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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 orcid ; Lindgren, David LU ; Vallon-Christersson, Johan LU orcid ; Isaksson, Anders ; Goransson, Hanna ; Juliusson, Gunnar LU ; Rosenquist, Richard ; Höglund, Mattias LU ; Borg, Åke LU and Ringnér, Markus LU orcid (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
; ; ; ; ; ; ; ; and
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Genome Biology
volume
9
issue
9
article number
R136
publisher
BioMed Central (BMC)
external identifiers
  • wos:000260586900014
  • scopus:53349171050
ISSN
1474-7596
DOI
10.1186/gb-2008-9-9-r136
language
English
LU publication?
yes
additional info
The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Hematology/Transplantation (013022014), Division of Clinical Genetics (013022003), Oncology, MV (013035000)
id
5b54b24b-1df9-486f-8ea5-522e65f79402 (old id 1283451)
date added to LUP
2016-04-01 11:57:11
date last changed
2025-10-14 12:13:10
@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.}},
  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 (BMC)}},
  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}},
  doi          = {{10.1186/gb-2008-9-9-r136}},
  volume       = {{9}},
  year         = {{2008}},
}