HLA DNA typing: past, present, and future

The human leukocyte antigen (HLA) class I and class II loci are the most polymorphic genes in the human genome, with a highly clustered and patchwork pattern of sequence motifs. In the three decades since the first HLA gene was isolated by molecular cloning (a cDNA clone of HLA-B7), thousands of alleles have been identified and the names and sequences of all known alleles have been curated in the IMGT/HLA database. This extensive allelic diversity made and continues to make high-resolution HLA DNA typing very challenging. The first attempt at HLA DNA typing involved restriction fragment length polymorphism (RFLP) analysis, but this approach had many limitations. The development of PCR in 1985 allowed for the amplification of the polymorphic exons of the HLA class I and class II genes and the analysis of the polymorphic sequence motifs with sequence-specific oligonucleotide (SSO) hybridization probes. The immobilization of these probes on membranes and later on beads, along with primer sets for sequence-specific priming (SSP), gave rise to the current set of HLA typing reagents. Sanger sequencing has provided high-resolution typing but, in many cases, genotyping 'ambiguity' remains an issue. In the past few years, the introduction of next-generation sequencing, with the critical properties of massively parallel and clonal sequencing, has significantly reduced HLA genotyping ambiguity. Here, our lab's efforts to develop high-resolution and high-throughput HLA DNA typing using the 454 Sequencing System are reviewed, and the potential future developments and applications of HLA DNA typing are discussed.