Targeted next generation sequencing panel for HPV genotyping in cervical cancer

Lippert, Jan; Bønløkke, Sara; Utke, A.; Knudsen, Birgitta R.; Sørensen, Boe Sandahl; Steiniche, Torben; Stougaard, Magnus

doi:10.1016/j.yexmp.2020.104568

Cited by 12 publications

(16 citation statements)

References 24 publications

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“…Compared with conventional HPV genotyping methods, NGS was associated with detection of HPV genotypes with high sensitivity. 20,21 To our knowledge, our study was the first to detect MB HPV with NGS technology and found a high sensitivity of 97.7%. Moreover, strengths of capture sequencing included detection of additional hrHPV infections and multiple hrHPV infections, identification of true-negative samples, and identification of the real hrHPV genotypes among those misidentified by conventional HPV testing.…”

Section: Discussionmentioning

confidence: 64%

Feasibility and Accuracy of Menstrual Blood Testing for High-risk Human Papillomavirus Detection With Capture Sequencing

et al. 2021

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Section: Discussionmentioning

confidence: 64%

Feasibility and Accuracy of Menstrual Blood Testing for High-risk Human Papillomavirus Detection With Capture Sequencing

et al. 2021

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“…It should be noted that numerous HPV tests and products have been developed in the world and successfully utilized for detecting HPV DNA integration into the cell genome [64][65][66][67]. Potentially, they can be used to identify prognostically unfavorable cases.…”

Section: Discussionmentioning

confidence: 99%

“…The presence of HPV DNA of 14 high risk genotypes (16,18,31,33,35,39,45,51,52,56,58,59,66,68) was determined in united scrapings from endo-and exocervix of 173 CC patients before treatment. Real-time PCR on "Rotor-Gene" (Corbett Research, Sydney, Australia) was performed using the test-systems "AmpliSens HPV HCR screen-titer-FL" and "AmpliSens HPV HCR genotype-titer FL" (Central Research Institute of Epidemiology, Moscow, Russia).…”

Section: Polymerase Chain Reaction (Pcr)mentioning

confidence: 99%

HPV Status and Individual Characteristics of Human Papillomavirus Infection as Predictors for Clinical Outcome of Locally Advanced Cervical Cancer

Мкртчян

Замулаева

Крикунова

et al. 2021

JPM

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This study is aimed at searching for an informative predictor of the clinical outcome of cervical cancer (CC) patients. The study included 135 patients with locally advanced cervical cancer (FIGO stage II–III) associated with human papillomavirus (HPV) 16/18 types or negative status of HPV infection. Using logistic regression, we analyzed the influence of the treatment method, clinical and morphological characteristics, and the molecular genetic parameters of HPV on the disease free survival (DFS) of patients treated with radiotherapy or chemoradiotherapy. Multivariate analysis revealed three factors that have prognostic significance for DFS, i.e., HPV-related biomarker (HPV-negativity or HPV DNA integration into the cell genome) (OR = 9.67, p = 1.2 × 10−4), stage of the disease (OR = 4.69, p = 0.001) and age (OR = 0.61, p = 0.025). The predictive model has a high statistical significance (p = 5.0 × 10−8; Nagelkirk’s R2 = 0.336), as well as sensitivity (Se = 0.74) and specificity (Sp = 0.75). Thus, simultaneous accounting for the clinical and molecular genetic predictors (stage of the disease, patient age and HPV-related biomarker) makes it possible to effectively differentiate patients with prognostically favorable and unfavorable outcome of the disease.

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“…Previously, a study from our group demonstrated the use of a small targeted NGS panel for HPV detection and genotyping in both formalin-fixed, paraffin-embedded (FFPE) samples and plasma samples. Furthermore, the study demonstrated the use of the targeted NGS panel for detection of viral integration of HPV16 [32].…”

Section: Introductionmentioning

confidence: 95%

“…To confirm the presence of DNA in each sample, an amplicon for each of five human reference genes (BTF3, PABPN1, PPIE, RAB1B, SRSF3) were included in the panel as well. How to select appropriate human reference genes is described in a previous publication [32]. The panel was designed with short amplicons of approximately 90 base pairs using the circulating free DNA (cfDNA) pipeline of the AmpliSeq Designer.…”

Section: Ngs Panel Designmentioning

confidence: 99%

Targeted Next Generation Sequencing for Human Papillomavirus Genotyping in Cervical Liquid-Based Cytology Samples

Andersen

Holm

Tranberg

et al. 2022

Cancers

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At present, human papillomavirus (HPV) testing is replacing morphology-based cytology as the primary tool for cervical cancer screening in several countries. However, the HPV assays approved for screening lack detection for all but one of the possibly carcinogenic HPV types and do not genotype all included HPV types. This study demonstrates the use of a targeted HPV next generation sequencing (NGS) panel to detect and genotype all 25 carcinogenic, probably carcinogenic, and possibly carcinogenic HPV types as well as the low-risk types HPV6 and HPV11. The panel was validated using a cohort of 93 paired liquid-based cytology samples (general practitioner (GP)-collected cervical samples and cervico-vaginal self-samples (SS)). Overall, the targeted panel had a sensitivity (GP = 97.7%, SS = 92.1%) and specificity (GP = 98.0%, SS = 96.4%) similar to the commercial HPV assays, Cobas® 4800 HPV DNA test (Roche) and CLART® HPV4S assay (GENOMICA). Interestingly, of the samples that tested positive with the NGS panel, three (6.4%) of the GP-collected samples and four (9.1%) of the self-samples tested positive exclusively for HPV types only included in the NGS panel. Thus, targeted HPV sequencing has great potential to improve the HPV screening programs since, as shown here, it can identify additional HPV positive cases, cases with HPV integration, variants in the HPV genome, and which HPV type is dominant in multi-infected cases.

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Targeted next generation sequencing panel for HPV genotyping in cervical cancer

Cited by 12 publications

References 24 publications

Feasibility and Accuracy of Menstrual Blood Testing for High-risk Human Papillomavirus Detection With Capture Sequencing

Feasibility and Accuracy of Menstrual Blood Testing for High-risk Human Papillomavirus Detection With Capture Sequencing

HPV Status and Individual Characteristics of Human Papillomavirus Infection as Predictors for Clinical Outcome of Locally Advanced Cervical Cancer

Targeted Next Generation Sequencing for Human Papillomavirus Genotyping in Cervical Liquid-Based Cytology Samples

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