Profiling critical cancer gene mutations in clinical tumor samples.
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.
MacConaill
Laura E
LE
Center for Cancer Genome Discovery, Dana-Farber Cancer Institute and Harvard Medical School, Boston, Massachusetts, USA.
Campbell
Catarina D
CD
Kehoe
Sarah M
SM
Bass
Adam J
AJ
Hatton
Charles
C
Niu
Lili
L
Davis
Matt
M
Yao
Keluo
K
Hanna
Megan
M
Mondal
Chandrani
C
Luongo
Lauren
L
Emery
Caroline M
CM
Baker
Alissa C
AC
Philips
Juliet
J
Goff
Deborah J
DJ
Fiorentino
Michelangelo
M
Rubin
Mark A
MA
Polyak
Kornelia
K
Chan
Jennifer
J
Wang
Yuexiang
Y
Fletcher
Jonathan A
JA
Santagata
Sandro
S
Corso
Gianni
G
Roviello
Franco
F
Shivdasani
Ramesh
R
Kieran
Mark W
MW
Ligon
Keith L
KL
Stiles
Charles D
CD
Hahn
William C
WC
Meyerson
Matthew L
ML
Garraway
Levi A
LA
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
D003062:Codon; D017931:DNA Primers; C482119:BRAF protein, human; D048493:Proto-Oncogene Proteins B-raf