A Technical Comparison of Human Papillomavirus Genotyping Assays from a Population-Based Cervical Cancer Screening in South Central Ethiopia

Figures & data

Table 1 Spectrum of HPV Genotypes in Three HPV Genotyping Assays

Assay	Oncogenic Potential
	High-Risk HPV	Low-Risk HPV
MPG-Luminex Assay	16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, 82	6, 11, 42, 43, 54, 57, 70, 72, 90
EUROArray HPV Assay	16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 73, 82	6, 11, 40, 42, 43, 44, 54, 61, 72, 70, 81, 89
Anyplex™ II HPV HR Detection Assay	16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, 68	Not included

Note: The highlighting color designates the 14 hr-HPV genotypes common for all three genotyping assays.

Table 2 HPV Positivity Result for the 110 Samples Tested with MPG-Luminex Assay, EUROArray HPV Assay, and Anyplex™ II HPV HR Detection Assay

	MPG-Luminex Assay	EUROArray HPV Assay	Anyplex™ II HPV HR Detection	κ–value
	n (%)	n (%)	n (%)
hr- and probable hr-HPV positive	24 (21.82)	18 (16.36)	24 (21.82)	0.734
lr-HPV positive	6 (5.45)	8 (7.27)	Not included	0.237
HPV negative	84 (76.36)	88 (80.00)	86 (78.2)

Table 3 Genotype-Specific Prevalence of HPV Genotypes in 110 Cervical Samples, by HPV Assay Used

HPV Genotype		Number of Positive Samples			κ-value	Meaning
		MPG-Luminex Assay	EUROArray HPV Assay	Anyplex™ II HPV HR Detection Assay
High-risk	16	7	4	4	0.790	Substantial
	18	0	0	1	−0.003	Poor^a)
	31	1	1	3	0.594	Moderate
	33	0	0	1	−0.003	Poor
	35	4	4	5	0.920	Almost perfect
	39	1	1	2	0.747	Substantial
	45	0	0	1	−0.003	Poor
	51	2	0	2	−0.012	Poor
	52	7	3	7	0.628	Substantial
	56	2	1	2	0.594	Moderate
	58	0	0	1	−0.003	Poor
	59	0	0	1	−0.003	Poor
	66	1	1	1	1	Almost perfect
	68	3	0	3	0.491	Moderate
Probable high-risk	26	0	0	NI^c)	CNC^b)
	53	4	3	NI	0.852	Almost perfect
	73	0	1	NI	−0.005	Poor
	82	5	5	NI	1	Almost perfect
Low-risk	6	2	2	NI
	11	0	0	NI
	40	NI	0	NI
	42	1	2	NI
	43	0	4	NI
	44	NI	0	NI
	54	0	0	NI
	57	1	NI	NI
	61	NI	0	NI
	70	0	0	NI
	72	0	0	NI
	81	NI	0	NI
	89	NI	0	NI
	90	2	NI	NI

Notes: ^a)Poor assay concordance results from too few samples positive for this genotype and generally a restricted power for this analysis. ^b)CNC, cannot be computed since none of the test kits identified this genotype.

Abbreviation: ^c)NI, not included.

Table 4 Detection Performance for High-Risk HPVs of EUROArray HPV and Anyplex™ II HPV HR Detection Assays

HPV Assay	n	14 hr-HPV Positive, n	14 hr-HPV Negatives, n	Sensitivity	Specificity
EUROArray HPV	110	14	96	70%	100%
Anyplex™ II HPV HR	110	24	86	100%	95.6%
MPG-Luminex Assay	110	20	90	Comparator assay

Table 5 Discordant Cases for Hr-HPV Genotypes in the Comparison Among the Three HPV DNA Genotyping Assays

Sample Lab. ID	HPV DNA Assay
	MPG-Luminex Assay	EUROArray HPV Assay	Anyplex™ II HPV HR Detection Assay	Discordant HPV Genotype
991530	Negative	Negative	Positive	Pos for HPV18
991760	Negative	Negative	Positive	Pos for HPV51
991365	Positive	Negative	Positive	Neg for HPV68
991374	Positive	Negative	Negative	Pos for HPV52
991376	Positive	Negative	Positive	Neg for HPV51, 52
991429	Negative	Negative	Positive	Pos for HPV56
991442	Positive	Negative	Negative	Pos for HPV51
181506	Negative	Negative	Positive	Pos for HPV51
181665	Negative	Negative	Positive	Pos for HPV31
181719	Positive	Negative	Positive	Neg for HPV31, 53
181735	Positive	Negative	Positive	Neg for HPV16, 68

Note: The highlighting color designates discordant results between the different assays.