Detection of alpha human papillomaviruses in archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens

Journal of Clinical Virology

Volumn 76, Issue , 2016, Pages S88-S97

  Kocjan, Boštjan J ^a   Hošnjak, Lea ^a   Poljak, Mario ^a,b  

^a UNIVERSITY OF LJUBLJANA   (Slovenia)

^b European Study Group for Biofilms (ESGB)   (Switzerland)

Author keywords

Achival tissues specimens; FFPE; Formalin fixed; HPV; Human papillomaviruses; Paraffin embedded tissue

Indexed keywords

FIXATIVE; FORMALDEHYDE; NUCLEIC ACID; PARAFFIN; VIRUS DNA; VIRUS RNA;

ALPHAPAPILLOMAVIRUS; ENVIRONMENTAL FACTOR; FORMALIN FIXED PARAFFIN EMBEDDED TISSUE; GENETIC ANALYSIS; HUMAN; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEIC ACID AMPLIFICATION; PH; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROCEDURES; PURIFICATION; REVIEW; TEMPERATURE; TISSUE FIXATION; TISSUE PRESERVATION; TISSUE SECTION; VIRUS DETECTION; CERVICAL INTRAEPITHELIAL NEOPLASIA; CHEMISTRY; CLASSIFICATION; COMPLICATION; FEMALE; GENETICS; HIGH THROUGHPUT SEQUENCING; HUMAN PAPILLOMAVIRUS DNA TEST; ISOLATION AND PURIFICATION; PAPILLOMAVIRUS INFECTIONS; UTERINE CERVICAL NEOPLASMS; VIROLOGY;

ALPHAPAPILLOMAVIRUS; CERVICAL INTRAEPITHELIAL NEOPLASIA; DNA, VIRAL; FEMALE; FIXATIVES; FORMALDEHYDE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMAN PAPILLOMAVIRUS DNA TESTS; HUMANS; PAPILLOMAVIRUS INFECTIONS; PARAFFIN EMBEDDING; POLYMERASE CHAIN REACTION; RNA, VIRAL; TISSUE FIXATION; UTERINE CERVICAL NEOPLASMS;

EID: 84960397404     PISSN: 13866532     EISSN: 18735967     Source Type: Journal    
DOI: 10.1016/j.jcv.2015.10.007     Document Type: Review

References (119)

1. zur Hausen H. Papillomaviruses in the causation of human cancers-a brief historical account. Virology 2009, 384:260-265.
2. Forman D., de Martel C., Lacey C.J., Soerjomataram I., Lortet-Tieulent J., et al. Global burden of human papillomavirus and related diseases. Vaccine 2012, 30(Suppl. 5):F12-F23.
3. Ndiaye C., Mena M., Alemany L., Arbyn M., Castellsagué X., et al. HPV DNA: E6/E7 mRNA, and p16INK4a detection in head and neck cancers: a systematic review and meta-analysis. Lancet Oncol. 2014, 15(12):1319-1331.
4. Komloš K.F., Kocjan B.J., Košorok P., Luzar B., Meglič L., et al. Tumor-specific and gender-specific pre-vaccination distribution of human papillomavirus types 6 and 11 in anogenital warts and laryngeal papillomas: a study on 574 tissue specimens. J. Med. Virol. 2012, 84(8):1233-1241.
5. But-Hadzic J., Jenko K., Poljak M., Kocjan B.J., Gale N., et al. Sinonasal inverted papilloma associated with squamous cell carcinoma. Radiol. Oncol. 2011, 45(4):267-272.
6. Komloš K.F., Kocjan B.J., Košorok P., Rus T., Toplak J., et al. Distribution of HPV genotypes in Slovenian patients with anal carcinoma: preliminary results. Acta Dermatovenerol. Alp Pannonica Adriat. 2011, 20(3):141-143.
7. Guimera N., Lloveras B., Lindeman J., Alemany L., van de Sandt M., et al. RIS HPV TTHPV VVAPO study groups. The occasional role of low-risk human papillomaviruses 6, 11, 42, 44, and 70 in anogenital carcinoma defined by laser capture microdissection/PCR methodology: results from a global study. Am. J. Surg. Pathol. 2013, 37(9):1299-1310.
