ArticleNPJ precision oncology2023
Multicentric pilot study to standardize clinical whole exome sequencing (WES) for cancer patients.
Article in NPJ precision oncology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
24 citing papers in PubMed, 29 citations in OpenAlex.
- Oncogenicity Variant Interpreter (OncoVI) Supports Harmonized Somatic Variant Interpretation in Precision Oncology.The Journal of molecular diagnostics : JMD · 2026Article
- Pre-Analytical and Analytical Challenges in Whole-Exome Sequencing of Formalin-Fixed Paraffin-Embedded Breast and Prostate Cancer Tissue: A Real-World Multicenter Study.Diagnostics (Basel, Switzerland) · 2026Article
- Clinical validation of a high-performance somatic exome sequencing assay: from target-enrichment strategy to variant calling.NPJ genomic medicine · 2026Article
- Time dependent outcomes modeling in a real-world analysis of the molecular tumor board at University Cancer Center Hamburg (2016-2022).The oncologist · 2026Article
- CBC3T-3: a novel patient-derived cisplatin-resistant distal cholangiocarcinoma cell line harboring multiple TP53 missense mutations.Human cell · 2026Article
- Clinical benefit of additional whole-exome sequencing over panel sequencing in an all-comer real-world molecular tumor board.ESMO open · 2025Article
- Unveiling Metabolic Signatures as Potential Biomarkers in Common Cancers: Insights from Lung, Breast, Colorectal, Liver, and Gastric Tumours.Biomolecules · 2025Review
- CG>TG mutation frequency as negative predictor of homologous recombination deficiency in ovarian and breast cancer.Communications biology · 2025Article
- HRProfiler Detects Homologous Recombination Deficiency in Breast and Ovarian Cancers Using Whole-Genome and Whole-Exome Sequencing Data.Cancer research · 2025Article
- Advances in personalized medicine: translating genomic insights into targeted therapies for cancer treatment.Annals of translational medicine · 2025Review
- The MHC-I-dependent neoantigen presentation pathway predicts response rate to PD-1/PD-L1 blockade.Biomolecules & biomedicine · 2025Article
- Individualized Neoantigen-Directed Melanoma Therapy.American journal of clinical dermatology · 2025Review
- RNA sequencing enables neoantigen discovery and vaccine validation in breast and lung cancer.Frontiers in immunology · 2025Article
- Enhancing Clinical Applications by Evaluation of Sensitivity and Specificity in Whole Exome Sequencing.International journal of molecular sciences · 2024Article
- Whole exome sequencing identifies risk variants associated with intracranial epidermoid cyst deterioration: A case report.World journal of clinical oncology · 2024Article
- BRCA-mutated breast cancer: the unmet need, challenges and therapeutic benefits of genetic testing.British journal of cancer · 2024Review
- Tumour mutational burden: clinical utility, challenges and emerging improvements.Nature reviews. Clinical oncology · 2024Review
- Current practices and challenges in implementing precision medicine for upper gastrointestinal cancers in European academic centers: an EORTC survey.ESMO gastrointestinal oncology · 2024Article
- [The collaborative project "Personalized medicine for oncology" (PM4Onco) as part of the Medical Informatics Initiative (MII)].Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz · 2024Article
- [Molecular pathological analysis through the ages].Pathologie (Heidelberg, Germany) · 2024Review
Corrections and comments
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Authors and funding
44 authors at 7 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A growing number of druggable targets and national initiatives for precision oncology necessitate broad genomic profiling for many cancer patients. Whole exome sequencing (WES) offers unbiased analysis of the entire coding sequence, segmentation-based detection of copy number alterations (CNAs), and accurate determination of complex biomarkers including tumor mutational burden (TMB), homologous recombination repair deficiency (HRD), and microsatellite instability (MSI). To assess the inter-institution variability of clinical WES, we performed a comparative pilot study between German Centers of Personalized Medicine (ZPMs) from five participating institutions. Tumor and matched normal DNA from 30 patients were analyzed using custom sequencing protocols and bioinformatic pipelines. Calling of somatic variants was highly concordant with a positive percentage agreement (PPA) between 91 and 95% and a positive predictive value (PPV) between 82 and 95% compared with a three-institution consensus and full agreement for 16 of 17 druggable targets. Explanations for deviations included low VAF or coverage, differing annotations, and different filter protocols. CNAs showed overall agreement in 76% for the genomic sequence with high wet-lab variability. Complex biomarkers correlated strongly between institutions (HRD: 0.79-1, TMB: 0.97-0.99) and all institutions agreed on microsatellite instability. This study will contribute to the development of quality control frameworks for comprehensive genomic profiling and sheds light onto parameters that require stringent standardization.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.