Article reference:


J. Hehir-Kwa, M. Egmont-Petersen, I. Janssen, D. Smeets, A. Geurts van Kessel. J. Veltman. "Genome-wide copy number profiling on high-density BAC, SNP and oligonucleotide microarrays: a platform comparison based on statistical power analysis," to appear in DNA Research, 2007.



Recently, comparative genomic hybridization onto BAC arrays (array CGH) 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 megabase. The capacity to reliably detect single copy number variations below 100 kilobases, 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 variation.

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