Aims To determine whether 0.6 mm cores of formalin-fixed paraffin-embedded (FFPE) tissue, as commonly used to construct immunohistochemical tissue microarrays, may be a valid alternative to tissue sections as source material for quantitative real-time PCR-based transcriptional profiling of breast cancer.
Methods Four matched 0.6 mm cores of invasive breast tumour and two 10 μm whole sections were taken from eight FFPE blocks. RNA was extracted and reverse transcribed, and TaqMan® assays were performed on the 21 genes of the Oncotype DX® Breast Cancer assay. Expression of the 16 recurrence-related genes was normalised to the set of five reference genes, and the recurrence score (RS) was calculated.
Results RNA yield was lower from 0.6 mm cores than from 10 μm whole sections, but was still more than sufficient to perform the assay. RS and single gene data from cores were highly comparable with those from whole sections (RS p=0.005). Greater variability was seen between cores than between sections.
Conclusions FFPE sections are preferable to 0.6 mm cores for RNA profiling in order to maximise RNA yield and to allow for standard histopathological assessment. However, 0.6 mm cores are sufficient and would be appropriate to use for large cohort studies.
- Breast cancer
- gene expression
- molecular pathology
- tissue microarray core
- tumour markers
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SD and JS contributed equally to this paper.
Funding We wish to acknowledge funding from Breakthrough Breast Cancer and NHS funding to the NIHR Biomedical Research Centre.
Competing interests Dr Rick Baehner is Director of Pathology for Genomic Health Inc. Dr Steve Shak is Chief Medical Officer for Genomic Health Inc.
Provenance and peer review Not commissioned; externally peer reviewed.