Evaluation of the Xpert® HPV assay in the detection of Human Papillomavirus in formalin-fixed paraffin-embedded oropharyngeal carcinomas

Maria Gabriella Donà, Francesca Rollo, Barbara Pichi, Giuseppe Spriano, Raul Pellini, Renato Covello, Edoardo Pescarmona, Giulia Fabbri, Manuela Scalfari, Tarik Gheit, Maria Benevolo

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Abstract

© 2017 Elsevier Ltd Objectives The increasing incidence of HPV-related Oropharyngeal Squamous Cell Carcinoma (OPSCC) and the improved survival of HPV-positive OPSCC highlight the need for effective tools in evaluating HPV status on formalin-fixed paraffin-embedded (FFPE) cancers. To date, there is no agreement regarding the most appropriate method for HPV testing on FFPE materials. We aimed to investigate the performance of the Xpert® HPV assay (Cepheid) on crude lysates from OPSCC FFPE tissues. Materials and methods Crude lysates were obtained by proteinase K digestion of FFPE tissues that had already been analyzed by the INNO-LiPA HPV assay and p16 ink4a immunostaining. Results 159 FFPE OPSCCs were evaluated. All the samples provided valid results with the Xpert, whereas three samples (1.8%) were invalid using the INNO-LiPA. Among the remaining 156 cases, 65 (41.7%) were concordantly positive and 87 (55.8%) concordantly negative (raw agreement 0.97, 95% CI: 0.93–0.99; Cohen K 0.95, 95% CI: 0.90–0.99). Type-specific data for the cases that were positive by both methods were completely concordant. Three samples were HPV16-positive with Xpert but negative with INNO-LiPA, while one OPSCC tested negative with Xpert and positive with INNO-LiPA. A very good agreement was observed between the Xpert and the p16 results, which was slightly higher than that for INNO-LiPA (Cohen K 0.87 vs. 0.85). Conclusion The Xpert HPV assay appears to be a very good method for HPV detection and genotyping on FFPE OPSCCs, and requires no prior purification of nucleic acids. This assay showed a very good agreement with INNO-LiPA and p16 findings.
Original languageEnglish
Pages (from-to)117-122
Number of pages6
JournalOral Oncology
Volume72
DOIs
Publication statusPublished - Sep 1 2017

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Paraffin
Formaldehyde
Carcinoma
Squamous Cell Carcinoma
Endopeptidase K
Nucleic Acids
Digestion
Survival
Incidence
Neoplasms

Keywords

  • FFPE
  • Head and neck cancer
  • HPV DNA tests
  • Human Papillomavirus
  • Orophrayngeal neoplasms
  • p16 ink4a

Cite this

Evaluation of the Xpert® HPV assay in the detection of Human Papillomavirus in formalin-fixed paraffin-embedded oropharyngeal carcinomas. / Donà, Maria Gabriella; Rollo, Francesca; Pichi, Barbara; Spriano, Giuseppe; Pellini, Raul; Covello, Renato; Pescarmona, Edoardo; Fabbri, Giulia; Scalfari, Manuela; Gheit, Tarik; Benevolo, Maria.

In: Oral Oncology, Vol. 72, 01.09.2017, p. 117-122.

