SSP and SSOP methods assay which parts of HLA alleles?

The SSP (Sequence-Specific Primer) and SSOP (Sequence-Specific Oligonucleotide Probe) methods are designed to detect specific alleles of HLA (Human Leukocyte Antigen) genes. These methods primarily target hypervariable regions of HLA alleles. Hypervariable regions are characterized by their extensive polymorphism, which means these areas exhibit a high degree of variability between different alleles.

This variability is essential for the identification of specific HLA alleles because it allows for the discrimination of even closely related alleles based on unique sequence differences. The high mutation rate in these regions directly correlates with the immune system's need for diversity in the HLA molecules presented on cell surfaces, which is crucial for the recognition and presentation of antigens by T cells.

In contrast, conserved regions of HLA genes do not vary much between different alleles, making them less useful for allele-specific assays. Similarly, promoter regions, while important for gene expression regulation, do not have the specific sequence diversity necessary for distinguishing between different HLA alleles and are not the target regions in these assays. Introns, which are non-coding regions within a gene, also do not provide the necessary allele specificity required for the performance of SSP and SSOP