Next-generation sequencing for simultaneous determination of human papillomavirus load, subtype, and associated genomic copy number changes in tumors

Journal of Molecular Diagnostics

Volumn 14, Issue 2, 2012, Pages 104-111

  Conway, Caroline ^a   Chalkley, Rebecca ^a   High, Alec ^b   MacLennan, Kenneth ^a   Berri, Stefano ^a   Chengot, Preetha ^a   Alsop, Melissa ^a   Egan, Philip ^a   Morgan, Joanne ^a   Taylor, Graham R ^a   Chester, John ^a   Sen, Mehmet ^a   Rabbitts, Pamela ^a   Wood, Henry M ^a  

^a ST JAMES S UNIVERSITY HOSPITAL   (United Kingdom)

^b LEEDS DENTAL INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 2A; VIRUS DNA;

ARTICLE; CANCER CELL CULTURE; CANCER TISSUE; CHROMOSOMAL INSTABILITY; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; GENE SEQUENCE; HEAD AND NECK CARCINOMA; HUMAN; HUMAN CELL; HUMAN PAPILLOMAVIRUS TYPE 16; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; INTERMETHOD COMPARISON; NEXT GENERATION SEQUENCING; NONHUMAN; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; VIRUS DETECTION; VIRUS ISOLATION; VIRUS LOAD; VIRUS TYPING; WART VIRUS;

CARCINOMA, SQUAMOUS CELL; DNA, VIRAL; FEMALE; GENE DOSAGE; HEAD AND NECK NEOPLASMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; IMMUNOENZYME TECHNIQUES; MIDDLE AGED; NEOPLASM PROTEINS; PAPILLOMAVIRIDAE; PAPILLOMAVIRUS INFECTIONS; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; TUMOR VIRUS INFECTIONS; VIRAL LOAD;

EID: 84857261896     PISSN: 15251578     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmoldx.2011.10.003     Document Type: Article

References (34)

