Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity

We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy...

Descripción completa

Detalles Bibliográficos
Autores principales: Rasmussen, Markus, Sundström, Magnus, Kultima, Hanna Göransson, Botling, Johan, Micke, Patrick, Birgisson, Helgi, Glimelius, Bengt, Isaksson, Anders
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333778/
https://www.ncbi.nlm.nih.gov/pubmed/22023820
http://dx.doi.org/10.1186/gb-2011-12-10-r108
_version_ 1782230519595925504
author Rasmussen, Markus
Sundström, Magnus
Kultima, Hanna Göransson
Botling, Johan
Micke, Patrick
Birgisson, Helgi
Glimelius, Bengt
Isaksson, Anders
author_facet Rasmussen, Markus
Sundström, Magnus
Kultima, Hanna Göransson
Botling, Johan
Micke, Patrick
Birgisson, Helgi
Glimelius, Bengt
Isaksson, Anders
author_sort Rasmussen, Markus
collection PubMed
description We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analysis of cancer samples indicates that TAPS is well suited to investigate samples with aneuploidy and tumor heterogeneity, which is commonly found in many types of solid tumors.
format Online
Article
Text
id pubmed-3333778
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-33337782012-04-23 Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity Rasmussen, Markus Sundström, Magnus Kultima, Hanna Göransson Botling, Johan Micke, Patrick Birgisson, Helgi Glimelius, Bengt Isaksson, Anders Genome Biol Method We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analysis of cancer samples indicates that TAPS is well suited to investigate samples with aneuploidy and tumor heterogeneity, which is commonly found in many types of solid tumors. BioMed Central 2011 2011-10-24 /pmc/articles/PMC3333778/ /pubmed/22023820 http://dx.doi.org/10.1186/gb-2011-12-10-r108 Text en Copyright ©2011 Rasmussen 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
Rasmussen, Markus
Sundström, Magnus
Kultima, Hanna Göransson
Botling, Johan
Micke, Patrick
Birgisson, Helgi
Glimelius, Bengt
Isaksson, Anders
Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
title Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
title_full Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
title_fullStr Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
title_full_unstemmed Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
title_short Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
title_sort allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3333778/
https://www.ncbi.nlm.nih.gov/pubmed/22023820
http://dx.doi.org/10.1186/gb-2011-12-10-r108
work_keys_str_mv AT rasmussenmarkus allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity
AT sundstrommagnus allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity
AT kultimahannagoransson allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity
AT botlingjohan allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity
AT mickepatrick allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity
AT birgissonhelgi allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity
AT glimeliusbengt allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity
AT isakssonanders allelespecificcopynumberanalysisoftumorsampleswithaneuploidyandtumorheterogeneity

Ejemplares similares