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

doi:10.1186/gb-2008-9-5-r86

Genome Biology

Volume 9
Issue 5

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Lyng H
Lando M
Brøvig RS
Svendsrud DH
Johansen M
Galteland E
Brustugun OT
Meza-Zepeda LA
Myklebost O
Kristensen GB
Hovig E
Stokke T

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Lyng H
Lando M
Brøvig RS
Svendsrud DH
Johansen M
Galteland E
Brustugun OT
Meza-Zepeda LA
Myklebost O
Kristensen GB
Hovig E
Stokke T
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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

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

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

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

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

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

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

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

author email corresponding author email

Genome Biology 2008, 9:R86doi: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.