title: Droplet Digital™ PCR quantitation of HER2 expression in FFPE breast cancer samples.
abstract: The human epidermal growth factor receptor 2 (HER2, also known as erbB2) gene is involved in signal transduction for cell growth and differentiation. It is a cell surface receptor tyrosine kinase and a proto-oncogene. Overexpression of HER2 is of clinical relevance in breast cancer due to its prognostic value correlating elevated expression with worsening clinical outcome. At the same time, HER2 assessment is also of importance because successful anti-tumor treatment with Herceptin® is strongly correlated with HER2 overexpression in the tumor (approximately 30% of all breast tumors overexpress HER2). In a comprehensive national study, Wolff et al. [1] state that "Approximately 20% of current HER2 testing may be inaccurate" which underscores the importance of developing more accurate methods to determine HER2 status. Droplet Digital™ PCR (ddPCR™) has the potential to improve upon HER2 measurements due to its ability to quantitate DNA and RNA targets with high precision and accuracy. Here we present a study which investigates whether ddPCR can be used to assess HER2 transcript levels in formalin-fixed paraffin embedded (FFPE) human breast tumors and whether these ddPCR measurements agree with prior assessments of these same samples by pathologists using immunohistochemistry (IHC) and in some cases fluorescence in situ hybridization (FISH). We also determined the copy number of HER2 in these samples as compared to the CEP17 reference gene.
  
  
  RESULTS
  Clinical FFPE samples were successfully studied using ddPCR and compared to results from standard FISH and IHC methodology. The results demonstrate that ddPCR can rank order the samples in complete agreement with the current standard methods and that ddPCR has the added benefit of providing quantitative results, rather than relying on the expert skill of a seasoned pathologist for determination.
authors.affiliation: Digital Biology Center, Bio-Rad Laboratories Inc., 7068 Koll Center Pkwy, Ste. 401, Pleasanton, CA 94566, USA.
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Heredia
authors.forename: Phillip
authors.initials: P
authors.lastname: Belgrader
authors.forename: Shenglong
authors.initials: S
authors.lastname: Wang
authors.forename: Ryan
authors.initials: R
authors.lastname: Koehler
authors.forename: Jack
authors.initials: J
authors.lastname: Regan
authors.forename: Angela M
authors.initials: AM
authors.lastname: Cosman
authors.forename: Serge
authors.initials: S
authors.lastname: Saxonov
authors.forename: Benjamin
authors.initials: B
authors.lastname: Hindson
authors.forename: Stephanie C
authors.initials: SC
authors.lastname: Tanner
authors.forename: Alexandra S
authors.initials: AS
authors.lastname: Brown
authors.forename: George
authors.initials: G
authors.lastname: Karlin-Neumann
mesh_terms: D001943:Breast Neoplasms / Q000378:metabolism*; D002503:Centromere / Q000235:genetics; D005260:Female; D005404:Fixatives / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D018628:Gene Dosage; D015870:Gene Expression; D006801:Humans; D007150:Immunohistochemistry; D017404:In Situ Hybridization, Fluorescence; D025202:Molecular Diagnostic Techniques / Q000592:standards*; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction / Q000592:standards*; D000090063:Proto-Oncogene Mas; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D018719:Erb-b2 Receptor Tyrosine Kinases / Q000235:genetics* / Q000378:metabolism; D012015:Reference Standards
chemical_list: D005404:Fixatives; D005557:Formaldehyde; D000090063:Proto-Oncogene Mas; D012333:RNA, Messenger; D018719:Erb-b2 Receptor Tyrosine Kinases; C000715470:MAS1 protein, human; C508053:ERBB2 protein, human