title: Absolute quantification of somatic DNA alterations in human cancer.
abstract: We describe a computational method that infers tumor purity and malignant cell ploidy directly from analysis of somatic DNA alterations. The method, named ABSOLUTE, can detect subclonal heterogeneity and somatic homozygosity, and it can calculate statistical sensitivity for detection of specific aberrations. We used ABSOLUTE to analyze exome sequencing data from 214 ovarian carcinoma tumor-normal pairs. This analysis identified both pervasive subclonal somatic point-mutations and a small subset of predominantly clonal and homozygous mutations, which were overrepresented in the tumor suppressor genes TP53 and NF1 and in a candidate tumor suppressor gene CDK12. We also used ABSOLUTE to infer absolute allelic copy-number profiles from 3,155 diverse cancer specimens, revealing that genome-doubling events are common in human cancer, likely occur in cells that are already aneuploid, and influence pathways of tumor progression (for example, with recessive inactivation of NF1 being less common after genome doubling). ABSOLUTE will facilitate the design of clinical sequencing studies and studies of cancer genome evolution and intra-tumor heterogeneity.
authors.affiliation: The Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA. scarter@broadinstitute.org
authors.forename: Scott L
authors.initials: SL
authors.lastname: Carter
authors.forename: Kristian
authors.initials: K
authors.lastname: Cibulskis
authors.forename: Elena
authors.initials: E
authors.lastname: Helman
authors.forename: Aaron
authors.initials: A
authors.lastname: McKenna
authors.forename: Hui
authors.initials: H
authors.lastname: Shen
authors.forename: Travis
authors.initials: T
authors.lastname: Zack
authors.forename: Peter W
authors.initials: PW
authors.lastname: Laird
authors.forename: Robert C
authors.initials: RC
authors.lastname: Onofrio
authors.forename: Wendy
authors.initials: W
authors.lastname: Winckler
authors.forename: Barbara A
authors.initials: BA
authors.lastname: Weir
authors.forename: Rameen
authors.initials: R
authors.lastname: Beroukhim
authors.forename: David
authors.initials: D
authors.lastname: Pellman
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Levine
authors.forename: Eric S
authors.initials: ES
authors.lastname: Lander
authors.forename: Matthew
authors.initials: M
authors.lastname: Meyerson
authors.forename: Gad
authors.initials: G
authors.lastname: Getz
mesh_terms: D000483:Alleles; D000782:Aneuploidy; D001709:Biotechnology / Q000379:methods; D045744:Cell Line, Tumor; D002469:Cell Separation; D018844:Cyclin-Dependent Kinases / Q000235:genetics; D004247:DNA / Q000235:genetics*; D004252:DNA Mutational Analysis / Q000379:methods*; D018450:Disease Progression; D005260:Female; D005434:Flow Cytometry; D018628:Gene Dosage; D005821:Genetic Techniques; D015894:Genome, Human; D006720:Homozygote; D006801:Humans; D008297:Male; D009369:Neoplasms / Q000235:genetics*; D025542:Neurofibromin 1 / Q000235:genetics; D010051:Ovarian Neoplasms / Q000235:genetics; D011003:Ploidies; D017354:Point Mutation; D016159:Tumor Suppressor Protein p53 / Q000235:genetics
chemical_list: D025542:Neurofibromin 1; C495901:TP53 protein, human; D016159:Tumor Suppressor Protein p53; D004247:DNA; C447339:CDK12 protein, human; D018844:Cyclin-Dependent Kinases