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Comparison of GeneChip, nCounter, and Real-Time PCR–Based Gene Expressions Predicting Locoregional Tumor Control after Primary and Postoperative Radiochemotherapy in Head and Neck Squamous Cell Carcinoma

2020; Elsevier BV; Volume: 22; Issue: 6 Linguagem: Inglês

10.1016/j.jmoldx.2020.03.005

1943-7811

Stefan E. Schmidt, Annett Linge, Marianne Großer, Fabian Lohaus, Volker Gudziol, Alexander Nowak, Ingeborg Tinhofer, Volker Budach, Ali Sak, Martin Stuschke, Panagiotis Balermpas, Claus Rödel, Henning Schäfer, Anca‐Ligia Grosu, Amir Abdollahi, Jürgen Debus, Ute Ganswindt, Claus Belka, Steffi Pigorsch, Stephanie E. Combs, David Mönnich, Daniel Zips, Gustavo Baretton, Frank Buchholz, Michaël Baumann, Mechthild Krause, Steffen Löck,

Lung Cancer Diagnosis and Treatment

This article compares the expression and applicability of biomarkers, from single genes and gene signatures, identified in patients with locally advanced head and neck squamous cell carcinoma using the GeneChip Human Transcriptome Array 2.0, nCounter, and real-time PCR analyses. Two multicenter, retrospective cohorts of patients with head and neck squamous cell carcinoma from the German Cancer Consortium Radiation Oncology Group who received postoperative radiochemotherapy or primary radiochemotherapy were considered. Real-time PCR was performed for a limited number of 38 genes of the cohort who received postoperative radiochemotherapy only. Correlations between the methods were evaluated by the Spearman rank correlation coefficient. Patients were stratified based on the expression of putative cancer stem cell markers, hypoxia-associated gene signatures, and a previously developed seven-gene signature. Locoregional tumor control was compared between these patient subgroups using log-rank tests. Gene expressions obtained from nCounter analyses were moderately correlated to GeneChip analyses (median ρ = approximately 0.68). A higher correlation was obtained between nCounter analyses and real-time PCR (median ρ = 0.84). Significant associations with locoregional tumor control were observed for most of the considered biomarkers evaluated by GeneChip and nCounter analyses. In general, all applied biomarkers (single genes and gene signatures) classified approximately 70% to 85% of the patients similarly. Overall, gene signatures seem to be more robust and had a better transferability among different measurement methods. This article compares the expression and applicability of biomarkers, from single genes and gene signatures, identified in patients with locally advanced head and neck squamous cell carcinoma using the GeneChip Human Transcriptome Array 2.0, nCounter, and real-time PCR analyses. Two multicenter, retrospective cohorts of patients with head and neck squamous cell carcinoma from the German Cancer Consortium Radiation Oncology Group who received postoperative radiochemotherapy or primary radiochemotherapy were considered. Real-time PCR was performed for a limited number of 38 genes of the cohort who received postoperative radiochemotherapy only. Correlations between the methods were evaluated by the Spearman rank correlation coefficient. Patients were stratified based on the expression of putative cancer stem cell markers, hypoxia-associated gene signatures, and a previously developed seven-gene signature. Locoregional tumor control was compared between these patient subgroups using log-rank tests. Gene expressions obtained from nCounter analyses were moderately correlated to GeneChip analyses (median ρ = approximately 0.68). A higher correlation was obtained between nCounter analyses and real-time