1. K.K. Ang, J. Harris, R. Wheeler, R. Weber, D.I. Rosenthal, P.F. Nguyen-Tan, W.H. Westra, C.H. Chung, R.C. Jordan, C. Lu, H. Kim, R. Axelrod, C.C. Silverman, K.P. Redmond, M.L. Gillison Human papillomavirus and survival of patients with oropharyngeal cancer N Engl J Med 363 2010 24 35
2. C. Fakhry, W.H. Westra, S. Li, A. Cmelak, J.A. Ridge, H. Pinto, A. Forastiere, M.L. Gillison Improved survival of patients with human papillomavirus-positive head and neck squamous cell carcinoma in a prospective clinical trial J Natl Cancer Inst 100 2008 261 269 (Pubitemid 351480538)
3. C.R. Leemans, B.J. Braakhuis, R.H. Brakenhoff The molecular biology of head and neck cancer Nat Rev Cancer 11 2011 9 22
4. J.S. Lewis Jr., W.L. Thorstad, R.D. Chernock, B.H. Haughey, J.H. Yip, Q. Zhang, S.K. El-Mofty p16 positive oropharyngeal squamous cell carcinoma: an entity with a favorable prognosis regardless of tumor HPV status Am J Surg Pathol 34 2010 1088 1096
5. D. Cao, S. Begum, S.Z. Ali, W.H. Westra Expression of p16 in benign and malignant cystic squamous lesions of the neck Hum Pathol 41 2010 535 539
6. S. Begum, D. Cao, M. Gillison, M. Zahurak, W.H. Westra Tissue distribution of human papillomavirus 16 DNA integration in patients with tonsillar carcinoma Clin Cancer Res 11 2005 5694 5699 (Pubitemid 41170292)
7. B. Klingenberg, H.C. Hafkamp, A. Haesevoets, J.J. Manni, P.J. Slootweg, S.J. Weissenborn, J.P. Klussmann, E.J. Speel p16 INK4A overexpression is frequently detected in tumour-free tonsil tissue without association with HPV Histopathology 56 2010 957 967
8. S.J. Smeets, A.T. Hesselink, E.J. Speel, A. Haesevoets, P.J. Snijders, M. Pawlita, C.J. Meijer, B.J. Braakhuis, C.R. Leemans, R.H. Brakenhoff A novel algorithm for reliable detection of human papillomavirus in paraffin embedded head and neck cancer specimen Int J Cancer 121 2007 2465 2472 (Pubitemid 350022416)
9. M. Robinson, P. Sloan, R. Shaw Refining the diagnosis of oropharyngeal squamous cell carcinoma using human papillomavirus testing Oral Oncol 46 2010 492 496
10. A.D. Singhi, W.H. Westra Comparison of human papillomavirus in situ hybridization and p16 immunohistochemistry in the detection of human papillomavirus-associated head and neck cancer based on a prospective clinical experience Cancer 116 2010 2166 2173
11. F.P. Worden, B. Kumar, J.S. Lee, G.T. Wolf, K.G. Cordell, J.M. Taylor, S.G. Urba, A. Eisbruch, T.N. Teknos, D.B. Chepeha, M.E. Prince, C.I. Tsien, N.J. D'Silva, K. Yang, D.M. Kurnit, H.L. Mason, T.H. Miller, N.E. Wallace, C.R. Bradford, T.E. Carey Chemoselection as a strategy for organ preservation in advanced oropharynx cancer: response and survival positively associated with HPV16 copy number J Clin Oncol 26 2008 3138 3146
12. B. Kumar, K.G. Cordell, J.S. Lee, F.P. Worden, M.E. Prince, H.H. Tran, G.T. Wolf, S.G. Urba, D.B. Chepeha, T.N. Teknos, A. Eisbruch, C.I. Tsien, J.M. Taylor, N.J. D'Silva, K. Yang, D.M. Kurnit, J.A. Bauer, C.R. Bradford, T.E. Carey EGFR, p16 HPV Titer, Bcl-xL and p53, sex, and smoking as indicators of response to therapy and survival in oropharyngeal cancer J Clin Oncol 26 2008 3128 3137
13. H.M. Wood, O. Belvedere, C. Conway, C. Daly, R. Chalkley, M. Bickerdike, C. McKinley, P. Egan, L. Ross, B. Hayward, J. Morgan, L. Davidson, K. MacLennan, T.K. Ong, K. Papagiannopoulos, I. Cook, D.J. Adams, G.R. Taylor, P. Rabbitts Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens Nucleic Acids Res 38 2010 e151
14. P. Rabbitts, J. Douglas, M. Daly, V. Sundaresan, B. Fox, P. Haselton, F. Wells, D. Albertson, J. Waters, J. Bergh Frequency and extent of allelic loss in the short arm of chromosome 3 in nonsmall-cell lung cancer Genes Chromosomes Cancer 1 1989 95 105 (Pubitemid 20093345)
15. R. Glaser, H.Y. Zhang, K.T. Yao, H.C. Zhu, F.X. Wang, G.Y. Li, D.S. Wen, Y.P. Li Two epithelial tumor cell lines (HNE-1 and HONE-1) latently infected with Epstein-Barr virus that were derived from nasopharyngeal carcinomas Proc Natl Acad Sci U S A 86 1989 9524 9528 (Pubitemid 20010459)
16. M. Lieber, B. Smith, A. Szakal, W. Nelson-Rees, G. Todaro A continuous tumor-cell line from a human lung carcinoma with properties of type II alveolar epithelial cells Int J Cancer 17 1976 62 70
17. F. Friedl, I. Kimura, T. Osato, Y. Ito Studies on a new human cell line (SiHa) derived from carcinoma of uterus I Its establishment and morphology Proc Soc Exp Biol Med 135 1970 543 545
