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

Bioinformatics. 2022 Mar 4;38(6):1724-1726. 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