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Background  An absence of reliable molecular markers has hampered individualised breast cancer treatments, and a major limitation for translational research is the lack of fresh tissue. There are, however, abundant banks of formalin-fixed paraffin-embedded (FFPE) tissue. This study evaluated two platforms available for the analysis of DNA copy number and gene expression using FFPE samples.    Methods  The cDNA-mediated annealing, selection, extension, and ligation assay (DASL™) has been developed for gene expression analysis and the Molecular Inversion Probes assay (Oncoscan™), were used for copy number analysis using FFPE tissues. Gene expression and copy number were evaluated in core-biopsy samples from patients with breast cancer undergoing neoadjuvant chemotherapy (NAC).    Results  Forty-three core-biopsies were evaluated and characteristic copy number changes in breast cancers, gains in 1q, 8q, 11q, 17q and 20q and losses in 6q, 8p, 13q and 16q, were confirmed. Regions that frequently exhibited gains in tumours showing a pathological complete response (pCR) to NAC were 1q  (55%) , 8q  (40%)  and 17q  (40%),  whereas 11q11 ( 37% ) gain was the most frequent change in non-pCR tumours. Gains associated with poor survival were 11q13  (62%) , 8q24  (54%)  and 20q  (47%) . Gene expression assessed by DASL correlated with immunohistochemistry (IHC) analysis for oestrogen receptor (ER) [area under the curve (AUC) = 0.95], progesterone receptor (PR)(AUC = 0.90) and human epidermal growth factor type-2 receptor (HER-2) (AUC = 0.96). Differential expression analysis between ER+ and ER– cancers identified over-expression of  TTF1, LAF-4 and C-MYB  ( p  ≤ 0.05), and between pCR vs non-pCRs, over-expression of  CXCL9, AREG, B-MYB  and under-expression of  ABCG2 .    Conclusion  This study was an integrative analysis of copy number and gene expression using FFPE core biopsies and showed that molecular marker data from FFPE tissues were consistent with those in previous studies using fresh-frozen samples. FFPE tissue can provide reliable information and will be a useful tool in molecular marker studies.    Trial Registration  Trial registration number  ISRCTN09184069  and registered retrospectively on 02/06/2010.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3867-3) contains supplementary material, which is available to authorized users.

bmc genomics

Integrative analysis of copy number and gene expression in breast cancer using formalin-fixed paraffin-embedded core biopsy tissue: a feasibility study