NanoString Technology for Human Papillomavirus Typing
Abstract
:1. Introduction
2. Materials and Methods
2.1. Overview of Study
2.2. CodeSets
2.3. Samples
2.4. Sample Preparation
2.5. Hybridization and Imaging
2.6. HPV TypeSeq Assay
2.7. Data Analysis and Statistics
3. Results
3.1. Results of Direct Testing of DNA Extracts (No-PCR)
3.2. Results of PCR-45 Test
3.3. Results of PCR-15 Test
3.4. Concordance between PCR-15 and HPV TypeSeq
3.5. Z-Test Results
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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HPV Types in Analysis | No-PCR Results | LA Results | Total | Agreement (%, k) $ | McNemar’s p-Value | Positive Agreement (%) | Sensitivity (%) | Specificity (%) | |
---|---|---|---|---|---|---|---|---|---|
+ | − | ||||||||
37 Types included in LA | + | 138 | 61 | 199 | 91 (1346/1480); k = 0.621 (95% CI 0.562–0.679) (substantial) | 0.342 | 67 | 65 (138/211) | 95.2 (1208/1269) |
− | 73 | 1208 | 1261 | ||||||
Total | 211 | 1269 | 1480 | ||||||
14 HR types | + | 72 | 24 | 96 | 90.7 (508/560) k = 0.678 (95% CI 0.597–0.760) (substantial) | 0.678 | 73 | 72 (72/100) | 95 (436/460) |
− | 28 | 436 | 464 | ||||||
Total | 100 | 460 | 560 | ||||||
HPV16/18 only | + | 21 | 3 | 24 | 90 (72/80) k = 0.767 (95% CI 0.615–0.919) (substantial) | 0.727 | 84 | 81 (21/26) | 94 (51/54) |
− | 5 | 51 | 56 | ||||||
Total | 26 | 54 | 80 |
HPV Types in Analysis | PCR-45 Results | LA Results | Total | Agreement (%, k) $ | McNemar’s p-Value | Positive Agreement (%) | Sensitivity (%) | Specificity (%) | |
---|---|---|---|---|---|---|---|---|---|
+ | − | ||||||||
All 37 LA types | + | 212 | 9 | 221 | 96.2 (1425/1480) k = 0.862 (95% CI 0.828–0.898) (substantial) | <0.000001 | 89 | 82 (212/258) | 99.3 (1213/1222) |
− | 46 | 1213 | 1259 | ||||||
Total | 258 | 1222 | 1480 | ||||||
14 HR types | + | 103 | 1 | 104 | 97.1 (544/560) k = 0.91 (95% CI 0.867–0.953) (almost perfect agreement) | <0.000519 | 93 | 87.3 (103/118) | 99.8 (441/442) |
− | 15 | 441 | 456 | ||||||
Total | 118 | 442 | 560 | ||||||
HPV16/18 only | + | 25 | 0 | 25 | 100 (80/80) k = 1.00 (95% CI 1.00–1.00) (perfect agreement) | 1.00 | 100 | 100 (25/25) | 100 (55/55) |
− | 0 | 55 | 55 | ||||||
Total | 25 | 55 | 80 |
HPV Type * | +/+ | +/− | Test Results ** −/+ | −/− | Agreement (%) | Positive Agreement (%) | Kappa | 95% CI | Interpretation | p-Value |
---|---|---|---|---|---|---|---|---|---|---|
All 37 types | 272 | 95 | 24 | 2384 | 95.7 | 82.1 | 0.796 | 0.761–0.832 | Substantial | <0.000001 |
14 HR types | 134 | 34 | 6 | 876 | 96.2 | 87.0 | 0.848 | 0.802–0.894 | Almost perfect | <0.0001 |
LR types | 138 | 61 | 18 | 1508 | 95.4 | 77.7 | 0.752 | 0.700–0.804 | Substantial | <0.0000001 |
HPV16/18 | 30 | 1 | 0 | 119 | 99.3 | 98.4 | 0.979 | 0.939–1.00 | Almost perfect | 1 |
16 β | 16 | 1 | 0 | 58 | 98.7 | 97 | 0.961 | 0.886–1.00 | Almost perfect | 1 |
18 β | 14 | 0 | 0 | 61 | 100 | 100 | 1.000 | 1.000–1.000 | Perfect | 1 |
31 β | 8 | 3 | 1 | 63 | 94.7 | 80.0 | 0.77 | 0.554–0.985 | Substantial | 0.617 |
33 β | 6 | 3 | 0 | 66 | 96 | 80.0 | 0.779 | 0.54–1.00 | Substantial | 0.248 |
35 | 7 | 3 | 0 | 65 | 96 | 82.4 | 0.802 | 0.586–1.00 | Almost perfect | 0.248 |
39 | 9 | 3 | 1 | 62 | 94.7 | 81.9 | 0.787 | 0.587–0.987 | Substantial | 0.617 |
45 β | 11 | 2 | 0 | 62 | 97.3 | 91.7 | 0.901 | 0.766–1.00 | Almost perfect | 0.479 |
51 | 13 | 2 | 0 | 60 | 97.3 | 92.9 | 0.912 | 0.793–1.00 | Almost perfect | 0.479 |
52 β | 15 | 3 | 0 | 57 | 96 | 90.9 | 0.884 | 0.756–1.00 | Almost perfect | 0.248 |
56 | 5 | 3 | 1 | 66 | 94.7 | 71.4 | 0.686 | 0.397–0.974 | Substantial | 0.617 |
58 β | 9 | 2 | 1 | 63 | 96 | 85.7 | 0.834 | 0.651–1.00 | Almost perfect | 1 |
59 | 11 | 4 | 1 | 59 | 93.3 | 81.5 | 0.775 | 0.587–0.962 | Substantial | 0.371 |
66 | 5 | 4 | 0 | 66 | 94.7 | 71.4 | 0.687 | 0.404–0.971 | Substantial | 0.133 |
68b | 5 | 1 | 1 | 68 | 97.3 | 83.3 | 0.819 | 0.574–1.00 | Almost perfect | 0.479 |
11 | 4 | 1 | 0 | 70 | 98.7 | 88.9 | 0.882 | 0.654–1.00 | Almost perfect | 1 |
26 | 4 | 1 | 0 | 70 | 98.7 | 88.9 | 0.882 | 0.654–1.00 | Almost perfect | 1 |
40 | 4 | 1 | 0 | 70 | 98.7 | 88.9 | 0.882 | 0.654–1.00 | Almost perfect | 1 |
42 | 11 | 2 | 1 | 61 | 96 | 88.0 | 0.856 | 0.697–1.00 | Almost perfect | 1 |
53 | 11 | 2 | 0 | 62 | 97.3 | 91.7 | 0.901 | 0.766–1.00 | Almost perfect | 0.479 |
54 | 7 | 3 | 0 | 65 | 96 | 82.4 | 0.802 | 0.586–1.00 | Substantial | 0.248 |
55 | 5 | 4 | 0 | 66 | 94.7 | 71.4 | 0.687 | 0.404–0.971 | Substantial | 0.133 |
61 | 6 | 2 | 1 | 66 | 96 | 80.0 | 0.778 | 0.536–1.00 | Substantial | 1 |
62 | 13 | 2 | 1 | 59 | 96 | 89.7 | 0.872 | 0.730–1.00 | Almost perfect | 1 |
64 | 3 | 4 | 0 | 68 | 94.7 | 60.0 | 0.576 | 0.210–0.942 | Moderate | 0.133 |
67 | 5 | 4 | 1 | 65 | 93.3 | 66.7 | 0.631 | 0.336–0.926 | Substantial | 0.371 |
69 | 3 | 3 | 0 | 69 | 96 | 66.7 | 0.648 | 0.282–1.00 | Substantial | 0.248 |
6 | 8 | 6 | 0 | 61 | 92 | 72.7 | 0.684 | 0.455–0.914 | Substantial | 0.041 |
70 | 6 | 4 | 0 | 65 | 94.7 | 75.0 | 0.722 | 0.468–0.97 | Substantial | 0.133 |
71 | 3 | 0 | 0 | 72 | 100 | 100 | 1 | 1.000–1.000 | Perfect | 1 |
72 | 6 | 1 | 0 | 68 | 98.7 | 92.3 | 0.916 | 0.753–1.00 | Almost perfect | 1 |
73 | 7 | 1 | 2 | 65 | 96 | 82.4 | 0.801 | 0.583–1.00 | Almost perfect | 1 |
81 | 6 | 1 | 0 | 68 | 98.7 | 92.3 | 0.916 | 0.753–1.00 | Almost perfect | 1 |
