ArticleBMC biology2024
Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine.
Article in BMC biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 15 citations in OpenAlex.
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- A HRH1-YAP1 feedback loop drives pancreatic cancer progression and predicts therapeutic response.Oncology letters · 2026Article
- Alternative splicing regulatesiScience · 2026Article
- Multi-Omics Profiling Uncovers Predictive Factors for Tumor-Infiltrating Lymphocyte Therapy in Ovarian Cancer.Journal of clinical laboratory analysis · 2026Article
- Mechanistic insights into the immune biomarker of perioperative immune checkpoint inhibitors for non-small cell lung cancer.Translational lung cancer research · 2025Review
- Utility and real-world clinical outcomes of next-generation sequencing in advanced non-small-cell lung cancer in the South Indian population.The oncologist · 2025Observational
- Comprehensive Evaluation of a 1021-Gene Panel in FFPE and Liquid Biopsy for Analytical and Clinical Use.International journal of molecular sciences · 2025Article
- High Tumor Mutation Burden (TMB) and a Novel Somatic Mutation in the TREX1 Gene in a Patient with Aggressive and Refractory High-Grade B-Cell Lymphoma: A Case Report.International journal of molecular sciences · 2025Article
- Different NGS identification methods of somatic mutation sites in solid tumors impact TMB results.BMC cancer · 2025Article
- SMARCB1-deficient malignant melanocytic uveal tumours: a new neural crest-derived tumour entity with SMARCB1-related germline predisposition.The Journal of pathology · 2025Article
- Identification of prognostic biomarkers for endometrioid endometrial carcinoma based on the miRNA and mRNA co-expression network regulated by estradiol.Clinics (Sao Paulo, Brazil) · 2025Article
- Genetic subtyping by Whole Exome Sequencing across Diffuse Large B Cell Lymphoma and Plasmablastic Lymphoma.PloS one · 2025Article
- The impact of targeted therapies on molecular alterations identified by an institutional molecular tumor board: an approach based on ESCAT classification.ESMO real world data and digital oncology · 2024Article
- Expanding the clinicopathologic spectrum and genomic landscape of tumors with SMARCA2/4::CREM fusions.The Journal of pathology · 2024Article
- Advancing Cancer Care in Colombia: Results of the First In Situ Implementation of Comprehensive Genomic Profiling.Journal of personalized medicine · 2024Article
- Prognostic significance of CNNM4 in ovarian cancer: a comprehensive bioinformatics analysis.Frontiers in oncology · 2024Article
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Authors and funding
30 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh tumor mutational burden (TMB) was reported to predict the efficacy of immune checkpoint inhibitors (ICIs). Pembrolizumab, an anti-PD-1, received FDA-approval for the treatment of unresectable/metastatic tumors with high TMB as determined by the FoundationOne®CDx test. It remains to be determined how TMB can also be calculated using other tests.
resultsFFPE/frozen tumor samples from various origins were sequenced in the frame of the Institut Curie (IC) Molecular Tumor Board using an in-house next-generation sequencing (NGS) panel. A TMB calculation method was developed at IC (IC algorithm) and compared to the FoundationOne® (FO) algorithm. Using IC algorithm, an optimal 10% variant allele frequency (VAF) cut-off was established for TMB evaluation on FFPE samples, compared to 5% on frozen samples. The median TMB score for MSS/POLE WT tumors was 8.8 mut/Mb versus 45 mut/Mb for MSI/POLE-mutated tumors. When focusing on MSS/POLE WT tumor samples, the highest median TMB scores were observed in lymphoma, lung, endometrial, and cervical cancers. After biological manual curation of these cases, 21% of them could be reclassified as MSI/POLE tumors and considered as "true TMB high." Higher TMB values were obtained using FO algorithm on FFPE samples compared to IC algorithm (40 mut/Mb [10-3927] versus 8.2 mut/Mb [2.5-897], p < 0.001).
conclusionsWe herein propose a TMB calculation method and a bioinformatics tool that is customizable to different NGS panels and sample types. We were not able to retrieve TMB values from FO algorithm using our own algorithm and NGS panel.
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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.