PMID: 11916510Mar 28, 2002Paper

Estimating an oncogenetic tree when false negatives and positives are present

Mathematical Biosciences
Aniko Szabo, Kenneth M Boucher

Abstract

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.

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Citations

Jul 3, 2009·Diseases of the Colon and Rectum·Martha L SlatteryWade Samowitz
Jul 12, 2012·Bioinformatics·Thomas Sakoparnig, Niko Beerenwinkel
Apr 15, 2011·Cancer Prevention Research·Kathleen SprouffskeCarlo C Maley
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Aug 14, 2012·Biometrical Journal. Biometrische Zeitschrift·Katrin HainkeRoland Fried
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Jan 9, 2015·PLoS Computational Biology·Thomas SakoparnigNiko Beerenwinkel
Oct 10, 2014·PloS One·Loes Olde LoohuisBud Mishra
Jul 1, 2016·Proceedings of the National Academy of Sciences of the United States of America·Giulio CaravagnaBud Mishra
Jun 10, 2004·Genes, Chromosomes & Cancer·Zhongxi HuangKaitai Yao
Feb 14, 2017·Nature Reviews. Genetics·Russell Schwartz, Alejandro A Schäffer
Jul 1, 2016·PloS One·E Michael GertzAlejandro A Schäffer
Oct 12, 2019·Experimental and Therapeutic Medicine·Xiao-Jun YuFang-Ming Zhong
Oct 9, 2021·Colorectal Disease : the Official Journal of the Association of Coloproctology of Great Britain and Ireland·Mariola Monika GolasBjoern Sander

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