title: Classifications within molecular subtypes enables identification of BRCA1/BRCA2 mutation carriers by RNA tumor profiling.
abstract: Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants of unclear pathogen significance are found in the families, constituting an increasing clinical challenge. New methods are therefore needed to improve the detection rate and aid the interpretation of the clinically uncertain variants. In this study we analyzed a series of 33 BRCA1, 22 BRCA2, and 128 sporadic tumors by RNA profiling to investigate the classification potential of RNA profiles to predict BRCA1/2 mutation status. We found that breast tumors from BRCA1 and BRCA2 mutation carriers display characteristic RNA expression patterns, allowing them to be distinguished from sporadic tumors. The majority of BRCA1 tumors were basal-like while BRCA2 tumors were mainly luminal B. Using RNA profiles, we were able to distinguish BRCA1 tumors from sporadic tumors among basal-like tumors with 83% accuracy and BRCA2 from sporadic tumors among luminal B tumors with 89% accuracy. Furthermore, subtype-specific BRCA1/2 gene signatures were successfully validated in two independent data sets with high accuracies. Although additional validation studies are required, indication of BRCA1/2 involvement ("BRCAness") by RNA profiling could potentially be valuable as a tool for distinguishing pathogenic mutations from benign variants, for identification of undetected mutation carriers, and for selecting patients sensitive to new therapeutics such as PARP inhibitors.
authors.affiliation: Department of Clinical Genetics, Odense University Hospital, Odense, Denmark.
authors.forename: Martin J
authors.initials: MJ
authors.lastname: Larsen
authors.forename: Torben A
authors.initials: TA
authors.lastname: Kruse
authors.forename: Qihua
authors.initials: Q
authors.lastname: Tan
authors.forename: Anne-Vibeke
authors.initials: AV
authors.lastname: Lænkholm
authors.forename: Martin
authors.initials: M
authors.lastname: Bak
authors.forename: Anne E
authors.initials: AE
authors.lastname: Lykkesfeldt
authors.forename: Kristina P
authors.initials: KP
authors.lastname: Sørensen
authors.forename: Thomas V O
authors.initials: TV
authors.lastname: Hansen
authors.forename: Bent
authors.initials: B
authors.lastname: Ejlertsen
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Gerdes
authors.forename: Mads
authors.initials: M
authors.lastname: Thomassen
mesh_terms: D000328:Adult; D019313:BRCA1 Protein / Q000235:genetics*; D024682:BRCA2 Protein / Q000235:genetics*; D001943:Breast Neoplasms / Q000145:classification* / Q000235:genetics* / Q000473:pathology; D016000:Cluster Analysis; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006579:Heterozygote; D006801:Humans; D008875:Middle Aged; D009154:Mutation / Q000235:genetics*; D012334:RNA, Neoplasm / Q000235:genetics* / Q000378:metabolism; D015203:Reproducibility of Results
chemical_list: D019313:BRCA1 Protein; D024682:BRCA2 Protein; D012334:RNA, Neoplasm