title: A second-generation microRNA-based assay for diagnosing tumor tissue origin.
abstract: BACKGROUND
  Cancers of unknown primary origin (CUP) constitute 3%-5% (50,000 to 70,000 cases) of all newly diagnosed cancers per year in the United States. Including cancers of uncertain primary origin, the total number increases to 12%-15% (180,000 to 220,000 cases) of all newly diagnosed cancers per year in the United States. Cancers of unknown/uncertain primary origins present major diagnostic and clinical challenges because the tumor tissue of origin is crucial for selecting optimal treatment. MicroRNAs are a family of noncoding, regulatory RNA genes involved in carcinogenesis. MicroRNAs that are highly stable in clinical samples and tissue specific serve as ideal biomarkers for cancer diagnosis. Our first-generation assay identified the tumor of origin based on 48 microRNAs measured on a quantitative real-time polymerase chain reaction platform and differentiated 25 tumor types.
  
  
  METHODS
  We present here the development and validation of a second-generation assay that identifies 42 tumor types using a custom microarray. A combination of a binary decision-tree and a k-nearest-neighbor classifier was developed to identify the tumor of origin based on the expression of 64 microRNAs.
  
  
  RESULTS
  Overall assay sensitivity (positive agreement), measured blindly on a validation set of 509 independent samples, was 85%. The sensitivity reached 90% for cases in which the assay reported a single answer (>80% of cases). A clinical validation study on 52 true CUP patients showed 88% concordance with the clinicopathological evaluation of the patients.
  
  
  CONCLUSIONS
  The abilities of the assay to identify 42 tumor types with high accuracy and to maintain the same performance in samples from patients clinically diagnosed with CUP promise improved utility in the diagnosis of cancers of unknown/uncertain primary origins.
authors.affiliation: Rosetta Genomics, Rehovot, Israel.
authors.forename: Eti
authors.initials: E
authors.lastname: Meiri
authors.forename: Wolf C
authors.initials: WC
authors.lastname: Mueller
authors.forename: Shai
authors.initials: S
authors.lastname: Rosenwald
authors.forename: Merav
authors.initials: M
authors.lastname: Zepeniuk
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Klinke
authors.forename: Tina Bocker
authors.initials: TB
authors.lastname: Edmonston
authors.forename: Margot
authors.initials: M
authors.lastname: Werner
authors.forename: Ulrike
authors.initials: U
authors.lastname: Lass
authors.forename: Iris
authors.initials: I
authors.lastname: Barshack
authors.forename: Meora
authors.initials: M
authors.lastname: Feinmesser
authors.forename: Monica
authors.initials: M
authors.lastname: Huszar
authors.forename: Franz
authors.initials: F
authors.lastname: Fogt
authors.forename: Karin
authors.initials: K
authors.lastname: Ashkenazi
authors.forename: Mats
authors.initials: M
authors.lastname: Sanden
authors.forename: Eran
authors.initials: E
authors.lastname: Goren
authors.forename: Nir
authors.initials: N
authors.lastname: Dromi
authors.forename: Orit
authors.initials: O
authors.lastname: Zion
authors.forename: Ilanit
authors.initials: I
authors.lastname: Burnstein
authors.forename: Ayelet
authors.initials: A
authors.lastname: Chajut
authors.forename: Yael
authors.initials: Y
authors.lastname: Spector
authors.forename: Ranit
authors.initials: R
authors.lastname: Aharonov
mesh_terms: D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D001681:Biological Assay; D014408:Biomarkers, Tumor / Q000032:analysis* / Q000235:genetics; D003663:Decision Trees; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000032:analysis* / Q000235:genetics; D008875:Middle Aged; D009382:Neoplasms, Unknown Primary / Q000145:classification / Q000175:diagnosis* / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction / Q000379:methods; D012680:Sensitivity and Specificity; D015398:Signal Transduction; D014481:United States
chemical_list: D014408:Biomarkers, Tumor; D035683:MicroRNAs