uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Screening for copy-number alterations and loss of heterozygosity in chronic lymphocytic leukemia-A comparative study of four differently designed, high resolution microarray platforms
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
Show others and affiliations
2008 (English)In: Genes, Chromosomes and Cancer, ISSN 1045-2257, E-ISSN 1098-2264, Vol. 47, no 8, 697-711 p.Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2008. Vol. 47, no 8, 697-711 p.
National Category
Medical and Health Sciences
URN: urn:nbn:se:uu:diva-16518DOI: 10.1002/gcc.20575ISI: 000256874100006PubMedID: 18484635OAI: oai:DiVA.org:uu-16518DiVA: diva2:44289
Available from: 2008-05-27 Created: 2008-05-27 Last updated: 2010-05-07Bibliographically approved

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Jansson, MattiasGöransson, HannaLiljedahl, UlrikaMansouri, MahmoudSyvänen, Ann-ChristineIsaksson, AndersRosenquist, Richard
By organisation
Department of Genetics and PathologyDepartment of Medical Sciences
In the same journal
Genes, Chromosomes and Cancer
Medical and Health Sciences

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 272 hits
ReferencesLink to record
Permanent link

Direct link