ArticleBMC medical genomics2022
Inter-assay variability of next-generation sequencing-based gene panels.
Article in BMC medical genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Assessing VirScan serosurvey epitope profiling variability between in-clinic venous blood draw and capillary blood self-sampling device.Microbiology spectrum · 2026Article
- CRISPR-driven diagnostics: Molecular mechanisms, clinical efficacy and translational challenges.Clinical and translational medicine · 2025Review
- An analysis of FDA drug approvals for oncological hematological malignancies in relation to companion diagnostics.Frontiers in oncology · 2025Article
- A clinically feasible algorithm for the parallel detection of glioma-associated copy number variation markers based on shallow whole genome sequencing.The journal of pathology. Clinical research · 2024Article
- The discrepancy of somatic BRCA1/2 pathogenic variants from two different platforms in epithelial ovarian, fallopian tube, and peritoneal cancer.Scientific reports · 2024Article
- Companion Diagnostics (CDx) Based on Molecular Biology Techniques.Life (Basel, Switzerland) · 2024Review
- Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients.NPJ precision oncology · 2023Article
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTumor heterogeneity has been known to cause inter-assay discordance among next-generation sequencing (NGS) results. However, whether preclinical factors such as sample type, sample quality and analytical features of gene panel can affect the concordance between two different assays remains largely unexplored.
methodsReplicate sets of DNA samples extracted from formalin-fixed paraffin-embedded tissues (FFPE) (n = 20) and fresh frozen (FF) tissues (n = 10) were herein analyzed using a tumor-only (TO) and paired tumor-normal (TN) gene panel in laboratories certified by the Clinical Laboratory Improvement Amendment. Reported variants from the TO and TN panels were then compared. Furthermore, additional FFPE samples were sequentially sliced from the same FFPE block and submitted to another TN panel assay.
resultsSubstantial discordance (71.8%) was observed between the results of the two panels despite using identical DNA samples, with the discordance rate being significantly higher for FFPE samples (p < 0.05). Among the 99 variants reported only in the TO panel, 32.3% were consistent with germline variants, which were excluded in the TN panel, while 30.3% had an allele frequency of less than 5%, some of which were highly likely to be artificial calls. The comparison of two independent TN panel assay results from the same FFPE block also showed substantial discordance rate (55.3%).
conclusionsIn the context of clinical settings, our comparative analysis revealed that inter-NGS assay discordance commonly occurred due to sample types and the different analytical features of each panel.
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