Deep Learning Based HPV Status Prediction for Oropharyngeal Cancer Patients
Abstract
:Simple Summary
Abstract
1. Introduction
2. Material and Methods
2.1. Data
2.2. Deep Neural Network
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
HPV | human papillomavirus |
OPC | oropharyngeal cancer |
CT | computed tomography |
AUC | area under the receiver operating characteristic curve |
CNN | convolutional neural network |
FDG-PET | fluorodeoxyglucose—positron emission tomography |
GTV | gross tumor volume |
IHC | immunohistochemistry |
DNA | deoxyribonucleic acid |
ROC | receiver operating characteristic |
AJCC | American Joint Committee of Cancer |
Appendix A
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2lClinical Variable | Training Set | Validation Set | Test Set | ||
---|---|---|---|---|---|
Cohort | OPC | HNSCC | HN PET-CT | HN1 | |
Number of patients | 412 | 263 | 90 | 80 | |
HPV: pos/neg | 290/122 | 223/40 | 71/19 | 23/57 | |
HPV status | |||||
Age | |||||
pos | 58.81 (52.00–64.75) | 57.87 (52.00–64.00) | 62.32 (58.00–66.00) | 57.52 (52.00–62.50) | |
neg | 64.82 (58.00–72.75) | 60.02 (54.50–67.25) | 59.11 (49.50–69.50) | 60.91 (56.00–66.00) | |
Sex: Female/Male | |||||
pos | 47/243 | 32/191 | 14/56 | 5/18 | |
neg | 34/88 | 15/25 | 4/15 | 12/45 | |
T-stage: T1/T2/T3/T4 | |||||
pos | 46/93/94/57 | 60/93/41/29 | 10/37/15/9 | 4/8/9/8 | |
neg | 9/35/43/35 | 6/12/12/10 | 3/4/8/4 | 9/16/9/23 | |
N-stage: N0/N1/N2/N3 | |||||
pos | 33/22/215/20 | 19/30/170/4 | 11/10/47/3 | 6/2/15/0 | |
neg | 36/16/62/8 | 5/2/31/2 | 2/1/13/3 | 14/10/31/2 | |
Tumor size [cm] | |||||
pos | 29.35 (10.52–37.78) | 11.78 (3.94–14.04) | 34.63 (14.91–41.77) | 23.00 (10.83–34.29) | |
neg | 36.99 (15.72–45.35) | 23.57 (5.80–22.85) | 35.09 (17.32–47.82) | 40.19 (11.77–54.42) | |
transversal voxel spacing [mm] | 0.97 (0.98–0.98) | 0.59 (0.49–0.51) | 1.06 (0.98–1.17) | 0.98 (0.98–0.98) | |
longitudinal voxel spacing [mm] | 2.00 (2.00–2.00) | 1.53 (1.00-2.50) | 2.89 (3.00–3.27) | 2.99 (3.00–3.00) | |
manufacturer | |||||
GE Med. Sys. | 272 | 238 | 45 | 0 | |
Toshiba | 138 | 3 | 0 | 0 | |
Philips | 2 | 12 | 45 | 0 | |
CMS Inc. | 0 | 0 | 0 | 43 | |
Siemens | 0 | 4 | 0 | 37 | |
other | 0 | 6 | 0 | 0 |
Metric | 3D Video Pre-Trained | 3D from Scratch | 2D ImageNet Pre-Trained |
---|---|---|---|
AUC | 0.81 (0.02) | 0.64 (0.05) | 0.73 (0.02) |
sensitivity | 0.75 (0.06) | 0.67 (0.12) | 0.84 (0.07) |
specificity | 0.72 (0.09) | 0.49 (0.09) | 0.40 (0.13) |
PPV | 0.53 (0.07) | 0.35 (0.03) | 0.37 (0.04) |
NPV | 0.88 (0.02) | 0.79 (0.05) | 0.87 (0.03) |
score | 0.62 (0.02) | 0.45 (0.05) | 0.51 (0.03) |
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Share and Cite
Lang, D.M.; Peeken, J.C.; Combs, S.E.; Wilkens, J.J.; Bartzsch, S. Deep Learning Based HPV Status Prediction for Oropharyngeal Cancer Patients. Cancers 2021, 13, 786. https://doi.org/10.3390/cancers13040786
Lang DM, Peeken JC, Combs SE, Wilkens JJ, Bartzsch S. Deep Learning Based HPV Status Prediction for Oropharyngeal Cancer Patients. Cancers. 2021; 13(4):786. https://doi.org/10.3390/cancers13040786
Chicago/Turabian StyleLang, Daniel M., Jan C. Peeken, Stephanie E. Combs, Jan J. Wilkens, and Stefan Bartzsch. 2021. "Deep Learning Based HPV Status Prediction for Oropharyngeal Cancer Patients" Cancers 13, no. 4: 786. https://doi.org/10.3390/cancers13040786
APA StyleLang, D. M., Peeken, J. C., Combs, S. E., Wilkens, J. J., & Bartzsch, S. (2021). Deep Learning Based HPV Status Prediction for Oropharyngeal Cancer Patients. Cancers, 13(4), 786. https://doi.org/10.3390/cancers13040786