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Table 3 Human papillomavirus (HPV) genotyping agreement for tissue specimens* tested with four different genotyping methods

From: Detection of HPV DNA in paraffin-embedded cervical samples: a comparison of four genotyping methods

HPV Method 1 Method 2 Percenta Kappa  
Type Name Positive Name Positive agreement Value 95 % CI P
Oncogenicb          
Any Onclarity 54 Inno-LiPA 51 81.7 0.2 −0.15 0.48 0.5
Any Onclarity 54 Linear Array 48 86.7 0.5 0.19 0.78 0.07
Any Onclarity 54 SPF-LiPA25 57 91.7 0.4 −0.01 0.82 0.4
Any Linear Array 48 Inno-LiPA 51 81.7 0.4 0.07 0.67 0.5
Any Linear Array 48 SPF-LiPA25 57 85.0 0.3 0.05 0.65 0.004
Any SPF-LiPA25 57 Inno-LiPA 51 86.7 0.3 −0.06 0.62 0.07
By single probe          
16 Onclarity 26 Linear Array 24 90.0 0.79 0.64 0.95 0.7
16 Onclarity 26 Inno-LiPA 25 91.7 0.83 0.69 0.97 1.0
16 Linear Array 24 Inno-LiPA 25 95.0 0.9 0.78 1.0 1.0
16 SPF-LiPA25 29 Onclarity 26 88.3 0.77 0.6 0.93 0.5
16 SPF-LiPA25 29 Inno-LiPA 25 90.0 0.8 0.65 0.95 0.2
16 SPF-LiPA25 29 Linear Array 24 91.7 0.83 0.69 0.97 0.1
18 Onclarity 8 Inno-LiPA 7 98.3 0.92 0.78 1.0 1.0
18 Onclarity 8 Linear Array 5 95.0 0.74 0.47 1.0 0.3
18 Linear Array 5 Inno-LiPA 7 96.7 0.82 0.57 1.0 0.5
18 SPF-LiPA25 8 Linear Array 5 95.0 0.74 0.47 1.0 0.3
18 SPF-LiPA25 8 Inno-LiPA 7 98.3 0.92 0.78 1.0 1.0
18 SPF-LiPA25 8 Onclarity 8 96.7 0.86 0.66 1.0 1.0
31 Onclarity 7 Inno-LiPA 7 96.7 0.84 0.62 1.0 1.0
31 Onclarity 7 Linear Array 6 98.3 0.91 0.75 1.0 1.0
31 Linear Array 6 Inno-LiPA 7 98.3 0.91 0.75 1.0 1.0
31 SPF-LiPA25 7 Linear Array 6 98.3 0.91 0.75 1.0 1.0
31 SPF-LiPA25 7 Onclarity 7 96.7 0.84 0.62 1.0 1.0
31 SPF-LiPA25 7 Inno-LiPA 7 100 NA NA NA NA
33 Linear Array 2 Inno-LiPA 2 100 NA NA NA NA
33 SPF-LiPA25 2 Linear Array 2 100 NA NA NA NA
33 SPF-LiPA25 2 Inno-LiPA 2 100 NA NA NA NA
35 Linear Array 0 Inno-LiPA 0 NA NA NA NA NA
35 SPF-LiPA25 0 Inno-LiPA 0 NA NA NA NA NA
35 SPF-LiPA25 0 Linear Array 0 NA NA NA NA NA
39 Linear Array 2 Inno-LiPA 2 100 NA NA NA NA
39 SPF-LiPA25 2 Inno-LiPA 2 100 NA NA NA NA
39 SPF-LiPA25 2 Linear Array 2 100 NA NA NA NA
45 Onclarity 5 Inno-LiPA 2 91.7 0.25 −0.19 0.69 0.4
45 Onclarity 5 Linear Array 3 93.3 0.47 0.03 0.91 0.6
45 Linear Array 3 Inno-LiPA 2 95.0 0.38 −0.18 0.93 1.0
45 SPF-LiPA25 5 Linear Array 3 96.7 0.73 0.38 1.0 0.5
45 SPF-LiPA25 5 Inno-LiPA 2 95.0 0.55 0.11 0.99 0.3
45 SPF-LiPA25 5 Onclarity 5 96.7 0.78 0.49 1.0 1.0
51 Onclarity 1 Inno-LiPA 2 98.3 0.66 0.04 1.0 1.0
51 Onclarity 1 Linear Array 1 100 NA NA NA NA
51 Linear Array 1 Inno-LiPA 2 98.3 0.66 0.04 1.0 1.0
51 SPF-LiPA25 2 Linear Array 1 98.3 0.66 0.04 1.0 1.0
51 SPF-LiPA25 2 Onclarity 1 98.3 0.66 0.04 1.0 1.0
51 SPF-LiPA25 2 Inno-LiPA 2 100 NA NA NA NA
52 Onclarity 5 Inno-LiPA 3 93.3 0.47 0.03 0.91 0.6
52 Onclarity 5 Linear Array 2 95.0 0.55 0.11 0.99 0.3
52 Linear Array 2 Inno-LiPA 3 98.3 0.79 0.4 1.0 1.0
52 SPF-LiPA25 6 Linear Array 2 93.3 0.47 0.05 0.9 0.1
52 SPF-LiPA25 6 Inno-LiPA 3 95.0 0.64 0.27 1.0 0.3
52 SPF-LiPA25 6 Onclarity 5 95.0 0.7 0.38 1.0 1.0
56 Linear Array 1 Inno-LiPA 1 100 NA NA NA NA
56 SPF-LiPA25 1 Linear Array 1 100 NA NA NA NA
56 SPF-LiPA25 1 Inno-LiPA 1 100 NA NA NA NA
58 Linear Array 3 Inno-LiPA 3 100 NA NA NA NA
58 SPF-LiPA25 3 Linear Array 3 100 NA NA NA NA
58 SPF-LiPA25 3 Inno-LiPA 3 100 NA NA NA NA
59 Linear Array 2 Inno-LiPA 0 NA NA NA NA NA
59 SPF-LiPA25 1 Linear Array 2 98.3 0.66 0.04 1.0 1.0
59 SPF-LiPA25 1 Inno-LiPA 0 NA NA NA NA NA
66 Linear Array 0 Inno-LiPA 0 NA NA NA NA NA
66 SPF-LiPA25 1 Inno-LiPA 0 NA NA NA NA NA
66 SPF-LiPA25 1 Linear Array 0 NA NA NA NA NA
68 Linear Array 1 Inno-LiPA 0 NA NA NA NA NA
  1. * Genotyping agreement for 60 formalin-fixed and paraffin embedded (FFPE) specimens in the SUCCEED study; Onclarity, The BD Onclarity™ HPV Assay; Inno-LiPA, The Inno-LiPA system; Linear Array, The PGMY09/11 Linear Array, and SPF-LiPA25, The SPF10-DEIA, LiPA25 (version 1); p, p-value of the McNerman test; b Any, includes a specimen positive for any of the 14 HPV types; NA, not apply or cannot be calculated; HPV 52 was positive when there was a test negative for HPV 33, 35, and 58 individually but positive for the combined probe 52/33/35/58 (for Linear Array)