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

Staaf, Johan LU ; Lindgren, David LU ; Vallon-Christersson, Johan LU ; Isaksson, Anders; Goransson, Hanna; Juliusson, Gunnar LU ; Rosenquist, Richard; Höglund, Mattias LU ; Borg, Åke LU and Ringnér, Markus LU (2008) In Genome Biology 9(9).
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.
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Genome Biology
volume
9
issue
9
publisher
BioMed Central
external identifiers
  • wos:000260586900014
  • scopus:53349171050
ISSN
1474-7596
DOI
10.1186/gb-2008-9-9-r136
project
CREATE Health
language
English
LU publication?
yes
id
5b54b24b-1df9-486f-8ea5-522e65f79402 (old id 1283451)
date added to LUP
2009-02-10 11:42:41
date last changed
2017-10-22 03:42:01
@article{5b54b24b-1df9-486f-8ea5-522e65f79402,
  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.},
  articleno    = {R136},
  author       = {Staaf, Johan and Lindgren, David and Vallon-Christersson, Johan and Isaksson, Anders and Goransson, Hanna and Juliusson, Gunnar and Rosenquist, Richard and Höglund, Mattias and Borg, Åke and Ringnér, Markus},
  issn         = {1474-7596},
  language     = {eng},
  number       = {9},
  publisher    = {BioMed Central},
  series       = {Genome Biology},
  title        = {Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays},
  url          = {http://dx.doi.org/10.1186/gb-2008-9-9-r136},
  volume       = {9},
  year         = {2008},
}