HPV Prevalence in the Dutch cervical cancer screening population (DuSC study): HPV testing using automated HC2, cobas and Aptima workflows

Background: Primary high risk (hr)HPV screening will be introduced in The Netherlands in January 2017. Our aim was to determine the hrHPV prevalence in the Dutch cervical cancer screening population (DuSC study). Methods: A total of 12,113 residual PreservCyt cervical samples from the Dutch population based cytology screening program were rendered anonymous, randomized and tested for hrHPV using 3 HPV assays on their respective automated platforms: QIAGEN's digene® HC2 HPV DNA Test® (HC2, signal amplification), Roche Cobas® HPV test (DNA amplification) and Hologic Aptima® HPV Test (RNA amplification). To determine the agreement between results generated using the different assays, pair wise comparison of the systems was performed by determining kappa coefficients. Results: The selected samples were representative for the population based screening program with respect to age distribution and cytology classification. HrHPV prevalences found were: 8.5% for HC2 (n = 959), 8.1% for cobas (n = 919) and 7.5% for Aptima (n = 849), resulting in a mean hrHPV prevalence of 8.0 ± 0.5%. Although the hrHPV prevalences of the different assays are in the range of 8%, there was a significant difference in prevalence for the HC2 vs. Aptima assay (p-value = 0.007). A clear age dependency was found, with an hrHPV prevalence ranging from 18.7 ± 1.2% in women 29-33 years of age to 4.2 ± 0.2% in women 59-63 years of age. Furthermore, a correlation between hrHPV prevalence and severity of cytology was observed, ranging from 5.5 ± 0.4% in normal cytology to 95.2 ± 1.7% in severe dysplasia. Indeed, kappa coefficients of 0.77, 0.71 and 0.72 (HC2 vs cobas, cobas vs Aptima and Aptima vs HC2, respectively) indicated substantial agreement between the results generated by the different systems. However, looking at the hrHPV positive samples, only 48% of the samples tested positive with all 3 assays. Conclusions: A hrHPV prevalence of 8% was found in this unselected population based screening cohort independently of using HC2, Aptima or cobas. This prevalence is higher than the previously reported 4-5% (POBASCAM and VUSA-Screen trials). Furthermore, the complete automated hrHPV detection workflow solutions from QIAGEN, Roche, and Hologic were successfully used and will be valuable for reliably implementing high throughput hrHPV testing in cervical cancer screening

Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics

Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity

Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics

Next-generation sequencing (NGS) panel analysis on DNA from formalin-fixed paraffin-embedded (FFPE) tissue is increasingly used to also identify actionable copy number gains (gene amplifications) in addition to sequence variants. While guidelines for the reporting of sequence variants are available, guidance with respect to reporting copy number gains from gene-panel NGS data is limited. Here, we report on Dutch consensus recommendations obtained in the context of the national Predictive Analysis for THerapy (PATH) project, which aims to optimize and harmonize routine diagnostics in molecular pathology. We briefly discuss two common approaches to detect gene copy number gains from NGS data, i.e., the relative coverage and B-allele frequencies. In addition, we provide recommendations for reporting gene copy gains for clinical purposes. In addition to general QC metrics associated with NGS in routine diagnostics, it is recommended to include clinically relevant quantitative parameters of copy number gains in the clinical report, such as (i) relative coverage and estimated copy numbers in neoplastic cells, (ii) statistical scores to show significance (e.g., z-scores), and (iii) the sensitivity of the assay and restrictions of NGS-based detection of copy number gains. Collectively, this information can guide clinical and analytical decisions such as the reliable detection of high-level gene amplifications and the requirement for additional in situ assays in case of borderline results or limited sensitivity