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Published on: April 11, 2016
Enhancing the quality of panel-based tumor mutation burden assessment: a comprehensive study of real-world and
Yuanfeng Zhang1,2,3, Duo Wang1,2,3, Zihong Zhao1,3,4
1National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, PR China.
Abstract:
Targeted panel-based tumor mutation burden (TMB) assays are widely employed to guide immunotherapy for patients with solid tumors. However, the accuracy and consistency of this method can be compromised due to the variability in technical details across different laboratories, particularly in terms of panel size, somatic mutation detection and TMB calculation rules. Currently, systematic evaluations of the impact of these technical factors on existing assays and best practice recommendations remain lacking. We assessed the performance of 50 participating panel-based TMB assays involving 38 unique methods using cell line samples. In silico experiments utilizing TCGA MC3 datasets were performed to further dissect the impact of technical factors. Here we show that the panel sizes beyond 1.04 Mb and 389 genes are necessary for the basic discrete accuracy, as determined by over 40,000 synthetic panels. The somatic mutation detection should maintain a reciprocal gap of recall and precision less than 0.179 for reliable psTMB calculation results. The inclusion of synonymous, nonsense and hotspot mutations could enhance the accuracy of panel-based TMB assay. A 5% variant allele frequency cut-off is suitable for TMB assays using tumor samples with at least 20% tumor purity. In conclusion, this multicenter study elucidates the major technical factors as sources of variability in panel-based TMB assays and proposed comprehensive recommendations for the enhancement of accuracy and consistency. These findings will assist clinical laboratories in optimizing the methodological details through bioinformatic experiments to enhance the reliability of panel-based methods.
Insights
Standardizing tumor mutation burden (TMB) assays is crucial for immunotherapy. This study identifies key technical factors and provides recommendations to improve the accuracy and consistency of panel-based TMB testing.
Area of Science:
- Oncology
- Genomics
- Bioinformatics
Background:
- Targeted panel-based tumor mutation burden (TMB) assays are essential for guiding cancer immunotherapy.
- Variability in technical aspects like panel size and mutation detection impacts assay accuracy and consistency.
- Lack of systematic evaluations and best practice recommendations hinders reliable TMB assessment.
Purpose of the Study:
- To systematically evaluate the impact of technical factors on panel-based TMB assays.
- To propose recommendations for enhancing the accuracy and consistency of TMB testing.
- To address the variability in TMB assay methodologies across laboratories.
Main Methods:
- Performance assessment of 50 panel-based TMB assays using cell line samples.
- In silico experiments with TCGA MC3 datasets to analyze technical factor impacts.
- Evaluation of panel size, mutation detection parameters, and variant allele frequency cut-offs.
Main Results:
- Panel sizes exceeding 1.04 Mb and 389 genes are required for basic accuracy.
- Somatic mutation detection needs a recall-precision gap below 0.179 for reliable psTMB calculation.
- Including synonymous, nonsense, and hotspot mutations, along with a 5% VAF cutoff for samples with ≥20% purity, enhances accuracy.
Conclusions:
- Identified major technical factors causing variability in panel-based TMB assays.
- Proposed comprehensive recommendations to improve TMB assay accuracy and consistency.
- Findings support clinical laboratories in optimizing bioinformatic and methodological details for reliable TMB testing.
