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Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia-A comparative study of four differently designed, high resolution microarray platforms.

Gunnarsson, Rebeqa LU ; Staaf, Johan LU orcid ; Jansson, Mattias ; Ottesen, Anne Marie ; Göransson, Hanna ; Liljedahl, Ulrika ; Ralfkiær, Ulrik ; Mansouri, Mahmoud ; Buhl, Anne Mette and Smedby, Karin Ekström , et al. (2008) In Genes, Chromosomes and Cancer 47(8). p.697-711
Abstract
Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. However, detection of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported... (More)
Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. However, detection of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported copy-number variations. LOH analysis using dChip revealed concordance of mainly large regions, but showed numerous, small nonoverlapping regions and LOH escaping detection. Evaluation of baseline variation and copy-number ratio response showed the best performance for the Agilent platform and confirmed the robustness of BAC arrays. Accordingly, these platforms demonstrated a higher degree of platform-specific CNAs. The SNP arrays displayed higher technical variation, although this was compensated by high density of elements. Affymetrix detected a higher degree of CNAs compared to Illumina, while the latter showed a lower noise level and higher detection rate in the LOH analysis. Large-scale studies of genomic aberrations are now feasible, but new tools for LOH analysis are requested. (Less)
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organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Genes, Chromosomes and Cancer
volume
47
issue
8
pages
697 - 711
publisher
John Wiley & Sons Inc.
external identifiers
  • wos:000256874100006
  • pmid:18484635
  • scopus:45349086985
ISSN
1045-2257
DOI
10.1002/gcc.20575
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: Oncology, MV (013035000), Hematology/Transplantation (013022014)
id
71490540-af1d-4a8f-bd3c-1a73ff63a83f (old id 1154053)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/18484635?dopt=Abstract
date added to LUP
2016-04-01 11:56:04
date last changed
2022-08-20 23:52:01
@article{71490540-af1d-4a8f-bd3c-1a73ff63a83f,
  abstract     = {{Screening for gene copy-number alterations (CNAs) has improved by applying genome-wide microarrays, where SNP arrays also allow analysis of loss of heterozygozity (LOH). We here analyzed 10 chronic lymphocytic leukemia (CLL) samples using four different high-resolution platforms: BAC arrays (32K), oligonucleotide arrays (185K, Agilent), and two SNP arrays (250K, Affymetrix and 317K, Illumina). Cross-platform comparison revealed 29 concordantly detected CNAs, including known recurrent alterations, which confirmed that all platforms are powerful tools when screening for large aberrations. However, detection of 32 additional regions present in 2-3 platforms illustrated a discrepancy in detection of small CNAs, which often involved reported copy-number variations. LOH analysis using dChip revealed concordance of mainly large regions, but showed numerous, small nonoverlapping regions and LOH escaping detection. Evaluation of baseline variation and copy-number ratio response showed the best performance for the Agilent platform and confirmed the robustness of BAC arrays. Accordingly, these platforms demonstrated a higher degree of platform-specific CNAs. The SNP arrays displayed higher technical variation, although this was compensated by high density of elements. Affymetrix detected a higher degree of CNAs compared to Illumina, while the latter showed a lower noise level and higher detection rate in the LOH analysis. Large-scale studies of genomic aberrations are now feasible, but new tools for LOH analysis are requested.}},
  author       = {{Gunnarsson, Rebeqa and Staaf, Johan and Jansson, Mattias and Ottesen, Anne Marie and Göransson, Hanna and Liljedahl, Ulrika and Ralfkiær, Ulrik and Mansouri, Mahmoud and Buhl, Anne Mette and Smedby, Karin Ekström and Hjalgrim, Henrik and Syvänen, Ann-Christine and Borg, Åke and Isaksson, Anders and Jurlander, Jesper and Juliusson, Gunnar and Rosenquist, Richard}},
  issn         = {{1045-2257}},
  language     = {{eng}},
  number       = {{8}},
  pages        = {{697--711}},
  publisher    = {{John Wiley & Sons Inc.}},
  series       = {{Genes, Chromosomes and Cancer}},
  title        = {{Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia-A comparative study of four differently designed, high resolution microarray platforms.}},
  url          = {{http://dx.doi.org/10.1002/gcc.20575}},
  doi          = {{10.1002/gcc.20575}},
  volume       = {{47}},
  year         = {{2008}},
}