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Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays

Johan Staaf12, David Lindgren1, Johan Vallon-Christersson12, Anders Isaksson3, Hanna Göransson3, Gunnar Juliusson4, Richard Rosenquist5, Mattias Höglund1, Åke Borg124 and Markus Ringnér12*

Author Affiliations

1 Department of Oncology, Clinical Sciences, Lund University, SE-22185 Lund, Sweden

2 CREATE Health Strategic Centre for Clinical Cancer Research, Lund University, SE-22184 Lund, Sweden

3 Department of Medical Sciences, Cancer Pharmacology and Informatics, Uppsala University, SE-75185 Uppsala, Sweden

4 Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Lund University, SE-22184 Lund, Sweden

5 Department of Genetics and Pathology, Uppsala University, SE-75185 Uppsala, Sweden

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Genome Biology 2008, 9:R136  doi:10.1186/gb-2008-9-9-r136

Published: 16 September 2008


We present a strategy for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome single nucleotide polymorphism genotyping data. Using a dilution series of a tumor cell line mixed with its paired normal cell line and data generated on Affymetrix and Illumina platforms, including paired tumor-normal samples and tumors characterized by fluorescent in situ hybridization, we demonstrate a high sensitivity and specificity of the strategy for detecting both minute and gross allelic imbalances in heterogeneous tumor samples.