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http://dx.doi.org/10.5808/GI.2010.8.3.138

Comparison of the Affymetrix SNP Array 5.0 and Oligoarray Platforms for Defining CNV  

Kim, Ji-Hong (Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine)
Jung, Seung-Hyun (Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine)
Hu, Hae-Jin (Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine)
Yim, Seon-Hee (Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine)
Chung, Yeun-Jun (Integrated Research Center for Genome Polymorphism, The Catholic University of Korea School of Medicine)
Publication Information
Genomics & Informatics / v.8, no.3, 2010 , pp. 138-141 More about this Journal
Abstract
Together with single nucleotide polymorphism (SNP), copy number variations (CNV) are recognized to be the major component of human genetic diversity and used as a genetic marker in many disease association studies. Affymetrix Genome-wide SNP 5.0 is one of the commonly used SNP array platforms for SNP-GWAS as well as CNV analysis. However, there has been no report that validated the accuracy and reproducibility of CNVs identified by Affymetrix SNP array 5.0. In this study, we compared the characteristics of CNVs from the same set of genomic DNAs detected by three different array platforms; Affymetrix SNP array 5.0, Agilent 2X244K CNV array and NimbleGen 2.1M CNV array. In our analysis, Affymetrix SNP array 5.0 seems to detect CNVs in a reliable manner, which can be applied for association studies. However, for the purpose of defining CNVs in detail, Affymetrix Genome-wide SNP 5.0 might be relatively less ideal than NimbleGen 2.1M CNV array and Agilent 2X244K CNV array, which outperform Affymetrix array for defining the small-sized single copy variants. This result will help researchers to select a suitable array platform for CNV analysis.
Keywords
copy number variation (CNV); single nucleotide polymorphism (SNP);
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