title: High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing.
abstract: Knowledge of "actionable" somatic genomic alterations present in each tumor (e.g., point mutations, small insertions/deletions, and copy-number alterations that direct therapeutic options) should facilitate individualized approaches to cancer treatment. However, clinical implementation of systematic genomic profiling has rarely been achieved beyond limited numbers of oncogene point mutations. To address this challenge, we utilized a targeted, massively parallel sequencing approach to detect tumor genomic alterations in formalin-fixed, paraffin-embedded (FFPE) tumor samples. Nearly 400-fold mean sequence coverage was achieved, and single-nucleotide sequence variants, small insertions/deletions, and chromosomal copynumber alterations were detected simultaneously with high accuracy compared with other methods in clinical use. Putatively actionable genomic alterations, including those that predict sensitivity or resistance to established and experimental therapies, were detected in each tumor sample tested. Thus, targeted deep sequencing of clinical tumor material may enable mutation-driven clinical trials and, ultimately, "personalized" cancer treatment.
  
  
  CONCLUSIONS
  Despite the rapid proliferation of targeted therapeutic agents, systematic methods to profile clinically relevant tumor genomic alterations remain underdeveloped. We describe a sequencingbased approach to identifying genomic alterations in FFPE tumor samples. These studies affirm the feasibility and clinical utility of targeted sequencing in the oncology arena and provide a foundation for genomics-based stratification of cancer patients.
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts, USA.
authors.forename: Nikhil
authors.initials: N
authors.lastname: Wagle
authors.forename: Michael F
authors.initials: MF
authors.lastname: Berger
authors.forename: Matthew J
authors.initials: MJ
authors.lastname: Davis
authors.forename: Brendan
authors.initials: B
authors.lastname: Blumenstiel
authors.forename: Matthew
authors.initials: M
authors.lastname: Defelice
authors.forename: Panisa
authors.initials: P
authors.lastname: Pochanard
authors.forename: Matthew
authors.initials: M
authors.lastname: Ducar
authors.forename: Paul
authors.initials: P
authors.lastname: Van Hummelen
authors.forename: Laura E
authors.initials: LE
authors.lastname: Macconaill
authors.forename: William C
authors.initials: WC
authors.lastname: Hahn
authors.forename: Matthew
authors.initials: M
authors.lastname: Meyerson
authors.forename: Stacey B
authors.initials: SB
authors.lastname: Gabriel
authors.forename: Levi A
authors.initials: LA
authors.lastname: Garraway
mesh_terms: D045744:Cell Line, Tumor; D004252:DNA Mutational Analysis / Q000379:methods; D018628:Gene Dosage; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D009369:Neoplasms / Q000235:genetics*