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

  • Johan Staaf
  • David Lindgren
  • Johan Vallon-Christersson
  • Anders Isaksson
  • Hanna Goransson
  • Gunnar Juliusson
  • Richard Rosenquist
  • Mattias Höglund
  • Åke Borg
  • Markus Ringnér
Publishing year: 2008
Language: English
Publication/Series: Genome Biology
Volume: 9
Issue: 9
Document type: Journal article
Publisher: BioMed Central

Abstract english

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.


  • Cancer and Oncology
  • Medical Genetics
  • Hematology


  • CREATE Health
  • ISSN: 1474-7596
Åke Borg
Åke Borg
E-mail: ake [dot] borg [at] med [dot] lu [dot] se

Principal investigator

Oncology and Pathology, MV

+46 46 275 25 52

MV 404 C21B2


Project manager

Familial Breast Cancer



Oncology and Pathology, MV

MV 404 C21C2