Abstract
Background
The increase in genetic alterations targeted by specific chemotherapy in lung cancer has led to the need for universal use of more comprehensive genetic testing, which has highlighted the development of a lung cancer diagnostic panel using next-generation sequencing.
Objective
We developed a hybridization capture-based massively parallel sequencing assay named Friendly, Integrated, Research-based, Smart and Trustworthy (FIRST)-lung cancer panel (LCP), and evaluated its performance.
Methods
FIRST-LCP comprises 64 lung cancer-related genes to test for various kinds of genetic alterations including single nucleotide variations (SNVs), insertions and deletions (indels), copy number variations (CNVs), and structural variations. To assess the performance of FIRST-LCP, we compiled test sets using HapMap samples or tumor cell lines with disclosed genetic information, and also tested our clinical lung cancer samples whose genetic alterations were known by conventional methods.
Results
FIRST-LCP accomplished high sensitivity (99.4%) and specificity (100%) of the detection of SNVs. High precision was also achieved, with intra- or inter-run concordance rate of 0.99, respectively. FIRST-LCP detected indels and CNVs close to the expected allele frequency and magnitude, respectively. Tests with samples from lung cancer patients also identified all SNVs, indels and fusions.
Conclusion
Based on the current state of the art, continuous application of the panel design and analysis pipeline following up-to-date knowledge could ensure precision medicine for lung cancer patients.
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Funding
This research was supported by grants from the Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health and Welfare, Republic of Korea (Grant numbers HI14C1277 and HI13C2148).
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Conflict of interest
Nak-Jung Kwon is an employee of Macrogen Inc. Sun-Wha Im, Jeesoo Chae, Se Song Jang, Jaeyong Choi, Jihui Yun, Soojin Cha, Yoon Kyung Jeon, Yoohwa Hwang, Miso Kim, Tae Min Kim, Dong-Wan Kim, Jong-Il Kim and Young Tae Kim declare that they have no conflict of interest.
Ethical approval
This study had been approved by the Seoul National University Hospital (No. 1012-130-346 and 1105-075-362). Informed consent was obtained from all individual participants included in the study.
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Im, SW., Chae, J., Jang, S.S. et al. A newly developed capture-based sequencing panel for genomic assay of lung cancer. Genes Genom 42, 751–759 (2020). https://doi.org/10.1007/s13258-020-00949-1
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DOI: https://doi.org/10.1007/s13258-020-00949-1