KRAS Mutation Analysis Using Cell-free DNA of Pancreatic Cancer

BACKGROUND/AIM

Detection of pancreatic cancer using small samples of the pancreas obtained by endoscopic ultrasound-guided fine-needle aspiration (EUS-FNA) remains a challenge. The purpose of this study was to investigate whether the detection of KRAS mutations in cell-free DNA (cfDNA) extracted from supernatants of liquid-based fixed cytology (LBC) specimens obtained using EUS-FNA in solid pancreatic cancer can be an auxiliary test for differential diagnosis. The purpose of this study was to investigate whether the detection of KRAS mutations in cell-free DNA (cfDNA) extracted from supernatants of liquid-based fixed cytology (LBC) specimens obtained using EUS-FNA in solid pancreatic cancer can be an auxiliary test for differential diagnosis.

PATIENTS AND METHODS

This was a single-institution cohort study that included 50 patients with pancreatic lesions. cfDNA was isolated from the supernatant of fixed LBC samples, and KRAS mutation status was compared between cfDNA samples and FFPE small fragment tissues.

RESULTS

Of the 50 cfDNA samples, 84% (42/50) were valid. KRAS mutations were detected in 57.1% (24/42) of the 42 valid samples. The sensitivity, specificity, and accuracy of KRAS mutation detection using cfDNA samples in the pancreatic lesions were 63.2% (24/38), 100.0% (4/4), and 66.7% (28/42), respectively. KRAS mutation status between FFPE small tissues and cfDNA samples were comparable.

CONCLUSION

Gene mutation analysis using cfDNA from the supernatant of fixed LBC samples is an effective ancillary diagnostic tool for pancreatic cancer.

Screening system for epidermal growth factor receptor mutation detection in cytology cell-free DNA of cerebrospinal fluid based on assured sample quality

BACKGROUND

The cobas^® epidermal growth factor receptor (EGFR) Mutation Test v2 designed for cell-free DNA (cfDNA) is approved as a companion diagnostic for osimertinib therapy. The aim of this study was to evaluate the concordance of EGFR mutation detection between paired primary or recurrent samples, and cerebrospinal fluid (CSF) cytology samples of lung cancer patients.

METHODS

In total, 26 lung cancer patients with supernatant cytology cfDNA in CSF were analysed for EGFR mutations using the cobas^® EGFR Mutation Test v2.0 designed for cfDNA, and the concordance rates between CSF cfDNA and primary or recurrent samples were investigated.

RESULTS

Of the 26 CSF cytology cfDNA samples, 46.1% (12/26) were valid and 53.9% (14/26) were invalid. Sensitivity, specificity and accuracy between the valid CSF cfDNA samples and primary or recurrent samples for detection of EGFR mutation, including T790M were 87.5%, 100.0% and 91.7%, respectively. Amounts of both inflammatory cells and tumour cells in CSF cytology were higher in the valid evaluation samples than in the invalid samples (P < .05), and mutant EGFR was detected in 80.0% (4/5) of the valid CSF cytology cfDNA samples with a negative cytology diagnosis.

CONCLUSIONS

The cobas^® EGFR Mutation Test v2.0 can accurately detect EGFR mutations, including T790M, from supernatant cfDNA of CSF cytology samples. Utilisation of supernatant cytology cfDNA in CSF will allow us to perform both EGFR mutation analysis and cytopathological diagnosis at the same time. This represents a new role of cytology in patient treatment, based on assured sample quality.

Epidermal growth factor receptor mutation status in cell-free DNA supernatant of bronchial washings and brushings

BACKGROUND

The aim of the current study was to examine whether it would be possible to detect epidermal growth factor receptor (EGFR) mutations in cytology cell-free DNA (ccfDNA) from the supernatant fluids of bronchial cytology samples.

METHODS

This study investigated cell damage via immunostaining with a cleaved caspase 3 antibody and the quantity of cell-free DNA in supernatant fluid from 2 cancer cell lines, and the EGFR mutation status was evaluated via polymerase chain reaction (PCR) analysis. EGFR mutations were also evaluated via PCR analysis in 74 clinical samples of ccfDNA from bronchial washing samples with physiological saline or from bronchial brushing liquid-based cytology samples with CytoRich Red.

RESULTS

The quantity and fragmentation of cell-free DNA in the supernatant fluid and the cell damage and cleaved caspase 3 expression in the sediment gradually increased in a time-dependent manner in the cell lines. In the 74 clinical samples, the quantity of ccfDNA extracted from the supernatant was adequate to perform the PCR assay, whereas the quality of ccfDNA in physiological saline was often decreased. The detection of EGFR mutations with ccfDNA showed a sensitivity of 88.0%, a specificity of 100%, a positive predictive value of 100%, a negative predictive value of 89.7%, and an accuracy of 94.1% in samples with malignant or atypical cells.

CONCLUSIONS

These results suggest that activating EGFR mutations can be detected with ccfDNA extracted from the supernatant fluid of liquid-based samples via a PCR assay. This could be a rapid and sensitive method for achieving a parallel diagnosis by both morphology and DNA analysis in non-small cell lung cancer patients.