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Background  Tumour DNA methylation profiling has shown potential to refine disease subtyping and improve the diagnosis and prognosis prediction of breast cancer. However, limited data exist regarding invasive lobular breast cancer (ILBC). Here, we investigated the genome-wide variability of DNA methylation levels across ILBC tumours and assessed the association between methylation levels at the variably methylated regions and overall survival in women with ILBC.    Methods  Tumour-enriched DNA was prepared by macrodissecting formalin-fixed paraffin embedded (FFPE) tumour tissue from 130 ILBCs diagnosed in the participants of the Melbourne Collaborative Cohort Study (MCCS). Genome-wide tumour DNA methylation was measured using the HumanMethylation 450K (HM450K) BeadChip array. Variably methylated regions (VMRs) were identified using the  DMRcate  package in R. Cox proportional hazards regression models were used to assess the association between methylation levels at the ten most significant VMRs and overall survival. Gene set enrichment analyses were undertaken using the web-based tool  Metaspace . Replication of the VMR and survival analysis findings was examined using data retrieved from The Cancer Genome Atlas (TCGA) for 168 ILBC cases. We also examined the correlation between methylation and gene expression for the ten VMRs of interest using TCGA data.    Results  We identified 2771 VMRs ( P  < 10 −8 ) in ILBC tumours. The ten most variably methylated clusters were predominantly located in the promoter region of the genes:  ISM1 ,  APC ,  TMEM101, ASCL2, NKX6, HIST3H2A/HIST3H2BB ,  HCG4P3, HES5, CELF2  and  EFCAB4B . Higher methylation level at several of these VMRs showed an association with reduced overall survival in the MCCS. In TCGA, all associations were in the same direction, however stronger than in the MCCS. The pooled analysis of the MCCS and TCGA data showed that methylation at four of the ten genes was associated with reduced overall survival, independently of age and tumour stage;  APC:  Hazard Ratio (95% Confidence interval) per one-unit  M -value increase: 1.18 (1.02–1.36),  TMEM101 : 1.23 (1.02–1.48),  HCG4P3 : 1.37 (1.05–1.79) and  CELF2 : 1.21 (1.02–1.43). A negative correlation was observed between methylation and gene expression for  CELF2  ( R  = − 0.25,  P  = 0.001), but not for  TMEM101  and  APC .    Conclusions  Our study identified regions showing greatest variability across the ILBC tumour genome and found methylation at several genes to potentially serve as a biomarker of survival for women with ILBC.

Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer