Article Figures & Data
Tables
- Table 1.
Genotype data comparing the PCR-SSO test with the HLA-B*27 targeted tag-SNP assay. Both tag SNP were 100% concordant. The HLA-B allele designation corresponding to the false-positive and -negative calls were false-positive (HLA-B*39:06/*49:XX) and false-negative samples (HLA-B*27:05/*35:XX; HLA-B*27:05/*18:01; HLA-B*27:05/*52:01, and HLA-B*27:05/*35:XX). Values are n unless otherwise specified.
Variables PCR-SSO HLA-B*27 Tag-SNP, rs4349859 HLA-B*27 Tag-SNP, rs116488202 HLA-B*27–positive samples 172 167 167 HLA-B*27–negative samples 828 831 832 False-positive samples N/A 1 1 False-negative samples N/A 4 4 Analytical sensitivity, % 100 97.6 97.6 Analytical specificity, % 100 99.9 99.9 Analytical accuracy, % 100 99.6 99.6 Analytical precision1, % 100 N/A 100 Samples with reportable genotype 1000 998† 999# ↵1 Precision analysis was performed using 89 samples run in duplicate only for the rs116488202 assay.
↵† Two samples failed to generate a result for the rs4349859 assay due to insufficient DNA for amplification (1 sample) and a variant under the primer-binding site (1 sample).
↵# A single sample failed to generate a result for the rs116488202 assay due to insufficient DNA for amplification. PCR-SSO: PCR-sequence–specific oligonucleotide; SNP: single-nucleotide polymorphism; N/A: not applicable.
- Table 2.
Economic and time comparison of the HLA-B locus PCR-SSO test with the HLA-B*27 targeted tag-SNP assay (rs116488202).
Variables HLA-B Locus PCR-SSO HLA-B*27 Tag-SNP Cost per sample, $ 64.91 4.61 3.28 Cost per run, $ 714.00 92.16 190.02 Hands-on time per run, min 209 151 403 Hands-on time per sample, min 19 6.30 6.30 Samples tested per run, n 11† 20 58 ↵† The HLA-B locus kit is sufficient to perform 16 reactions (11 samples, 4 rotating positive controls, 1 non-template control). Given that it is easy to mix up sample order during the wash cycle step for the PCR-SSO kit, a minimum of 4 controls is strongly recommended. Hands-on time represents the total time for run preparation paperwork, wet work, quality control, result analysis, interpretation, second checking, and reporting. PCR-SSO: PCR-sequence–specific oligonucleotide; SNP: single-nucleotide polymorphism.
