Evaluation of using composite HPV genotyping assay results to monitor human papillomavirus infection burden through simulation

Lin, Carol Y

doi:10.1186/s12879-015-0851-x

Table 2 Composite prevalence estimates when the “true” underlying type-specific infection burden is pre-specified as the reported prevalence in the Northwest Territories, Canada

From: Evaluation of using composite HPV genotyping assay results to monitor human papillomavirus infection burden through simulation

No. of HPV types*	Time^§	Pre-specified true composite prevalence (SD)	Composite prevalence estimate (SD)	Est. to true ratio	Composite prevalence estimate (SD)	Est. to true ratio	Composite prevalence estimate (SD)	Est. to true ratio	Composite prevalence estimate (SD)	Est. to true ratio
a: Sensitivity ≤ Specificity
			Sen. = 0.95		Sen. = 0.90		Sen. = 0.85		Sen. = 0.80
			Spe. = 0.95		Spe. = 0.95		Spe. = 0.95		Spe. = 0.95
2	Baseline	0.053 (0.004)	0.142 (0.006)	2.676	0.140 (0.005)	2.642	0.138 (0.005)	2.604	0.135 (0.005)	2.547
	Reduced	0.027 (0.003)	0.120 (0.005)	4.444	0.119 (0.005)	4.407	0.117 (0.005)	4.333	0.116 (0.005)	4.296
	% red.	49.1	15.5		15.0		15.2		14.1
4	Baseline	0.064 (0.004)	0.231 (0.007)	3.609	0.229 (0.006)	3.578	0.226 (0.006)	3.531	0.224 (0.006)	3.500
	Reduced	0.033 (0.003)	0.207 (0.006)	6.272	0.206 (0.006)	6.242	0.204 (0.006)	6.181	0.203 (0.007)	6.152
	% red.	48.4	10.4		10.0		9.7		9.4
22	Baseline	0.216 (0.006)	0.701 (0.007)	3.245	0.697 (0.007)	3.227	0.694 (0.004)	3.213	0.690 (0.007)	3.194
	Reduced	0.194 (0.006)	0.694 (0.007)	3.577	0.691 (0.007)	3.562	0.687 (0.007)	3.541	0.684 (0.007)	3.526
	% red.	10.2	0.9		0.9		1.0		0.9
45	Baseline	0.287 (0.007)	0.841 (0.006)	2.930	0.839 (0.006)	2.923	0.836 (0.006)	2.913	0.834 (0.006)	2.906
	Reduced	0.265 (0.007)	0.838 (0.006)	3.162	0.835 (0.006)	3.151	0.833 (0.006)	3.143	0.831 (0.006)	3.136
	% red.	7.6	0.4		0.5		0.4		0.4
b: Sensitivity ≥ Specificity
			Sen. = 0.95		Sen. = 0.95		Sen. = 0.95		Sen. = 0.95
			Spe. = 0.95		Spe. = 0.90		Spe. = 0.85		Spe. = 0.80
2	Baseline	0.052 (0.004)	0.142 (0.006)	2.731	0.229 (0.006)	4.404	0.311 (0.007)	5.981	0.387 (0.008)	7.442
	Reduced	0.027 (0.003)	0.120 (0.005)	4.444	0.209 (0.007)	7.74	0.293 (0.007)	10.85	0.371 (0.008)	13.74
	% red.	49.1	15.5		8.7		5.8		4.1
4	Baseline	0.064 (0.004)	0.231 (0.007)	3.609	0.375 (0.007)	5.859	0.497 (0.008)	7.766	0.599 (0.008)	9.359
	Reduced	0.033 (0.003)	0.207 (0.006)	6.272	0.356 (0.008)	10.78	0.482 (0.009)	14.61	0.588 (0.008)	17.82
	% red.	48.4	10.4		5.1		3.0		1.8
22	Baseline	0.216 (0.007)	0.701 (0.007)	3.245	0.883 (0.005)	4.088	0.954 (0.003)	4.417	0.983 (0.002)	4.551
	Reduced	0.194 (0.006)	0.694 (0.007)	3.577	0.881 (0.005)	4.541	0.954 (0.003)	4.917	0.982 (0.002)	5.062
	% red.	10.2	0.9		0.2		0		0.1
45	Baseline	0.288 (0.007)	0.841 (0.006)	2.920	0.961 (0.003)	3.337	0.990 (0.002)	3.438	0.997 (0.001)	3.462
	Reduced	0.265 (0.007)	0.838 (0.006)	3.162	0.960 (0.003)	3.623	0.990 (0.002)	3.736	0.997 (0.001)	3.762
	% red.	7.6	0.4		0.1		0		0

*2: high-risk vaccine types(HPV 16, 18); 4: vaccine types (HPV 6, 11, 16, 18); 23: high-risk types (HPV 16, 18, 26, 30, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 67, 68, 69, 70, 73, 82, 85); 45: any types (HPV 6, 11, 13, 16, 18, 26, 30, 31, 32, 33, 35, 39, 40, 42, 43, 44, 45, 51, 52, 53, 54, 56, 58, 59, 61, 62, 66, 67, 68, 69, 70, 71, 72, 73, 74, 81, 82, 83, 84, 85, 86, 87, 89, 90, 91).
^§Pre-specified type-specific prevalence at baseline:HPV6 = 0.009, HPV11 = 0.003, HPV13 = 0.001, HPV16 = 0.041, HPV18 = 0.013, HPV26 = 0, HPV30 = 0.002, HPV31 = 0.021, HPV32 = 0.001, HPV33 = 0.007, HPV35 = 0.007, HPV39 = 0.016, HPV40 = 0.005, HPV42 = 0.013, HPV43 = 0.002, HPV44 = 0.003, HPV45 = 0.015, HPV51 = 0.016, HPV52 = 0.014, HPV53 = 0.005,HPV54 = 0.008, HPV56 = 0.010, HPV58 = 0.013, HPV59 = 0.012, HPV62 = 0.016, HPV66 = 0.019, HPV67 = 0.013, HPV68 = 0.003, HPV69 = 0.003, HPV70 = 0.011, HPV72 = 0.007, HPV73 = 0.005, HPV74 = 0.007, HPV81 = 0.007, HPV82 = 0.002, HPV83 = 0.007, HPV84 = 0.004, HPV85 = 0.003, HPV89 = 0.010, HPV90 = 0.004, HPV86 = 0.004, HPV87 = 0.001, HPV91 = 0.001, HPV61 = 0.001, HPV71 = 0.
Reduced: vaccine types (HPV 6, 11, 16, 18) are reduced 50%.

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