title: Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing.
abstract: As more clinically relevant cancer genes are identified, comprehensive diagnostic approaches are needed to match patients to therapies, raising the challenge of optimization and analytical validation of assays that interrogate millions of bases of cancer genomes altered by multiple mechanisms. Here we describe a test based on massively parallel DNA sequencing to characterize base substitutions, short insertions and deletions (indels), copy number alterations and selected fusions across 287 cancer-related genes from routine formalin-fixed and paraffin-embedded (FFPE) clinical specimens. We implemented a practical validation strategy with reference samples of pooled cell lines that model key determinants of accuracy, including mutant allele frequency, indel length and amplitude of copy change. Test sensitivity achieved was 95-99% across alteration types, with high specificity (positive predictive value >99%). We confirmed accuracy using 249 FFPE cancer specimens characterized by established assays. Application of the test to 2,221 clinical cases revealed clinically actionable alterations in 76% of tumors, three times the number of actionable alterations detected by current diagnostic tests.
authors.affiliation: 1] Foundation Medicine, Cambridge, Massachusetts, USA. [2].
authors.forename: Garrett M
authors.initials: GM
authors.lastname: Frampton
authors.forename: Alex
authors.initials: A
authors.lastname: Fichtenholtz
authors.forename: Geoff A
authors.initials: GA
authors.lastname: Otto
authors.forename: Kai
authors.initials: K
authors.lastname: Wang
authors.forename: Sean R
authors.initials: SR
authors.lastname: Downing
authors.forename: Jie
authors.initials: J
authors.lastname: He
authors.forename: Michael
authors.initials: M
authors.lastname: Schnall-Levin
authors.forename: Jared
authors.initials: J
authors.lastname: White
authors.forename: Eric M
authors.initials: EM
authors.lastname: Sanford
authors.forename: Peter
authors.initials: P
authors.lastname: An
authors.forename: James
authors.initials: J
authors.lastname: Sun
authors.forename: Frank
authors.initials: F
authors.lastname: Juhn
authors.forename: Kristina
authors.initials: K
authors.lastname: Brennan
authors.forename: Kiel
authors.initials: K
authors.lastname: Iwanik
authors.forename: Ashley
authors.initials: A
authors.lastname: Maillet
authors.forename: Jamie
authors.initials: J
authors.lastname: Buell
authors.forename: Emily
authors.initials: E
authors.lastname: White
authors.forename: Mandy
authors.initials: M
authors.lastname: Zhao
authors.forename: Sohail
authors.initials: S
authors.lastname: Balasubramanian
authors.forename: Selmira
authors.initials: S
authors.lastname: Terzic
authors.forename: Tina
authors.initials: T
authors.lastname: Richards
authors.forename: Vera
authors.initials: V
authors.lastname: Banning
authors.forename: Lazaro
authors.initials: L
authors.lastname: Garcia
authors.forename: Kristen
authors.initials: K
authors.lastname: Mahoney
authors.forename: Zac
authors.initials: Z
authors.lastname: Zwirko
authors.forename: Amy
authors.initials: A
authors.lastname: Donahue
authors.forename: Himisha
authors.initials: H
authors.lastname: Beltran
authors.forename: Juan Miguel
authors.initials: JM
authors.lastname: Mosquera
authors.forename: Mark A
authors.initials: MA
authors.lastname: Rubin
authors.forename: Snjezana
authors.initials: S
authors.lastname: Dogan
authors.forename: Cyrus V
authors.initials: CV
authors.lastname: Hedvat
authors.forename: Michael F
authors.initials: MF
authors.lastname: Berger
authors.forename: Lajos
authors.initials: L
authors.lastname: Pusztai
authors.forename: Matthias
authors.initials: M
authors.lastname: Lechner
authors.forename: Chris
authors.initials: C
authors.lastname: Boshoff
authors.forename: Mirna
authors.initials: M
authors.lastname: Jarosz
authors.forename: Christine
authors.initials: C
authors.lastname: Vietz
authors.forename: Alex
authors.initials: A
authors.lastname: Parker
authors.forename: Vincent A
authors.initials: VA
authors.lastname: Miller
authors.forename: Jeffrey S
authors.initials: JS
authors.lastname: Ross
authors.forename: John
authors.initials: J
authors.lastname: Curran
authors.forename: Maureen T
authors.initials: MT
authors.lastname: Cronin
authors.forename: Philip J
authors.initials: PJ
authors.lastname: Stephens
authors.forename: Doron
authors.initials: D
authors.lastname: Lipson
authors.forename: Roman
authors.initials: R
authors.lastname: Yelensky
mesh_terms: D056915:DNA Copy Number Variations; D004252:DNA Mutational Analysis / Q000379:methods*; D005787:Gene Frequency; D006801:Humans; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA / Q000379:methods*