82 Subtype IS39 | 5 | 8 | 1 | 61 | 88.0 | 52.6 | 0.468 | 0.184–0.752 | Moderate | 0.045 |
82 | 3 | 5 | 4 | 63 | 88.0 | 40.0 | 0.334 | 0.002–0.669 | Fair | 1 |
83 | 3 | 1 | 1 | 70 | 97.3 | 75.0 | 0.736 | 0.385–1.00 | Substantial | 0.479 |
84 | 6 | 5 | 5 | 59 | 86.7 | 54.5 | 0.467 | 0.186–0.748 | moderate | 0.751 |
89 | 9 | 0 | 1 | 65 | 98.7 | 94.7 | 0.94 | 0.823–1.00 | Almost perfect | 1 |
HPV Type * | +/+ | +/− | Test Results ** −/+ | −/− | Agreement (%) | Positive Ageement (%) | Kappa | 95% CI | Interpretation | p-Value |
---|---|---|---|---|---|---|---|---|---|---|
All 47 types | 218 | 72 | 33 | 1745 | 94.9 | 80.6 | 0.777 | 0.736–0.888 | Substantial | 0.000178 |
14 HR types | 108 | 17 | 10 | 481 | 95.6 | 88.9 | 0.862 | 0.811–0.912 | Almost perfect | 0.247789 |
33 LR types | 110 | 55 | 23 | 1264 | 94.6 | 73.8 | 0.709 | 0.648–0.770 | Substantial | 0.000378 |
HPV16/18 | 22 | 3 | 0 | 63 | 96.6 | 93.6 | 0.913 | 0.817–1.00 | Almost perfect | 0.248 |
16 β | 13 | 2 | 0 | 29 | 95.5 | 92.9 | 0.895 | 0.755–1.00 | Almost perfect | 0.479 |
18 β | 9 | 1 | 0 | 34 | 97.7 | 94.7 | 0.933 | 0.803–1.00 | Almost perfect | 1.000 |
31 β | 8 | 1 | 0 | 35 | 97.7 | 94.1 | 0.927 | 0.786–1.00 | Almost perfect | 1.000 |
33 β | 5 | 1 | 0 | 38 | 97.7 | 90.9 | 0.896 | 0.696–1.00 | Almost perfect | 1.000 |
35 | 7 | 1 | 2 | 34 | 93.2 | 82.4 | 0.781 | 0.545–1.00 | Substantial | 1.000 |
39 | 7 | 0 | 0 | 37 | 100.0 | 100.0 | 1.000 | 1.00–1.00 | Almost perfect | 1.000 |
45 β | 7 | 2 | 1 | 34 | 93.2 | 82.4 | 0.781 | 0.545–1.00 | Substantial | 1.000 |
51 | 8 | 2 | 0 | 34 | 95.5 | 88.9 | 0.861 | 0.674–1.00 | Almost perfect | 0.479 |
52 β | 14 | 1 | 0 | 29 | 97.7 | 96.6 | 0.949 | 0.849–1.00 | Almost perfect | 1.000 |
56 | 3 | 3 | 3 | 35 | 86.4 | 50.0 | 0.421 | 0.037–0.805 | Moderte | 0.683 |
58 β | 8 | 0 | 1 | 35 | 97.7 | 94.1 | 0.927 | 0.786–1.00 | Almost perfect | 1.000 |
59 | 11 | 1 | 1 | 31 | 95.5 | 91.7 | 0.885 | 0.730–1.00 | Almost perfect | 0.479 |
66 | 4 | 2 | 0 | 38 | 95.5 | 80.0 | 0.776 | 0.479–1.00 | Substantial | 0.479 |
68b | 4 | 0 | 2 | 38 | 95.5 | 80.0 | 0.776 | 0.479–1.00 | Substantial | 0.479 |
6 | 8 | 1 | 0 | 35 | 97.7 | 94.1 | 0.927 | 0.786–1.00 | Almost perfect | 1.000 |
11 | 2 | 0 | 0 | 42 | 100.0 | 100.0 | 1.000 | 1.00–1.00 | Almost perfect | 1.000 |
13 | 0 | 2 | 0 | 42 | 95.5 | 0.0 | 0.000 | 0 | Poor | 0.479 |
26 | 2 | 0 | 0 | 42 | 100.0 | 100.0 | 1.000 | 1.00–1.00 | Almost perfect | 1.000 |
30 | 4 | 1 | 1 | 38 | 95.5 | 80.0 | 0.774 | 0.474–1.00 | Substantial | 0.479 |
40 | 1 | 1 | 1 | 41 | 95.5 | 50.0 | 0.476 | 0.143–1.00 | Moderate | 0.479 |
42 | 7 | 0 | 2 | 35 | 95.5 | 87.5 | 0.848 | 0.644–1.00 | Almost perfect | 0.479 |
