Chromosome abnormalities in ovarian adenocarcinoma: III. Using breakpoint data to infer and test mathematical models for oncogenesis

Richard Simon, Richard Desper, Christos H. Papadimitriou, Amy Peng, David S. Alberts, Raymond Taetle, Jeffrey M. Trent, Alejandro A. Schäffer

Research output: Contribution to journalArticle

Abstract

Cancer geneticists seek to identify genetic changes in tumor cells and to relate the genetic changes to tumor development. Because single changes can disrupt the cell cycle and promote other genetic changes, it is extremely hard to distinguish cause from effect. In this article we illustrate how 7 techniques from statistics, theoretical computer science, and phylogenetics can be used to infer and test possible models of tumor progression from single genome-wide descriptions of aberrations in a large sample of tumors. Specifically, we propose 4 tree models for tumor progression inferred from the large ovarian cancer data set described in the first 2 articles in this series. The models are derived from 2 different methods to select the non- random genetic aberrations and 2 different methods to infer the trees, given a set of events. Various aspects of the tree models are tested and extended by 5 methods: overall tests of independence, likelihood ratio tests, principal components analysis, directed acyclic graph modeling, and Bayesian survival analysis. All our methods lead to strikingly consistent conclusions about chromosomal breakpoints in ovarian adenocarcinoma, including (1) the non-random breakpoints in ovarian adenocarcinoma do not occur independently; (2) breakpoints in regions 1p3 and 11p1 are important early events and distinguish a class of tumors associated with poor prognosis; and (3) breakpoints in 1p1, 3p1, and 1q2 distinguish a class of ovarian tumors, and the breaks at 1p1 and 3p1 are associated with poor prognosis. (C) 2000 Wiley- Liss, Inc.

Original languageEnglish (US)
Pages (from-to)106-120
Number of pages15
JournalGenes Chromosomes and Cancer
Volume28
Issue number1
DOIs
StatePublished - May 2000
Externally publishedYes

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Chromosome Aberrations
Carcinogenesis
Adenocarcinoma
Theoretical Models
Neoplasms
Psychological Techniques
Bayes Theorem
Survival Analysis
Principal Component Analysis
Ovarian Neoplasms
Cell Cycle
Genome

ASJC Scopus subject areas

  • Cancer Research
  • Genetics

Cite this

Chromosome abnormalities in ovarian adenocarcinoma : III. Using breakpoint data to infer and test mathematical models for oncogenesis. / Simon, Richard; Desper, Richard; Papadimitriou, Christos H.; Peng, Amy; Alberts, David S.; Taetle, Raymond; Trent, Jeffrey M.; Schäffer, Alejandro A.

In: Genes Chromosomes and Cancer, Vol. 28, No. 1, 05.2000, p. 106-120.

Research output: Contribution to journalArticle

Simon, Richard ; Desper, Richard ; Papadimitriou, Christos H. ; Peng, Amy ; Alberts, David S. ; Taetle, Raymond ; Trent, Jeffrey M. ; Schäffer, Alejandro A. / Chromosome abnormalities in ovarian adenocarcinoma : III. Using breakpoint data to infer and test mathematical models for oncogenesis. In: Genes Chromosomes and Cancer. 2000 ; Vol. 28, No. 1. pp. 106-120.
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