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

Castro, Felipe A.; Koshiol, Jill; Quint, Wim; Wheeler, Cosette M.; Gillison, Maura L.; Vaughan, Laurence M.; Kleter, Bernhard; van Doorn, Leen-Jan; Chaturvedi, Anil K.; Hildesheim, Allan; Schiffman, Mark; Wang, Sophia S.; Zuna, Rosemary E.; Walker, Joan L.; Dunn, S. Terence; Wentzensen, Nicolas

doi:10.1186/s12879-015-1281-5

BMC Infectious Diseases

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		Percent^a	Kappa
Type	Name	Positive	Name	Positive	agreement	Value	95 % CI		P
Oncogenic^b
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

* 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)

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