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

Markus Rasmussen1, Magnus Sundström2, Hanna Göransson Kultima1, Johan Botling2, Patrick Micke2, Helgi Birgisson3, Bengt Glimelius45 and Anders Isaksson1*

Author Affiliations

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

2 Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, SE-751 85 Uppsala, Sweden

3 Department of Surgical Sciences, Uppsala University, Akademiska sjukhuset, SE-751 85 Uppsala, Sweden

4 Department of Radiology, Oncology and Radiation Sciences, Uppsala University Akademiska sjukhuset, SE-751 85 Uppsala Sweden

5 Department of Oncology and Pathology, Karolinska Institutet, SE-17177 Stockholm, Sweden

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Genome Biology 2011, 12:R108  doi:10.1186/gb-2011-12-10-r108

Published: 24 October 2011

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.