Research output: Contribution to journalArticle

Donà, MG, Rollo, F, Pichi, B, Spriano, G, Pellini, R, Covello, R, Pescarmona, E, Fabbri, G, Scalfari, M, Gheit, T & Benevolo, M 2017, 'Evaluation of the Xpert® HPV assay in the detection of Human Papillomavirus in formalin-fixed paraffin-embedded oropharyngeal carcinomas', Oral Oncology, vol. 72, pp. 117-122. https://doi.org/10.1016/j.oraloncology.2017.07.016
Donà, Maria Gabriella ; Rollo, Francesca ; Pichi, Barbara ; Spriano, Giuseppe ; Pellini, Raul ; Covello, Renato ; Pescarmona, Edoardo ; Fabbri, Giulia ; Scalfari, Manuela ; Gheit, Tarik ; Benevolo, Maria. / Evaluation of the Xpert® HPV assay in the detection of Human Papillomavirus in formalin-fixed paraffin-embedded oropharyngeal carcinomas. In: Oral Oncology. 2017 ; Vol. 72. pp. 117-122.
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abstract = "{\circledC} 2017 Elsevier Ltd Objectives The increasing incidence of HPV-related Oropharyngeal Squamous Cell Carcinoma (OPSCC) and the improved survival of HPV-positive OPSCC highlight the need for effective tools in evaluating HPV status on formalin-fixed paraffin-embedded (FFPE) cancers. To date, there is no agreement regarding the most appropriate method for HPV testing on FFPE materials. We aimed to investigate the performance of the Xpert{\circledR} HPV assay (Cepheid) on crude lysates from OPSCC FFPE tissues. Materials and methods Crude lysates were obtained by proteinase K digestion of FFPE tissues that had already been analyzed by the INNO-LiPA HPV assay and p16 ink4a immunostaining. Results 159 FFPE OPSCCs were evaluated. All the samples provided valid results with the Xpert, whereas three samples (1.8{\%}) were invalid using the INNO-LiPA. Among the remaining 156 cases, 65 (41.7{\%}) were concordantly positive and 87 (55.8{\%}) concordantly negative (raw agreement 0.97, 95{\%} CI: 0.93–0.99; Cohen K 0.95, 95{\%} CI: 0.90–0.99). Type-specific data for the cases that were positive by both methods were completely concordant. Three samples were HPV16-positive with Xpert but negative with INNO-LiPA, while one OPSCC tested negative with Xpert and positive with INNO-LiPA. A very good agreement was observed between the Xpert and the p16 results, which was slightly higher than that for INNO-LiPA (Cohen K 0.87 vs. 0.85). Conclusion The Xpert HPV assay appears to be a very good method for HPV detection and genotyping on FFPE OPSCCs, and requires no prior purification of nucleic acids. This assay showed a very good agreement with INNO-LiPA and p16 findings.",
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AU - Spriano, Giuseppe

AU - Pellini, Raul

AU - Covello, Renato

AU - Pescarmona, Edoardo

AU - Fabbri, Giulia

AU - Scalfari, Manuela

AU - Gheit, Tarik

AU - Benevolo, Maria

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N2 - © 2017 Elsevier Ltd Objectives The increasing incidence of HPV-related Oropharyngeal Squamous Cell Carcinoma (OPSCC) and the improved survival of HPV-positive OPSCC highlight the need for effective tools in evaluating HPV status on formalin-fixed paraffin-embedded (FFPE) cancers. To date, there is no agreement regarding the most appropriate method for HPV testing on FFPE materials. We aimed to investigate the performance of the Xpert® HPV assay (Cepheid) on crude lysates from OPSCC FFPE tissues. Materials and methods Crude lysates were obtained by proteinase K digestion of FFPE tissues that had already been analyzed by the INNO-LiPA HPV assay and p16 ink4a immunostaining. Results 159 FFPE OPSCCs were evaluated. All the samples provided valid results with the Xpert, whereas three samples (1.8%) were invalid using the INNO-LiPA. Among the remaining 156 cases, 65 (41.7%) were concordantly positive and 87 (55.8%) concordantly negative (raw agreement 0.97, 95% CI: 0.93–0.99; Cohen K 0.95, 95% CI: 0.90–0.99). Type-specific data for the cases that were positive by both methods were completely concordant. Three samples were HPV16-positive with Xpert but negative with INNO-LiPA, while one OPSCC tested negative with Xpert and positive with INNO-LiPA. A very good agreement was observed between the Xpert and the p16 results, which was slightly higher than that for INNO-LiPA (Cohen K 0.87 vs. 0.85). Conclusion The Xpert HPV assay appears to be a very good method for HPV detection and genotyping on FFPE OPSCCs, and requires no prior purification of nucleic acids. This assay showed a very good agreement with INNO-LiPA and p16 findings.

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