References
- Ferlay J, Shin H R, Bray F, Forman D, Mathers C, Parkin D M. Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008. Int J Cancer. 2010;127(12):2893-2917. https://doi.org/10.1002/ijc.25516
- Decker J, Goldstein JC. Risk factors in head and neck cancer. N Engl J Med. 1982;306:1151-1155. https://doi.org/10.1056/NEJM198205133061905
- Licitra L, Locati LD, Bossi P. Head and neck cancer. Ann Oncol. 2004;15(Suppl4):iv267-273. https://doi.org/10.1093/annonc/mdh937
- Ang KK, Harris J, Wheeler R, et al. Human papillomavirus and survival of patients with oropharyngeal cancer. N Engl J Med. 2010;363:24-35. https://doi.org/10.1056/NEJMoa0912217
- Ragin CC, Taioli E. Survival of squamous cell carcinoma of the head and neck in relation to human papillomavirus infection: review and meta-analysis. Int J Cancer. 2007;121:1813-1820. https://doi.org/10.1002/ijc.22851
- Fakhry C, Westra WH, Li S, et al. Improved survival of patients with human papillomavirus-positive head and neck squamous cell carcinoma in a prospective clinical trial. J Natl Cancer Inst. 2008;100:261-269. https://doi.org/10.1093/jnci/djn011
- Vidal L, Gillison LV. Human papillomavirus in HNSCC: recognition of a distinct disease type. Hematol Oncol Clin N Am. 2008;22:1125-1142. https://doi.org/10.1016/j.hoc.2008.08.006
- Snietura M, Piglowski W., Jaworska M, Mucha-Malecka A, Wozniak G, Lange D, Suwinski R. Impact of HPV infection on the clinical outcome of p-CAIR trial in head and neck cancer. Eur Arch Otorhinolaryngol. 2011;268:721-726. https://doi.org/10.1007/s00405-010-1396-7
- Kujdowicz M, Januś D, Taczanowska-Niemczuk A, Lankosz MW, Adamek D. Raman Spectroscopy as a Potential Adjunct of Thyroid Nodule Evaluation: A Systematic Review. Int J Mol Sci. 2023;24(20):15131. https://doi.org/10.3390/ijms242015131
- Kujdowicz M, Placha W, Mech B, Chrabaszcz K, Okoń K, Malek K. In Vitro Spectroscopy-Based Profiling of Urothelial Carcinoma: A Fourier Transform Infrared and Raman Imaging Study. Cancers (Basel). 2021;13(1):123. https://doi.org/10.3390/cancers13010123
- Neto V, Esteves-Ferreira S, Inácio I, et al. Metabolic Profile Characterization of Different Thyroid Nodules Using FTIR Spectroscopy: A Review. Metabolites. 2022;12(1):53. https://doi.org/10.3390/metabo12010053
- Wahadoszamen M, Rahaman A, Hoque NM, I Talukder A, Abedin KM, Haider AF. Laser raman spectroscopy with different excitation sources and extension to surface enhanced raman spectroscopy. J Spectrosc. 2015;2015:1-8. https://doi.org/10.1155/2015/895317
- Śnietura M, Brewczynski A, Waniczek D, Kopec A, Stanek-Widera A, Muc-Wierzgoń M, Rutkowski T. Is p16 expression still a surrogate marker for human papillomavirus infection in oral squamous cell carcinomas? J Biol RegulHomeost Agents. 2020;34(3):1153-1156. https://doi.org/10.23812/19-423-L-58
- Smeets SJ, Hesselink AT, Speel E-JM, et al. A novel algorithm for reliable detection of human papillomavirus in paraffin embedded head and neck cancer specimen. Int J Cancer. 2007;121(11):2465-2472. https://doi.org/10.1002/ijc.22980
- Huang S, Erickson B, Tang N, et al. Clinical performance of Abbott RealTime High Risk HPV test for detection of high-grade cervical intraepithelial neoplasia in women with abnormal cytology. J Clin Virol. 2009;45(Suppl 1):S19-23. https://doi.org/10.1016/S1386-6532(09)70004-6
- Huang S, Tang N, Mak W-B, et al. Principles and analytical performance of Abbott RealTime High Risk HPV test. J Clin Virol. 2009;45(Suppl 1):S13-17. https://doi.org/10.1016/S1386-6532(09)70003-4
- Snietura M, Piglowski W, Jaworska M, et al. Impact of HPV infection on the clinical outcome of p-CAIR trial in head and neck cancer. Eur Arch Otorhinolaryngol. 2011;268(5):721-726. https://doi.org/10.1007/s00405-010-1396-7
- Kocjan BJ, Maver PJ, Hosnjak L, et al. Comparative evaluation of the Abbott RealTime High Risk HPV test and INNO-LiPA HPV Genotyping Extra test for detecting and identifying human papillomaviruses in archival tissue specimens of head and neck cancers. Acta Dermatovenerol Alp PannonicaAdriat. 2012;21(4):73-75.
- R Core Team. R: A language and environment for statistical computing. R 2.5.2 Foundation for Statistical Computing, Vienna, Austria. 2016; URL https://www.R-project.org/.
- Beleites C, Sergo V.: hyperSpec: a package to handle hyperspectral data sets in R, R package version 0.98-20161118.
- HovdeLiland, Helge Mevik B. Baseline: Baseline Correction of Spectra, 2015; URL https://CRAN.R-project.org/package=baseline. R package version 1.2-1.
- Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society Series B. 1995;57:289-300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x
- Mardia KV, Kent JT, Bibby JM. Multivariate Analysis, London: Academic Press.1979.
- Murtagh F, Legendre P. Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion? Journal of Classification. 2014;31:274-295. https://doi.org/10.1007/s00357-014-9161-z
- Perez-Enciso M, Tenenhaus M. Prediction of clinical outcome with microarray data: a partial least squares discriminant analysis (PLSDA) approach. Human Genetics. 2003;112:581-592. https://doi.org/10.1007/s00439-003-0921-9
- Smith EM, Wang D, Kim Y, et al. p16INK4a Expression, human papillomavirus, and survival in head and neck cancer. Oral Oncology. 2008;44(2):133-142. https://doi.org/10.1016/j.oraloncology.2007.01.010
- AW Auner, JC Thomas, Double-Stranded DNA Damage Assessed with Raman Spectroscopy. Biochemistry & Analytical Biochemistry. 2016;5(3). https://doi.org/10.4172/2161-1009.1000284
- Lipiec E, Bambery KR, Heraud P, et al. Monitoring UVR induced damage in single cells and isolated nuclei using SR-FTIR microspectroscopy and 3D confocal Raman imaging. Analyst. 2014;139(17):4200-4209. https://doi.org/10.1039/C4AN00838C
- Sánchez V, Redmann K, Wistuba J, et al. Oxidative DNA damage in human sperm can be detected by Raman microspectroscopy. FertilSteril. 2012;98(5):1124-1129.e1-3. https://doi.org/10.1016/j.fertnstert.2012.07.1059
- Kelly JG, Najand GM, Martin FL. Characterisation of DNA methylation status using spectroscopy (mid-IR versus Raman) with multivariate analysis. J Biophotonics. 2011;4(5):345-354. https://doi.org/10.1002/jbio.201000085
- Krafft C. Bioanalytical applications of Raman spectroscopy. Anal Bioanal Chem. 2004;378(1):60-62. https://doi.org/10.1007/s00216-003-2266-6
- Nijssen A, Koljenović S, Bakker Schut TC, Caspers PJ, Puppels GJ. Towards oncological application of Raman spectroscopy. J Biophotonics. 2009;2(1-2):29-36. https://doi.org/10.1002/jbio.200810055
- Kendall C, Isabelle M, Bazant-Hegemark F, et al. Vibrational spectroscopy: a clinical tool for cancer diagnostics. Analyst. 2009;134(6):1029-1045. https://doi.org/10.1039/b822130h
- Kondepati VR, Heise HM, Backhaus J. Recent applications of near-infrared spectroscopy in cancer diagnosis and therapy. Anal Bioanal Chem. 2008;390(1):125-139. https://doi.org/10.1007/s00216-007-1651-y
- Ramos IRM, Malkin A, Lyng FM. Current Advances in the Application of Raman Spectroscopy for Molecular Diagnosis of Cervical Cancer. Biomed Res Int. 2015;2015:561242. https://doi.org/10.1155/2015/561242
- Hewitt SM, Lewis FA, Cao Y, et al. Tissue Handling and Specimen Preparation in Surgical Pathology: Issues Concerning the Recovery of Nucleic Acids From Formalin-Fixed, Paraffin-Embedded Tissue. Archives of Pathology & Laboratory Medicine. 2008;132(12):1929-1935. https://doi.org/10.5858/132.12.1929
