Open Access Method

GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data

Heidi Lyng1*, Malin Lando1, Runar S Brøvig1, Debbie H Svendsrud1, Morten Johansen2, Eivind Galteland1, Odd T Brustugun1,3, Leonardo A Meza-Zepeda2,4, Ola Myklebost2,4, Gunnar B Kristensen5,6, Eivind Hovig2,6,7 and Trond Stokke1

Author Affiliations

1 Department of Radiation Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway

2 Department of Tumor Biology, Institute for Cancer Research, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway

3 Department of Oncology, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway

4 Norwegian Microarray Consortium, Department of Molecular Bioscience, University of Oslo, NO-0316 Oslo, Norway

5 Department of Gynecologic Oncology, Norwegian Radium Hospital, Montebello, NO-0310 Oslo, Norway

6 Department of Medical Informatics, University of Oslo, NP-0316 Oslo, Norway

7 Institute of Informatics, University of Oslo, NO-0316 Oslo, Norway

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Genome Biology 2008, 9:R86 doi:10.1186/gb-2008-9-5-r86

Published: 23 May 2008

Abstract

Absolute tumor DNA copy numbers can currently be achieved only on a single gene basis by using fluorescence in situ hybridization (FISH). We present GeneCount, a method for genome-wide calculation of absolute copy numbers from clinical array comparative genomic hybridization data. The tumor cell fraction is reliably estimated in the model. Data consistent with FISH results are achieved. We demonstrate significant improvements over existing methods for exploring gene dosages and intratumor copy number heterogeneity in cancers.