title: Identification of BRCA1 Deficiency Using Multi-Analyte Estimation of BRCA1 and Its Repressors in FFPE Tumor Samples from Patients with Triple Negative Breast Cancer.
abstract: OBJECTIVE
  Apart from germ-line BRCA1-mutated breast cancers, a significant proportion of women with sporadic triple negative breast cancer (TNBC) sub-type are known to harbour varying levels of BRCA1-dysfuction. There is currently no established diagnostic method to identify these patients.
  
  
  METHODS
  The analysis was performed on 183 primary breast cancer tumor specimens from our longitudinal case-series archived as formalin-fixed-paraffin-embedded (FFPE) blocks comprising 71 TNBCs and 112 Hormone receptor positive HER2 negative (HR+HER2-) tumors. Transcript levels of BRCA1 and two of its repressors ID4 and microRNA182 were determined by TaqMan quantitative PCR. BRCA1 protein was detected immunohistochemically with the MS110 antibody.
  
  
  RESULTS
  The representation of BRCA1 and its repressor ID4 as a ratio led to improved separation of TNBCs from HR+HER2- compared to either measure by itself. We then dichotomised the continuous distribution of each of the three measurements (Protein, MIRNA and transcript:repressor ratio) into categories of deficient (0) and adequate (1). A composite BRCA1 Deficiency Score (BDS) was computed by the addition of the score for all three measures. Samples deficient on 2 or more measures were deemed to be BRCA1 deficient; and 40% of all TNBCs met this criterion.
  
  
  CONCLUSIONS
  We propose here a simple multi-level assay of BRCA1 deficiency using the BRCA1:ID4 ratio as a critical parameter that can be performed on FFPE samples in clinical laboratories by the estimation of only 3 bio-markers. The ease of testing will hopefully encourage adoption and clinical validation.
authors.affiliation: Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
authors.forename: Aruna
authors.initials: A
authors.lastname: Korlimarla
authors.affiliation: Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
authors.forename: Jyothi S
authors.initials: JS
authors.lastname: Prabhu
authors.affiliation: Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
authors.forename: Jose
authors.initials: J
authors.lastname: Remacle
authors.affiliation: Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
authors.forename: Savitha
authors.initials: S
authors.lastname: Rajarajan
authors.affiliation: Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
authors.forename: Uma
authors.initials: U
authors.lastname: Raja
authors.affiliation: Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
authors.forename: Anupama
authors.initials: A
authors.lastname: C E
authors.affiliation: Sri Shankara Cancer Hospital & Research Centre, Bangalore, India.
authors.forename: B S
authors.initials: BS
authors.lastname: Srinath
authors.affiliation: Department of Surgical Oncology, St. John's Medical College and Hospital, Bangalore, India.
authors.forename: Suraj
authors.initials: S
authors.lastname: Manjunath
authors.affiliation: Rangadore Memorial Hospital, Bangalore, India.
authors.forename: Gopinath
authors.initials: G
authors.lastname: K S
authors.affiliation: Department of Pathology, St John's Medical College and Hospital, Bangalore, India.
authors.forename: Marjorrie
authors.initials: M
authors.lastname: Correa
authors.affiliation: Sri Shankara Cancer Hospital & Research Centre, Bangalore, India.
authors.forename: Prasad
authors.initials: P
authors.lastname: M S N
authors.affiliation: Division of Molecular Medicine, St. John's Research Institute, Bangalore, India.
authors.forename: T S
authors.initials: TS
authors.lastname: Sridhar
mesh_terms: D019313:BRCA1 Protein / Q000172:deficiency* / Q000235:genetics*; D016190:Carboplatin / Q000494:pharmacology / Q000627:therapeutic use; D005260:Female; D005557:Formaldehyde; D015972:Gene Expression Regulation, Neoplastic / Q000187:drug effects; D006801:Humans; D051796:Inhibitor of Differentiation Proteins / Q000235:genetics; D035683:MicroRNAs / Q000235:genetics; D008875:Middle Aged; D009367:Neoplasm Staging; D016612:Paraffin Embedding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016707:Tissue Fixation; D016896:Treatment Outcome; D064726:Triple Negative Breast Neoplasms / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism / Q000473:pathology*
chemical_list: D019313:BRCA1 Protein; C490128:ID4 protein, human; D051796:Inhibitor of Differentiation Proteins; D035683:MicroRNAs; C538984:Mirn182 microRNA, human; D012333:RNA, Messenger; D005557:Formaldehyde; D016190:Carboplatin