Table 3.: Comparison of Genotype Detection by Direct PCR and Conventional PCR: Overall Agreement, Positive Agreement, Kappa Index, and McNemar Test

HPV Genotype Direct PCR/ Conventional PCR Agreement Positive Agreement Kappa McNemar p-Value
+/+ +/- -/+ -/-
6 15 7 11 62 81.05 15.79 0.499 0.481
11 8 4 8 75 87.37 8.42 0.499 0.388
16 52 6 1 36 92.63 54.74 0.849 0.125
18 16 0 1 78 98.95 16.84 0.963 1
26 0 1 0 94 98.95 0.00 - -
31 6 3 2 84 94.74 6.32 0.677 1
33 5 0 3 87 96.84 5.26 0.753 0.25
35 3 1 1 90 97.89 3.16 0.739 1
39 7 1 2 85 96.84 7.37 0.806 1
40 0 1 1 93 97.89 0.00 - -
42 12 0 1 82 98.95 12.63 0.954 1
43 5 4 2 84 93.68 5.26 0.591 0.687
44/55 2 0 1 92 98.95 2.11 0.795 1
45 4 0 2 89 97.89 4.21 0.789 0.5
51 7 1 0 87 98.95 7.37 0.928 1
52 8 4 0 83 95.79 8.42 0.778 0.125
53 4 3 3 85 93.68 4.21 0.537 1
54 6 0 2 87 97.89 6.32 0.846 0.5
56 4 1 1 89 97.89 4.21 0.789 1
58 5 1 1 88 97.89 5.26 0.822 1
59 1 2 2 90 95.79 1.05 0.312 1
61 1 0 3 91 96.84 1.05 0.390 0.25
62/81 7 2 2 84 95.79 7.37 0.755 1
66 3 3 3 86 93.68 3.16 0.466 1
67 1 0 2 92 97.89 1.05 0.492 0.5
68 2 2 1 90 96.84 2.11 0.555 1
69 1 0 0 94 100.00 1.05 1 1
70 3 1 2 89 96.84 3.16 0.650 1
72 0 1 1 93 97.89 0.00 - -
73 2 0 2 91 97.89 2.11 0.657 0.5
82 3 2 1 89 96.84 3.16 0.65 1
84 2 1 0 92 98.95 2.11 0.795 1
89 3 0 0 92 100.00 3.16 1 1

N: number. CI: confidence interval. Calculations were done considering the 95 HPV samples found to be HPV-positive with at least one of the protocols.