Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays

We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance prof...

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Autores principales: Popova, Tatiana, Manié, Elodie, Stoppa-Lyonnet, Dominique, Rigaill, Guillem, Barillot, Emmanuel, Stern, Marc Henri
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2009
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810663/
https://www.ncbi.nlm.nih.gov/pubmed/19903341
http://dx.doi.org/10.1186/gb-2009-10-11-r128
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author Popova, Tatiana
Manié, Elodie
Stoppa-Lyonnet, Dominique
Rigaill, Guillem
Barillot, Emmanuel
Stern, Marc Henri
author_facet Popova, Tatiana
Manié, Elodie
Stoppa-Lyonnet, Dominique
Rigaill, Guillem
Barillot, Emmanuel
Stern, Marc Henri
author_sort Popova, Tatiana
collection PubMed
description We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes.
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spelling pubmed-28106632010-01-26 Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays Popova, Tatiana Manié, Elodie Stoppa-Lyonnet, Dominique Rigaill, Guillem Barillot, Emmanuel Stern, Marc Henri Genome Biol Method We describe a method for automatic detection of absolute segmental copy numbers and genotype status in complex cancer genome profiles measured with single-nucleotide polymorphism (SNP) arrays. The method is based on pattern recognition of segmented and smoothed copy number and allelic imbalance profiles. Assignments were verified by DNA indexes of primary tumors and karyotypes of cell lines. The method performs well even for poor-quality data, low tumor content, and highly rearranged tumor genomes. BioMed Central 2009 2009-11-11 /pmc/articles/PMC2810663/ /pubmed/19903341 http://dx.doi.org/10.1186/gb-2009-10-11-r128 Text en Copyright ©2009 Popova 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
Popova, Tatiana
Manié, Elodie
Stoppa-Lyonnet, Dominique
Rigaill, Guillem
Barillot, Emmanuel
Stern, Marc Henri
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
title Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
title_full Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
title_fullStr Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
title_full_unstemmed Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
title_short Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays
title_sort genome alteration print (gap): a tool to visualize and mine complex cancer genomic profiles obtained by snp arrays
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2810663/
https://www.ncbi.nlm.nih.gov/pubmed/19903341
http://dx.doi.org/10.1186/gb-2009-10-11-r128
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