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Absolute quantification of somatic DNA alterations in human cancer.

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.

Pubmed ID: 22544022

Authors

  • Carter SL
  • Cibulskis K
  • Helman E
  • McKenna A
  • Shen H
  • Zack T
  • Laird PW
  • Onofrio RC
  • Winckler W
  • Weir BA
  • Beroukhim R
  • Pellman D
  • Levine DA
  • Lander ES
  • Meyerson M
  • Getz G

Journal

Nature biotechnology

Publication Data

May 18, 2012

Associated Grants

  • Agency: NIGMS NIH HHS, Id: 5 T32 GM008313
  • Agency: NIGMS NIH HHS, Id: 5R01 GM083299-14
  • Agency: NCI NIH HHS, Id: F32CA113126
  • Agency: NCI NIH HHS, Id: K08 CA122833
  • Agency: NCI NIH HHS, Id: K08CA122833
  • Agency: NHGRI NIH HHS, Id: T32 HG002295
  • Agency: NCI NIH HHS, Id: U24 CA143882
  • Agency: NCI NIH HHS, Id: U24CA126546
  • Agency: NCI NIH HHS, Id: U24CA143845
  • Agency: NCI NIH HHS, Id: U24CA143867
  • Agency: NCI NIH HHS, Id: U54 CA143798
  • Agency: NCI NIH HHS, Id: U54CA143798

Mesh Terms

  • Alleles
  • Aneuploidy
  • Biotechnology
  • Cell Line, Tumor
  • Cell Separation
  • Cyclin-Dependent Kinases
  • DNA
  • DNA Mutational Analysis
  • Disease Progression
  • Female
  • Flow Cytometry
  • Gene Dosage
  • Genetic Techniques
  • Genome, Human
  • Homozygote
  • Humans
  • Male
  • Neoplasms
  • Neurofibromin 1
  • Ovarian Neoplasms
  • Ploidies
  • Point Mutation
  • Tumor Suppressor Protein p53