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Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction
Published on: August 21, 2016
Single-day HER2neu amplification assessment using chip-based digital PCR in formalin-fixed paraffin-embedded breast
Parth S Shah1,2, Shiva Murarka1, Anupam Joshi3
1Department of Molecular Genetics, Supratech Micropath Laboratory and Research Institute, Ahmedabad, India, shiva.murarka@supratechlabs.com.
Introduction:
Human epidermal growth factor receptor 2 (HER2) amplification is present in almost 15%-20% of breast cancer tumors, making it an important parameter for testing. The present study was designed to evaluate a chip-based digital PCR (dPCR) system for assessing HER2 amplification from formalin-fixed paraffin-embedded breast carcinoma tissue and to compare this system with immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH).
Materials And Methods:
A total of 84 breast carcinoma tissue samples were analyzed by IHC, FISH, and chip-based dPCR in a blinded manner.
Results:
All nine IHC-positive and 35 IHC-negative samples had equivalent results with dPCR, taking an amplification ratio threshold of 1.8 as a positive result. Of the 40 IHC equivocal samples, 10 were assessed as positive, 27 as negative, and three as equivocal by dPCR.
Conclusion:
These results demonstrate that chip-based dPCR is suitable for HER2 amplification detection in formalin-fixed paraffin-embedded samples in a clinical setting, providing the advantages of superior turnaround time, cost-effectiveness, and increased precision with absolute quantification compared with conventional tests such as FISH and IHC. This methodology was especially beneficial in tissue samples with low DNA concentration.
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