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Six hundred twenty-one samples from Portugal, the Cabo Verde archipelago, and Guinea-Bissau were typed for HLA-A, HLA-B, and HLADRB1 using the polymerase chain reaction–sequence-specific oligonucleotide probe (PCR-SSOP) method and the sequence-based typing (SBT) method to characterize and compare discrepancies between the two methods. Fifty-three alleles (4.27% of 1,242 chromosomes typed) identified by the PCR-SSOP method were not concordant with the results obtained using the SBT method. Thirty-four (2.74% of total chromosomes typed) PCR-SSOP mistyping results were discrepancies inside the same allele group and 19 others (1.53% of total chromosomes typed) were relative to nonconcordant results between different groups. PCR-SSOP allele mistyping is the result of interpretation difficulties resulting from less intense, absent, or dubious hybridization patterns. Noncommercial PCR-SSOP procedures are highly exigent on the technicians’ experience and the availability of properly calibrated high-precision equipment.