Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay
Abstract
:1. Introduction
2. Methods and Materials
2.1. Sample Collection
2.2. DNA Extraction
2.3. Next Generation Sequencing
2.4. Hybrid Capture II
2.5. VisionArray® HPV Chips
2.6. Statistical Analysis
3. Results
3.1. Next Generation Sequencing and VisionArray® HPV Chips Analysis Comparison
3.1.1. Discrepant Results
3.1.2. Statistical Measures of Performance
3.2. Hybrid Capture II High-Risk HPV DNA Analysis and VisionArray® HPV Chips Analysis Comparison
3.2.1. Discrepant Results
3.2.2. Statistical Measures of Performance
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Data Availability Statement
Conflicts of Interest
References
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Sample | Sex | Age | Sample Type | Site Region |
---|---|---|---|---|
S1 | M | 43 | FrB | Anogenital-Anus |
S2 | M | 45 | FrB | Anogenital-Anus |
S3 | F | 34 | FrB | Anogenital-Anus |
S4 | M | 61 | FFPE | Oropharyngeal-Lymph node |
S5 | M | 67 | FFPE | Oropharyngeal-Tonsil |
S6 | F | 24 | FrB | Anogenital-Cervix |
S7 | M | 57 | FFPE | Oropharyngeal-Lymph node |
S8 | F | 60 | FFPE | Anogenital-Anus |
S9 | F | 43 | FrB | Anogenital-Anus |
S10 | M | 41 | FFPE | Oropharyngeal-Tonsil |
S11 | F | 48 | FrB | Anogenital-Anus |
S12 | F | 20 | FrB | Anogenital-Anus |
S13 | M | 53 | FrB | Anogenital-Anus |
S14 | F | 66 | FFPE | Oropharyngeal-Tonsil |
S15 | F | 69 | FFPE | Oropharyngeal-Tonsil |
S16 | M | 66 | FFPE | Oropharyngeal-Tongue |
S17 | M | 70 | FrB | Anogenital-Anus |
S18 | F | 63 | FFPE | Oropharyngeal-Tonsil |
S19 | F | 39 | FrB | Anogenital-Anus |
S20 | F | 44 | FrB^ | Anogenital-Cervix |
S21 | F | 28 | FFPE | Anogenital-Anus |
S22 | M | 55 | FFPE | Oropharyngeal-Lymph node |
S23 | M | 28 | FrB | Anogenital-Anus |
S24 | M | 42 | FFPE | Oropharyngeal-Tongue |
S25 | F | 53 | FFPE | Oropharyngeal-Tonsil |
S26 | F | 19 | FrB | Anogenital-Cervix |
S27 | F | 61 | FrB | Anogenital-Cervix |
S28 | F | 32 | FrB | Anogenital-Cervix |
S29 | F | 61 | FrB | Anogenital-Cervix |
S30 | F | 39 | FrB | Anogenital-Cervix |
S31 | F | 46 | FrB | Anogenital-Cervix |
S32 | F | 30 | FrB | Anogenital-Cervix |
S33 | F | 33 | FrB | Anogenital-Cervix |
S34 | F | 46 | FrB | Anogenital-Cervix |
S35 | F | 31 | FrB | Anogenital-Cervix |
S36 | F | 49 | FrB | Anogenital-Cervix |
S37 | F | 45 | FrB | Anogenital-Cervix |
S38 | F | 46 | FrB | Anogenital-Cervix |
S39 | F | 70 | FrB | Anogenital-Cervix |
S40 | F | 59 | FrB | Anogenital-Cervix |
S41 | F | 48 | FrB | Anogenital-Cervix |
S42 | F | 21 | FrB | Anogenital-Cervix |
S43 | F | 40 | FrB | Anogenital-Cervix |
S44 | F | 33 | FrB | Anogenital-Cervix |
S45 | F | 32 | FrB | Anogenital-Cervix |
S46 | F | 46 | FrB | Anogenital-Cervix |
S47 | F | 46 | FrB | Anogenital-Cervix |
S48 | F | 33 | FrB | Anogenital-Cervix |
S49 | F | 41 | FrB | Anogenital-Cervix |
S50 | F | 33 | FrB | Anogenital-Cervix |
Sample | NGS | VisionArray® | Site Region |
---|---|---|---|
S1 | HPV11 | HPV11 | Anogenital-Anus |
S2 | Neg | Neg | Anogenital-Anus |
S3 | Neg | Neg | Anogenital-Anus |
S4 * | NE | Neg | Oropharyngeal-Lymph node |
S5 * | NE | HPV16+42 | Oropharyngeal-Tonsil |
S6 * | HPV6+66 | HPV6+66+61+73+82+90 | Anogenital-Cervix |
S7 * | NE | HPV16 | Oropharyngeal-Lymph node |
S8 | HPV16 | HPV16 | Anogenital-Anus |
S9 | HPV11 | HPV11 | Anogenital-Anus |
S10 | Neg | Neg | Oropharyngeal-Tonsil |
S11 | HPV6 | HPV6 | Anogenital-Anus |
S12 | Neg | Neg | Anogenital-Anus |
S13 | HPV33+54 | HPV33+54 | Anogenital-Anus |
S14 | Neg | Neg | Oropharyngeal-Tonsil |
S15 | HPV35 | HPV35 | Oropharyngeal-Tonsil |
S16 | HPV33 | HPV33 | Oropharyngeal-Tongue |