PCR (median ρ = 0.84). Significant associations with locoregional tumor control were observed for most of the considered biomarkers evaluated by GeneChip and nCounter analyses. In general, all applied biomarkers (single genes and gene signatures) classified approximately 70% to 85% of the patients similarly. Overall, gene signatures seem to be more robust and had a better transferability among different measurement methods. Patients with locally advanced head and neck squamous cell carcinomas (HNSCC) have a heterogeneous response to radiochemotherapy (RCT), thus leading to an overall survival of only approximately 50%.1Baumann M. Krause M. Overgaard J. Debus J. Bentzen S.M. Daartz J. Richter C. Zips D. Bortfeld T. Radiation oncology in the era of precision medicine.Nat Rev Cancer. 2016; 16: 234-249Crossref PubMed Scopus (490) Google Scholar To date, several prognostic biomarkers have been identified2Solomon B. Young R.J. Rischin D. Head and neck squamous cell carcinoma: genomics and emerging biomarkers for immunomodulatory cancer treatments.Semin Cancer Biol. 2018; 52: 228-240Crossref PubMed Scopus (201) Google Scholar, 3Shen S. Bai J. Wei Y. Wang G. Li Q. Zhang R. Duan W. Yang S. Du M. Zhao Y. Christiani D.C. Chen F. A seven-gene prognostic signature for rapid determination of head and neck squamous cell carcinoma survival.Oncol Rep. 2017; 38: 3403-3411PubMed Google Scholar, 4Kostareli E. Hielscher T. Zucknick M. Baboci L. Wichmann G. Holzinger D. Mücke O. Pawlita M. Del Mistro A. Boscolo-Rizzo P. Da Mosto M.C. Tirelli G. Plinkert P. Dietz A. Plass C. Weichenhan D. Hess J. Gene promoter methylation signature predicts survival of head and neck squamous cell carcinoma patients.Epigenetics. 2016; 11: 61-73Crossref PubMed Scopus (27) Google Scholar, 5Leemans C.R. Braakhuis B.J.M. Brakenhoff R.H. The molecular biology of head and neck cancer.Nat Rev Cancer. 2011; 11: 9-22Crossref PubMed Scopus (1887) Google Scholar, 6Nordsmark M. Overgaard J. A confirmatory prognostic study on oxygenation status and loco-regional control in advanced head and neck squamous cell carcinoma treated by radiation therapy.Radiother Oncol. 2000; 57: 39-43Abstract Full Text Full Text PDF PubMed Scopus (260) Google Scholar that may help to stratify patients with HNSCC regarding their response to primary RCT7Stangl S. Tontcheva N. Sievert W. Shevtsov M. Niu M. Schmid T.E. Pigorsch S. Combs S.E. Haller B. Balermpas P. Rödel F. Rödel C. Fokas E. Krause M. Linge A. Lohaus F. Baumann M. Tinhofer I. Budach V. Stuschke M. Grosu A.-L. Abdollahi A. Debus J. Belka C. Maihöfer C. Mönnich D. Zips D. Multhoff G. Heat shock protein 70 and tumor-infiltrating NK cells as prognostic indicators for patients with squamous cell carcinoma of the head and neck after radiochemotherapy: a multicentre retrospective study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG).Int J Cancer. 2018; 142: 1911-1925Crossref PubMed Scopus (37) Google Scholar, 8De-Colle C. Menegakis A. Mönnich D. Welz S. Boeke S. Sipos B. Fend F. Mauz P.-S. Tinhofer I. Budach V. Abu Jawad J. Stuschke M. Balermpas P. Rödel C. Grosu A.-L. Abdollahi A. Debus J. Belka C. Ganswindt U. Pigorsch S. Combs S.E. Lohaus F. Linge A. Krause M. Baumann M. Zips D. DKTK-ROGSDF-1/CXCR4 expression is an independent negative prognostic biomarker in patients with head and neck cancer after primary radiochemotherapy.Radiother Oncol. 2018; 126: 125-131Abstract Full Text Full Text PDF PubMed Scopus (20) Google Scholar, 9Linge A. Lohaus F. Löck S. Nowak A. Gudziol V. Valentini C. von Neubeck C. Jütz M. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Krause M. Baumann M. HPV status, cancer stem cell marker expression, hypoxia gene signatures and tumour volume identify good prognosis subgroups in patients with HNSCC after primary radiochemotherapy: a multicentre retrospective study of the German Cancer Consortium Radiation.Radiother Oncol. 2016; 121: 364-373Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar, 10Hess J. Unger K. Maihoefer C. Schüttrumpf L. Wintergerst L. Heider T. Weber P. Marschner S. Braselmann H. Samaga D. Kuger S. Pflugradt U. Baumeister P. Walch A. Woischke C. Kirchner T. Werner M. Werner K. Baumann M. Budach V. Combs S.E. Debus J. Grosu A.L. Krause M. Linge A. Rödel C. Stuschke M. Zips D. Zitzelsberger H.F. Ganswindt U. Henke M. Belka C. A five-microRNA signature predicts survival and disease control of patients with head and neck cancer negative for HPV-infection.Clin Cancer Res. 2018; 25: 1505-1516Crossref PubMed Scopus (47) Google Scholar, 11de Jong M.C. Pramana J. van der Wal J.E. Lacko M. Peutz-Kootstra C.J. de Jong J.M. Takes R.P. Kaanders J.H. van der Laan B.F. Wachters J. Jansen J.C. Rasch C.R. van Velthuysen M.-L.F. Grénman R. Hoebers F.J. Schuuring E. van den Brekel M.W. Begg A.C. CD44 expression predicts local recurrence after radiotherapy in larynx cancer.Clin Cancer Res. 2010; 16: 5329-5338Crossref PubMed Scopus (132) Google Scholar or adjuvant RCT.12Schmidt S. Linge A. Zwanenburg A. Leger S. Lohaus F. Krenn C. Appold S. Gudziol V. Nowak A. Von Neubeck C. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rodel C. Bunea H. Grosu A.L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Monnich D. Zips D. Baretton G.B. Buchholz F. Baumann M. Krause M. Lock S. Development and validation of a gene signature for patients with head and neck carcinomas treated by postoperative radio(chemo)therapy.Clin Cancer Res. 2018; 24: 1364-1374Crossref PubMed Scopus (37) Google Scholar, 13De-Colle C. Mönnich D. Welz S. Boeke S. Sipos B. Fend F. Mauz P.-S. Tinhofer I. Budach V. Jawad J.A. Stuschke M. Balermpas P. Rödel C. Grosu A.-L. Abdollahi A. Debus J. Bayer C. Belka C. Pigorsch S. Combs S.E. Lohaus F. Linge A. Krause M. Baumann M. Zips D. Menegakis A. SDF-1/CXCR4 expression in head and neck cancer and outcome after postoperative radiochemotherapy.Clin Transl Radiat Oncol. 2017; 5: 28-36Abstract Full Text Full Text PDF PubMed Scopus (17) Google Scholar, 14Balermpas P. Rödel F. Krause M. Linge A. Lohaus F. Baumann M. Tinhofer I. Budach V. Sak A. Stuschke M. Gkika E. Grosu A.-L. Abdollahi A. Debus J. Stangl S. Ganswindt U. Belka C. Pigorsch S. Multhoff G. Combs S.E. Welz S. Zips D. Lim S.Y. Rödel C. Fokas E. DKTK-ROGThe PD-1/PD-L1 axis and human papilloma virus in patients with head and neck cancer after adjuvant chemoradiotherapy: a multicentre study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG).Int J Cancer. 2017; 141: 594-603Crossref PubMed Scopus (63) Google Scholar, 15Linge A. Löck S. Gudziol V. Nowak A. Lohaus F. von Neubeck C. Jütz M. Abdollahi A. Debus J. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.-L. Bayer C. Belka C. Pigorsch S. Combs S.E. Welz S. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Baumann M. Krause M. DKTK-ROGLow cancer stem cell marker expression and low hypoxia identify good prognosis subgroups in HPV(-) HNSCC after postoperative radiochemotherapy: a multicenter study of the DKTK-ROG.Clin Cancer Res. 2016; 22: 2639-2649Crossref PubMed Scopus (96) Google Scholar, 16Tinhofer I. Budach V. Saki M. Konschak R. Niehr F. Jöhrens K. Weichert W. Linge A. Lohaus F. Krause M. Neumann K. Endris V. Sak A. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.L. Abdollahi A. Debus J. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Baumann M. Targeted next-generation sequencing of locally advanced squamous cell carcinomas of the head and neck reveals druggable targets for improving adjuvant chemoradiation.Eur J Cancer. 2016; 57: 78-86Abstract Full Text Full Text PDF PubMed Scopus (56) Google Scholar, 17Balermpas P. Rödel F. Rödel C. Krause M. Linge A. Lohaus F. Baumann M. Tinhofer I. Budach V. Gkika E. Stuschke M. Avlar M. Grosu A.-L. Abdollahi A. Debus J. Bayer C. Stangl S. Belka C. Pigorsch S. Multhoff G. Combs S.E. Mönnich D. Zips D. Fokas E. CD8+ tumour-infiltrating lymphocytes in relation to HPV status and clinical outcome in patients with head and neck cancer after postoperative chemoradiotherapy: a multicentre study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG): CD8+.Int J Cancer. 2016; 138: 171-181Crossref PubMed Scopus (148) Google Scholar, 18Lohaus F. Linge A. Tinhofer I. Budach V. Gkika E. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.L. Abdollahi A. Debus J. Bayer C. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Von Neubeck C. Baretton G.B. Löck S. Thames H.D. Krause M. Baumann M. HPV16 DNA status is a strong prognosticator of loco-regional control after postoperative radiochemotherapy of locally advanced oropharyngeal carcinoma: results from a multicentre explorative study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG).Radiother Oncol. 2014; 113: 317-323Abstract Full Text Full Text PDF PubMed Scopus (115) Google Scholar, 19Wintergerst L. Selmansberger M. Maihoefer C. Schüttrumpf L. Walch A. Wilke C. Pitea A. Woischke C. Baumeister P. Kirchner T. Belka C. Ganswindt U. Zitzelsberger H. Unger K. Hess J. A prognostic mRNA expression signature of four 16q24.3 genes in radio(chemo)therapy-treated head and neck squamous cell carcinoma (HNSCC).Mol Oncol. 2018; 12: 2085-2101Crossref PubMed Scopus (16) Google Scholar, 20Chen J. Fu G. Chen Y. Zhu G. Wang Z. Gene-expression signature predicts survival benefit from postoperative chemoradiotherapy in head and neck squamous cell carcinoma.Oncol Lett. 2018; 16: 2565-2578PubMed Google Scholar However, molecular methods are varying from array-based approaches to single-gene assays, thus impeding the comparability, transferability, and reproducibility of the results. Common approaches include chip-based whole transcriptome arrays (GeneChip analyses), customized nanoString (NanoString Technologies, Seattle, WA) gene panels (nCounter analyses), and real-time PCR analyses. To date, several studies have found a high correlation between the expressions obtained by GeneChip and nCounter analyses.21Brant R. Sharpe A. Liptrot T. Dry J.R. Harrington E.A. Barrett J.C. Whalley N. Womack C. Smith P. Hodgson D.R. Clinically viable gene expression assays with potential for predicting benefit from MEK inhibitors.Clin Cancer Res. 2017; 23: 1471-1480Crossref PubMed Scopus (20) Google Scholar, 22Ho T.H. Serie D.J. Parasramka M. Cheville J.C. Bot B.M. Tan W. Wang L. Joseph R.W. Hilton T. Leibovich B.C. Parker A.S. Eckel-Passow J.E. Differential gene expression profiling of matched primary renal cell carcinoma and metastases reveals upregulation of extracellular matrix genes.Ann Oncol. 2017; 28: 604-610Abstract Full Text Full Text PDF PubMed Scopus (54) Google Scholar, 23Altenbuchinger M. Schwarzfischer P. Rehberg T. Reinders J. Kohler C.W. Gronwald W. Richter J. Szczepanowski M. Masqué-Soler N. Klapper W. Oefner P.J. Spang R. Molecular signatures that can be transferred across different omics platforms.Bioinformatics. 2017; 33: i333-i340Crossref PubMed Scopus (12) Google Scholar, 24Hess A.-K. Müer A. Mairinger F.D. Weichert W. Stenzinger A. Hummel M. Budach V. Tinhofer I. MiR-200b and miR-155 as predictive biomarkers for the efficacy of chemoradiation in locally advanced head and neck squamous cell carcinoma.Eur J Cancer. 