title: Profiling critical cancer gene mutations in clinical tumor samples.
abstract: BACKGROUND
  Detection of critical cancer gene mutations in clinical tumor specimens may predict patient outcomes and inform treatment options; however, high-throughput mutation profiling remains underdeveloped as a diagnostic approach. We report the implementation of a genotyping and validation algorithm that enables robust tumor mutation profiling in the clinical setting.
  
  
  METHODS
  We developed and implemented an optimized mutation profiling platform ("OncoMap") to interrogate approximately 400 mutations in 33 known oncogenes and tumor suppressors, many of which are known to predict response or resistance to targeted therapies. The performance of OncoMap was analyzed using DNA derived from both frozen and FFPE clinical material in a diverse set of cancer types. A subsequent in-depth analysis was conducted on histologically and clinically annotated pediatric gliomas. The sensitivity and specificity of OncoMap were 93.8% and 100% in fresh frozen tissue; and 89.3% and 99.4% in FFPE-derived DNA. We detected known mutations at the expected frequencies in common cancers, as well as novel mutations in adult and pediatric cancers that are likely to predict heightened response or resistance to existing or developmental cancer therapies. OncoMap profiles also support a new molecular stratification of pediatric low-grade gliomas based on BRAF mutations that may have immediate clinical impact.
  
  
  CONCLUSIONS
  Our results demonstrate the clinical feasibility of high-throughput mutation profiling to query a large panel of "actionable" cancer gene mutations. In the future, this type of approach may be incorporated into both cancer epidemiologic studies and clinical decision making to specify the use of many targeted anticancer agents.
authors.affiliation: Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Laura E
authors.initials: LE
authors.lastname: MacConaill
authors.forename: Catarina D
authors.initials: CD
authors.lastname: Campbell
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Kehoe
authors.forename: Adam J
authors.initials: AJ
authors.lastname: Bass
authors.forename: Charles
authors.initials: C
authors.lastname: Hatton
authors.forename: Lili
authors.initials: L
authors.lastname: Niu
authors.forename: Matt
authors.initials: M
authors.lastname: Davis
authors.forename: Keluo
authors.initials: K
authors.lastname: Yao
authors.forename: Megan
authors.initials: M
authors.lastname: Hanna
authors.forename: Chandrani
authors.initials: C
authors.lastname: Mondal
authors.forename: Lauren
authors.initials: L
authors.lastname: Luongo
authors.forename: Caroline M
authors.initials: CM
authors.lastname: Emery
authors.forename: Alissa C
authors.initials: AC
authors.lastname: Baker
authors.forename: Juliet
authors.initials: J
authors.lastname: Philips
authors.forename: Deborah J
authors.initials: DJ
authors.lastname: Goff
authors.forename: Michelangelo
authors.initials: M
authors.lastname: Fiorentino
authors.forename: Mark A
authors.initials: MA
authors.lastname: Rubin
authors.forename: Kornelia
authors.initials: K
authors.lastname: Polyak
authors.forename: Jennifer
authors.initials: J
authors.lastname: Chan
authors.forename: Yuexiang
authors.initials: Y
authors.lastname: Wang
authors.forename: Jonathan A
authors.initials: JA
authors.lastname: Fletcher
authors.forename: Sandro
authors.initials: S
authors.lastname: Santagata
authors.forename: Gianni
authors.initials: G
authors.lastname: Corso
authors.forename: Franco
authors.initials: F
authors.lastname: Roviello
authors.forename: Ramesh
authors.initials: R
authors.lastname: Shivdasani
authors.forename: Mark W
authors.initials: MW
authors.lastname: Kieran
authors.forename: Keith L
authors.initials: KL
authors.lastname: Ligon
authors.forename: Charles D
authors.initials: CD
authors.lastname: Stiles
authors.forename: William C
authors.initials: WC
authors.lastname: Hahn
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Meyerson
authors.forename: Levi A
authors.initials: LA
authors.lastname: Garraway
mesh_terms: D000465:Algorithms; D003062:Codon; D004252:DNA Mutational Analysis; D017931:DNA Primers / Q000235:genetics; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D005838:Genotype; D005910:Glioma / Q000235:genetics; D006801:Humans; D009154:Mutation; D009369:Neoplasms / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D048493:Proto-Oncogene Proteins B-raf / Q000235:genetics; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
chemical_list: D003062:Codon; D017931:DNA Primers; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf