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

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 fra...

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Autores principales: Lyng, Heidi, Lando, Malin, Brøvig, Runar S, Svendsrud, Debbie H, Johansen, Morten, Galteland, Eivind, Brustugun, Odd T, Meza-Zepeda, Leonardo A, Myklebost, Ola, Kristensen, Gunnar B, Hovig, Eivind, Stokke, Trond
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441472/
https://www.ncbi.nlm.nih.gov/pubmed/18500990
http://dx.doi.org/10.1186/gb-2008-9-5-r86
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author Lyng, Heidi
Lando, Malin
Brøvig, Runar S
Svendsrud, Debbie H
Johansen, Morten
Galteland, Eivind
Brustugun, Odd T
Meza-Zepeda, Leonardo A
Myklebost, Ola
Kristensen, Gunnar B
Hovig, Eivind
Stokke, Trond
author_facet Lyng, Heidi
Lando, Malin
Brøvig, Runar S
Svendsrud, Debbie H
Johansen, Morten
Galteland, Eivind
Brustugun, Odd T
Meza-Zepeda, Leonardo A
Myklebost, Ola
Kristensen, Gunnar B
Hovig, Eivind
Stokke, Trond
author_sort Lyng, Heidi
collection PubMed
description 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.
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spelling pubmed-24414722008-07-01 GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data Lyng, Heidi Lando, Malin Brøvig, Runar S Svendsrud, Debbie H Johansen, Morten Galteland, Eivind Brustugun, Odd T Meza-Zepeda, Leonardo A Myklebost, Ola Kristensen, Gunnar B Hovig, Eivind Stokke, Trond Genome Biol Method 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. BioMed Central 2008 2008-05-23 /pmc/articles/PMC2441472/ /pubmed/18500990 http://dx.doi.org/10.1186/gb-2008-9-5-r86 Text en Copyright © 2008 Lyng et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Lyng, Heidi
Lando, Malin
Brøvig, Runar S
Svendsrud, Debbie H
Johansen, Morten
Galteland, Eivind
Brustugun, Odd T
Meza-Zepeda, Leonardo A
Myklebost, Ola
Kristensen, Gunnar B
Hovig, Eivind
Stokke, Trond
GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
title GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
title_full GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
title_fullStr GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
title_full_unstemmed GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
title_short GeneCount: genome-wide calculation of absolute tumor DNA copy numbers from array comparative genomic hybridization data
title_sort genecount: genome-wide calculation of absolute tumor dna copy numbers from array comparative genomic hybridization data
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2441472/
https://www.ncbi.nlm.nih.gov/pubmed/18500990
http://dx.doi.org/10.1186/gb-2008-9-5-r86
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