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Updated: May 12, 2025
Next Generation Sequencing for the Detection of Actionable Mutations in Solid and Liquid Tumors
Published on: September 20, 2016
Clinical Sequence Revealed the Prevalence and Biological Significance of Somatic Pathogenic Variants in Thoracic
Takahiro Fukushima1, Kohei Nakamura2, Hideki Terai3
1Division of Pulmonary Medicine, Department of Medicine, Keio University, School of Medicine, Tokyo, Japan.
Purpose:
Presumed germline pathogenic variants (PGPVs) are occasionally detected in thoracic cancer and their frequency and functional significance remain underexplored. We investigated the prevalence and biological significance of PGPVs identified in comprehensive genomic profiling (CGP) panels in patients with thoracic cancer.
Patients And Methods:
Between January 2021 and August 2023, 204 patients with thoracic cancer were included in this study. A somatic cancer genomic profile system-FoundationOne CDx or an in-house system (Rapid-Neo)-was used for next-generation sequencing-based cancer gene panel tests. Potential PGPVs were identified by evaluating the variant allele frequency (VAF; cutoff > 10%) and pathogenicity based on ClinVar.
Results:
PGPVs were detected at a frequency of 9.7% from cohort 1 and 8.1% from cohort 2 in thoracic cancer, based on real-world comprehensive genomic profiling panel testing. Copy number plot did not indicate any homologous recombination deficiency patterns in cases with BRCA1, BRCA2, and RAD51D pathogenic variants in thoracic cancer compared with those in hereditary breast and ovarian cancers. Only one hit of MSH6 pathogenic germline variant was observed for lung cancer tissue in the case of Lynch syndrome; therefore, high tumor mutational burden/microsatellite instability or mismatch repair deficiency was not observed, unlike that in endometrial cancer tissue in the same individual.
Conclusion:
This study underscores the importance of identifying PGPVs through CGP testing conducted in patients with thoracic cancer. Using frequency and functional analysis. Further investigation is warranted regarding the clinical significance of these PGPVs in managing patients with thoracic cancer and their families.
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