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Updated: Mar 5, 2026
Author Spotlight: Advancements in Molecular Biomarker Testing for Non-Squamous Non-Small Cell Lung Cancer
Published on: September 8, 2023
Routine genetic testing of lung cancer specimens derived from surgery, bronchoscopy and fluid aspiration by next
Gou Yamamoto1, Mari Kikuchi1, Shiho Kobayashi1
1Department of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Ina, Kitaadachi, Saitama 362-0806, Japan.
Abstract:
After the development of EGFR tyrosine kinase inhibitors (TKIs), genetic testing of EGFR became required for effective treatment of lung cancer. Initially, the testing was conducted separately for each mutated region. However, many EGFR mutations have since been identified that determine the efficacy of EGFR-TKIs. Therefore, genetic testing of EGFR by next generation sequencing (NGS) may be a suitable strategy for lung cancer. Here we examined the applicability of the NGS method in regard to sensitivity, time and cost. A total of 939 specimens were obtained from 686 lung cancer patients at our hospital. DNA and RNA were simultaneously extracted from specimens derived from surgery, bronchoscopy, and fluid aspiration. Specimens included cerebrospinal fluid, pleural effusion, abdominal fluid, and pericardial effusion. From RNA, target regions (EGFR, KRAS, ALK fusion and RET fusion) were enriched by RT-PCR and sequenced with MiSeq. From DNA, PCR or PCR-RFLP conventional methods were performed. NGS and conventional methods were carried out routinely per week. Among the total 939 specimens, 38 specimens could not be examined with NGS. Among these, 34 specimens were analyzed by conventional testing with simultaneously extracted DNA. The remaining four specimens could not be tested with either method. Compared with the conventional method, the concordance rate of mutations was 99% (892/901), excluding specimens with NGS failure. The time period required from processing of specimens to results was 4 days, and the cost per sample was sufficiently low. In conclusion, the genetic testing with NGS method was useful for lung cancer treatment. The cost, sensitivity and time were able to tolerate routine examinations.
Insights
Next-generation sequencing (NGS) is a sensitive, cost-effective, and timely method for genetic testing in lung cancer patients, aiding effective treatment decisions. This approach offers high concordance with conventional methods for identifying EGFR mutations.
Area of Science:
- Oncology
- Genetics
- Molecular Diagnostics
Background:
- EGFR tyrosine kinase inhibitors (TKIs) require EGFR genetic testing for effective lung cancer treatment.
- Traditional genetic testing methods analyze specific mutated regions separately.
- The identification of numerous EGFR mutations necessitates comprehensive genetic analysis.
Purpose of the Study:
- To evaluate the applicability of next-generation sequencing (NGS) for lung cancer genetic testing.
- To assess NGS sensitivity, turnaround time, and cost-effectiveness.
- To compare NGS performance against conventional genetic testing methods.
Main Methods:
- Simultaneous DNA and RNA extraction from 939 lung cancer specimens (surgery, bronchoscopy, fluid aspiration).
- Targeted enrichment (RT-PCR) and sequencing (MiSeq) of EGFR, KRAS, ALK, and RET fusion regions from RNA.
- Conventional PCR or PCR-RFLP methods used for DNA analysis.
- Routine weekly comparison of NGS and conventional methods.
Main Results:
- NGS successfully analyzed 901 out of 939 specimens, with 34 analyzed by conventional methods.
- A high concordance rate of 99% was observed between NGS and conventional methods for mutation detection.
- Turnaround time for NGS was 4 days, with a sufficiently low cost per sample.
- NGS demonstrated high sensitivity, acceptable turnaround time, and cost-effectiveness for routine use.
Conclusions:
- NGS is a valuable tool for genetic testing in lung cancer, supporting personalized treatment strategies.
- The NGS method is suitable for routine clinical application due to its efficiency and accuracy.
- NGS provides a comprehensive genetic profile, improving the management of lung cancer patients.