8. de Villiers E.M., Fauquet C., Broker T.R., Bernard H.U., zur Hausen H. Classification of papillomaviruses. Virology 2014, 324(1):17-27.
9. Poljak M., Cuzick J., Kocjan B.J., Iftner T., Dillner J., et al. Nucleic acid tests for the detection of alpha human papillomaviruses. Vaccine 2012, 30(Suppl. 5):F100-F106.
10. Arbyn M., Snijders P.J., Meijer C.J., Berkhof J., Cuschieri K., et al. Which high-risk HPV assays fulfil criteria for use in primary cervical cancer screening?. Clin. Microbiol. Infect. 2015, 21(9):817-826.
11. Kreuter A., Potthoff A., Brockmeyer N.H., Gambichler T., Swoboda J., et al. German competence network HIV/AIDS. Anal carcinoma in human immunodeficiency virus-positive men: results of a prospective study from Germany. Br. J. Dermatol. 2010, 162(6):1269-1277.
12. Miloševič M., Poljak M., Mlakar B. Anal HPV infection in Slovenian men who have sex with men. Cent. Eur. J. Med. 2010, 5:698-703.
13. Bottalico D., Chen Z., Dunne A., Ostoloza J., McKinney S., et al. The oral cavity contains abundant known and novel human papillomaviruses from the betapapillomavirus and gammapapillomavirus genera. J. Infect. Dis. 2011, 204(5):787-792.
14. Meyer M.F., Huebbers C.U., Siefer O.G., Vent J., Engbert I., et al. Prevalence and risk factors for oral human papillomavirus infection in 129 women screened for cervical HPV infection. Oral Oncol. 2014, 50(1):27-31.
15. Mlakar B., Kocjan B.J., Hošnjak L., Fujs Komloš K., Milošević M., et al. Betapapillomaviruses in the anal canal of HIV positive and HIV negative men who have sex with men. J. Clin.Virol. 2014, 61(2):237-241.
16. Pathak N., Dodds J., Zamora J., Khan K. Accuracy of urinary human papillomavirus testing for presence of cervical HPV: systematic review and meta-analysis. BMJ 2014, 349:g5264.
17. Cobo F. Application of molecular diagnostic techniques for viral testing. Open Virol. J. 2012, 6:104-114.
18. Khardori N. Future of diagnostic microbiology. Indian J. Med. Microbiol. 2014, 32:371-377.
19. Thavarajah R., Mudimbaimannar V.K., Elizabeth J., Rao U.K., Ranganathan K. Chemical and physical basics of routine formaldehyde fixation. J. Oral Maxillofac. Pathol. 2012, 16(3):400-405.
20. Titford M.E., Horenstein M.G. Histomorphologic assessment of formalin substitute fixatives for diagnostic surgical pathology. Arch. Pathol. Lab. Med. 2005, 129(4):502-506.
21. Gilbert M.T., Haselkorn T., Bunce M., Sanchez J.J., Lucas S.B., et al. The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when?. PLoS One 2007, 2(6):e537.
22. Moelans C.B., ter Hoeve N., van Ginkel J.W., ten Kate F.J., van Diest P.J. Formaldehyde substitute fixatives. Analysis of macroscopy, morphologic analysis, and immunohistochemical analysis. Am. J. Clin. Pathol. 2011, 136(4):548-556.
23. Nuovo G.J., Richart R.M. Buffered formalin is the superior fixative for the detection of HPV DNA by in situ hybridization analysis. Am. J. Pathol. 1989, 134(4):837-842.
24. Park J.S., Leake J.F., Sharma B.K., Toki T., Kessis T.D., et al. Variability in beta-globin and HPV DNA amplification by PCR from fixed tissues. Mod. Pathol. 1991, 4(5):667-670.
25. Bonin S., Petrera F., Rosai J., Stanta G. DNA and RNA obtained from Bouin's fixed tissues. J. Clin. Pathol. 2005, 58(3):313-316.
26. Powell N., Boyde A., Tristram A., Hibbitts S., Fiander A. The potential impact of human papillomavirus vaccination in contemporary cytologically screened populations may be underestimated: an observational retrospective analysis of invasive cervical cancers. Int. J. Cancer 2009, 125(10):2425-2427.
