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. 2022 Aug 3;14(15):3784.
doi: 10.3390/cancers14153784.

A Prospective Validation Study of Lung Cancer Gene Panel Testing Using Cytological Specimens

Kei Morikawa  1 , Hirotaka Kida  1 , Hiroshi Handa  1 , Takeo Inoue  1 , Hisashi Saji  2 , Junki Koike  3 , Seiji Nakamura  4 , Yoshiharu Sato  4 , Yumi Ueda  4 , Fumihiko Suzuki  4 , Ryo Matoba  4 , Masamichi Mineshita  1
Affiliations

A Prospective Validation Study of Lung Cancer Gene Panel Testing Using Cytological Specimens

Kei Morikawa et al. Cancers (Basel). .

Abstract

Background: Genetic panel tests require sufficient tissue samples, and therefore, cannot always be performed. Although collecting cytological specimens is easier than tissue collection, there are no validation studies on the diagnostic accuracy of lung cancer gene panel tests using cytology samples. Methods: Using an amplicon-based high-sensitivity next-generation sequencing panel test capable of measuring eight druggable genes, we prospectively enrolled consecutive patients who underwent diagnostic procedures. We evaluated the analysis accuracy rate, nucleic acid yield, and the quality of cytological specimens under brushing, needle aspiration, and pleural effusion. We then compared these specimens with collected tissue samples. Results: In 163 prospectively enrolled cases, nucleic acid extraction and analysis accuracy was 100% in cases diagnosed with adenocarcinoma. Gene mutations were found in 68.7% of cases with 99.5% (95% CI: 98.2-99.9) concordance to companion diagnostics. The median DNA/RNA yield and DNA/RNA integrity number were 475/321 ng and 7.9/5.7, respectively. The correlation coefficient of the gene allele ratio in 64 cases compared with tissue samples was 0.711. Conclusion: The success of gene analysis using cytological specimens was high, and the yield and quality of the extracted nucleic acid were sufficient for panel analysis. Moreover, the allele frequency of gene mutations in cytological specimens showed high correlations with tissue specimens.

Keywords: cytology specimens; gene panel analysis; lung cancer compact panel (LCCP); non-small cell carcinoma (NSCLC); variant allele frequency (VAF).

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Conflict of interest statement

Dr Morikawa received lecture fees from the DNA Chip Research Institute.

Figures

Figure 1
Figure 1
Cytological specimen collection using a GM tube. ROSE: Rapid on-site cytologic evaluation.
Figure 2
Figure 2
Flow diagram of sample selection. FFPE: Formalin-fixed paraffin-embedded, LCCP: Lung cancer compact panel.
Figure 3
Figure 3
DNR/RNA yield from 163 cytology samples.
Figure 4
Figure 4
DIN/RIN values for purified nucleotides from cytology samples. EBUS-TBB: Endobronchial ultrasonography-guided transbronchial brushing. EBUS-TBNA: Endobronchial ultrasonography-guided transbronchial needle aspiration. EUS-FNA: Endoscopic ultrasound-guided fine needle aspiration. CT: Computed tomography. US: ultrasound. EBUS-TBB: Endobronchial ultrasonography-guided transbronchial brushing. EBUS-TBNA: Endobronchial ultrasonography-guided transbronchial needle aspiration. EUS-FNA: Endoscopic ultrasound-guided fine needle aspiration. CT: Computed tomography. US: Ultrasound.
Figure 5
Figure 5
Correlation of estimated %VAF between FFPE tissue sample and cytology sample. VAF: Variant allele frequency. FFPE: Formalin-fixed paraffin-embedded.
Figure 6
Figure 6
Pie chart of mutation call variants detected by LCCP assay of cytology samples. LCCP: Lung cancer compact panel.
See this image and copyright information in PMC

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