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Genome Biol. 2011 Oct 24;12(10):R108. doi: 10.1186/gb-2011-12-10-r108.

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

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1
Science for Life Laboratory, Department of Medical Sciences, Uppsala University, Akademiska sjukhuset, SE-751 85 Uppsala, Sweden.

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.

PMID:
22023820
PMCID:
PMC3333778
DOI:
10.1186/gb-2011-12-10-r108
[Indexed for MEDLINE]
Free PMC Article
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