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. 2013 Apr 16;20(1):22.
doi: 10.1186/1423-0127-20-22.

Detection of epidermal growth factor receptor mutations in formalin fixed paraffin embedded biopsies in Malaysian non-small cell lung cancer patients

Tiffany Ng Shi Yeen  1 , Rajadurai Pathmanathan, Mohd Sidik Shiran, Fattah Azman Ahmad Zaid, Yoke Kqueen Cheah
Affiliations

Detection of epidermal growth factor receptor mutations in formalin fixed paraffin embedded biopsies in Malaysian non-small cell lung cancer patients

Tiffany Ng Shi Yeen et al. J Biomed Sci. .

Abstract

Background: Somatic mutations of the epidermal growth factor receptor (EGFR) are reportedly associated with various responses in non-small cell lung cancer (NSCLC) patients receiving the anti-EGFR agents. Detection of the mutation therefore plays an important role in therapeutic decision making. The aim of this study was to detect EGFR mutations in formalin fixed paraffin embedded (FFPE) samples using both Scorpion ARMS and high resolution melt (HRM) assay, and to compare the sensitivity of these methods.

Results: All of the mutations were found in adenocarcinoma, except one that was in squamous cell carcinoma. The mutation rate was 45.7% (221/484). Complex mutations were also observed, wherein 8 tumours carried 2 mutations and 1 tumour carried 3 mutations.

Conclusions: Both methods detected EGFR mutations in FFPE samples. HRM assays gave more EGFR positive results compared to Scorpion ARMS.

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Figures

Figure 1
Figure 1
Amplification plots from Scorpion ARMS assay. Panel A: Amplification plots of EGFR positive controls. Panel B: Amplification plot showing the presence of deletions in sample 408. Panel C: Amplification plot showing the presence of L858R mutation in sample 429.
Figure 2
Figure 2
Difference plots of EGFR exons 18–21. Panel A: The difference plot of EGFR exon 18 shows melting profile for four positive samples (S162 in yellow, S455 in pink, S49/12 in green and S87/12 in blue). Panel B: The difference plot of EGFR exon 19 shows melting profiles for seven positive samples (S101 in yellow, S047 in pink, S063 in brown, S552 in green, S065 in blue, S046 in purple and S048 in orange). Panel C: The difference plot of EGFR exon 20 shows melting profile for four positive samples (S13 in yellow, S19 in purple, S28 in green, S68 in pink). Panel D: The difference plot of EGFR exon 21 shows melting profile for seven positive samples (S105/12 in purple, S115/12 in light blue, S210/12 in brown, S211/12 in green, S212/12 in dark blue, S217/12 in orange and S220/12 in pink).
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