Comprehensive approach to high-resolution KIR typing

Abstract

Multiple studies suggest that prospective KIR typing may be beneficial for the outcome of bone marrow transplants, but to date no practical high-resolution KIR typing system has been developed. Here we propose a comprehensive high-resolution typing approach that provides allele level KIR typing. Based on the low-resolution typing obtained by SSO, the 14 KIR loci are divided in groups according to the level of polymorphism in exons coding for extracellular Ig-like domains and cytoplasmic tail. The first group is typed by sequence-specific oligonucleotide only; the second is typed by sequence-based typing (SBT) based on the amplification of a fragment coding the Ig-like domains; and the third is typed by SBT based on amplification of a fragment coding the cytoplasmic tail. SBT for the fourth group includes both the Ig-like and cytoplasmic domains. Because of a considerable number of polymorphisms scattered throughout all nine KIR exons, SBT results may still produce a number of ambiguities, which can be resolved by sequence-specific primers. This combined high-resolution approach was applied to the complete KIR typing of 205 Caucasian hematopoietic stem cell donors in support of the National Marrow Donor Program High-resolution KIR Typing Pilot Project. High-resolution typing of several KIR loci produced numerous novel alleles, whereas some loci demonstrated very limited polymorphism. Several of the novel alleles appeared in more than four donors, suggesting that these alleles are not rare. Our results showed that the comprehensive KIR typing approach presented here provides the balance of high-resolution typing and cost effectiveness.