18. R.A. Pattillo, R.O. Hussa, M.T. Story, A.C. Ruckert, M.R. Shalaby, R.F. Mattingly Tumor antigen and human chorionic gonadotropin in CaSki cells: a new epidermoid cervical cancer cell line Science 196 1977 1456 1458 (Pubitemid 8122337)
19. Y. Shimada, M. Imamura, T. Wagata, N. Yamaguchi, T. Tobe Characterization of 21 newly established esophageal cancer cell lines Cancer 69 1992 277 284
20. A.M. de Roda Husman, J.M. Walboomers, A.J. van den Brule, C.J. Meijer, P.J. Snijders 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 76 Pt 4 1995 1057 1062
21. N.R. Griffin, I.S. Bevan, F.A. Lewis, M. Wells, L.S. Young Demonstration of multiple HPV types in normal cervix and in cervical squamous cell carcinoma using the polymerase chain reaction on paraffin wax embedded material J Clin Pathol 43 1990 52 56 (Pubitemid 20063714)
22. H. Li, R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 2009 1754 1760
23. H. Li, B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin 1000 Genome Project Data Processing Subgroup The Sequence Alignment/Map format and SAMtools Bioinformatics 25 2009 2078 2079
24. 1000 Genomes Project Consortium. A map of human genome variation from population-scale sequencing. Nature 467:10611073
25. W. Qu, G. Jiang, Y. Cruz, C.J. Chang, G.Y. Ho, R.S. Klein, R.D. Burk PCR detection of human papillomavirus: comparison between MY09/MY11 and GP5+/GP6+ primer systems J Clin Microbiol 35 1997 1304 1310 (Pubitemid 27216785)
26. S.T. Lindau, M.L. Drum, E. Gaumer, H. Surawska, J.A. Jordan Prevalence of high-risk human papillomavirus among older women Obstet Gynecol 112 2008 979 989
27. Y.D. Choi, W.W. Jung, J.H. Nam, H.S. Choi, C.S. Park Detection of HPV genotypes in cervical lesions by the HPV DNA Chip and sequencing Gynecol Oncol 98 2005 369 375
28. A.T. Hesselink, M.A. van Ham, D.A. Heideman, Z.M. Groothuismink, L. Rozendaal, J. Berkhof, F.J. van Kemenade, L.A. Massuger, W.J. Melchers, C.J. Meijer, P.J. Snijders Comparison of GP5+/6+-PCR and SPF10-line blot assays for detection of high-risk human papillomavirus in samples from women with normal cytology results who develop grade 3 cervical intraepithelial neoplasia J Clin Microbiol 46 2008 3215 3221
29. M.A. Cohen, S.R. Basha, D.K. Reichenbach, E. Robertson, D.A. Sewell Increased viral load correlates with improved survival in HPV-16-associated tonsil carcinoma patients Acta Otolaryngol 128 2008 583 589 (Pubitemid 351550952)
30. Alvarez K, Kash SF, Lyons-Weiler MA, Kim HJ, Peterson LE, Mathai B, Hagenkord JM, Monzon FA: Reproducibility and performance of virtual karyotyping with SNP microarrays for the detection of chromosomal imbalances in formalin-fixed paraffin-embedded tissues. Diagn Mol Pathol 19:127134
31. C. Conway, A. Mitra, R. Jewell, J. Randerson-Moor, S. Lobo, J. Nsengimana, S. Edward, D.S. Sanders, M. Cook, B. Powell, A. Boon, F. Elliott, F. de Kort, M.A. Knowles, D.T. Bishop, J. Newton-Bishop Gene expression profiling of paraffin-embedded primary melanoma using the DASL assay identifies increased osteopontin expression as predictive of reduced relapse-free survival Clin Cancer Res 15 2009 6939 6946
32. J. Hicks, A. Krasnitz, B. Lakshmi, N.E. Navin, M. Riggs, E. Leibu, D. Esposito, J. Alexander, J. Troge, V. Grubor, S. Yoon, M. Wigler, K. Ye, A.L. Borresen-Dale, B. Naume, E. Schlicting, L. Norton, T. Hagerstrom, L. Skoog, G. Auer, S. Maner, P. Lundin, A. Zetterberg Novel patterns of genome rearrangement and their association with survival in breast cancer Genome Res 16 2006 1465 1479 (Pubitemid 44878486)
33. B.S. Taylor, N. Schultz, H. Hieronymus, A. Gopalan, Y. Xiao, B.S. Carver, V.K. Arora, P. Kaushik, E. Cerami, B. Reva, Y. Antipin, N. Mitsiades, T. Landers, I. Dolgalev, J.E. Major, M. Wilson, N.D. Socci, A.E. Lash, A. Heguy, J.A. Eastham, H.I. Scher, V.E. Reuter, P.T. Scardino, C. Sander, C.L. Sawyers, W.L. Gerald Integrative genomic profiling of human prostate cancer Cancer Cell 18 2010 11 22
34. J.P. Klussmann, J.J. Mooren, M. Lehnen, S.M. Claessen, M. Stenner, C.U. Huebbers, S.J. Weissenborn, I. Wedemeyer, S.F. Preuss, J.M. Straetmans, J.J. Manni, A.H. Hopman, E.J. Speel Genetic signatures of HPV-related and unrelated oropharyngeal carcinoma and their prognostic implications Clin Cancer Res 15 2009 1779 1786