Comparison of two methods to extract DNA from formalin-fixed, paraffin-embedded tissues and their impact on EGFR mutation detection in non-small cell lung carcinoma.
OBJECTIVE
Molecular pathology tests are often carried for clinicopathological diagnosis and pathologists have established large collections of formalin-fixed, paraffin-embedded tissue (FFPE) banks. However, extraction of DNA from FFPE is a laborious and challenging for researchers in clinical laboratories. The aim of this study was to compare two widely used DNA extraction methods: using a QIAamp DNA FFPE kit from Qiagen and a Cobas Sample Preparation Kit from Roche, and evaluated the effect of the DNA quality on molecular diagnostics.


METHODS
DNA from FFPE non-small cell lung carcinoma tissues including biopsy and surgical specimens was extracted with both QIAamp DNA FFPE and Cobas Sample Preparation Kits and EGFR mutations of non-small cell lung carcinomas were detected by real-time quantitative PCR using the extracted DNA.


CONCLUSIONS
Our results showed that DNA extracted by QIAamp and Cobas methods were both suitable to detect downstream EGFR mutation in surgical specimens. Howover, Cobas method could yield more DNA from biopsy specimens, and gain much better EGFR mutation results.
Department of Pathology, The First College of Clinical Medical Sciences, China Three Gorges University, Yichang, China E-mail : hl-chen@whu.edu.cn.
Yu-Chang
YC
Hu
Qian
Q
Zhang
Yan-Hua
YH
Huang
Yu-Fei
YF
Liu
Hong-Lei
HL
Chen
D000230:Adenocarcinoma / Q000235:genetics*; D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D002294:Carcinoma, Squamous Cell / Q000235:genetics*; D004247:DNA / Q000235:genetics / Q000302:isolation & purification*; D066246:ErbB Receptors / Q000235:genetics*; D005557:Formaldehyde; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D009154:Mutation / Q000235:genetics*; D016612:Paraffin Embedding; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods
D005557:Formaldehyde; D004247:DNA; C512478:EGFR protein, human; D066246:ErbB Receptors