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

ABSTRACT: 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.

SUBMITTER: Rasmussen M

PROVIDER: S-EPMC3333778 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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

Rasmussen Markus M Sundström Magnus M Göransson Kultima Hanna H Botling Johan J Micke Patrick P Birgisson Helgi H Glimelius Bengt B Isaksson Anders A

Genome biology 20111024 10

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 ...[more]

PMID: 22023820

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

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