Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection

Li, Tengguo; Unger, Elizabeth R.; Rajeevan, Mangalathu S.

doi:10.1186/s12864-019-5598-0

Table 1 Reproducibility of mapping parameters for HPV type determination based on eWGS

From: Universal human papillomavirus typing by whole genome sequencing following target enrichment: evaluation of assay reproducibility and limit of detection

Sample No.	HPV types (Expected)	HPV (copy number)	HPV type (eWGS call)	Mapped reads (Mean ± SD)^a	CV^b	Average depth (Mean ± SD)	CV	Fraction of genome covered (Mean ± SD)	CV
1	11, 16, 31, 45, 52	625	11	7824.75 ± 1033.9	13.2	98.7 ± 13	13.2	1 ± 0.0009	0.1
			16	6916 ± 1056.3	15.3	87.5 ± 13.4	15.3	0.94 ± 0.017	1.8
			31	6606.75 ± 1099	16.6	83.5 ± 13.9	16.6	1 ± 0.0011	0.1
			45	10,152 ± 1195.1	11.8	129 ± 15.2	11.8	0.99 ± 0.0002	0.0
			52	9860.75 ± 1094.3	11.1	124.2 ± 13.8	11.1	1 ± 0.0008	0.1
2	11, 16, 31, 45, 52	125	11	1858.25 ± 99.2	5.3	23.4 ± 1.3	5.3	0.98 ± 0.0122	1.2
			16	1612 ± 215.9	13.4	20.4 ± 2.7	13.4	0.88 ± 0.0076	0.9
			31	1540.25 ± 49.3	3.2	19.5 ± 0.6	3.2	0.96 ± 0.0085	0.9
			45	2542 ± 84.9	3.3	32.3 ± 1.1	3.3	0.98 ± 0.0038	0.4
			52	2170.5 ± 209.3	9.6	27.3 ± 2.6	9.6	0.99 ± 0.0056	0.6
3	11, 16, 31, 45, 52	25	11	254 ± 67.7	26.6	3.2 ± 0.9	26.6	0.47 ± 0.0879	18.6
			16	264.5 ± 84.3	31.9	3.3 ± 1.1	31.9	0.49 ± 0.0536	11.0
			31	295.25 ± 91.8	31.1	3.7 ± 1.2	31.1	0.59 ± 0.1011	17.1
			45	496.5 ± 56.7	11.4	6.3 ± 0.7	11.4	0.75 ± 0.0245	3.3
			52	351.5 ± 116.6	33.2	4.4 ± 1.5	33.2	0.62 ± 0.0507	8.2
4	11, 16, 31, 45, 52	5	11	91.5 ± 25.8	28.2	1.2 ± 0.3	28.2	0.18 ± 0.0674	37.3
			16	89 ± 47	52.8	1.1 ± 0.6	52.8	0.26 ± 0.1169	45.2
			31	84.5 ± 35.2	41.7	1.1 ± 0.4	41.7	0.16 ± 0.0793	48.4
			45	191.5 ± 67.1	35.0	2.4 ± 0.9	35.0	0.4 ± 0.1125	27.8
			52	58.5 ± 31.1	53.2	0.7 ± 0.4	53.3	0.18 ± 0.0779	43.5
5	11, 16, 31, 45, 52	1	11	12 ± 4.3	36.0	0.2 ± 0.1	36.0	0.05 ± 0.015	28.9
			16	22.75 ± 16.2	71.0	0.3 ± 0.2	71.0	0.11 ± 0.0748	66.8
			31	21.5 ± 5.6	25.9	0.3 ± 0.1	25.9	0.08 ± 0.0289	36.8
			45	38.25 ± 18.3	47.8	0.5 ± 0.2	47.8	0.1 ± 0.0434	42.9
			52	0 ± 0		0 ± 0		0 ± 0
6	6, 18, 33, 58	625	6	5601.5 ± 141	2.5	70.1 ± 1.8	2.5	1 ± 0.0019	0.2
			18	10,845 ± 1721	15.9	138 ± 21.9	15.9	1 ± 0.0001	0.0
			33	9550.25 ± 893.6	9.4	120.8 ± 11.3	9.4	0.99 ± 0.0007	0.1
			58	10,873 ± 619	5.7	139 ± 7.9	5.7	1 ± 0.0001	0.0
7	6, 18, 33, 58	125	6	1023.75 ± 243.6	23.8	12.8 ± 3	23.8	0.85 ± 0.0103	1.2
			18	2277.25 ± 144.2	6.3	29 ± 1.8	6.3	0.98 ± 0.0049	0.5
			33	1875 ± 62	3.3	23.7 ± 0.8	3.3	0.96 ± 0.0072	0.7
			58	1818.25 ± 212.8	11.7	23.2 ± 2.7	11.7	0.98 ± 0.0082	0.8
8	6, 18, 33, 58	25	6	205.75 ± 17.4	8.5	2.6 ± 0.2	8.5	0.4 ± 0.0625	15.5
			18	258.25 ± 37.5	14.5	3.3 ± 0.5	14.5	0.55 ± 0.0781	14.3
			33	329.25 ± 110.2	33.5	4.2 ± 1.4	33.5	0.54 ± 0.2009	36.9
			58	443.5 ± 56.9	12.8	5.7 ± 0.7	12.8	0.66 ± 0.0429	6.5
9	6, 18, 33, 58	5	6	16.75 ± 11.5	68.5	0.2 ± 0.1	68.5	0.07 ± 0.0443	59.2
			18	60.75 ± 34.8	57.3	0.8 ± 0.4	57.3	0.25 ± 0.088	35.6
			33	70 ± 8.3	11.8	0.9 ± 0.1	11.8	0.24 ± 0.0235	9.8
			58	97.75 ± 41.6	42.6	1.2 ± 0.5	42.6	0.3 ± 0.0832	27.5
10	6, 18, 33, 58	1	6	14.5 ± 16.9	116.7	0.2 ± 0.2	116.7	0.04 ± 0.0452	117.0
			18	9.5 ± 11	116.1	0.1 ± 0.1	116.1	0.08 ± 0.068	84.9
			33	15.75 ± 17.1	108.3	0.2 ± 0.2	108.3	0.05 ± 0.0451	89.0
			58	29.25 ± 4.3	14.9	0.4 ± 0.1	14.9	0.09 ± 0.0251	29.1
11	WHO HPV16	10,000	16	136,765.25 ± 13,297.7	9.7	1729.9 ± 168.2	9.7	0.99 ± 0.0001	0.0
12	WHO HPV18	10,000	18	57,105.5 ± 7675.3	13.4	726.8 ± 97.7	13.4	1 ± 0.0001	0.0
13	H2O		Neg
14	Placental DNA		Neg
15	SiHa		16	266,625.5 ± 16,411.4	6.2	3372.4 ± 207.6	6.2	0.92 ± 0.0095	1.0
16	Hela		18	326,684.25 ± 10,950	3.4	4157.9 ± 139.4	3.4	0.63 ± 0.008	1.3

^aMean and SD were calculated based on 4 replicates for each sample;
^bCV Coefficient of Variation

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