title: DNA methylation profiling to assess pathogenicity of BRCA1 unclassified variants in breast cancer.
abstract: Germline pathogenic mutations in BRCA1 increase risk of developing breast cancer. Screening for mutations in BRCA1 frequently identifies sequence variants of unknown pathogenicity and recent work has aimed to develop methods for determining pathogenicity. We previously observed that tumor DNA methylation can differentiate BRCA1-mutated from BRCA1-wild type tumors. We hypothesized that we could predict pathogenicity of variants based on DNA methylation profiles of tumors that had arisen in carriers of unclassified variants. We selected 150 FFPE breast tumor DNA samples [47 BRCA1 pathogenic mutation carriers, 65 BRCAx (BRCA1-wild type), 38 BRCA1 test variants] and analyzed a subset (n=54) using the Illumina 450K methylation platform, using the remaining samples for bisulphite pyrosequencing validation. Three validated markers (BACH2, C8orf31, and LOC654342) were combined with sequence bioinformatics in a model to predict pathogenicity of 27 variants (independent test set). Predictions were compared with standard multifactorial likelihood analysis. Prediction was consistent for c.5194-12G>A (IVS 19-12 G>A) (P>0.99); 13 variants were considered not pathogenic or likely not pathogenic using both approaches. We conclude that tumor DNA methylation data alone has potential to be used in prediction of BRCA1 variant pathogenicity but is not independent of estrogen receptor status and grade, which are used in current multifactorial models to predict pathogenicity.
authors.affiliation: a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK.
authors.forename: Kirsty J
authors.initials: KJ
authors.lastname: Flower
authors.affiliation: a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK.
authors.forename: Natalie S
authors.initials: NS
authors.lastname: Shenker
authors.affiliation: b Department of Histopathology ; Hammersmith Hospital; Imperial College London ; UK.
authors.forename: Mona
authors.initials: M
authors.lastname: El-Bahrawy
authors.affiliation: c Huntsman Cancer Institute; University of Utah ; Salt Lake City , UT , USA.
authors.forename: David E
authors.initials: DE
authors.lastname: Goldgar
authors.affiliation: d QIMR Berghofer Medical Research Institute ; Brisbane , QLD , Australia.
authors.forename: Michael T
authors.initials: MT
authors.lastname: Parsons
authors.affiliation: d QIMR Berghofer Medical Research Institute ; Brisbane , QLD , Australia.
authors.forename: Amanda B
authors.initials: AB
authors.lastname: Spurdle
authors.affiliation: f Genome Stability Unit; School of Cancer Sciences; University of Birmingham ; UK.
authors.forename: Joanna R
authors.initials: JR
authors.lastname: Morris
authors.affiliation: a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK.|g Section of Molecular Pathology; Institute for Cancer Research ; Sutton , UK.
authors.forename: Robert
authors.initials: R
authors.lastname: Brown
authors.affiliation: a Epigenetics Unit; Department of Surgery and Cancer; Imperial College London ; UK.
authors.forename: James M
authors.initials: JM
authors.lastname: Flanagan
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D019295:Computational Biology; D019175:DNA Methylation; D004252:DNA Mutational Analysis; D005260:Female; D019398:Genes, BRCA1; D005819:Genetic Markers; D020022:Genetic Predisposition to Disease; D006801:Humans
chemical_list: D005819:Genetic Markers
keywords: BRCA1; breast cancer; epigenetic; methylation; variants