27. Bonin S., Stanta G. Nucleic acid extraction methods from fixed and paraffin-embedded tissues in cancer diagnostics. Expert Rev. Mol. Diagn. 2013, 13(3):271-282.
28. Dietrich D., Uhl B., Sailer V., Holmes E.E., Jung M., et al. Improved PCR performance using template DNA from formalin-fixed and paraffin-embedded tissues by overcoming PCR inhibition. PLoS One 2013, 8(10):e77771.
29. Unlocking your FFPE archive: critical factors for molecular analysis of FFPE samples. Qiagen. URL: , 2013 (accessed: 15.08.15). http://www.qiagen.com/literature/render.aspx%3Fid=200780.
30. G. Rolls, Fixation and Fixatives (2)-Factors influencing chemical fixation, formaldehyde and glutaraldehyde. Leica Biosystems. URL: , 2012 (accessed 15.08.15). http://www.leicabiosystems.com/pathologyleaders/fixation-and-fixatives-2-factors-influencing-chemical-fixation-formaldehyde-and-glutaraldehyde/.
31. J. Randolph-Habecker, Tips about Fixation and Formalin. Fred Hutchinson Cancer Research Center. URL: (accessed 15.08.15). http://sharedresources.fhcrc.org/training/tips-about-fixation-and-formalin.
32. Ganjali H., Ganjali M. Fixation in tissue processing. IJFAS 2013, 68:686-689.
33. Zsikla V., Baumann M., Cathomas G. Effect of buffered formalin on amplification of DNA from paraffin wax embedded small biopsies using real-time PCR. J. Clin. Pathol. 2004, 57(6):654-656.
34. Colley E.C., Stead R.H. Fixation and other pre-analytical factors. Immunohistochemical Staining Methods 2013, 20-39. Dako Denmark A/S, An Agilent Technologies Company. C.R. Taylor, L. Rudbeck (Eds.).
35. Bass B.P., Engel K.B., Greytak S.R., Moore H.M. A review of preanalytical factors affecting molecular, protein, and morphological analysis of formalin-fixed, paraffin-embedded (FFPE) tissue: how well do you know your FFPE specimen?. Arch. Pathol. Lab. Med. 2014, 138(11):1520-1530.
36. Gillio-Tos A., De Marco L., Fiano V., Garcia-Bragado F., Dikshit R., et al. Efficient DNA extraction from 25-year-old paraffin-embedded tissues: study of 365 samples. Pathology (Philadelphia) 2007, 39(3):345-348.
37. Xie R., Chung J.Y., Ylaya K., Williams R.L., Guerrero N., et al. Factors influencing the degradation of archival formalin-fixed paraffin-embedded tissue sections. J. Histochem. Cytochem. 2011, 59(4):356-365.
38. Do H., Wong S.Q., Li J., Dobrovic A. Reducing sequence artifacts in amplicon-based massively parallel sequencing of formalin-fixed paraffin-embedded DNA by enzymatic depletion of uracil-containing templates. Clin. Chem. 2013, 59(9):1376-1383.
39. Kocjan B.J., Seme K., Poljak M. Comparison of the Abbott RealTime High Risk HPV test and INNO-LiPA HPV Genotyping Extra test for the detection of human papillomaviruses in formalin-fixed, paraffin-embedded cervical cancer specimens. J. Virol. Methods 2011, 175(1):117-119.
40. Kocjan B.J., Maver P.J., Hosnjak L., Zidar N., Odar K., 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 Pannonica Adriat. 2012, 21(4):73-75.
41. de Sanjose S., Quint W.G., Alemany L., Geraets D.T., Klaustermeier J.E., et al. Retrospective international survey and HPV time trends study group. Human papillomavirus genotype attribution in invasive cervical cancer: a retrospective cross-sectional worldwide study. Lancet Oncol. 2010, 11(11):1048-1056.
42. Quint W., Jenkins D., Molijn A., Struijk L., van de Sandt M., et al. One virus, one lesion-individual components of CIN lesions contain a specific HPV type. J. Pathol. 2012, 227(1):62-71.
