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

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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, R.; Staaf, J.; Jansson, M.; Ottesen, A.M.; Goransson, H.; Liljedahl, U.; Ralfkiaer, U.; Mansouri, M.; Buhl, A.M.; Smedby, K.E.; Hjalgrim, H.; Syvanen, A.C.; Borg, A.; Isaksson, A.; Jurlander, J.; Juliusson, G.; Rosenquist, R.

I: Genes, Chromosomes & Cancer, Bind 47, Nr. 8, 2008, s. 697-711.

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningfagfællebedømt

Harvard

Gunnarsson, R, Staaf, J, Jansson, M, Ottesen, AM, Goransson, H, Liljedahl, U, Ralfkiaer, U, Mansouri, M, Buhl, AM, Smedby, KE, Hjalgrim, H, Syvanen, AC, Borg, A, Isaksson, A, Jurlander, J, Juliusson, G & Rosenquist, R 2008, 'Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms', Genes, Chromosomes & Cancer, bind 47, nr. 8, s. 697-711.

APA

Gunnarsson, R., Staaf, J., Jansson, M., Ottesen, A. M., Goransson, H., Liljedahl, U., ... Rosenquist, R. (2008). Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms. Genes, Chromosomes & Cancer, 47(8), 697-711.

Vancouver

Gunnarsson R, Staaf J, Jansson M, Ottesen AM, Goransson H, Liljedahl U o.a. Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms. Genes, Chromosomes & Cancer. 2008;47(8):697-711.

Author

Gunnarsson, R. ; Staaf, J. ; Jansson, M. ; Ottesen, A.M. ; Goransson, H. ; Liljedahl, U. ; Ralfkiaer, U. ; Mansouri, M. ; Buhl, A.M. ; Smedby, K.E. ; Hjalgrim, H. ; Syvanen, A.C. ; Borg, A. ; Isaksson, A. ; Jurlander, J. ; Juliusson, G. ; Rosenquist, R. / Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms. I: Genes, Chromosomes & Cancer. 2008 ; Bind 47, Nr. 8. s. 697-711.

Bibtex

@article{6be642e0f36211ddbf70000ea68e967b,
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",
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 Udgivelsesdato: 2008/8",
author = "R. Gunnarsson and J. Staaf and M. Jansson and A.M. Ottesen and H. Goransson and U. Liljedahl and U. Ralfkiaer and M. Mansouri and A.M. Buhl and K.E. Smedby and H. Hjalgrim and A.C. Syvanen and A. Borg and A. Isaksson and J. Jurlander and G. Juliusson and R. Rosenquist",
year = "2008",
language = "English",
volume = "47",
pages = "697--711",
journal = "Genes, Chromosomes & Cancer",
issn = "1045-2257",
publisher = "JohnWiley & Sons, Inc.",
number = "8",

}

RIS

TY - JOUR

T1 - Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia--a comparative study of four differently designed, high resolution microarray platforms

AU - Gunnarsson, R.

AU - Staaf, J.

AU - Jansson, M.

AU - Ottesen, A.M.

AU - Goransson, H.

AU - Liljedahl, U.

AU - Ralfkiaer, U.

AU - Mansouri, M.

AU - Buhl, A.M.

AU - Smedby, K.E.

AU - Hjalgrim, H.

AU - Syvanen, A.C.

AU - Borg, A.

AU - Isaksson, A.

AU - Jurlander, J.

AU - Juliusson, G.

AU - Rosenquist, R.

PY - 2008

Y1 - 2008

N2 - 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 Udgivelsesdato: 2008/8

AB - 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 Udgivelsesdato: 2008/8

M3 - Journal article

VL - 47

SP - 697

EP - 711

JO - Genes, Chromosomes & Cancer

JF - Genes, Chromosomes & Cancer

SN - 1045-2257

IS - 8

ER -

ID: 10151503