled DNA, here described for the first time in a HSCT population, is a useful method for the systematic evaluation of multigeneic traits.