Human Lymphocyte Antigen Typing: Direct DNA Typing-The Only Choice?

Abstract

Exact human lymphocyte antigen (HLA) allele matching and sequence variation are important for matching organ donors, immune response studies, and disease association investigations. The number of HLAs has reached several hundred within each of the different classes. This level of heterogeneity makes routine DNA typing to the allele level problematic using fixed probe and primer technologies. Routine large-batch screening programs where only intermediate-level typing is required can be performed in automated fashion by several DNA technologies. Screening large numbers of samples with probe-based technologies, even oligo array chips, is cost effective. Allele-specific typing is most easily performed using direct sequencing. New sequencing technologies based on cycle sequencing and high-speed capillary gels have made routine sequencing for clinical typing a reality. The complexity of the class I locus requires a detailed analysis of all the polymorphisms within exons 2 and 3. Sequencing strategies are thus designed to use informative variable regions within the flanking introns and the flanking region as well as the untranslated regions. Simliar strategies are being adapted to the complex class II DRB alleles, which now number about 200 different alleles. Greater understanding of HLA diversity and distribution throughout humans and their relatives facilitates organ matching and the history and origins of human populations. Knowledge of parasites and their role in the selection of alleles will ultimately lead to better prediction and manipulation of the immune system response to these organisms. HLA typing is used to determine relative risk to a variety of autoimmune diseases. Future uses of molecular HLA typing may include the prevention and cessation of these self-destructing diseases.