title: Systematic Functional Interrogation of Rare Cancer Variants Identifies Oncogenic Alleles.
abstract: Cancer genome characterization efforts now provide an initial view of the somatic alterations in primary tumors. However, most point mutations occur at low frequency, and the function of these alleles remains undefined. We have developed a scalable systematic approach to interrogate the function of cancer-associated gene variants. We subjected 474 mutant alleles curated from 5,338 tumors to pooled in vivo tumor formation assays and gene expression profiling. We identified 12 transforming alleles, including two in genes (PIK3CB, POT1) that have not been shown to be tumorigenic. One rare KRAS allele, D33E, displayed tumorigenicity and constitutive activation of known RAS effector pathways. By comparing gene expression changes induced upon expression of wild-type and mutant alleles, we inferred the activity of specific alleles. Because alleles found to be mutated only once in 5,338 tumors rendered cells tumorigenic, these observations underscore the value of integrating genomic information with functional studies.
  
  
  
  Experimentally inferring the functional status of cancer-associated mutations facilitates the interpretation of genomic information in cancer. Pooled in vivo screen and gene expression profiling identified functional variants and demonstrated that expression of rare variants induced tumorigenesis. Variant phenotyping through functional studies will facilitate defining key somatic events in cancer. Cancer Discov; 6(7); 714-26. ©2016 AACR.See related commentary by Cho and Collisson, p. 694This article is highlighted in the In This Issue feature, p. 681.
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
authors.forename: Eejung
authors.initials: E
authors.lastname: Kim
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
authors.forename: Nina
authors.initials: N
authors.lastname: Ilic
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Yashaswi
authors.initials: Y
authors.lastname: Shrestha
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
authors.forename: Lihua
authors.initials: L
authors.lastname: Zou
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
authors.forename: Atanas
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authors.lastname: Kamburov
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Cong
authors.initials: C
authors.lastname: Zhu
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Yang
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Rakela
authors.initials: R
authors.lastname: Lubonja
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Nancy
authors.initials: N
authors.lastname: Tran
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Cindy
authors.initials: C
authors.lastname: Nguyen
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Michael S
authors.initials: MS
authors.lastname: Lawrence
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Federica
authors.initials: F
authors.lastname: Piccioni
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Mukta
authors.initials: M
authors.lastname: Bagul
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: John G
authors.initials: JG
authors.lastname: Doench
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Candace R
authors.initials: CR
authors.lastname: Chouinard
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Xiaoyun
authors.initials: X
authors.lastname: Wu
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Larson
authors.initials: L
authors.lastname: Hogstrom
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Ted
authors.initials: T
authors.lastname: Natoli
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medicine, University of California, San Diego, La Jolla, California.
authors.forename: Pablo
authors.initials: P
authors.lastname: Tamayo
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts.
authors.forename: Heiko
authors.initials: H
authors.lastname: Horn
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Corsello
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Surgery, Massachusetts General Hospital, Boston, Massachusetts.
authors.forename: Kasper
authors.initials: K
authors.lastname: Lage
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: David E
authors.initials: DE
authors.lastname: Root
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Aravind
authors.initials: A
authors.lastname: Subramanian
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
authors.forename: Todd R
authors.initials: TR
authors.lastname: Golub
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Cancer Center and Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts.
authors.forename: Gad
authors.initials: G
authors.lastname: Getz
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts.
authors.forename: Jesse S
authors.initials: JS
authors.lastname: Boehm
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts. Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts. william_hahn@dfci.harvard.edu.
authors.forename: William C
authors.initials: WC
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mesh_terms: D000483:Alleles; D000818:Animals; D045744:Cell Line, Tumor; D002471:Cell Transformation, Neoplastic / Q000235:genetics*; D004195:Disease Models, Animal; D020869:Gene Expression Profiling / Q000379:methods; D056726:Genetic Association Studies; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D064593:Heterografts; D057166:High-Throughput Screening Assays; D006801:Humans; D008297:Male; D051379:Mice; D009369:Neoplasms / Q000175:diagnosis / Q000235:genetics*; D009857:Oncogenes; D015203:Reproducibility of Results