Table 2.
Hierarchical classification of HPV genotypes detected by cobas and Linear Arraya
| cobas group and subgroup | No. found by Linear Array |
||||
|---|---|---|---|---|---|
| HPV16 | HPV18 | Other high-risk genotype | Negative for all high-risk genotypes | Total (column %) | |
| All womenb | |||||
| HPV16 | 233 | 2 | 8 | 10 | 253 (13.9) |
| HPV18 | 0 | 69 | 4 | 7 | 80 (4.4) |
| Other high-risk HPV genotype | 4 | 1 | 658 | 61 | 724 (39.7) |
| Negative for all high-risk HPV genotypes | 9 | 0 | 77 | 681 | 767 (42.1) |
| Total (row %) | 246 (13.5) | 72 (4.0) | 747 (41.0) | 759 (41.6) | 1,824 (100) |
| HC2 negativec | |||||
| HPV16 | 16 | 0 | 1 | 6 | 23 (2.8) |
| HPV18 | 0 | 11 | 1 | 4 | 16 (2.0) |
| Other high-risk HPV genotype | 0 | 1 | 87 | 37 | 125 (15.2) |
| Negative for all high-risk HPV genotypes | 8 | 0 | 53 | 594 | 655 (80.0) |
| Total (row %) | 24 (2.9) | 12 (1.5) | 142 (17.3) | 641 (78.3) | 819 (100) |
| HC2 positived | |||||
| HPV16 | 217 | 2 | 7 | 4 | 230 (22.9) |
| HPV18 | 0 | 58 | 3 | 3 | 64 (6.4) |
| Other high-risk HPV genotype | 4 | 0 | 571 | 24 | 599 (59.6) |
| Negative for all high-risk HPV genotypes | 1 | 0 | 24 | 87 | 112 (11.1) |
| Total (row %) | 224 (22.2) | 60 (5.9) | 608 (60.2) | 118 (11.7) | 1,005 (100.0) |
Classification of specimens taken at 1-year follow-up visit after a previous HC2-positive test result, stratified by HC2 status at follow-up. LA and cobas results were categorized hierarchically according to cancer risk: HPV16 positive (possibly positive for another high-risk HPV genotype), HPV18 positive (HPV16 negative, HPV18 positive, and possibly positive for another high-risk HPV genotype), positive for one or more other high-risk HPV genotypes (HPV31, -33, -35, -39, -45, -51, -52, -56, -58, -59, and -68 as well as HPV66 but negative for both HPV16 and -18), and negative for all high-risk HPV genotypes (negative for HPV16, -18, -31, -33, -35, -39, -45, -51, -52, -56, -58, -59, and -68 as well as HPV66). Bold type indicates values that indicate that cobas tended to classify more women as HPV 16 positive than LA when the tests disagreed; underlining indicates values that indicate cobas tended to classify more women as HPV18 positive than LA when the tests disagreed; italics indicate total; shading indicates agreement between cobas and LA. Of 37 specimens that were HPV66 positive by LA and negative for all 13 carcinogenic HPV genotypes, 26 (70.3%) were HC2 positive. Comparatively, 31 (86.1% of 36; one specimen was missing a cobas result) were cobas positive for any of the carcinogenic HPV genotypes.
Agreement, 90.0%; overall kappa, 0.844 (95% CI, 0.822-0.866); weighted kappa, 0.871 (95% CI, 0.850-0.891); exact P value for symmetry, 0.029.
Agreement, 86.4%; overall kappa, 0.609 (95% CI, 0.543-0.675); weighted kappa, 0.629 (95% CI, 0.556-0.702); exact P value for symmetry, 0.229.
Agreement, 92.8%; overall kappa, 0.875 (95% CI, 0.848-0.903); weighted kappa, 0.901 (95% CI, 0.876-0.925); exact P value for symmetry, 0.101.