Estimating an oncogenetic tree when false negatives and positives are present

Math Biosci. 2002 Apr;176(2):219-36. doi: 10.1016/s0025-5564(02)00086-x.


Human solid tumors are believed to be caused by a sequence of genetic abnormalities arising in the tumor cells. The understanding of these sequences is extremely important for improving cancer treatment. Models for the occurrence of the abnormalities include linear structure and a recently proposed tree-based structure. In this paper we extend the pure oncogenetic tree model by introducing false positive and false negative observations. We state conditions sufficient for the reconstruction of the generating tree. As an example we analyze a comparative genomic hybridization data set and show that addition of the error model significantly improves the ability of the model to describe the data.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Adenocarcinoma, Clear Cell / genetics
  • Algorithms
  • Chromosome Aberrations
  • False Negative Reactions
  • False Positive Reactions
  • Female
  • Humans
  • Kidney Neoplasms / genetics
  • Male
  • Models, Genetic*
  • Neoplasms / genetics*
  • Nucleic Acid Hybridization
  • Oncogenes / genetics*