43. Guimera N., Lloveras B., Alemany L., Iljazovic E., Shin H.R., et al. Laser capture microdissection shows HPV11 as both a causal and a coincidental infection in cervical cancer specimens with multiple HPV types. Histopathology 2013, 63(2):287-292.
44. Hawkins M.G., Winder D.M., Ball S.L., Vaughan K., Sonnex C., Stanley M.A., Sterling J.C., Goon P.K. Detection of specific HPV subtypes responsible for the pathogenesis of condylomata acuminata. Virol. J. 2013, 10:137.
45. Steinau M., Patel S.S., Unger E.R. Efficient DNA extraction for HPV genotyping in formalin-fixed, paraffin-embedded tissues. J. Mol. Diagn. 2011, 13:377-381.
46. Cannavo I., Loubatier C., Chevallier A., Giordanengo V. Improvement of DNA extraction for human papillomavirus genotyping from formalin-fixed paraffin-embedded tissues. Biores. Open Access 2012, 1:333-337.
47. Bateman A.C., Katundu K., Polepole P., Shibemba A., Mwanahamuntu M., et al. Identification of human papillomaviruses from formalin-fixed, paraffin-embedded pre-cancer and invasive cervical cancer specimens in Zambia: a cross-sectional study. Virol. J. 2015, 12:2.
48. Lin J., Kennedy S.H., Svarovsky T., Rogers J., Kemnitz J.W., Xu A., Zondervan K.T. High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil. Anal. Biochem. 2009, 395(2):265-267.
49. Heikal N., Nussenzveig R.H., Agarwal A.M. Deparaffinization with mineral oil: a simple procedure for extraction of high-quality DNA from archival formalin-fixed paraffin-embedded samples. Appl. Immunohistochem. Mol. Morphol. 2014, 22(8):623-626.
50. Chan P.K., Chan D.P., To K.F., Yu M.Y., Cheung J.L., et al. Evaluation of extraction methods from paraffin wax embedded tissues for PCR amplification of human and viral DNA. J. Clin. Pathol. 2001, 54(5):401-403.
51. Kocjan B.J., Hošnjak L., Poljak M. Commercially available kits for manual and automatic extraction of nucleic acids from formalin-fixed, paraffin-embedded (FFPE) tissues. Acta Dermatovenerol. Alp Pannonica Adriat. 2015, 24(2):21-23.
52. Bonin S., Hlubek F., Benhattar J., Denkert C., Dietel M., et al. Multicentre validation study of nucleic acids extraction from FFPE tissues. Virchows Arch. 2010, 457(3):309-317.
53. Kapp J.R., Diss T., Spicer J., Gandy M., Schrijver I., et al. Variation in pre-PCR processing of FFPE samples leads to discrepancies in BRAF and EGFR mutation detection: a diagnostic RING trial. J. Clin. Pathol. 2015, 68(2):111-118.
54. de Sanjosé S., Alemany L., Ordi J., Tous S., Alejo M., et al. Worldwide human papillomavirus genotype attribution in over 2000 cases of intraepithelial and invasive lesions of the vulva. Eur. J. Cancer 2013, 49(16):3450-3461.
55. Pirog E.C., Lloveras B., Molijn A., Tous S., Guimerà N., et al. RIS HPV. TT study group. HPV prevalence and genotypes in different histological subtypes of cervical adenocarcinoma, a worldwide analysis of 760 cases. Mod. Pathol. 2014, 27(12):1559-1567.
56. Alemany L., Saunier M., Alvarado-Cabrero I., Quirós B., Salmeron J., et al. HPV VVAP study group. Human papillomavirus DNA prevalence and type distribution in anal carcinomas worldwide. Int. J. Cancer 2015, 136(1):98-107.
57. de Melo Maia B., Lavorato-Rocha A.M., Rodrigues I.S., Baiocchi G., Cestari F.M., et al. Prognostic significance of c-KIT in vulvar cancer: bringing this molecular marker from bench to bedside. J. Transl. Med. 2012, 10:150.