43 | 1 | 0 | 0 | 43 | 100 | 100.0 | 1.000 | 1.00–1.00 | Almost perfect | 1.000 |
44 | 3 | 2 | 1 | 38 | 93.2 | 66.7 | 0.629 | 0.245–1.00 | Substantial | 1.000 |
53 | 10 | 2 | 1 | 31 | 93.2 | 87.0 | 0.824 | 0.632–1.00 | Almost perfect | 1.000 |
54 | 4 | 3 | 0 | 37 | 93.2 | 72.7 | 0.692 | 0.371–1.00 | Substantial | 0.248 |
55 | 3 | 2 | 0 | 39 | 95.5 | 75.0 | 0.727 | 0.371–1.00 | Substantial | 0.479 |
61 | 3 | 3 | 0 | 38 | 93.2 | 66.7 | 0.633 | 0.261–1.00 | Substantial | 0.248 |
62 | 10 | 1 | 0 | 33 | 97.7 | 95.2 | 0.938 | 0.817–1.00 | Almost perfect | 1.000 |
64 | 3 | 2 | 2 | 37 | 90.9 | 60.0 | 0.549 | 0.156–0.941 | Moderte | 0.617 |
67 | 5 | 0 | 1 | 38 | 97.7 | 90.9 | 0.896 | 0.696–1.00 | Almost perfect | 1.000 |
68a | 0 | 8 | 0 | 36 | 81.8 | 0.0 | 0.000 | 0 | Poor | 0.013 |
69 | 1 | 2 | 0 | 41 | 95.5 | 50.0 | 0.482 | 0.117–1.00 | Moderte | 0.479 |
70 | 2 | 3 | 0 | 39 | 93.2 | 57.1 | 0.542 | 0.097–0.987 | Moderte | 0.248 |
71 | 2 | 0 | 0 | 42 | 100 | 100.0 | 1.000 | 1.00–1.00 | Almost perfect | 1.000 |
72 | 3 | 1 | 0 | 40 | 97.7 | 85.7 | 0.845 | 0.549–1.00 | Almost perfect | 1.000 |
73 | 5 | 1 | 1 | 37 | 95.5 | 83.3 | 0.807 | 0.548–1.00 | Almost perfect | 0.479 |
74 | 5 | 0 | 4 | 35 | 90.9 | 71.4 | 0.665 | 0.371–0.960 | Moderate | 0.133 |
81 | 5 | 0 | 0 | 39 | 100.0 | 100.0 | 1.000 | 1.00–1.00 | Almost perfect | 1.000 |
82 Subtype IS39 | 2 | 3 | 1 | 38 | 90.9 | 50.0 | 0.453 | 0.008–0.899 | Moderate | 0.617 |
82 | 3 | 4 | 1 | 36 | 88.6 | 54.5 | 0.486 | 0.107–0.865 | Moderate | 0.371 |
83 | 0 | 2 | 1 | 41 | 93.2 | 0.0 | 0 | 0 | Poor | 1.000 |
84 | 4 | 4 | 1 | 35 | 88.6 | 61.5 | 0.553 | 0.211–0.894 | Moderate | 0.371 |
87 | 2 | 2 | 1 | 39 | 93.2 | 57.1 | 0.535 | 0.073–0.998 | Moderate | 1.000 |
89 | 5 | 1 | 2 | 36 | 93.2 | 76.9 | 0.73 | 0.440–1.00 | Substantial | 1.000 |
90 | 3 | 1 | 0 | 40 | 97.7 | 85.7 | 0.845 | 0.549–1.00 | Almost perfect | 1.000 |
91 | 2 | 0 | 2 | 40 | 95.5 | 66.7 | 0.645 | 0.196–1.00 | Substantial | 0.479 |
114 | 0 | 3 | 0 | 41 | 93.2 | 0.0 | 0.000 | 0 | Poor | 0.248 |
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Rajeevan, M.S.; Patel, S.; Li, T.; Unger, E.R. NanoString Technology for Human Papillomavirus Typing. Viruses 2021, 13, 188. https://doi.org/10.3390/v13020188
Rajeevan MS, Patel S, Li T, Unger ER. NanoString Technology for Human Papillomavirus Typing. Viruses. 2021; 13(2):188. https://doi.org/10.3390/v13020188
Chicago/Turabian StyleRajeevan, Mangalathu S., Sonya Patel, Tengguo Li, and Elizabeth R. Unger. 2021. "NanoString Technology for Human Papillomavirus Typing" Viruses 13, no. 2: 188. https://doi.org/10.3390/v13020188