2017; 77: 3-12Abstract Full Text Full Text PDF PubMed Scopus (45) Google Scholar An even higher correlation is stated between the gene expression measurements obtained with nCounter and real-time PCR measurements.25Geiss G.K. Bumgarner R.E. Birditt B. Dahl T. Dowidar N. Dunaway D.L. Fell H.P. Ferree S. George R.D. Grogan T. James J.J. Maysuria M. Mitton J.D. Oliveri P. Osborn J.L. Peng T. Ratcliffe A.L. Webster P.J. Davidson E.H. Hood L. Dimitrov K. Direct multiplexed measurement of gene expression with color-coded probe pairs.Nat Biotechnol. 2008; 26: 317-325Crossref PubMed Scopus (1554) Google Scholar,26Reis P.P. Waldron L. Goswami R.S. Xu W. Xuan Y. Perez-Ordonez B. Gullane P. Irish J. Jurisica I. Kamel-Reid S. mRNA transcript quantification in archival samples using multiplexed, color-coded probes.BMC Biotechnol. 2011; 11: 46Crossref PubMed Scopus (215) Google Scholar However, most of these studies were based on a limited number of patients or samples and were performed using versions of Affymetrix (Thermo Fisher Scientific, Santa Clara, CA) arrays considered outdated today.27Veldman-Jones M.H. Lai Z. Wappett M. Harbron C.G. Barrett J.C. Harrington E.A. Thress K.S. Reproducible, quantitative, and flexible molecular subtyping of clinical DLBCL samples using the NanoString nCounter system.Clin Cancer Res. 2015; 21: 2367-2378Crossref PubMed Scopus (56) Google Scholar Therefore, the aim of this study was to compare gene expression data obtained by the three approaches, GeneChip analyses, nCounter analyses, and real-time PCR, that are available to a large number of patients and that were also based on the same RNA as starting material. We report on the two retrospective HNSCC cohorts of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG), including 327 patients in total who were diagnosed with locally advanced disease and received postoperative or primary RCT. For these cohorts, the impact of the putative cancer stem cell (CSC) markers CD44, MET, and SLC3A2, hypoxia-associated gene panels, and a seven-gene signature (postoperative RCT only) have previously been investigated and reported using nCounter gene expression data.9Linge A. Lohaus F. Löck S. Nowak A. Gudziol V. Valentini C. von Neubeck C. Jütz M. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Krause M. Baumann M. HPV status, cancer stem cell marker expression, hypoxia gene signatures and tumour volume identify good prognosis subgroups in patients with HNSCC after primary radiochemotherapy: a multicentre retrospective study of the German Cancer Consortium Radiation.Radiother Oncol. 2016; 121: 364-373Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar,12Schmidt S. Linge A. Zwanenburg A. Leger S. Lohaus F. Krenn C. Appold S. Gudziol V. Nowak A. Von Neubeck C. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rodel C. Bunea H. Grosu A.L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Monnich D. Zips D. Baretton G.B. Buchholz F. Baumann M. Krause M. Lock S. Development and validation of a gene signature for patients with head and neck carcinomas treated by postoperative radio(chemo)therapy.Clin Cancer Res. 2018; 24: 1364-1374Crossref PubMed Scopus (37) Google Scholar,15Linge A. Löck S. Gudziol V. Nowak A. Lohaus F. von Neubeck C. Jütz M. Abdollahi A. Debus J. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.-L. Bayer C. Belka C. Pigorsch S. Combs S.E. Welz S. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Baumann M. Krause M. DKTK-ROGLow cancer stem cell marker expression and low hypoxia identify good prognosis subgroups in HPV(-) HNSCC after postoperative radiochemotherapy: a multicenter study of the DKTK-ROG.Clin Cancer Res. 2016; 22: 2639-2649Crossref PubMed Scopus (96) Google Scholar,18Lohaus F. Linge A. Tinhofer I. Budach V. Gkika E. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.L. Abdollahi A. Debus J. Bayer C. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Von Neubeck C. Baretton G.B. Löck S. Thames H.D. Krause M. Baumann M. HPV16 DNA status is a strong prognosticator of loco-regional control after postoperative radiochemotherapy of locally advanced oropharyngeal carcinoma: results from a multicentre explorative study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG).Radiother Oncol. 2014; 113: 317-323Abstract Full Text Full Text PDF PubMed Scopus (115) Google Scholar Here, the reproducibility of these results is tested using GeneChip analyses as well as real-time PCR gene expression data, which is important for conducting clinical trials, including multicenter biomarker trials, and may also play a role in meta-analyses of biomarker data. For this study, patients of the two retrospective HNSCC cohorts of the DKTK-ROG were considered. All patients were diagnosed with locally advanced disease and were treated with either postoperative RCT15Linge A. Löck S. Gudziol V. Nowak A. Lohaus F. von Neubeck C. Jütz M. Abdollahi A. Debus J. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.-L. Bayer C. Belka C. Pigorsch S. Combs S.E. Welz S. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Baumann M. Krause M. DKTK-ROGLow cancer stem cell marker expression and low hypoxia identify good prognosis subgroups in HPV(-) HNSCC after postoperative radiochemotherapy: a multicenter study of the DKTK-ROG.Clin Cancer Res. 2016; 22: 2639-2649Crossref PubMed Scopus (96) Google Scholar,18Lohaus F. Linge A. Tinhofer I. Budach V. Gkika E. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.L. Abdollahi A. Debus J. Bayer C. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Von Neubeck C. Baretton G.B. Löck S. Thames H.D. Krause M. Baumann M. HPV16 DNA status is a strong prognosticator of loco-regional control after postoperative radiochemotherapy of locally advanced oropharyngeal carcinoma: results from a multicentre explorative study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG).Radiother Oncol. 2014; 113: 317-323Abstract Full Text Full Text PDF PubMed Scopus (115) Google Scholar,28Linge A. Schötz U. Löck S. Lohaus F. von Neubeck C. Gudziol V. Nowak A. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Bunea H. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Lauber K. Pigorsch S. Combs S.E. Mönnich D. Zips D. Baretton G.B. Buchholz F. Krause M. Belka C. Baumann M. Comparison of detection methods for HPV status as a prognostic marker for loco-regional control after radiochemotherapy in patients with HNSCC.Radiother Oncol. 2018; 127: 27-35Abstract Full Text Full Text PDF PubMed Scopus (9) Google Scholar or primary R-CT9Linge A. Lohaus F. Löck S. Nowak A. Gudziol V. Valentini C. von Neubeck C. Jütz M. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Krause M. Baumann M. HPV status, cancer stem cell marker expression, hypoxia gene signatures and tumour volume identify good prognosis subgroups in patients with HNSCC after primary radiochemotherapy: a multicentre retrospective study of the German Cancer Consortium Radiation.Radiother Oncol. 2016; 121: 364-373Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar,28Linge A. Schötz U. Löck S. Lohaus F. von Neubeck C. Gudziol V. Nowak A. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Bunea H. