Implementing tumor mutational burden (TMB) analysis in routine diagnostics-a primer for molecular pathologists and clinicians - PubMed (original) (raw)

Review

doi: 10.21037/tlcr.2018.08.14.

Jan Budczies 1 2, Petros Christopoulos 3 4, Volker Endris 1, Amelie Lier 1, Eugen Rempel 1, Anna-Lena Volckmar 1, Martina Kirchner 1, Moritz von Winterfeld 1, Jonas Leichsenring 1, Olaf Neumann 1, Stefan Fröhling 5 6, Roland Penzel 1, Michael Thomas 3 4, Peter Schirmacher 1 2, Albrecht Stenzinger 1 2

Affiliations

Review

Implementing tumor mutational burden (TMB) analysis in routine diagnostics-a primer for molecular pathologists and clinicians

Michael Allgäuer et al. Transl Lung Cancer Res. 2018 Dec.

Abstract

Tumor mutational burden (TMB) is a new biomarker for prediction of response to PD-(L)1 treatment. Comprehensive sequencing approaches (i.e., whole exome and whole genome sequencing) are ideally suited to measure TMB directly. However, as their applicability in routine diagnostics is currently limited by high costs, long turnaround times and poor availability of fresh tissue, targeted next-generation sequencing (NGS) of formalin-fixed and paraffin-embedded (FFPE) samples appears to be a more feasible and straight-forward approach for TMB approximation, which can be seamlessly integrated in already existing diagnostic workflows and pipelines. In this work, we provide an overview of the clinical implications of TMB testing and highlight key parameters including pre-analysis, analysis and post-analytical steps that influence and shape TMB approximation by panel sequencing. Collectively, the data will not only serve as a field guide and state of the art knowledge source for molecular pathologists who consider implementation of TMB measurement in their lab, but also enable clinicians in understanding the specific parameters influencing TMB test results and reporting.

Keywords: Tumor mutational burden (TMB); mutational load; next-generation sequencing (NGS); panel; sequencing.

PubMed Disclaimer

Conflict of interest statement

Conflicts of Interest: V Endris: advisory board and lecture fees from AstraZeneca and ThermoFisher. J Leichsenring: consultancy contract with AstraZeneca. S Fröhling: speaker’s honoraria from Amgen, Lilly, PharmaMar and Roche; research funding from AstraZeneca, Pfizer and PharmaMar. M Thomas: advisory board honoraria from Novartis, Lilly, BMS, MSD, Roche, Celgene, Takeda, AbbVie, Boehringer, speaker’s honoraria from Lilly, MSD, Takeda, research funding from AstraZeneca, BMS, Celgene, Novartis, Roche and travel grants from BMS, MSD, Novartis, Boehringer. P Schirmacher: advisory board honoraria from Pfizer, Roche, Novartis, AstraZeneca as well as speaker’s honoraria and research funding from Roche, AstraZeneca and Novartis. A Stenzinger: advisory board honoraria from BMS, AstraZeneca, Novartis, ThermoFisher, speaker’s honoraria from BMS, Illumina, AstraZeneca, MSD, Novartis, Roche, ThermoFisher, and research funding from Chugai. The other authors have no conflicts of interest to declare.

Figures

Figure 1

Figure 1

One-stop shop approach to maximize specimen yield. Necessary molecular testing should best be indicated by the clinician or anticipated when the specimen is initially processed in the pathology laboratory. A sufficient number of slides should be precut to avoid re-cutting of the tissue block. Depicted are three groups of diagnostic tests that are often performed sequentially. # slides: approximated number of slides needed. In routine pathology, material usage is determined by the utilization of IHC stains. In molecular pathology, the number of slides/paraffin sections needed depends on the amount of tumor present and assays used.

Figure 2

Figure 2

Panel design influences TMB measurement. Amplicons (i.e., sequenced regions of exome) of arbitrary sequencing panels (Panels I–IV) are schematically depicted to illustrate differences in size and composition. Panel I is a small focused panel which might be used for entity specific investigations or when DNA is limited, like in liquid biopsies. Panel II and III are more comprehensive targeting additional exonic regions. Panel IV is a comprehensive tumor profiling panel developed for TMB detection. Indicated on exome are exemplified clonal (green), subclonal (red), and frameshift (orange) mutations, and indels (blue). TMB, tumor mutational burden.

Figure 3

Figure 3

Precision of TMB estimation using targeted sequencing panels of size 0.1 to 10 Mbp. An upper limit for the precision of TMB estimates is set by the combinatorial error that comes from estimating the mutation rate (in mut/Mbp) by the number of mutations in a sequence of a limited length. In the display, the precision of TMB estimation (reported as 95% confidence interval) is illustrated for a tumor with high TMB (20 mut/Mbp, typically classified as immune therapy responder) and a tumor with low TMB (5 mut/Mbp, typically classified as immune therapy non-responder). Sequencing panels larger than 1 Mbp are required to separate the tumors in the example with high precision. TMB, tumor mutational burden.

Similar articles

Cited by

References

    1. Topalian SL, Taube JM, Anders RA, et al. Mechanism-driven biomarkers to guide immune checkpoint blockade in cancer therapy. Nat Rev Cancer 2016;16:275-87. 10.1038/nrc.2016.36 - DOI - PMC - PubMed
    1. Goodman AM, Kato S, Bazhenova L, et al. Tumor Mutational Burden as an Independent Predictor of Response to Immunotherapy in Diverse Cancers. Mol Cancer Ther 2017;16:2598-608. 10.1158/1535-7163.MCT-17-0386 - DOI - PMC - PubMed
    1. Yarchoan M, Hopkins A, Jaffee EM. Tumor Mutational Burden and Response Rate to PD-1 Inhibition. N Engl J Med 2017;377:2500-1. 10.1056/NEJMc1713444 - DOI - PMC - PubMed
    1. Snyder A, Makarov V, Merghoub T, et al. Genetic basis for clinical response to CTLA-4 blockade in melanoma. N Engl J Med 2014;371:2189-99. 10.1056/NEJMoa1406498 - DOI - PMC - PubMed
    1. Van Allen EM, Miao D, Schilling B, et al. Genomic correlates of response to CTLA-4 blockade in metastatic melanoma. Science 2015;350:207-11. 10.1126/science.aad0095 - DOI - PMC - PubMed

Publication types

LinkOut - more resources