ArticleVirchows Archiv : an international journal of pathology2019
Recommendations for the clinical interpretation and reporting of copy number gains using gene panel NGS analysis in routine diagnostics.
Article in Virchows Archiv : an international journal of pathology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 36 citations in OpenAlex.
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- Analytical Validation and Performance Evaluation of Amplicon-Based Next-Generation Sequencing Assays for DetectingCancers · 2024Article
- Detection ofBiomedicines · 2024Article
- Targeted molecular profiling of solid tumours-Indian tertiary cancer centre experience.Journal of cancer research and clinical oncology · 2023Article
- PD-L1 gene amplification and focality: relationship with protein expression.Journal for immunotherapy of cancer · 2023Article
- Digital PCR-Based Method for Detecting CDKN2A Loss in Brain Tumours.Molecular diagnosis & therapy · 2022Article
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- HER2 Amplification by Next-Generation Sequencing in Lung Carcinoma: A Comparison of NGS Amplified and Non-amplified Cases by Immunohistochemistry and In Situ HybridizationBalkan medical journal · 2022Article
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- Therapeutic implications of cancer gene amplifications without mRNA overexpression: silence may not be golden.Journal of hematology & oncology · 2021Article
- Comparison ofOncotarget · 2021Article
- Validation of the EuroClonality-NGS DNA capture panel as an integrated genomic tool for lymphoproliferative disorders.Blood advances · 2021Article
- Clinical Value of EGFR Copy Number Gain Determined by Amplicon-Based Targeted Next Generation Sequencing in Patients with EGFR-Mutated NSCLC.Targeted oncology · 2021Article
- Unraveling Neuroendocrine Gallbladder Cancer: Comprehensive Clinicopathologic and Molecular Characterization.JCO precision oncology · 2021Article
- Comprehensive routine diagnostic screening to identify predictive mutations, gene amplifications, and microsatellite instability in FFPE tumor material.BMC cancer · 2020Article
- Somatic mutations and copy number variations in breast cancers with heterogeneous HER2 amplification.Molecular oncology · 2020Article
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Authors and funding
25 authors at 13 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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