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Screening for copy-...
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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- Gunnarsson, Rebeqa (author)
- Lund University,Lunds universitet,Stamcellscentrum (SCC),Avdelningen för stamcellsforskning,Institutionen för laboratoriemedicin,Medicinska fakulteten,Stem Cell Center,Division of stem cell research,Department of Laboratory Medicine,Faculty of Medicine
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- Staaf, Johan (author)
- Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine
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- Jansson, Mattias (author)
- Uppsala universitet,Institutionen för genetik och patologi
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Ottesen, Anne Marie (author)
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- Göransson, Hanna (author)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Cancer Pharmacology and Informatics
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- Liljedahl, Ulrika (author)
- Uppsala universitet,Institutionen för medicinska vetenskaper
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Ralfkiær, Ulrik (author)
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- Mansouri, Mahmoud (author)
- Uppsala universitet,Institutionen för genetik och patologi
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Buhl, Anne Mette (author)
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- Smedby, Karin Ekström (author)
- Karolinska Institutet
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Hjalgrim, Henrik (author)
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- Syvänen, Ann-Christine (author)
- Uppsala universitet,Institutionen för medicinska vetenskaper
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- Borg, Åke (author)
- Lund University,Lunds universitet,Bröstcancer-genetik,Sektion I,Institutionen för kliniska vetenskaper, Lund,Medicinska fakulteten,Breastcancer-genetics,Section I,Department of Clinical Sciences, Lund,Faculty of Medicine
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- Isaksson, Anders (author)
- Uppsala universitet,Institutionen för medicinska vetenskaper,Cancer Pharmacology and Informatics
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Jurlander, Jesper (author)
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- Juliusson, Gunnar (author)
- Lund University,Lunds universitet,Stamcellscentrum (SCC),Avdelningen för stamcellsforskning,Institutionen för laboratoriemedicin,Medicinska fakulteten,Stem Cell Center,Division of stem cell research,Department of Laboratory Medicine,Faculty of Medicine
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- Rosenquist, Richard (author)
- Uppsala universitet,Institutionen för genetik och patologi
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(creator_code:org_t)
- 2008
- 2008
- English.
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In: Genes, Chromosomes and Cancer. - : Wiley. - 1045-2257 .- 1098-2264. ; 93, s. 0536-0536
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http://dx.doi.org/10...
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Abstract
Subject headings
Close
- 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.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Cancer och onkologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Cancer and Oncology (hsv//eng)
- MEDICIN OCH HÄLSOVETENSKAP -- Klinisk medicin -- Hematologi (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Clinical Medicine -- Hematology (hsv//eng)
Keyword
- MEDICINE
- MEDICIN
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Gunnarsson, Rebe ...
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Staaf, Johan
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Jansson, Mattias
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Ottesen, Anne Ma ...
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Göransson, Hanna
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Liljedahl, Ulrik ...
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show more...
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Ralfkiær, Ulrik
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Mansouri, Mahmou ...
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Buhl, Anne Mette
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Smedby, Karin Ek ...
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Hjalgrim, Henrik
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Syvänen, Ann-Chr ...
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Borg, Åke
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Isaksson, Anders
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Jurlander, Jespe ...
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Juliusson, Gunna ...
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Rosenquist, Rich ...
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Cancer and Oncol ...
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Clinical Medicin ...
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and Hematology
- Articles in the publication
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Genes, Chromosom ...
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Haematologica-Th ...
- By the university
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Uppsala University
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Lund University
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Karolinska Institutet