alexa Molecular Classification of Breast Cancer Patients Using Formalin-fixed Paraffin-embedded Derived RNA Samples

Journal of Molecular Biomarkers & Diagnosis
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Research Article

Molecular Classification of Breast Cancer Patients Using Formalin-fixed Paraffin-embedded Derived RNA Samples

Godfrey Grech1*, Shawn Baldacchino1, Christian Saliba2, Keith Sacco1, Brendan Yee3 and Christian Scerri4,5

1Department of Pathology, Medical School, University of Malta, Malta

2Centre for Molecular Medicine and Biobanking, University of Malta, Malta

3Affymetrix Inc, Santa Clara, CA

4Department of Physiology and Biochemistry, University of Malta, Malta

5Molecular Genetics Clinic, Mater Dei Hospital, Malta

*Corresponding Author:
Godfrey Grech
Department of Pathology
Medical School, University of Malta
Msida, MSD2090 Malta
Tel: 00356 23403047

Received date: January 12, 2015; Accepted date: January 28, 2016; Published date: January 30, 2016

Citation Grech G, Baldacchino S, Saliba C, Sacco K, Yee B, et al. (2016) Molecular Classification of Breast Cancer Patients Using Formalin-fixed Paraffin-embedded Derived RNA Samples. J Mol Biomarkers Diagn S8:016. doi:10.4172/2155-9929.S8-016

Copyright: © 2016 Grech G, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited



The use of archival formalin-fixed paraffin-embedded (FFPE) material to analyse gene expression is limited by the low quality of extracted RNA. In this paper, we utilised an RNA based assay to quantify expression of luminal and basal markers, together with ERBB2 probes, in FFPE archival tissue from 2009 to 2010, all of which had clinical and therapeutic information of more than 5 years. Receptor status of the patients was characterised using the QuantiGene® Plex assay with 100% concordance to immunohistochemical (IHC) and fluorescence in situ hybridisation (FISH) results. A panel of molecular markers known to classify luminal and basal tumours were used and correlated with receptor status of the tumours. As expected, the triple negative breast cancer (TNBC) samples were classified as basal and oestrogen receptor (ER) positive cases as luminal. In summary, the QuantiGene® Plex technology provides a platform to quantitate novel panels of biomarkers on archival material. Moreover, multiplex analysis allows the use of minimal amounts of material providing an opportunity to utilise laser micro-dissected material. FFPE tissue samples are an invaluable resource for retrospective studies to interrogate current novel biomarkers, particularly to generate disease free survival and overall survival graphs to measure predictive value using well annotated retrospective samples with full clinical and pharmacological outcomes.


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