Multiplex PCR for the detection of high risk human papilloma virus types in formalin fixed paraffin embedded cervical tissues

Context.—Testing for high-risk human papillomavirus (HR-HPV) in head and neck squamous cell carcinomas (HNSCCs) is important for both prognostication and clinical management. Several testing platforms are available for HR-HPV; however, effective alternative automated approaches are needed. Objective.—To assess the performance of the automated Roche cobas 4800 HPV real-time polymerase chain reaction-based system on formalin-fixed, paraffin-embedded HNSCC specimens and compare results with standard methods of in situ hybridization (ISH) and p16 immunohistochemistry. Design.—Formalin-fixed, paraffin-embedded samples of HNSCC were collected from archival specimens in the Department of Pathology, Massachusetts General Hospital (Boston), and prepared using the automated system by deparaffinization and dehydration followed by tissue lysis. Samples were integrated into routine cervical cytology testing runs by cobas. Corresponding formalin-fixed, paraffin-embedded samples were evaluated for HR-HPV by ISH and p16 by immunohistochemistry. Discrepant cases were adjudicated by polymerase chain reaction. Results.—Sixty-two HNSCC samples were analyzed using the automated cobas system, ISH, and immunohistochemistry. Fifty-two percent (n = 32 of 62) of formalin-fixed, paraffin-embedded tumors were positive for HR-HPV by cobas. Eighty-eight percent (n = 28 of 32) of cases were the HPV 16 subtype and 12% (n = 4 of 32) were other HR-HPV subtypes. Corresponding testing with ISH was concordant in 92% (n = 57 of 62) of cases. Compared with the adjudication polymerase chain reaction standard, there were 3 false-positive cases by cobas. Conclusions.—Concordance in HNSCC HR-HPV status between cobas and ISH was more than 90%. The cobas demonstrated a sensitivity of 100% and a specificity of 91% for detection of HR-HPV. Advantages favoring cobas include its automation, cost efficiency, objective results, and ease of performance.

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Diagnosis of proliferative enteritis in frozen and formalin-fixed, paraffin-embedded tissues from a hamster, horse, deer and ostrich using a Lawsonia intracellularis-specific multiplex PCR assay

Veterinary Microbiology ◽

10.1016/s0378-1135(96)01264-3 ◽

1997 ◽

Vol 54 (1) ◽

pp. 47-62 ◽

Cited By ~ 65

Author(s):

D.M. Cooper ◽

D.L. Swanson ◽

C.J. Gebhart

Keyword(s):

Multiplex Pcr ◽

Lawsonia Intracellularis ◽

Pcr Assay ◽

Multiplex Pcr Assay ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Formalin Fixed

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Population-based p16 and HPV positivity rates in oropharyngeal cancer in Southeast Scotland

Journal of Clinical Pathology ◽

10.1136/jclinpath-2015-202947 ◽

2015 ◽

Vol 68 (10) ◽

pp. 849-852 ◽

Cited By ~ 2

Author(s):

L A R Wells ◽

E J Junor ◽

B Conn ◽

S Pattle ◽

K Cuschieri

Keyword(s):

Hpv Infection ◽

Population Based ◽

Papilloma Virus ◽

P16 Immunohistochemistry ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Hpv Types ◽

Positive Groups ◽

Formalin Fixed ◽

Cause Specific Survival

We assessed a population-based cohort of patients diagnosed with oropharyngeal squamous cell carcinoma in Southeast Scotland over 13 months. p16 and human papilloma virus (HPV) expression were determined, and correlated with stage, treatment, smoking and alcohol history, and disease outcomes. Retrospective analysis was performed on 60 patients. p16 immunohistochemistry and HPV genotyping were performed on formalin-fixed paraffin-embedded tissues. HPV infection (as defined by p16 positivity and/or HPV PCR positivity) was identified in 57% of samples, while dual positives were detected in 45% of cases. HPV16 was most prevalent of the HPV types and was associated with 90% of positive samples. Cause-specific 1-year and 2-year survivals were 82.5% and 78.2%, respectively. The p16-positive and HPV-positive groups demonstrated significantly increased cause-specific survival in comparison with their negative counterparts.

