Comparison of HPV detection rate in formalin‐fixed paraffin‐embedded tissues of head and neck carcinoma using two DNA extraction kits and three amplification methods

Božić, Ljiljana; Jovanović, Tanja; Šmitran, Aleksandra; Janković, Marko; Knežević, Aleksandra

doi:10.1111/eos.12746

Cited by 7 publications

(8 citation statements)

References 43 publications

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“…The use of high temperatures during extraction, however, has been suggested to interfere with multiplex qPCR performance [26], while lower de-cross-linking temperatures have been shown to be beneficial in the assessment of somatic variants in cancer patients [27]. The two protocols used in this study have been previously evaluated by Bozic et al [12] who found comparable detection rates of human papillomavirus in FFPE samples, albeit higher yields of total DNA were obtained with the FFPE kit. This was also the case in our study, where we determined higher ratios of the human single-copy gene RNase P and of viral findings in the samples extracted with the FFPE kit, although the difference to the standard protocol was not significant.…”

Section: Discussionmentioning

confidence: 98%

“…Most importantly, the analytical sensitivity of detection of low-copy viral nucleic acids in archival and/or highly degraded samples has not been assessed. Indeed, most of the existing reports on FFPE tissue specimens have been PCR-based and focused on oncogenic viruses in tumor samples, in which the viral copies are commonly very high [10][11][12][13][14]. For example, in cervical cancer, human papillomaviruses can have average copies of 10 7 /µg in contrast to 10 2 /µg of most persistent viruses in healthy tissues [15].…”

Section: Introductionmentioning

confidence: 99%

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Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation

Mielonen

Pratas

Hedman

et al. 2022

Viruses

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Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (±paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63–159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (<250 copies/million cells) and longer PCR amplicons (>150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.

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Section: Discussionmentioning

confidence: 98%

Section: Introductionmentioning

confidence: 99%

Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation

Mielonen

Pratas

Hedman

et al. 2022

Viruses

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“…During infection, viral DNA sequences of HPV are incorporated into cellular DNA and play a key role in the promotion of neoplasm growth and malignant transformation of SNIP [ 32 ]. The detection method and detection rate of HPV-PCR are important points, and there have been several studies that employ HPV-PCR in FFPE samples [ 33 , 34 , 35 ]. The internal control gene amplification was performed to assess the validity of the results obtained in this study.…”

Section: Discussionmentioning

confidence: 99%

Clinicopathologic Analysis of Sinonasal Inverted Papilloma, with Focus on Human Papillomavirus Infection Status

et al. 2022

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Sinonasal inverted papilloma (SNIP) can recur; however, the factors related to tumor recurrence remain unclear. This study aimed to analyze risk factors, including human papillomavirus (HPV) infection, as well as other factors associated with SNIP recurrence. Thirty-two patients who were diagnosed with SNIP and underwent surgery between 2010 and 2019 were enrolled: 24 men and 8 women, with a mean age of 59.2 years. The mean follow-up was 57.3 months. Demographics and information about history of smoking, diabetes mellitus (DM), hypertension, allergic rhinitis, alcohol consumption, tumor stage, surgical approach, and recurrence were reviewed retrospectively. Specimens were investigated using polymerase chain reaction to detect HPV DNA (high-risk subtypes: 16, 18, 31, 33, 35, 52b, and 58; low-risk subtypes: 6 and 11). Seven patients (21.9%) experienced recurrence. HPV DNA was detected in five (15.6%) patients (high-risk subtypes, n = 2; low-risk subtypes, n = 3). Patients with recurrence of SNIP had a higher proportion of young adults and displayed higher rates of HPV infection, DM, and advanced tumor stage than those without recurrence. HPV infection, young adulthood, DM, and advanced tumor stage could be associated with a high recurrence rate, which suggests that patients with these risk factors could require close follow-up after surgery.

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“…They concluded that the PGMY/GP+ nested PCR is the most appropriate primer set for the detection of HPV DNA using FFPE samples from OSCC. In turn, Božić et al [ 45 ] have compared HPV detection rate in FFPE of head and neck carcinoma using three amplification methods: single PCR and real-time PCR and nested PCR. In their study there was not HPV amplification in any of the 50 FFPE samples using the single PCR and real‐time PCR, whereas HPV DNA was detected in 22% of samples using nested PCR.…”

Section: Discussionmentioning

confidence: 99%

Low frequency of HPV positivity in breast tumors among patients from south-central Poland

Biesaga

Janecka-Widła

Kołodziej-Rzepa

et al. 2021

Infect Agents Cancer

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Background Some studies suggest that Human Papilloma Virus (HPV) infection is important factor in carcinogenesis of breast tumors. This study’ objective was to analyze HPV prevalence in breast cancers of patients from south-central Poland. Materials and methods The study was performed based on archival paraffin embebbed and formalin fixed blocks in the group of 383 patients with breast cancer. HPV prevalence and its genotype were assessed, respectively by: nested PCR (with two groups of primers: PGMY09/PGMY11 and GP5+/GP6+), quantitative PCR (qPCR). Tumors were classified as HPV positive in case of at least one positive result in nested PCR and positive results in genotyping procedure. For all HPV positive tissues P16 immunostaining was applied in order to confirm active viral infection. Results In the group of 383 breast cancers, HPV positivity was found in 17 samples (4.4%) in nested PCR. All these samples were subjected to HPV genotyping. This analysis revealed presence of HPV type 16 into two tumors (0.5%). In these two cancers, P16 overexpression was reported. Conclusion In breast tumors of patients from south-central Poland in Poland, HPV positivity is demonstrated in very low percentage of cases.

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Comparison of HPV detection rate in formalin‐fixed paraffin‐embedded tissues of head and neck carcinoma using two DNA extraction kits and three amplification methods

Abstract: zevi c A. Comparison of HPV detection rate in formalin-fixed paraffin-embedded tissues of head and neck carcinoma using two DNA extraction kits and three amplification methods.

Cited by 7 publications

References 43 publications

Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation

Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation

Clinicopathologic Analysis of Sinonasal Inverted Papilloma, with Focus on Human Papillomavirus Infection Status

Low frequency of HPV positivity in breast tumors among patients from south-central Poland

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