N11: A Dominantly Inherited 5’UTR Variant Causing Methylation Associated Silencing of BRCA1 As A Novel Cause Of Breast And Ovarian Cancer

D. G. Evans1, 2, 3, 4, 8, E. M. van Veen1, 5, 8, H. J. Byers1, 5, A. J. Wallace5, J. M. Ellingford1, 5, G. Beaman1, 5, J. Santoyo-Lopez6, T. J. Aitman6, D. M. Eccles7, F. I. Lalloo5, M. J. Smith1, 5, 8, W. G. Newman1, 4, 5, 8

1 – Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK. 2 – Prevention Breast Cancer Centre and Nightingale Breast Screening Centre, University Hospital of South Manchester, Manchester, UK. 3 – The Christie NHS Foundation Trust, Manchester, UK. 4 – Manchester Breast Centre, Manchester Cancer Research Centre, University of Manchester, Manchester, UK. 5 – Manchester Centre for Genomic Medicine, St. Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, UK. 6 – Centre for Genomic and Experimental Medicine, and Edinburgh Genomics, University of Edinburgh, Edinburgh, UK. 7 – Cancer Sciences Academic Unit and Southampton Clinical Trials Unit, Faculty of Medicine, University of Southampton and University Hospital Southampton Foundation Trust, Southampton, UK. 8 – Department of Genomic Medicine, St Mary’s Hospital, Manchester Universities NHS Foundation Trust Manchester M13 9WL


Aim: Pathogenic variants in BRCA1/BRCA2 are identified in ~20% of families with multiple individuals with early-onset breast/ovarian cancer. Extensive searches for additional highly penetrant genes/alternative mutational mechanisms altering BRCA1/2 have not explained the missing heritability. For the first time, we report a dominantly inherited 5’UTR variant associated with epigenetic silencing of BRCA1 due to promoter hypermethylation in two families with breast/ovarian cancer.

Method: BRCA1 promoter methylation of ten CpG dinucleotides in breast/ovarian cancer families without germline BRCA1/2 pathogenic variants was assessed by pyrosequencing and clonal bisulfite sequencing. BRCA1 RNA/DNA sequencing from lymphocytes was undertaken to establish allelic expression and germline variants.

Results: BRCA1 promoter hypermethylation was identified in 2/49 families with multiple women affected with grade-3 breast/high-grade-serous ovarian cancer. Soma-wide BRCA1 promoter hypermethylation was confirmed in blood/buccal mucosa/hair follicles. Methylation levels were ~50%, consistent with complete silencing of one allele. RNA sequencing revealed allelic BRCA1 expression loss in both families segregating with a novel heterozygous variant c.-107A>T in 5’UTR.

Conclusion: Our results indicate a novel mechanism for familial breast/ovarian cancer, caused by an in cis 5’UTR variant associated with epigenetic silencing of BRCA1 promoter. We propose methylation analyses are undertaken to establish the frequency of this mechanism in families affected by early onset breast/ovarian cancer without a BRCA1/2 pathogenic variant.