58. Wichmann G., Rosolowski M., Krohn K., Kreuz M., Boehm A., et al. The role of HPV RNA transcription, immune response-related gene expression and disruptive TP53 mutations in diagnostic and prognostic profiling of head and neck cancer. Int. J. Cancer. 2015, (Epub ahead of print). 10.1002/ijc.29649.
59. Gocze K., Gombos K., Juhasz K., Kovacs K., Kajtar B., et al. Unique microRNA expression profiles in cervical cancer. Anticancer Res. 2013, 33:2561-2567.
60. Halec G., Schmitt M., Dondog B., Sharkhuu E., Wentzensen N., et al. Biological activity of probable/possible high-risk human papillomavirus types in cervical cancer. Int. J. Cancer 2013, 132(1):63-71.
61. Halec G., Alemany L., Lloveras B., Schmitt M., Alejo M., et al. Retrospective international survey and HPV time trends study group; retrospective international survey and HPV time trends study group. Pathogenic role of the eight probably/possibly carcinogenic HPV types 26, 53, 66, 67, 68, 70, 73 and 82 in cervical cancer. J. Pathol. 2014, 234(4):441-451.
62. Greer C.E., Wheeler C.M., Manos M.M. Sample preparation and PCR amplification from paraffin-embedded tissues. PCR Methods Appl. 1994, 3(6):S113-S122.
63. van Duin M., Snijders P.J., Schrijnemakers H.F., Voorhorst F.J., Rozendaal L., et al. Human papillomavirus 16 load in normal and abnormal cervical scrapes: an indicator of CIN II/III and viral clearance. Int. J. Cancer 2002, 98(4):590-595.
64. Lo E.J., Bell D., Woo J.S., Li G., Hanna E.Y., et al. Human papillomavirus and WHO type I nasopharyngeal carcinoma. Laryngoscope 2010, 120(10):1990-1997.
65. Kansky A.A., Poljak M., Seme K., Kocjan B.J., Gale N., et al. Human papillomavirus DNA in oral squamous cell carcinomas and normal oral mucosa. Acta Virol. 2003, 47(1):11-16.
66. Alemany L., Saunier M., Tinoco L., Quirós B., Alvarado-Cabrero I., et al. Large contribution of human papillomavirus in vaginal neoplastic lesions: a worldwide study in 597 samples. Eur. J. Cancer 2014, 50(16):2846-2854.
67. Seme K., Lepej S.Z., Lunar M.M., Iscić-Bes J., Planinić A., et al. Digene HPV genotyping RH test RUO comparative evaluation with INNO-LiPA HPV Genotyping Extra Test for detection of 18 high-risk and probable high-risk human papillomavirus genotypes. J. Clin. Virol. 2009, 46(2):176-179.
68. Evans M.F., Adamson C.S., Simmons-Arnold L., Cooper K. Touchdown general primer (GP5+/GP6+) PCR and optimized sample DNA concentration support the sensitive detection of human papillomavirus. BMC Clin. Pathol. 2005, 16(5):10.
69. Pérez C., Klaustermeier J.E., Alemany L., Tous S., de Sanjosé S., et al. Comparison of 2 different PCR-based technologies for the detection of human papilloma virus from paraffin-embedded tissue: genómica clinical arrays versus SPF(10)-LiPA(25). Diagn. Mol. Pathol. 2012, 21(1):45-52.
70. Omland T., Lie K.A., Akre H., Sandlie L.E., Jebsen P., et al. Recurrent respiratory papillomatosis: HPV genotypes and risk of high-grade laryngeal neoplasia. PLoS One 2014, 9(6):e99114.
71. Iljazović E., Mena M., Tous S., Alemany L., Omeragić F., et al. Human papillomavirus genotype distribution in invasive cervical cancer in Bosnia and Herzegovina. Cancer Epidemiol. 2014, 38(5):504-510.
72. Jančar N., Kocjan B.J., Poljak M., Lunar M.M., Bokal E.V. Distribution of human papillomavirus genotypes in women with cervical cancer in Slovenia. Eur. J. Obstet. Gynecol. Reprod. Biol. 2009, 145(2):184-188.
73. Jenko K., Kocjan B., Zidar N., Poljak M., Strojan P., et al. In inverted papillomas HPV more likely represents incidental colonization than an etiological factor. Virchows Arch. 2011, 459(5):529-538.
