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Table 4 Human papillomavirus (HPV) genotyping agreement for paired cytology and tissue specimensa tested with different genotyping methods

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

Overall agreement Onclarity Inno-LiPA Linear Array SPF-LiPA25
with cytology N (%) N (%) N (%) N (%)
Identical 32 (53.3) 34 (56.7) 32 (53.3) 37 (61.7)
Compatible 19 (31.7) 17 (28.3) 15 (25.0) 20 (33.3)
Discrepant 9 (15.0) 9 (15.0) 13 (21.7) 3 (5.0)
HPV type %a kappa p %b kappa p %a kappa p %a kappa p
Any oncogenic typec 90.0 NA   85.0 NA   80.0 NA   95.0 NA  
Single probe             
HPV 16 83.3 0.7 0.1 88.3 0.8 0.02 86.7 0.7 0.01 88.3 0.8 0.5
HPV 18 95 0.8 1.0 96.7 0.9 0.5 93.3 0.7 0.1 98.3 0.9 1.0
HPV 31 95 0.8 1.0 98.3 0.9 1.0 96.7 0.8 0.5 98.3 0.9 1.0
HPV 33 NA    100 1.0 NA 100 1.0 NA 100 1.0 NA
HPV 35 NA    98.3 NA   98.3 NA   98.3 NA  
HPV 39 NA    96.7 0.7 0.5 96.7 0.7 0.5 96.7 0.7 0.5
HPV 45 91.7 0.6 0.1 90.0 0.4 0.03 91.7 0.5 0.1 95.0 0.7 0.3
HPV 51 91.7 0.3 0.1 93.3 0.5 0.1 91.7 0.3 0.1 93.3 0.5 0.1
HPV 52d 98.3 0.9 1.0 95.0 0.6 0.3 93.3 0.5 0.1 96.7 0.8 1.0
HPV 56 NA    95.0 0.4 0.3 95.0 0.4 0.3 95.0 0.4 0.3
HPV 58 NA    96.7 0.7 0.5 96.7 0.7 0.5 96.7 0.7 0.5
HPV 59 NA    NA    100 1.0 NA 98.3 0.7 1.0
HPV 66 NA    NA    NA    95.0 0.4 0.3
HPV 68 NA    NA    98.3 0.7 1.0 NA   
  1. a Genotyping agreement for 60 paired cytology- and 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); Identical, same number and type identified; Compatible, at least one type in common identified; Discrepant, no type in common identified or FFPE sample HPV negative; a Only single probes, but including probe combined probe 52/33/35/58 for Linear Array;b Percentage of overall agreement; c Includes a specimen positive for any of the 14 HPV types; d HPV 52 was positively identified in the linear Array test when the presence of HPV 33, 35, and 58 was excluded; p, p-value of the McNemar test; NA, not apply or cannot be calculated