Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays.
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.
Staaf
Johan
J
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden. johan.staaf@med.lu.se
Lindgren
David
D
Vallon-Christersson
Johan
J
Isaksson
Anders
A
Göransson
Hanna
H
Juliusson
Gunnar
G
Rosenquist
Richard
R
Höglund
Mattias
M
Borg
Ake
A
Ringnér
Markus
M
D022981:Allelic Imbalance; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D018628:Gene Dosage; D005821:Genetic Techniques; D006801:Humans; D019656:Loss of Heterozygosity; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity
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