74. Balslev Avnstorp M.B., Jensen R.G., Garnnæs E., Therkildsen M.H., Norrild B., et al. Human papillomavirus and oropharyngeal cancer in Greenland in 1994-2010. Int. J. Circumpolar Health 2013, 72:22386.
75. Dona M.G., Ronchetti L., Giuliani M., Carosi M., Rollo F., Congiu M., Mazza D., Pescarmona E., Vocaturo A., Benevolo M. Performance of the linear array HPV genotyping test on paired cytological and formalin-fixed, paraffin-embedded cervical samples. J. Mol. Diagn. 2013, 15(3):373-379.
76. Evans M., Newcombe R., Fiander A., Powell J., Rolles M., et al. Human papillomavirus-associated oropharyngeal cancer: an observational study of diagnosis, prevalence and prognosis in a UK population. BMC Cancer 2013, 13:220.
77. Mills A., Balasubramaniam R., Longacre T.A., Kong C.S., Pinsky B.A. Laboratory-developed L1 sequencing and type-specific, real-time polymerase chain reaction for the detection and typing of human papillomaviruses in formalin-fixed, paraffin-embedded tissues. Arch. Pathol. Lab. Med. 2013, 137(1):50-54.
78. Swangvaree S.S., Kongkaew P., Ngamkham J. Frequency and type-distribution of human papillomavirus from paraffin-embedded blocks of high grade cervical intraepithelial neoplasia lesions in Thailand. Asian Pac. J. Cancer Prev. 2013, 14(2):1023-1026.
79. Hernandez B.Y., Goodman M.T., Lynch C.F., Cozen W., Unger E.R., et al. HPV typing of cancer workgroup. Human papillomavirus prevalence in invasive laryngeal cancer in the United States. PLoS One 2014, 9(12):e115931.
80. Odar K., Kocjan B.J., Hošnjak L., Gale N., Poljak M., et al. Verrucous carcinoma of the head and neck- not a human papillomavirus-related tumour?. J. Cell. Mol. Med. 2014, 18(4):635-645.
81. Rödel F., Wieland U., Fraunholz I., Kitz J., Rave-Fränk M., Wolff H.A., Weiss C., Wirtz R., Balermpas P., Fokas E., Rödel C. Human papillomavirus DNA load and p16INK4a expression predict for local control in patients with anal squamous cell carcinoma treated with chemoradiotherapy. Int. J. Cancer 2015, 136(2):278-288.
82. Strojan P., Zadnik V., Šifrer R., Lanišnik B., Didanović V., et al. Incidence trends in head and neck squamous cell carcinoma in Slovenia, 1983-2009: role of human papillomavirus infection. Eur. Arch. Otorhinolaryngol. 2014, (December 27). (Epub ahead of print).
83. Antonsson A., Neale R.E., Boros S., Lampe G., Coman W.B., et al. Human papillomavirus status and p16(INK4A) expression in patients with mucosal squamous cell carcinoma of the head and neck in Queensland, Australia. Cancer Epidemiol. 2015, 39(2):174-181.
84. Mlakar J., Kocjan B.J., Hošnjak L., Pižem J., Beltram M., et al. Morphological characteristics of conjunctival squamous papillomas in relation to human papillomavirus infection. Br. J. Ophthalmol. 2015, 99(3):431-436.
85. Ingles D.J., Pierce Campbell C.M., Messina J.A., Stoler M.H., Lin H.Y., et al. Human papillomavirus virus (HPV) genotype- and age-specific analyses of external genital lesions among men in the HPV infection in men (HIM) study. J. Infect. Dis. 2015, 211(7):1060-1067.
86. Baay M.F., Quint W.G., Koudstaal J., Hollema H., Duk J.M., Burger M.P., Stolz E., Herbrink P. Comprehensive study of several general and type-specific primer pairs for detection of human papillomavirus DNA by PCR in paraffin-embedded cervical carcinomas. J. Clin. Microbiol. 1996, 34(3):745-747.
87. Lillsunde L., arsson G., Carlsson J., Karlsson M.G., Helenius G. Evaluation of HPV genotyping assays for archival clinical samples. J. Mol. Diagn. 2015, 17(3):293-301.