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Lauber K. Pigorsch S. Combs S.E. Mönnich D. Zips D. Baretton G.B. Buchholz F. Krause M. Belka C. Baumann M. Comparison of detection methods for HPV status as a prognostic marker for loco-regional control after radiochemotherapy in patients with HNSCC.Radiother Oncol. 2018; 127: 27-35Abstract Full Text Full Text PDF PubMed Scopus (9) Google Scholar at one of the eight DKTK-ROG partner sites. The retrospective postoperative RCT cohort of the DKTK-ROG included 221 patients and was previously described.15Linge A. Löck S. Gudziol V. Nowak A. Lohaus F. von Neubeck C. Jütz M. Abdollahi A. Debus J. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.-L. Bayer C. Belka C. Pigorsch S. Combs S.E. Welz S. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Baumann M. Krause M. DKTK-ROGLow cancer stem cell marker expression and low hypoxia identify good prognosis subgroups in HPV(-) HNSCC after postoperative radiochemotherapy: a multicenter study of the DKTK-ROG.Clin Cancer Res. 2016; 22: 2639-2649Crossref PubMed Scopus (96) Google Scholar,18Lohaus F. Linge A. Tinhofer I. Budach V. Gkika E. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.L. Abdollahi A. Debus J. Bayer C. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Von Neubeck C. Baretton G.B. Löck S. Thames H.D. Krause M. Baumann M. HPV16 DNA status is a strong prognosticator of loco-regional control after postoperative radiochemotherapy of locally advanced oropharyngeal carcinoma: results from a multicentre explorative study of the German Cancer Consortium Radiation Oncology Group (DKTK-ROG).Radiother Oncol. 2014; 113: 317-323Abstract Full Text Full Text PDF PubMed Scopus (115) Google Scholar,28Linge A. Schötz U. Löck S. Lohaus F. von Neubeck C. Gudziol V. Nowak A. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Bunea H. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Lauber K. Pigorsch S. Combs S.E. Mönnich D. Zips D. Baretton G.B. Buchholz F. Krause M. Belka C. Baumann M. Comparison of detection methods for HPV status as a prognostic marker for loco-regional control after radiochemotherapy in patients with HNSCC.Radiother Oncol. 2018; 127: 27-35Abstract Full Text Full Text PDF PubMed Scopus (9) Google Scholar Briefly, patients were treated between 2004 and 2012 with curatively intended cisplatinum-based postoperative RCT with a median dose of 64.0 Gy (range, 56.0 to 68.0 Gy) according to standard protocols. Each patient presented with a tumor stage pT4 and/or >3 positive lymph nodes and/or positive microscopic resection margins and/or extracapsular spread. The primary RCT cohort originally consisted of 158 patients and was previously described.9Linge A. Lohaus F. Löck S. Nowak A. Gudziol V. Valentini C. von Neubeck C. Jütz M. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Krause M. Baumann M. HPV status, cancer stem cell marker expression, hypoxia gene signatures and tumour volume identify good prognosis subgroups in patients with HNSCC after primary radiochemotherapy: a multicentre retrospective study of the German Cancer Consortium Radiation.Radiother Oncol. 2016; 121: 364-373Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar,28Linge A. Schötz U. Löck S. Lohaus F. von Neubeck C. Gudziol V. Nowak A. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Bunea H. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Lauber K. Pigorsch S. Combs S.E. Mönnich D. Zips D. Baretton G.B. Buchholz F. Krause M. Belka C. Baumann M. Comparison of detection methods for HPV status as a prognostic marker for loco-regional control after radiochemotherapy in patients with HNSCC.Radiother Oncol. 