TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power

Laura Fancello; Alessandro Guida; Gianmaria Frige; Arnaud Gerard Michel Ceol; Gabriele Babini; Giovanni Luca Scaglione; Mario Zanfardino; Tommaso Mazza; Lorenzo Ferrando; Pier Giuseppe Pelicci; Luca Mazzarella

doi:10.1093/bioinformatics/btab836

TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power

Bioinformatics. 2022 Mar 4;38(6):1724-1726. doi: 10.1093/bioinformatics/btab836.

Authors

Affiliations

¹ Unité Biosanté, Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Grenoble, France.
² Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy.
³ Biomedical Translational Imaging Centre, IWK Health Center, Halifax, NS, Canada.
⁴ Department of Diagnostic Radiology, Dalhousie University, Halifax, NS, Canada.
⁵ Department of Woman and Child Health and Public Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy.
⁶ Laboratory of Molecular Oncology, IDI-IRCCS, Rome, Italy.
⁷ Laboratory of Bioinformatics and Statistics, IRCCS SDN, Naples, Italy.
⁸ Laboratory of Bioinformatics, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, FG, Italy.
⁹ Dipartimento di Medicina Interna, Università Degli Studi di Genova, Genova, Italy.
¹⁰ Department of Oncology and Hemato-Oncology, University of Milan, 20142 Milan, Italy.
¹¹ Division of Early Drug Development, IEO, European Institute of Oncology IRCCS, Milan, Italy.

PMID: 34927668
DOI: 10.1093/bioinformatics/btab836

Abstract

Motivation: Tumor mutational burden (TMB) has been proposed as a predictive biomarker for immunotherapy response in cancer patients, as it is thought to enrich for tumors with high neoantigen load. TMB assessed by whole-exome sequencing is considered the gold standard but remains confined to research settings. In the clinical setting, targeted gene panels sampling various genomic sizes along with diverse strategies to estimate TMB were proposed and no real standard has emerged yet.

Results: We provide the community with TMBleR, a tool to measure the clinical impact of various strategies of panel-based TMB measurement.

Availability and implementation: R package and docker container (GPL-3 Open Source license): https://acc-bioinfo.github.io/TMBleR/. Graphical-user interface website: https://bioserver.ieo.it/shiny/app/tmbler.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Biomarkers, Tumor / genetics
Computational Biology
Humans
Immunotherapy
Mutation
Neoplasms* / pathology

Substances

Biomarkers, Tumor

Abstract

Publication types

MeSH terms

Substances

Grants and funding