Journal Article

Genome-wide Copy Number Profiling on High-density Bacterial Artificial Chromosomes, Single-nucleotide Polymorphisms, and Oligonucleotide Microarrays: A Platform Comparison based on Statistical Power Analysis

Jayne Y. Hehir-Kwa, Michael Egmont-Petersen, Irene M. Janssen, Dominique Smeets, Ad Geurts van Kessel and Joris A. Veltman

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 14, issue 1, pages 1-11
Published in print January 2007 | ISSN: 1340-2838
Published online March 2007 | e-ISSN: 1756-1663 | DOI: http://dx.doi.org/10.1093/dnares/dsm002

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Abstract

Recently, comparative genomic hybridization onto bacterial artificial chromosome (BAC) arrays (array-based comparative genomic hybridization) has proved to be successful for the detection of submicroscopic DNA copy-number variations in health and disease. Technological improvements to achieve a higher resolution have resulted in the generation of additional microarray platforms encompassing larger numbers of shorter DNA targets (oligonucleotides). Here, we present a novel method to estimate the ability of a microarray to detect genomic copy-number variations of different sizes and types (i.e. deletions or duplications). We applied our method, which is based on statistical power analysis, to four widely used high-density genomic microarray platforms. By doing so, we found that the high-density oligonucleotide platforms are superior to the BAC platform for the genome-wide detection of copy-number variations smaller than 1 Mb. The capacity to reliably detect single copy-number variations below 100 kb, however, appeared to be limited for all platforms tested. In addition, our analysis revealed an unexpected platform-dependent difference in sensitivity to detect a single copy-number loss and a single copy-number gain. These analyses provide a first objective insight into the true capacities and limitations of different genomic microarrays to detect and define DNA copy-number variations.

Keywords: array CGH; molecular cytogenetics; microdeletion; copy-number variation; power analysis

Journal Article.  6412 words.  Illustrated.

Subjects: Genetics and Genomics

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