2018; 127: 27-35Abstract Full Text Full Text PDF PubMed Scopus (9) Google Scholar Patients received primary RCT (based on cisplatinum or mitomycin-C) with a median dose of 72.0 Gy (range, 68.4 to 74.0 Gy) between 2005 and 2011. Some of the samples of the original patient cohorts had to be omitted from the analysis because of insufficient tumor material or a too low RNA yield. The frequency of RNA assay failure was 1.2% for nCounter, 1.8% for GeneChip, and 4.6% for real-time PCR analyses. Results of both GeneChip and nCounter analyses were available for 191 patients in the postoperative RCT cohort and 136 patients in the primary RCT cohort. For 187 patients in the postoperative RCT cohort, an additional analysis with real-time PCR was performed. Both cohorts are summarized in Table 1. Expression and outcome data are available in Supplemental Table S1.Table 1Patient and Tumor Characteristics for the Postoperative and Primary RCT CohortsCharacteristicsPostoperative RCT cohortPrimary RCT cohortFollow-up, median (95% CI), months56.7 (11.5–94.5)54.7 (10.9–81.1)Age, median (range), years57.0 (24.0–75.2)59.0 (39.2–81.9)Dose, Gy64.0 (56.0–68.4)72.0 (68.4–74.0)Sex, n (%) Male152 (76.6)112 (82.4) Female39 (30.4)24 (17.6)Localization Oropharynx113 (59.2)70 (51.5) Oral cavity53 (27.7)23 (16.9) Hypopharynx25 (13.1)43 (31.6)UICC stage 1 27 (3.7) 330 (15.7)12 (8.8) 4154 (80.6)124 (91.8)HPV16 status Negative125 (65.4)119 (87.5) Positive65 (34.0)16 (11.8) Unknown1 (0.5)1 (0.7)Locoregional recurrences28 (14.7)54 (39.7)Distant metastases36 (18.9)24 (17.7)Deaths61 (31.9)70 (51.5)Data are presented as n (%) of patients unless otherwise indicated. Compared with previous studies of these cohorts,9Linge A. Lohaus F. Löck S. Nowak A. Gudziol V. Valentini C. von Neubeck C. Jütz M. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Grosu A.-L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Krause M. Baumann M. HPV status, cancer stem cell marker expression, hypoxia gene signatures and tumour volume identify good prognosis subgroups in patients with HNSCC after primary radiochemotherapy: a multicentre retrospective study of the German Cancer Consortium Radiation.Radiother Oncol. 2016; 121: 364-373Abstract Full Text Full Text PDF PubMed Scopus (95) Google Scholar,12Schmidt S. Linge A. Zwanenburg A. Leger S. Lohaus F. Krenn C. Appold S. Gudziol V. Nowak A. Von Neubeck C. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rodel C. Bunea H. Grosu A.L. Abdollahi A. Debus J. Ganswindt U. Belka C. Pigorsch S. Combs S.E. Monnich D. Zips D. Baretton G.B. Buchholz F. Baumann M. Krause M. Lock S. Development and validation of a gene signature for patients with head and neck carcinomas treated by postoperative radio(chemo)therapy.Clin Cancer Res. 2018; 24: 1364-1374Crossref PubMed Scopus (37) Google Scholar,15Linge A. Löck S. Gudziol V. Nowak A. Lohaus F. von Neubeck C. Jütz M. Abdollahi A. Debus J. Tinhofer I. Budach V. Sak A. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.-L. Bayer C. Belka C. Pigorsch S. Combs S.E. Welz S. Zips D. Buchholz F. Aust D.E. Baretton G.B. Thames H.D. Dubrovska A. Alsner J. Overgaard J. Baumann M. Krause M. DKTK-ROGLow cancer stem cell marker expression and low hypoxia identify good prognosis subgroups in HPV(-) HNSCC after postoperative radiochemotherapy: a multicenter study of the DKTK-ROG.Clin Cancer Res. 2016; 22: 2639-2649Crossref PubMed Scopus (96) Google Scholar,18Lohaus F. Linge A. Tinhofer I. Budach V. Gkika E. Stuschke M. Balermpas P. Rödel C. Avlar M. Grosu A.L. Abdollahi A. Debus J. Bayer C. Belka C. Pigorsch S. Combs S.E. Mönnich D. Zips D. Von Neubeck C. Baretton G.B. Löck S. Thames H.D. Krause M. Baumann M. HPV16 DNA status is a strong prognosticator of loco-regional control after postoperative radiochemother