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Multiplex Polymerase Chain Reaction for the Detection of High-risk-Human Papillomavirus Types in Formalin-fixed Paraffin-embedded Cervical Tissues

Indian Journal of Medical Microbiology ◽

10.4103/ijmm.ijmm_15_277 ◽

2017 ◽

Vol 35 (1) ◽

pp. 113-115

Author(s):

Mini P. Singh ◽

Nalini Gupta ◽

T. Deepak ◽

Archit Kumar ◽

Radha Kanta Ratho

Keyword(s):

Polymerase Chain Reaction ◽

Human Papillomavirus ◽

High Risk ◽

Multiplex Polymerase Chain Reaction ◽

Chain Reaction ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Polymerase Chain ◽

Formalin Fixed

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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

Journal of Virological Methods ◽

10.1016/j.jviromet.2011.04.006 ◽

2011 ◽

Vol 175 (1) ◽

pp. 117-119 ◽

Cited By ~ 24

Author(s):

Boštjan J. Kocjan ◽

Katja Seme ◽

Mario Poljak

Keyword(s):

Cervical Cancer ◽

High Risk ◽

Human Papillomaviruses ◽

Hpv Genotyping ◽

Formalin Fixed Paraffin ◽

Hpv Test ◽

Formalin Fixed Paraffin Embedded ◽

High Risk Hpv ◽

Formalin Fixed

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97P Multiplex PCR of reference genes for accurate quantification of genes expression in formalin-fixed paraffin-embedded breast cancer tissues

Annals of Oncology ◽

10.1093/annonc/mdv519.46 ◽

2015 ◽

Vol 26 ◽

pp. ix16

Author(s):

A.S. Leshchenko ◽

N.Y. Matsenko ◽

V. Shamanin ◽

A.E. Kozyakov ◽

S. Kovalenko

Keyword(s):

Breast Cancer ◽

Multiplex Pcr ◽

Reference Genes ◽

Formalin Fixed Paraffin ◽

Genes Expression ◽

Formalin Fixed Paraffin Embedded ◽

Cancer Tissues ◽

Formalin Fixed ◽

Accurate Quantification

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High-risk human papillomavirus (HPV) detection in formalin-fixed paraffin-embedded cervical tissues: performances of Aptima HPV assay and Beckton Dickinson (BD) Onclarity assay

Journal of Clinical Pathology ◽

10.1136/jclinpath-2021-207657 ◽

2021 ◽

pp. jclinpath-2021-207657

Author(s):

Gozde Kir ◽

Humeyra Gunel ◽

Zeynep Cagla Olgun ◽

W Glenn McCluggage

Keyword(s):

Human Papillomavirus ◽

High Risk ◽

Hpv 16 ◽

Formalin Fixed Paraffin ◽

Formalin Fixed Paraffin Embedded ◽

Ffpe Tissues ◽

Hpv Types ◽

High Risk Hpv ◽

Hpv Assays ◽

Formalin Fixed

AimThere are many scenarios where high-risk human papillomavirus (HPV) detection in formalin-fixed paraffin-embedded (FFPE) specimens is important. However, there is no Food and Drug Administration (FDA)-approved and clinically validated technique for detecting high-risk HPV in FFPE tissues. In this study, we evaluated two commercially available HPV assays which are FDA-approved for use on cytology specimens, the Aptima HPV assay and the Beckton Dickinson (BD) Onclarity assay, to detect high-risk HPV in FFPE tissues of cervical high-grade squamous intraepithelial lesion (HSIL) and squamous cell carcinoma (SCC).MethodsA total of 189 cases (46 SCC, 107 HSIL and 36 benign/normal) were tested for high-risk HPV with the Aptima HPV assay and a subset of cases (n=97) with the BD Onclarity assay.ResultsThe sensitivities of the Aptima and BD Onclarity HPV assays were 99.4% (95% CI 96.46% to 99.98%) and 75.9% (95% CI 65.27% to 84.62%), respectively; the specificity and positive predictive value (PPV) of the two assays were 100%. Negative predictive values of the Aptima and BD Onclarity HPV assays were 97.3% (95% CI 83.61% to 99.61%) and 67.7% (95% CI 58.91% to 75.47%), respectively. The kappa value (0.96) for comparison of the distribution of high-risk HPV types between the two assays was high. HPV 16 was the most common high-risk HPV type for HSIL and SCC cases. However, SCC cases had higher percentages of HPV 16 and HPV 18/45 and lower percentages of other high-risk HPV types compared with HSIL cases.ConclusionBoth assays are reliable methods for high-risk HPV detection and genotype determination in FFPE specimens, with high PPV and specificity. The Aptima HPV assay has the advantage of higher sensitivity. As far as we are aware, this is the first study comparing the Aptima HPV assay and the BD Onclarity assay in FFPE tissues. Our study results should be tested and confirmed in larger cohorts.

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