88. St Guily J.L., Jacquard A.C., Prétet J.L., Haesebaert J., Beby-Defaux A., Clavel C., et al. Human papillomavirus genotype distribution in oropharynx and oral cavity cancer in France-the EDiTH VI study. J. Clin. Virol. 2011, 51(2):100-104.
89. Kleter B., van Doorn L.J., Schrauwen L., Molijn A., Sastrowijoto S., et al. Development and clinical evaluation of a highly sensitive PCR-reverse hybridization line probe assay for detection and identification of anogenital human papillomavirus. J. Clin. Microbiol. 1999, 37(8):2508-2517.
90. de Roda Husman A.M., Walboomers J.M., van den Brule A.J., Meijer C.J., Snijders P.J. The use of general primers GP5 and GP6 elongated at their 3' ends with adjacent highly conserved sequences improves human papillomavirus detection by PCR. J. Gen. Virol. 1995, 76:1057-1062.
91. de Vuyst H., Clifford G.M., Nascimento M.C., Madeleine M.M., Franceschi S. Prevalence and type distribution of human papillomavirus in carcinoma and intraepithelial neoplasia of the vulva, vagina and anus: a meta-analysis. Int. J. Cancer 2009, 124(7):1626-1636.
92. Miralles-Guri C., Bruni L., Cubilla A.L., Castellsagué X., Bosch F.X., et al. Human papillomavirus prevalence and type distribution in penile carcinoma. J. Clin. Pathol. 2009, 62(10):870-878.
93. Bzhalava D., Guan P., Franceschi S., Dillner J., Clifford G. A systematic review of the prevalence of mucosal and cutaneous human papillomavirus types. Virology 2013, 445(1-2):224-231.
94. Rabah R., Lancaster W.D., Thomas R., Gregoire L. Human papillomavirus-11-associated recurrent respiratory papillomatosis is more aggressive than human papillomavirus-6-associated disease. Pediatr. Dev. Pathol. 2001, 4(1):68-72.
95. Aubin F., Prétet J.L., Jacquard A.C., Saunier M., Carcopino X., et al. EDiTH Study Group. Human papillomavirus genotype distribution in external acuminata condylomata: a large French national study (EDiTH IV). Clin. Infect. Dis. 2008, 47(5):610-615.
96. Resnick R.M., Cornelissen M.T., Wright D.K., Eichinger G.H., Fox H.S., et al. Detection and typing of human papillomavirus in archival cervical cancer specimens by DNA amplification with consensus primers. J. Natl. Cancer Inst. 1990, 82(18):1477-1484.
97. Tieben L.M., Schegget J., Minnaar R.P., Bouwes B., avinck J.N., Berkhout R.J., et al. Detection of cutaneous and genital HPV types in clinical samples by PCR using consensus primers. J. Virol. Methods 1993, 42:265-279.
98. Sasagawa T., Minemoto Y., Basha W., Yamazaki H., Nakamura M., et al. A new PCR-based assay amplifies the E6-E7 genes of most mucosal human papillomaviruses (HPV). Virus Res. 2000, 67(2):127-139.
99. Gheit T., Landi S., Gemignani F., Snijders P.J., Vaccarella S., et al. Development of a sensitive and specific assay combining multiplex PCR and DNA microarray primer extension to detect high-risk mucosal human papillomavirus types. J. Clin. Microbiol. 2006, 44(6):2025-2031.
100. Kocjan B.J., Seme K., Poljak M. Detection and differentiation of human papillomavirus genotypes HPV-6 and HPV-11 by FRET-based real-time PCR. J. Virol. Methods 2008, 153(2):245-249.
101. Maver P.J., Poljak M., Seme K., Kocjan B.J. Detection and typing of low-risk human papillomavirus genotypes HPV 6, HPV 11, HPV 42, HPV 43 and HPV 44 by polymerase chain reaction and restriction fragment length polymorphism. J. Virol. Methods 2010, 169(1):215-218.
102. Kocjan B.J., Bzhalava D., Forslund O., Dillner J., Poljak M. Molecular methods for identification and characterization of novel papillomaviruses. Clin. Microbiol. Infect. 2015, 21(9):808-816.
