Journal Article

Tumor mutational burden assessment and standardized bioinformatics approach using custom NGS panels in clinical routine

Gutman, Tom, Trabelsi-Grati, Olfa, Le Tourneau, Christophe, Kamoun, Choumouss, Hescot, Ségolène, Borcoman, Edith, Romejon, Julien, Callens, Céline, Guillou, Isabelle, Neuzillet, Cindy, Masliah-Planchon, Julien, Sablin, Marie-Paule, Cyrta, Joanna, Galut, Michèle, Vibert, Roseline, Girard, Elodie, Wong, Jennifer, Halladjian, Maral, Dupain, Célia, Castel-Ajgal, Zahra, Melaabi, Samia, Bièche, Ivan, Allory, Yves, Antonio, Samantha, Franck, Coralie, Servant, Nicolas, Marret, Grégoire, Stoppa-Lyonnet, Dominique, Frouin, Eleonore, Kamal, Maud

2024

Overview

Background High 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. Results FFPE/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). Conclusions We 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.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Algorithms / Bioinformatics / Biomarkers / Biomedical and Life Sciences / Calculation / Cancer / Care and treatment / Cervical cancer / Comparative analysis / Computational biology / DNA sequencing / Drug approval / Drug therapy / Gene frequency / Gene mutations / Genetic aspects / Immune checkpoint inhibitors / Immunotherapy / Life Sciences / Lymphoma / Lymphomas / Mathematical analysis / Metastases / Metastasis / Methods / Molecular Tumor Board / Monoclonal antibodies / Mutation / Next-generation sequencing / Nucleotide sequencing / Oncology, Experimental / Panels / PD-1 protein / Pembrolizumab / Precision medicine / Prognosis / Research Article / Tumor mutational burden / Tumors