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1: Genome Biol. 2008;9(9):R136. Epub 2008 Sep 16.Click here to read Click here to read Links

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

Staaf J, Lindgren D, Vallon-Christersson J, Isaksson A, Göransson H, Juliusson G, Rosenquist R, Höglund M, Borg A, Ringnér M.

Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden. johan.staaf@med.lu.se

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.

PMID: 18796136 [PubMed - indexed for MEDLINE]

PMCID: PMC2592714