S17 | HPV6 | HPV6 | Anogenital-Anus |
S18 | HPV16 | HPV16 | Oropharyngeal-Tonsil |
S19 | Neg | Neg | Anogenital-Anus |
S20 | Neg | Neg | Anogenital-Cervix |
S21 * | Neg | HPV40 | Anogenital-Anus |
S22 * | HPV35 | HPV35+34 | Oropharyngeal-Lymph node |
S23 | HPV6+91 | HPV6+91 | Anogenital-Anus |
S24 | Neg | Neg | Oropharyngeal-Tongue |
S25 | HPV35 | HPV35 | Oropharyngeal-Tonsil |
VisionArray® vs. NGS | Sensitivity | Specificity | Overall Accuracy | PPV | NPV | Concordance (Cohen’s κ) (95% CI) |
---|---|---|---|---|---|---|
Positive: HR+PHR+LR | 0.81 | 1.0 | 0.84 | 1.0 | 0.75 | 0.702 (0.44–0.97) |
Positive: HR | 0.78 | 1.0 | 0.92 | 1.0 | 0.89 | 0.779 (0.55–1.0) |
Positive: HR/PHR | 0.73 | 1.0 | 0.88 | 1.0 | 0.82 | 0.775 (0.56–0.99) |
HR/PHR/LR | 0.81 | 1.0 | 0.84 | 1.0 | 0.75 | 0.818 (0.62–1.0) |
Sample | HC | VisionArray® | Site Region |
---|---|---|---|
S26 * | Neg | HPV42 | Anogenital-Cervix |
S27 * | Neg | HPV55 | Anogenital-Cervix |
S28 * | Neg | HPV42 | Anogenital-Cervix |
S29 | Neg | Neg | Anogenital-Cervix |
S30 * | Neg | 16+42 | Anogenital-Cervix |
S31 * | Neg | HPV6+11+53 | Anogenital-Cervix |
S32 | Neg | Neg | Anogenital-Cervix |
S33 | Neg | Neg | Anogenital-Cervix |
S34 | Neg | Neg | Anogenital-Cervix |
S35 | Neg | Neg | Anogenital-Cervix |
S36 | Neg | Neg | Anogenital-Cervix |
S37 | Neg | Neg | Anogenital-Cervix |
S38 | Neg | Neg | Anogenital-Cervix |
S39 | Pos | HPV16 | Anogenital-Cervix |
S40 | Pos | HPV35 | Anogenital-Cervix |
S41 | Pos | HPV51 | Anogenital-Cervix |
S42 | Pos | HPV56 | Anogenital-Cervix |
S43 | Pos | HPV56 | Anogenital-Cervix |
S44 | Pos | HPV16+39 | Anogenital-Cervix |
S45 | Pos | HPV16+52+53 | Anogenital-Cervix |
S46 | Pos | HPV16+54+56+66 | Anogenital-Cervix |
S47 | Pos | HPV16+61 | Anogenital-Cervix |
S48 | Pos | HPV16+18 | Anogenital-Cervix |
S49 * | Pos | HPV40+42+44+54 | Anogenital-Cervix |
S50 | Pos | HPV6+31 | Anogenital-Cervix |
VisionArray® vs. HC II | Sensitivity | Specificity | Overall Accuracy | PPV | NPV | Concordance (Cohen’s κ) (95% CI) |
---|---|---|---|---|---|---|
Positive HR+PHR+LR | 0.71 | 1.0 | 0.80 | 1.0 | 0.62 | 0.606 (0.32–0.89) |
Positive: HR | 0.92 | 0.92 | 0.92 | 0.92 | 0.92 | 0.84 (0.63–1.0) |
Positive: HR/PHR | 0.85 | 0.92 | 0.88 | 0.92 | 0.85 | 0.76 (0.51–1.0) |
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Acquaviva, G.; Visani, M.; Sanza, V.; De Leo, A.; Maloberti, T.; Pierotti, P.; Crucitti, P.; Collina, G.; Chiarelli Olivari, C.; Pession, A.; et al. Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay. J. Mol. Pathol. 2021, 2, 29-41. https://doi.org/10.3390/jmp2010004
Acquaviva G, Visani M, Sanza V, De Leo A, Maloberti T, Pierotti P, Crucitti P, Collina G, Chiarelli Olivari C, Pession A, et al. Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay. Journal of Molecular Pathology. 2021; 2(1):29-41. https://doi.org/10.3390/jmp2010004
Chicago/Turabian StyleAcquaviva, Giorgia, Michela Visani, Viviana Sanza, Antonio De Leo, Thais Maloberti, Paola Pierotti, Paola Crucitti, Guido Collina, Cecilia Chiarelli Olivari, Annalisa Pession, and et al. 2021. "Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay" Journal of Molecular Pathology 2, no. 1: 29-41. https://doi.org/10.3390/jmp2010004
APA StyleAcquaviva, G., Visani, M., Sanza, V., De Leo, A., Maloberti, T., Pierotti, P., Crucitti, P., Collina, G., Chiarelli Olivari, C., Pession, A., Tallini, G., & de Biase, D. (2021). Different Methods in HPV Genotyping of Anogenital and Oropharyngeal Lesions: Comparison between VisionArray® Technology, Next Generation Sequencing, and Hybrid Capture Assay. Journal of Molecular Pathology, 2(1), 29-41. https://doi.org/10.3390/jmp2010004