Table 2. Summary of four HPV genotyping methods (HPV major type and minor types detected by next-generation sequencing [NGS] for all samples/percentage of total reads obtained in the sequencing).
| Sample | Cytology | Nested-PCR | INNO-LiPA | DNA CHIP | NGS | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HPV major type (>50%) | NGS HPV minor type (<50%, top 10) | ||||||||||||||
| B511C | Normal | 16 | 16, 51 | 16, 51 | 16 (95.89%) | 109/0.36 | 164/0.27 | 50/0.26 | 168/0.25 | 119/0.16 | 59/0.15 | 87/0.14 | 98/0.14 | 24/0.13 | 11/0.13 |
| B198C | Normal | 70 | 74 | Negative | 70 (82.66%) | 109/1.55 | 164/1.38 | 168/1.1 | 82/0.95 | 50/0.94 | 87/0.91 | 119/0.73 | 59/0.68 | 98/0.65 | 153/0.6 |
| B135C | Normal | 16 | 52 | 16, 31, 39, 51, 52 | 16 (93.95%) | 109/0.59 | 164/0.46 | 168/0.41 | 50/0.34 | 31/0.28 | 119/0.26 | 59/0.23 | 98/0.22 | 153/0.22 | 172/0.21 |
| B12C | Normal | 18 | 18, 51, 52 | 16, 18, 39, 51, 58 | 18 (93.72%) | 16/0.77 | 107/0.45 | 87/0.45 | 164/0.31 | 168/0.3 | 45/0.28 | 33/0.27 | 50/0.27 | 119/0.18 | 24/0.17 |
| B603C | Normal | 16 | 16, 51, 52, 74 | 16, 58 | 16 (97.54%) | 87/0.3 | 11/0.2 | 109/0.14 | 168/0.11 | 97/0.1 | 50/0.1 | 164/0.1 | 119/0.08 | 59/0.06 | 167/0.06 |
| B807C | Normal | 6 | 39, 52 | 39, 51, 58, 59, 68 | 6 (94.03%) | 97/0.5 | 109/0.43 | 168/0.33 | 50/0.32 | 164/0.3 | 119/0.23 | 59/0.21 | 87/0.18 | 11/0.18 | 35/0.17 |
| S131C | Normal | 66 | 44, 56, 58, 66 | 58 | 66 (89.34%) | 109/1.07 | 50/0.76 | 164/0.75 | 168/0.67 | 119/0.48 | 24/0.45 | 59/0.43 | 172/0.42 | 57/0.39 | 163/0.38 |
| S113C | LSIL | 56 | 33 | 33, 56, 58 | 56 (92.78%) | 109/0.63 | 50/0.4 | 164/0.39 | 168/0.38 | 119/0.31 | 16/0.31 | 87/0.3 | 45/0.29 | 59/0.29 | 24/0.27 |
| S30C | LSIL | 16 | 16, 18, 56 | 16, 18 | 16 (67.49%) | 18/23.86 | 109/0.75 | 168/0.51 | 164/0.48 | 50/0.46 | 167/0.39 | 59/0.37 | 87/0.34 | 42/0.33 | 12/0.33 |
| S32C | LSIL | 16 | 51 | 16, 51 | 16 (64.19%) | 70/27.94 | 109/0.7 | 168/0.49 | 87/0.48 | 164/0.44 | 50/0.41 | 59/0.33 | 163/0.28 | 119/0.27 | 98/0.27 |
| S215C | LSIL | 16 | 16, 44, 56, 58, 66 | 16, 58 | 16 (88.64%) | 58/4.83 | 109/0.47 | 168/0.39 | 66/0.36 | 164/0.32 | 87/0.32 | 59/0.3 | 50/0.28 | 119/0.24 | 98/0.23 |
| S212C | LSIL | 56 | 16, 45, 53, 54, 56, 58, 73 | 16, 45, 56, 68 | 81 (71.94%) | 16/21.29 | 56/3.15 | 87/0.3 | 109/0.28 | 164/0.22 | 50/0.21 | 168/0.2 | 62/0.16 | 119/0.13 | 59/0.12 |
