Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays
2008
Staaf, Johan | Lindgren, David | Vallon-Christersson, Johan | Isaksson, Anders | Göransson, Hanna | Juliusson, Gunnar | Rosenquist, Richard | Höglund, Mattias | Borg, Åke | Ringnér, Markus
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.
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