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Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing
Published on: October 18, 2013
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Standardization of pleural effusion-based tumor mutation burden (TMB) estimation using capture-based targeted
Yongfeng Yu1, Lan Shen1, Wenxiang Ji1
1Shanghai Lung Cancer Center, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, China.
Annals of Translational Medicine
|February 11, 2021
Summary
Pleural effusion (PE) samples can reliably assess tumor mutation burden (TMB) using targeted sequencing panels, offering a promising alternative to tissue biopsies for predicting response to immune checkpoint inhibitors (ICIs). This study validates PE as a viable medium for TMB evaluation.
Area of Science:
- Oncology
- Genomics
- Biomarker Discovery
Background:
- Tumor mutation burden (TMB) is a key biomarker for predicting response to immune checkpoint inhibitors (ICIs).
- Current TMB assessment relies on tissue biopsies, often using whole-exome sequencing (WES) or targeted sequencing.
- Liquid biopsies are explored as alternatives, but TMB assessment using pleural effusion (PE) has not been reported.
Purpose of the Study:
- To evaluate the performance of targeted sequencing panels for TMB assessment in pleural effusion (PE) specimens.
- To determine if PE can serve as an alternative to traditional tissue biopsies for TMB evaluation.
Main Methods:
- Prospective enrollment of 32 advanced non-small cell lung cancer (NSCLC) patients with PE.
- Analysis of cell-free DNA (cfDNA) from PE supernatant using both WES and commercially available targeted sequencing panels.
Main Results:
- All five targeted sequencing panels showed good correlation with WES-derived TMB (correlation coefficients 0.68-0.81).
- Two- and three-tier classification systems based on PE TMB demonstrated concordance rates of 74% and 63% with WES-based classifications, respectively.
Conclusions:
- Targeted sequencing panels are effective for TMB evaluation using PE samples.
- Pleural effusion (PE) is a viable alternative medium for TMB assessment.
- This study establishes a foundation for standardized TMB protocols using PE.