| S25C | LSIL | 66 | 31, 39, 51, 66, 82 | 31, 39, 51, 58 | 66 (79.16%) | 31/12.85 | 58/1.79 | 6/0.58 | 109/0.51 | 164/0.41 | 50/0.36 | 168/0.36 | 87/0.35 | 62/0.23 | 119/0.22 |
| S11C | LSIL | 81 | 16, 39 | 16, 39 | 81 (63.23%) | 16/29.08 | 109/0.64 | 87/0.58 | 168/0.53 | 164/0.46 | 50/0.37 | 167/0.3 | 59/0.27 | 119/0.27 | 24/0.25 |
| S13C | LSIL | 66 | 52, 56, 66 | 52, 56 | 66 (57.15%) | 62/17.04 | 56/11.11 | 87/2.35 | 109/1.33 | 168/0.87 | 164/0.83 | 50/0.74 | 59/0.63 | 98/0.63 | 167/0.47 |
| S27C | LSIL | 66 | 33, 66 | 33, 59 | 33 (51.82%) | 66/34.51 | 109/1.37 | 168/0.93 | 164/0.89 | 50/0.77 | 167/0.67 | 59/0.61 | 98/0.52 | 119/0.51 | 163/0.49 |
| S34C | LSIL | 31 | 31, 33, 44, 51, 82 | 31, 51 | 31 (92.4%) | 109/0.79 | 50/0.49 | 164/0.46 | 168/0.4 | 59/0.33 | 24/0.31 | 163/0.29 | 119/0.28 | 98/0.26 | 12/0.25 |
| S38C | LSIL | 58 | 16, 39, 58 | 39, 58 | 58 (91.33%) | 109/0.84 | 164/0.59 | 168/0.59 | 50/0.52 | 59/0.37 | 119/0.3 | 98/0.3 | 12/0.28 | 68/0.28 | 35/0.28 |
| S272C | LSIL | 16 | 52 | 16, 39, 45, 52 | 16 (96.14%) | 11/0.33 | 87/0.31 | 109/0.31 | 168/0.2 | 50/0.18 | 164/0.17 | 58/0.13 | 119/0.11 | 167/0.11 | 59/0.11 |
| S312C | LSIL | 58 | 58, 70 | 52, 58 | 58 (96.21%) | 35/0.29 | 109/0.26 | 168/0.22 | 62/0.18 | 70/0.16 | 33/0.16 | 164/0.16 | 87/0.15 | 50/0.14 | 59/0.12 |
| S322C | LSIL | 11 | 39, 52 | 39, 52 | 11 (89.14%) | 81/3.2 | 87/0.74 | 109/0.65 | 50/0.65 | 168/0.44 | 164/0.41 | 119/0.32 | 24/0.28 | 172/0.26 | 16/0.25 |
| S28C | LSIL | 33 | 33, 58 | 16, 33, 58 | 33 (97.66%) | 109/0.18 | 58/0.16 | 16/0.16 | 35/0.14 | 164/0.12 | 50/0.11 | 168/0.1 | 18/0.09 | 97/0.08 | 59/0.07 |
| S96C | LSIL | 33 | 33 | 33, 58 | 33 (98.8%) | 35/0.12 | 97/0.09 | 18/0.07 | 109/0.06 | 50/0.06 | 164/0.06 | 58/0.05 | 87/0.05 | 168/0.04 | 16/0.03 |
| S9C | LSIL | 16 | 31 | 16, 31, 52, 68 | 16 (90.29%) | 31/0.95 | 109/0.92 | 168/0.65 | 164/0.59 | 50/0.47 | 59/0.39 | 119/0.36 | 167/0.33 | 98/0.29 | 24/0.28 |
| S137C | LSIL | 56 | 31, 33, 44, 66 | 16, 31, 56 | 66 (97.03%) | 31/1.33 | 87/0.41 | 97/0.09 | 16/0.08 | 109/0.08 | 56/0.06 | 81/0.06 | 168/0.06 | 33/0.06 | 50/0.06 |
| S820C | HSIL, ASC-H | 33 | 16, 33, 39 | 33, 39 | 33 (90.32%) | 109/0.97 | 168/0.77 | 164/0.59 | 50/0.44 | 119/0.44 | 42/0.42 | 110/0.41 | 167/0.38 | 68/0.35 | 98/0.34 |
| S853C | HSIL, CIN II | 45 | 16, 39, 45, 51 | 39, 45, 51 | 45 (96.73%) | 109/0.27 | 164/0.2 | 50/0.19 | 168/0.18 | 87/0.18 | 59/0.11 | 119/0.11 | 98/0.11 | 24/0.09 | 172/0.09 |
