HLA Diagnostic Sequencing – Conception, Application and Automation/Diagnostische HLA-Sequenzierung – Konzept, Anwendung und Automatisierung

Abstract

Sequencing gives the most reliable and accurate information of the DNA sequence of a gene and is therefore of particular interest for fully characterising the genetic complexity and allelic diversity of the HLA genes. The full complexity of allelic diversity in HLA class I and class II genes, as well as recent improvements in the convenience and quality of automated se-quencing, makes sequencing the method of choice for HLA low-and high-resolution typing. HLA typing by means of sequencing should be done whenever the HLA type of an individual is needed. The current developments with regard to HLA-sequencing systems, se-quencing instruments and software solutions for data interpretation have made sequencing equally simple and robust, providing formats for each level of throughput and automation in order to match each laboratory's individual requirements. Modern sequencing is based on direct sequencing of PCR products from genomic DNA with the help of fluorescent-labelling methods using dye terminator cycle sequencing chemistries with spe-cialised DNA polymerases and automated capillary se-quencers. The presently available HLA sequencing systems differ mainly in regard to their PCR amplification strategies and software solutions for allele identification. As the diversity of all HLA loci developed through extensive sequence exchanges, resulting in chimeric structures of each HLA allele, the allele-specific sequencing approach is the most successful for high-resolution typing (4 digits), as it is capable of determining the cis linkage of sequence motifs. This is achieved by applying multiple group-specific amplifications in parallel, thus splitting the alleles into individual groups. This approach increases the capacity for cis linkage definition and in turn decreases the number of ambiguities. When sequencing shall be established as the only method for 4-digit HLA typing, these group-specific approaches must be used. When sequencing shall be used also for 2-digit HLA typing, a gene-specific amplification approach for sequencing of both alleles simultaneously should be applied. Thus, the progress made in diagnostic HLA sequencing now offers a real alternative to the conventional molecular typing techniques, and will increasingly replace them for the patients' benefit.