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Paired analysis of tumor mutation burden calculated by targeted deep sequencing panel and whole exome sequencing in Non-Small Cell Lung Cancer
Sehhoon Park 1,# (Professor), Chung Lee 2,# (Senior researcher), Bo Mi Ku 3 (Researcher), Minjae Kim 2 (Researcher), Woong-Yang Park 2,4 (CEO), Nayoung K.D. Kim 2 (Director), Myung-Ju Ahn 1,* (Professor)
1Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University of School of Medicine, Seoul 06351, Republic of Korea,
2Geninus Inc., Seoul 05836, Republic of Korea,
3Research Institute for Future Medicine, Samsung Medical Center, Sungkyunkwan University of School of Medicine, Seoul 06351, Republic of Korea,
4Samsung Genome Institute, Samsung Medical Center, Seoul 06351, Republic of Korea
Abstract
Background: With the development of NGS (next generation sequencing), genomic alteration become as essential component of predictive biomarker which impact the treatment decision in many types of cancer. Among the biomarkers, the tumor mutation burden (TMB) identified by NGS is useful in predicting a clinical response of cancer immunotherapy. In this study, we directly compared the lab-developed-test (LDT) target sequencing panel, K-MASTER panel v3.0, with whole-exome sequencing (WES) to evaluate concordance of TMB.
Methods: As an initial step, the reference materials (n=3) using known TMB status were used as an exploratory test. For the validation, the one hundred samples from surgically resected non-small cell lung cancer (NSCLC) were used to evaluate the TMB. The TMB of each sample was tested using both LDT and WES using DNA extracted at the same time. In addition, we evaluate the impact of capture region which might lead to different consequences in TMB based on the size of NGS target sequencing panel.
Results: From the pilot study, TMB was evaluated by LDT and WES using duplicated reference sample which showed high concordance rate (R2 = 0.887). This was also reproduced in clinical sample (n=100) which showed R2 of 0.71. The difference between the coding sequence ratio (3.49%) and the ratio of mutations (4.8%) indicated relatively higher number of mutations identified by LDT panel.
Conclusions: TMB calculation using LDT is feasible which can be useful in clinical practice. Further customized approach of calculation of TMB based on the cancer type or specific clinical setting is warranted.
Abstract, Accepted Manuscript(in press) [Submitted on March 31, 2021, Accepted on June 2, 2021]
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