Cancer Res Treat.  2015 Oct;47(4):661-669. 10.4143/crt.2014.282.

Peptide Nucleic Acid Clamping Versus Direct Sequencing for the Detection of EGFR Gene Mutation in Patients with Non-small Cell Lung Cancer

• Yoon SH
• Choi YD
• Oh IJ
• Kim KS
• Choi H
• Chang J
• Shin HJ
• Park CK
• Kim YC

• KMID: 2403384
• DOI: http://doi.org/10.4143/crt.2014.282

Abstract

PURPOSE
Direct sequencing (DS) is the standard method for detection of epidermal growth factor receptor (EGFR) gene mutation in non-small cell lung cancer (NSCLC); however, low detection sensitivity is a problem. The aim of this study is to demonstrate higher detection rate of EGFR gene mutation with peptide nucleic acid (PNA) clamping compared with DS.
MATERIALS AND METHODS
This is a single arm, prospective study for patients with stage IIIB/IV or relapsed NSCLC. Using tumor DNA from 138 patients, both DS and PNA clamping for EGFR gene in exon 18, 19, 20, and 21 were performed. Discrepant results between the two methods were verified using Cobas and a mutant enrichment based next generation sequencing (NGS). Patients with activating mutations were treated with EGFR tyrosine kinase inhibitor (EGFR-TKI, gefitinib, or erlotinib) as first line treatment.
RESULTS
Of 138 paired test sets, 24 (17.4%) and 45 (32.6%) cases with activating mutations were detected by DS and PNA clamping, respectively. The difference of detection rate between the two methods was 15.2% (95% confidence interval, 8.7% to 17.8%; p < 0.001). Between the two methods, 25 cases showed discrepant results (n=23, PNA+/DS-; n=2, PNA-/DS+). Mutations were confirmed by Cobas or NGS in 22 of 23 PNA+/DS- cases. The response rates to EGFR-TKI were 72.2% in the PNA+/DS+ group and 85.0% in the PNA+/DS- group.
CONCLUSION
PNA clamping showed a significantly higher detection rate of EGFR gene mutation compared with DS. Higher sensitivity of PNA clamping was not compromised by the loss of predictive power of response to EGFR-TKI.

Keyword

Genes; erbB-1; Mutation; Peptide nucleic acids

MeSH Terms

Arm
Carcinoma, Non-Small-Cell Lung*
Constriction*
DNA
Exons
Genes, erbB-1*
Humans
Peptide Nucleic Acids
Prospective Studies
Protein-Tyrosine Kinases
Receptor, Epidermal Growth Factor
DNA
Peptide Nucleic Acids
Protein-Tyrosine Kinases
Receptor, Epidermal Growth Factor

Figure

• 

  Fig. 1. CONSORT diagram. NSCLC, non-small cell lung cancer; DS, direct sequencing; PNA, peptide nucleic acid clamping; NGS, next generation sequencing; EGFR-TKI, epidermal growth factor receptor–tyrosine kinase inhibitor.

Reference

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