| S835C | HSIL, CIN II | 16 | 16 | 16, 58 | 16 (97.03%) | 87/0.31 | 11/0.22 | 109/0.21 | 168/0.17 | 50/0.15 | 33/0.14 | 164/0.13 | 97/0.1 | 59/0.07 | 12/0.07 |
| S841C | HSIL, CIN II | 16 | 16, 52 | 16, 45, 52 | 16 (95.79%) | 168/0.35 | 109/0.29 | 87/0.28 | 50/0.28 | 164/0.22 | 11/0.21 | 110/0.15 | 59/0.13 | 42/0.13 | 163/0.13 |
| S842C | HSIL, CIN II | 58 | 31 , 44, 58 | 31, 58 | 58 (95.13%) | 109/0.38 | 35/0.28 | 168/0.27 | 164/0.22 | 50/0.19 | 59/0.18 | 62/0.18 | 167/0.18 | 98/0.17 | 87/0.17 |
| S878C | HSIL, CIN II | 16 | 16 | 16, 39 | 16 (96.42%) | 109/0.34 | 168/0.26 | 50/0.22 | 164/0.18 | 59/0.15 | 87/0.15 | 119/0.15 | 98/0.15 | 11/0.11 | 12/0.11 |
| S864C | HSIL, CIN III | 31 | 31, 33, 44, 52, 54 | 31 | 31 (94.19%) | 109/0.55 | 164/0.43 | 50/0.41 | 168/0.37 | 59/0.23 | 119/0.23 | 98/0.2 | 24/0.2 | 57/0.19 | 163/0.19 |
| S819C | HSIL, CIN III | 33 | 33, 52, 54 | 33, 51 | 33 (97.16%) | 35/0.24 | 109/0.2 | 18/0.17 | 168/0.15 | 87/0.14 | 164/0.13 | 50/0.13 | 97/0.11 | 52/0.08 | 58/0.08 |
| S839C | HSIL, CIN III | 45 | 16, 45 | 16, 45 | 45 (72.41%) | 16/23.26 | 109/0.36 | 87/0.3 | 164/0.25 | 168/0.22 | 50/0.18 | 97/0.17 | 33/0.16 | 18/0.16 | 54/0.16 |
| S859C | HSIL, CIN III | 16 | 16 | 16, 33, 68 | 16 (95.67%) | 109/0.36 | 87/0.33 | 164/0.22 | 11/0.21 | 168/0.21 | 50/0.17 | 59/0.16 | 119/0.14 | 167/0.14 | 98/0.14 |
| S871C | HSIL, CIN III | 18 | 18 | 18, 31 | 18 (86.82%) | 109/1.49 | 164/1.17 | 168/1.05 | 50/0.98 | 109/1.50 | 164/1.18 | 172/0.52 | 59/0.51 | 167/0.49 | 24/0.48 |
| S836C | HSIL, CIN III | 18 | 18, 52 | 18, 52 | 18 (95.96%) | 87/0.38 | 109/0.26 | 50/0.23 | 16/0.22 | 87/0.39 | 109/0.27 | 164/0.19 | 168/0.15 | 59/0.13 | 97/0.12 |
| T100C | CA | 33 | 16, 33, 58, 68 | 16, 33, 58, 59, 68 | 16 (85.38%) | 109/1.43 | 164/1.13 | 50/1.06 | 168/1.05 | 119/0.62 | 33/0.61 | 59/0.61 | 98/0.54 | 24/0.52 | 163/0.51 |
| T36C | CA | 16 | 16, 44, 52 | 16 | 16 (89.92%) | 109/1.05 | 164/0.78 | 50/0.73 | 168/0.7 | 59/0.44 | 119/0.43 | 98/0.39 | 172/0.37 | 57/0.35 | 167/0.34 |
| T26C | CA | 67 | Negative | 16, 56 | 56 (89.4%) | 109/0.99 | 16/0.87 | 164/0.74 | 50/0.69 | 168/0.64 | 119/0.43 | 59/0.41 | 98/0.38 | 163/0.36 | 24/0.36 |
| T32C | CA | 33 | 33 | 33, 39 | 33 (87.98%) | 81/6.44 | 109/0.64 | 50/0.49 | 164/0.43 | 168/0.3 | 59/0.24 | 172/0.21 | 12/0.2 | 24/0.2 | 119/0.2 |
| T37C | CA | 45 | 45, 52 | 31, 45, 51, 52 | 45 (98%) | 87/0.15 | 109/0.15 | 97/0.13 | 33/0.11 | 50/0.11 | 168/0.1 | 164/0.1 | 83/0.08 | 172/0.05 | 119/0.05 |
