title: Identification and validation of an anthracycline/cyclophosphamide-based chemotherapy response assay in breast cancer.
abstract: BACKGROUND
  There is no method routinely used to predict response to anthracycline and cyclophosphamide-based chemotherapy in the clinic; therefore patients often receive treatment for breast cancer with no benefit. Loss of the Fanconi anemia/BRCA (FA/BRCA) DNA damage response (DDR) pathway occurs in approximately 25% of breast cancer patients through several mechanisms and results in sensitization to DNA-damaging agents. The aim of this study was to develop an assay to detect DDR-deficient tumors associated with loss of the FA/BRCA pathway, for the purpose of treatment selection.
  
  
  METHODS
  DNA microarray data from 21 FA patients and 11 control subjects were analyzed to identify genetic processes associated with a deficiency in DDR. Unsupervised hierarchical clustering was then performed using 60 BRCA1/2 mutant and 47 sporadic tumor samples, and a molecular subgroup was identified that was defined by the molecular processes represented within FA patients. A 44-gene microarray-based assay (the DDR deficiency assay) was developed to prospectively identify this subgroup from formalin-fixed, paraffin-embedded samples. All statistical tests were two-sided.
  
  
  RESULTS
  In a publicly available independent cohort of 203 patients, the assay predicted complete pathologic response vs residual disease after neoadjuvant DNA-damaging chemotherapy (5-fluorouracil, anthracycline, and cyclophosphamide) with an odds ratio of 3.96 (95% confidence interval [Cl] =1.67 to 9.41; P = .002). In a new independent cohort of 191 breast cancer patients treated with adjuvant 5-fluorouracil, epirubicin, and cyclophosphamide, a positive assay result predicted 5-year relapse-free survival with a hazard ratio of 0.37 (95% Cl = 0.15 to 0.88; P = .03) compared with the assay negative population.
  
  
  CONCLUSIONS
  A formalin-fixed, paraffin-embedded tissue-based assay has been developed and independently validated as a predictor of response and prognosis after anthracycline/cyclophosphamide-based chemotherapy in the neoadjuvant and adjuvant settings. These findings warrant further validation in a prospective clinical study.
authors.affiliation: Affiliations of authors: Almac Diagnostics, Craigavon, UK (JMM, LAH, SD, KEK, OYR, FAM, EO, MB, SMW, PK, TSD, VP, PGJ, DPH, RDK); Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast, UK (GI, DB, JEQ, PBM, CRJ, JJ, TSD, MS-T, PGJ, DPH, RDK); Department of Health Science Research, Mayo Clinic, Scottsdale, AZ (NML); Department of Medical Genetics, Mayo Clinic, Rochester, MN (FJC).
authors.forename: Jude M
authors.initials: JM
authors.lastname: Mulligan
authors.forename: Laura A
authors.initials: LA
authors.lastname: Hill
authors.forename: Steve
authors.initials: S
authors.lastname: Deharo
authors.forename: Gareth
authors.initials: G
authors.lastname: Irwin
authors.forename: David
authors.initials: D
authors.lastname: Boyle
authors.forename: Katherine E
authors.initials: KE
authors.lastname: Keating
authors.forename: Olaide Y
authors.initials: OY
authors.lastname: Raji
authors.forename: Fionnuala A
authors.initials: FA
authors.lastname: McDyer
authors.forename: Eamonn
authors.initials: E
authors.lastname: O'Brien
authors.forename: Max
authors.initials: M
authors.lastname: Bylesjo
authors.forename: Jennifer E
authors.initials: JE
authors.lastname: Quinn
authors.forename: Noralane M
authors.initials: NM
authors.lastname: Lindor
authors.forename: Paul B
authors.initials: PB
authors.lastname: Mullan
authors.forename: Colin R
authors.initials: CR
authors.lastname: James
authors.forename: Steven M
authors.initials: SM
authors.lastname: Walker
authors.forename: Peter
authors.initials: P
authors.lastname: Kerr
authors.forename: Jacqueline
authors.initials: J
authors.lastname: James
authors.forename: Timothy S
authors.initials: TS
authors.lastname: Davison
authors.forename: Vitali
authors.initials: V
authors.lastname: Proutski
authors.forename: Manuel
authors.initials: M
authors.lastname: Salto-Tellez
authors.forename: Patrick G
authors.initials: PG
authors.lastname: Johnston
authors.forename: Fergus J
authors.initials: FJ
authors.lastname: Couch
authors.forename: D
authors.initials: D
authors.lastname: Paul Harkin
authors.forename: Richard D
authors.initials: RD
authors.lastname: Kennedy
mesh_terms: D000328:Adult; D000368:Aged; D018943:Anthracyclines / Q000008:administration & dosage; D000971:Antineoplastic Combined Chemotherapy Protocols / Q000494:pharmacology* / Q000627:therapeutic use; D001943:Breast Neoplasms / Q000188:drug therapy* / Q000235:genetics / Q000378:metabolism*; D017024:Chemotherapy, Adjuvant; D003520:Cyclophosphamide / Q000008:administration & dosage; D004249:DNA Damage / Q000187:drug effects*; D004273:DNA, Neoplasm / Q000187:drug effects*; D018572:Disease-Free Survival; D015251:Epirubicin / Q000008:administration & dosage; D005199:Fanconi Anemia / Q000235:genetics / Q000378:metabolism*; D005260:Female; D005472:Fluorouracil / Q000008:administration & dosage; D006801:Humans; D008875:Middle Aged; D020360:Neoadjuvant Therapy / Q000379:methods; D016017:Odds Ratio; D020411:Oligonucleotide Array Sequence Analysis; D011446:Prospective Studies
chemical_list: D018943:Anthracyclines; D004273:DNA, Neoplasm; D015251:Epirubicin; D003520:Cyclophosphamide; D005472:Fluorouracil