Analysis of the breast cancer methylome using formalin-fixed paraffin-embedded tumour.
Aberrant DNA methylation occurs frequently in breast carcinogenesis. Tools for translational epigenetic studies of breast cancer involving formalin-fixed paraffin-embedded (FFPE) human tissues have now been developed. Few studies have measured genome-wide methylation in DNA derived from paraffin-embedded tumour tissues and compared the DNA methylation in corresponding adjacent non-tumour ductal epithelium (ADJNT). These studies are technically challenging due to the spectrum of breast cancer pathologies, the variable suitability of DNA extracted from FFPE material and the difficulties in identifying ADJNT. We assessed the suitability of FFPE breast cancer material for genome-wide DNA methylation assessment of tumour and ADJNT.



Twenty-one archival breast tumour tissues with paired ADJNTobtained from separate blocks and at least 2 cm from the tumour were sourced from The Melbourne Collaborative Cohort Study (MCCS). DNA was prepared from macrodissected tissue samples and assessed for genome-wide methylation using the Infinium HumanMethylation450 Beadchip (HM450K) array.



The 1000 most differentially methylated probes between tumour and ADJNTin this FFPE-derived dataset differentiated tumour and ADJNTin The Cancer Genome Atlas Network data (TCGA; derived from high molecular weight DNA using the same HM450K array).



Large-scale studies of genome-wide DNA methylation using FFPE breast cancer specimens offer the opportunity to further refine the pathological classification of tumours, to include subtypes that are underrepresented in the TCGA data and provide the capacity to further explore intra-tumoural heterogeneity.
Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
Ee Ming
EM
Wong
Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia.
JiHoon E
JE
Joo
Anatomical Pathology, Alfred Health, The Alfred Hospital, Melbourne, VIC, 3181, Australia.
Catriona A
CA
McLean
Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France.|Gustave Roussy, 94805, Villejuif, France.|Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.|Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia.
Laura
L
Baglietto
Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.|Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia.
Dallas R
DR
English
Université Paris-Saclay, Univ. Paris-Sud, UVSQ, CESP, INSERM, Villejuif, France.|Gustave Roussy, 94805, Villejuif, France.|Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.|Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia.|HuGeF, Human Genetics Foundation, 10126, Turin, Italy.
Gianluca
G
Severi
Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
Hui-Chen
HC
Wu
Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA.
Mary Beth
MB
Terry
Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia.
John L
JL
Hopper
Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.|Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia.
Roger L
RL
Milne
Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia.|Centre for Epidemiology and Biostatistics, University of Melbourne, Melbourne, VIC, Australia.
Graham G
GG
Giles
Genetic Epidemiology Laboratory, Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia. msouthey@unimelb.edu.au.|Cancer Epidemiology Centre, Cancer Council Victoria, Melbourne, Australia. msouthey@unimelb.edu.au.
Melissa C
MC
Southey
D000328:Adult; D000368:Aged; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D018270:Carcinoma, Ductal, Breast / Q000235:genetics / Q000473:pathology; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods; D055106:Genome-Wide Association Study; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007150:Immunohistochemistry; D008875:Middle Aged; D059467:Transcriptome
Breast cancer; FFPE; Methylome