103. Chaturvedi A.K., Engels E.A., Pfeiffer R.M., Hernandez B.Y., Xiao W., et al. Human papillomavirus and rising oropharyngeal cancer incidence in the United States. J. Clin. Oncol. 2011, 29(32):4294-4301.
104. Schache A.G., Liloglou T., Risk J.M., Jones T.M., Ma X.J., et al. Validation of a novel diagnostic standard in HPV-positive oropharyngeal squamous cell carcinoma. Br. J. Cancer 2013, 108(6):1332-1339.
105. Baboci L., Boscolo-Rizzo P., Holzinger D., Bertorelle R., Biasini L., et al. Evidence of the causal role of human papillomavirus type 58 in an oropharyngeal carcinoma. Virol. J. 2013, 10:334.
106. Halec G., Holzinger D., Schmitt M., Flechtenmacher C., Dyckhoff G., et al. Biological evidence for a causal role of HPV16 in a small fraction of laryngeal squamous cell carcinoma. Br. J. Cancer 2013, 109(1):172-183.
107. Melchers L.J., Mastik M.F., Samaniego Cameron B., van Dijk B.A., de Bock G.H., et al. Detection of HPV-associated oropharyngeal tumours in a 16-year cohort: more than meets the eye. Br. J. Cancer 2015, 112(8):1349-1357.
108. Anantharaman D., Gheit T., Waterboer T., Halec G., Carreira C., et al. No causal association identified for human papillomavirus infections in lung cancer. Cancer Res. 2014, 74(13):3525-3534.
109. Hedegaard J., Thorsen K., Lund M.K., Hein A.M., Hamilton-Dutoit S.J., et al. Next-generation sequencing of RNA and DNA isolated from paired fresh-frozen and formalin-fixed paraffin-embedded samples of human cancer and normal tissue. PLoS One 2014, 9(5):e98187.
110. Boycott K.M., Vanstone M.R., Bulman D.E., MacKenzie A.E. Rare-disease genetics in the era of next-generation sequencing: discovery to translation. Nat. Rev. Genet. 2013, 14(10):681-691.
111. Frese K.S., Katus H.A., Meder B. Next-generation sequencing: from understanding biology to personalized medicine. Biology 2013, 2:378-398.
112. Simbolo M., Gottardi M., Corbo V., Fassan M., Mafficini A., et al. DNA qualification workflow for next generation sequencing of histopathological samples. PLoS One 2013, 8(6):e62692.
113. Agrawal N., Frederick M.J., Pickering C.R., Bettegowda C., Chang K., et al. Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in NOTCH1. Science 2011, 333:1154-1157.
114. Stransky N., Egloff A.M., Tward A.D., Kostic A.D., Cibulskis K., et al. The mutational landscape of head and neck squamous cell carcinoma. Science 2011, 333:1157-1160.
115. Lechner M., Frampton G.M., Fenton T., Feber A., Palmer G., et al. Targeted next-generation sequencing of head and neck squamous cell carcinoma identifies novel genetic alterations in HPV+ and HPV- tumors. Genome Med. 2013, 5(5):49.
116. Chung C.H., Guthrie V.B., Masica D.L., Tokheim C., Kang H., et al. Genomic alterations in head and neck squamous cell carcinoma determined by cancer gene-targeted sequencing. Ann. Oncol. 2015, 26(6):1216-1223.
117. Saba N.F., Wilson M., Doho G., DaSilva J., Benjamin Isett R., et al. Mutation and transcriptional profiling of formalin-fixed paraffin embedded specimens as companion methods to immunohistochemistry for determining therapeutic targets in oropharyngeal squamous cell carcinoma (OPSCC): a pilot of proof of principle. Head Neck Pathol. 2015, 9(2):223-235.
118. Okello J.B., Zurek J., Devault A.M., Kuch M., Okwi A.L., et al. Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues. Anal. Biochem. 2010, 400(1):110-117.
119. Ludyga N., Grünwald B., Azimzadeh O., Englert S., Höfler H., et al. Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses. Virchows Arch. 2012, 460(2):131-140.