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Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity |
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| Authors: | Rasmussen Markus Sundström Magnus Kultima Hanna Göransson Botling Johan Micke Patrick Birgisson Helgi Glimelius Bengt Isaksson Anders |
| Institution: | 1. Novartis Vaccines and Diagnostics, Via Fiorentina 1, 53100, Siena, Italy 2. Allegheny General Hospital, Allegheny-Singer Research Institute, Center for Genomic Sciences, Pittsburgh, Pennsylvania, 152123, USA 3. Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Kragujevac, MD, 21201, USA 4. The Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK 5. Laboratorio di Microbiologia Molecolare e Biotecnologia, Dipartimento di Biologia Molecolare, Universita’ di Siena, Policlinico Le Scotte, 53100, Siena, Italy 6. Division of Infection and Immunity, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK 7. Institute of Medical Microbiology and Immunology, Aarhus University, DK-8000, Aarhus, Denmark 8. University of Oxford Department of Paediatrics, Medical Sciences Division, John Radcliffe Hospital, Headington, OX3 9DU, UK |
| 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. |
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