Overview of different HLA typing techniques
Typing method | Basic mechanism | Advantages | Disadvantages |
---|---|---|---|
Serologic method | Detection of HLA molecules using antisera | • Rapid screening • Suitable for deceased donor typing |
• Low resolution • Limited availability of serological reagents • Typing limited to known alleles |
SSO | Hybridization with short oligonucleotide DNA probes | Multiple sample typing | • Low to intermediate resolution • Typing limited to known alleles • Certain amount of ambiguities |
SSP | Amplification of HLA alleles with sequence-specific primers | • Low cost • Applicable for deceased donor • Different resolutions can be obtained depending on the primers |
• Unsuitable for large numbers of samples • Low to intermediate resolution • Typing limited to known alleles • Certain amount of ambiguities |
SBT | Direct DNA sequencing | • High resolution • Able to sequence novel alleles |
• Requires longer time • High cost • Unable to set phase between polymorphisms • Not suitable for deceased donor typing |
NGS | Sequencing of small fragments of DNA in parallel | • High resolution • High throughput • Able to sequence novel alleles • Low ambiguity • Whole-gene coverage |
• Expensive sequencer • Requires suitable software for analysis • Not suitable for deceased donor typing |
TGS | • Individual DNA molecule sequencing in real time (PacBio SMRT sequencing) • Single DNA molecule sequencing through a nanopore (Oxford Nanopore sequencing) |
• High resolution • Able to sequence novel alleles • Low ambiguity and phasing • Whole-gene coverage • Applicable for deceased donor typing (Oxford Nanopore sequencing) |
• Expensive equipment • Relatively high error rate • Require suitable bioinformatics tools |
HLA, human leukocyte antigen; SSO, sequence-specific oligonucleotide; SSP, sequence-specific primers; SBT, sequence-based typing; NGS, next-generation sequencing; TGS, third-generation sequencing, SMRT, Single-Molecule Sequencing in Real Time.