- Howat WJ, Wilson BA. Tissue fixation and the effect of molecular fixatives on downstream staining procedures. Methods. 2014;70(1):12-19. https://doi.org/10.1016/j.ymeth.2014.01.022
- Shrivastava A, Aggarwal LM, Murali Krishna C, et al. Diagnostic and prognostic application of Raman spectroscopy in carcinoma cervix: A biomolecular approach. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2021;250:119356. https://doi.org/10.1016/j.saa.2020.119356
- Man Y, Moinfar F, Bratthauer GL, Kuhls EA, Tavassoli FA. An Improved Method for DNA Extraction from Paraffin Sections. Pathology - Research and Practice. 2001;197(9):635-642. https://doi.org/10.1078/0344-0338-00138
- Krishna CM, Sockalingum GD, Vadhiraja BM, et al. Vibrational spectroscopy studies of formalin-fixed cervix tissues. Biopolymers. 2007;85(3):214-221. https://doi.org/10.1002/bip.20631
- Lyng FM, Traynor D, Ramos IRM, Bonnier F, Byrne HJ. Raman spectroscopy for screening and diagnosis of cervical cancer. Anal Bioanal Chem. 2015;407(27):8279-8289. https://doi.org/10.1007/s00216-015-8946-1
- Yazdi Y, Ramanujam N, Lotan R, Mitchell MF, Hittelman W, Richards-Kortum R. Resonance Raman Spectroscopy at 257 nm Excitation of Normal and Malignant Cultured Breast and Cervical Cells. Appl Spectrosc, AS. 1999;53(1):82-85. https://doi.org/10.1366/0003702991945254
- Ostrowska KM, Malkin A, Meade A, et al. Investigation of the influence of high-risk human papillomavirus on the biochemical composition of cervical cancer cells using vibrational spectroscopy. Analyst. 2010;135(12):3087-3093. https://doi.org/10.1039/c0an00571a
- Snietura M, Lamch R, Kopec A, Waniczek D, Likus W, Lange D, Markowski J Oral and oropharyngeal papillomas are not associated with high-risk human papillomavirus infection. Eur Arch Otorhinolaryngol. 2017 Sep;274(9):3477-3483. https://doi.org/10.1007/s00405-017-4649-x
- Schäfer A, Lengenfelder D, Grillhösl C, Wieser C, Fleckenstein B, Ensser A. The latency-associated nuclear antigen homolog of herpesvirus saimiri inhibits lytic virus replication. J Virol. 2003;77(10):5911-5925. https://doi.org/10.1128/JVI.77.10.5911-5925.2003
- Vargis E, Tang Y-W, Khabele D, Mahadevan-Jansen A. Near-infrared Raman Microspectroscopy Detects High-risk Human Papillomaviruses. Transl Oncol. 2012;5(3):172-179. https://doi.org/10.1593/tlo.12106
- Ringelhan M, Heikenwalder M, Protzer U. Direct effects of hepatitis B virus-encoded proteins and chronic infection in liver cancer development. Dig Dis. 2013;31(1):138-151. https://doi.org/10.1159/000347209
- Moor K, Ohtani K, Myrzakozha D, Zhanserkenova O, Andriana BB, Sato H. Noninvasive and label-free determination of virus infected cells by Raman spectroscopy. J Biomed Opt. 2014;19(6):067003. https://doi.org/10.1117/1.JBO.19.6.067003
- Salman A, Shufan E, Zeiri L, Huleihel M. Characterization and detection of Vero cells infected with Herpes Simplex Virus type 1 using Raman spectroscopy and advanced statistical methods. Methods. 2014;68(2):364-370. https://doi.org/10.1016/j.ymeth.2014.02.022
- Ruokola P, Dadu E, Kazmertsuk A, Häkkänen H, Marjomäki V, Ihalainen JA. Raman Spectroscopic Signatures of Echovirus 1 Uncoating. J Virol. 2014;88(15):8504-8513. https://doi.org/10.1128/JVI.03398-13
- Hermann P, Hermelink A, Lausch V, et al. Evaluation of tip-enhanced Raman spectroscopy for characterizing different virus strains. Analyst. 2011;136(6):1148-1152. https://doi.org/10.1039/c0an00531b