Reliability of panel-based mutational signatures for immune-checkpoint-inhibition efficacy prediction in non-small cell lung cancer.

Objectives: Mutational signatures (MS) are gaining traction for deriving therapeutic insights for immune checkpoint inhibition (ICI). We asked if MS attributions from comprehensive targeted sequencing assays are reliable enough for predicting ICI efficacy in non-small cell lung cancer (NSCLC).
Methods: Somatic mutations of m = 126 patients were assayed using panel-based sequencing of 523 cancer-related genes. In silico simulations of MS attributions for various panels were performed on a separate dataset of m = 101 whole genome sequenced patients. Non-synonymous mutations were deconvoluted using COSMIC v3.3 signatures and used to test a previously published machine learning classifier.
Results: The ICI efficacy predictor performed poorly with an accuracy of 0.51 _-0.09 ^+0.09 , average precision of 0.52 _-0.11 ^+0.11 , and an area under the receiver operating characteristic curve of 0.50 _-0.09 ^+0.10 . Theoretical arguments, experimental data, and in silico simulations pointed to false negative rates (FNR) related to panel size. A secondary effect was observed, where deconvolution of small ensembles of point mutations lead to reconstruction errors and misattributions.
Conclusion: MS attributions from current targeted panel sequencing are not reliable enough to predict ICI efficacy. We suggest that, for downstream classification tasks in NSCLC, signature attributions be based on whole exome or genome sequencing instead.
Competing Interests: Declaration of Competing Interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: HCD: None to declare; KC: None to declare; GF: None to declare; HJMG: Consulting or Advisory Role: Novartis, Lilly. TJNH: Advisory/consultancy fees from AstraZeneca, Bristol-Myers-Squibb, Illumina, Merck Sharp Dohme, Roche, and research grants/funding from AstraZeneca, Hoffmann-La Roche. BM: None to declare; ES: Honoraria/speakers fee: Bio-Rad, Roche, Agena Bioscience, Illumina, Lilly; Consulting or Advisory Role: MSD/Merck, Astellas, Bayer, BMS, Agena Bioscience, Janssen Cilag (Johnson & Johnson), Novartis, Roche, AstraZeneca, Amgen, Lilly; Research Funding: Biocartis, Bio-Rad, Roche, Agena Bioscience, AstraZeneca, InVitae/Archer (all paid to UMCG); Travel, Accommodations, Expenses: Roche Molecular Diagnostics, Bio-Rad. PJV: None to declare; GAL: Research grant from Boehringer-Ingelheim. Owns shares in Genomics PLC.; BvE: None to declare.
(Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)