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

Johan Staaf¹^,2 , David Lindgren¹ , Johan Vallon-Christersson¹^,2 , Anders Isaksson³ , Hanna Göransson³ , Gunnar Juliusson⁴ , Richard Rosenquist⁵ , Mattias Höglund¹ , Åke Borg¹^,2^,4 and Markus Ringnér¹^,2

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

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

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

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

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

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Genome Biology 2008, 9:R136doi:10.1186/gb-2008-9-9-r136


Published:	16 September 2008

Subject areas: Genetics, Bioinformatics, Genome studies

Abstract

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.