| T44C | CA | 16 | 16, 33 | 16, 33 | 16 (92.73%) | 109/0.71 | 50/0.65 | 33/0.57 | 164/0.57 | 168/0.44 | 59/0.29 | 124/0.27 | 12/0.27 | 119/0.26 | 24/0.25 |
| T60C | CA | 18 | 18 | 18, 58 | 18 (66.46%) | 109/3.53 | 168/2.79 | 164/2.52 | 50/2.36 | 59/1.6 | 98/1.46 | 119/1.41 | 163/1.33 | 24/1.31 | 167/1.27 |
| T69C | CA | 67 | Negative | Negative | 67 (96.06%) | 109/0.34 | 50/0.25 | 168/0.24 | 97/0.23 | 164/0.22 | 31/0.16 | 24/0.14 | 119/0.14 | 57/0.13 | 172/0.13 |
| T85C | CA | 16 | 16 | 16, 31, 39 | 16 (88.68%) | 109/1.34 | 50/0.89 | 164/0.85 | 168/0.8 | 24/0.47 | 119/0.46 | 59/0.44 | 12/0.4 | 163/0.4 | 57/0.38 |
| T94C | CA | 16 | 16 | 16, 68 | 16 (96.7%) | 109/0.33 | 50/0.27 | 168/0.21 | 164/0.21 | 87/0.14 | 124/0.14 | 11/0.13 | 59/0.12 | 24/0.11 | 119/0.11 |
| T95C | CA | 18 | 18 | 16, 18 | 18 (98.62%) | 16/0.18 | 87/0.18 | 45/0.15 | 33/0.11 | 97/0.08 | 109/0.07 | 168/0.05 | 50/0.04 | 164/0.03 | 172/0.03 |
| T129C | CA | 18 | 18, 51 | 18, 51 | 18 (70.56%) | 109/3.27 | 168/2.69 | 164/2.22 | 50/2.21 | 110/1.31 | 119/1.22 | 59/1.2 | 98/1.1 | 167/1.09 | 163/1.06 |
| T134C | CA | 58 | 58 | 39, 52, 58 | 58 (97.85%) | 18/0.22 | 16/0.16 | 35/0.15 | 50/0.15 | 109/0.15 | 168/0.11 | 164/0.1 | 33/0.09 | 124/0.08 | 45/0.07 |
| T144C | CA | 45 | 51 | 45, 51 | 45 (98.5%) | 16/0.18 | 87/0.15 | 97/0.13 | 33/0.11 | 109/0.08 | 83/0.06 | 164/0.06 | 50/0.05 | 44/0.04 | 168/0.04 |
| T151C | CA | 16 | 16, 58 | 16, 31, 58 | 16 (97.42%) | 109/0.22 | 87/0.15 | 164/0.15 | 11/0.14 | 168/0.14 | 50/0.13 | 59/0.09 | 6/0.08 | 119/0.08 | 24/0.07 |
| T153C | CA | 16 | 16, 52 | 16, 52 | 16 (98.4%) | 11/0.14 | 87/0.12 | 109/0.12 | 50/0.09 | 164/0.09 | 168/0.08 | 97/0.06 | 33/0.05 | 119/0.05 | 59/0.04 |
| T180C | CA | 16 | 16 | 16, 58 | 16 (80.09%) | 109/2.52 | 168/1.53 | 164/1.53 | 50/1.32 | 59/1.02 | 119/0.89 | 12/0.85 | 167/0.84 | 98/0.79 | 172/0.79 |
| T29C | CA | 45 | 45 | 16, 45 | 45 (96%) | 109/0.43 | 168/0.3 | 164/0.25 | 50/0.23 | 16/0.15 | 68/0.15 | 87/0.15 | 59/0.14 | 163/0.13 | 119/0.13 |
| T28C | CA | 16 | 16 | 16, 18, 33, 52 | 16 (80.88%) | 109/2.29 | 50/1.53 | 164/1.45 | 168/1.4 | 59/0.9 | 119/0.85 | 24/0.77 | 172/0.75 | 12/0.73 | 163/0.72 |
| T19C | CA | 16 | 16 | 16, 33 | 16 (96.73%) | 109/0.31 | 168/0.22 | 164/0.22 | 50/0.21 | 87/0.15 | 11/0.14 | 59/0.12 | 119/0.12 | 98/0.11 | 68/0.11 |
| T23C | CA | 16 | 16, 52 | 16, 52 | 16 (83.06%) | 109/1.92 | 164/1.38 | 168/1.29 | 50/1.24 | 59/0.86 | 119/0.74 | 98/0.68 | 24/0.65 | 172/0.65 | 163/0.65 |
>30% 
20–29.9% 
10–19.9% 
1–9.9% 
<1%