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

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.

Figure 1

Detection of known and validated submicroscopic copy-number variations by high-density BAC, SNP, and oligonucleotide arrays. Individual chromosome plots are shown for Patient 8 (chromosome 9), with the log₂ T/R (test-over-reference) values plotted on the y-axis versus the genomic position on chromosome 9 on the x-axis. Results are shown for the tiling-resolution 32k BAC array (A), the 100k SNP array (B), the 250k SNP array (C), and the 385k oligonucleotide array (D). A known and validated microdeletion of 0.54 Mb on 9q33.1 is detected by all four genomic microarray platforms (see black arrow). In addition, a previously undetected microduplication is clearly visible on the chromosome profile obtained by the 250k SNP array (see grey arrow). This figure also shows the different levels of microarray noise present for the different microarray platforms.

Figure 2

Result of the power analysis of the four genomic microarray platforms for detection of a single copy-number gain or loss contained by different numbers of consecutive targets. The resulting power for a single copy-number gain (dotted) and a single copy-number loss (line) are displayed for the 32k BAC array platform (A), the 100k SNP array (B), the 250k SNP array (C), and 385k oligonucleotide array platform (D). The increase in number of targets has a varying impact on the resulting power across the four different microarray platforms. In addition, the number of consecutive targets required to detect single copy-number gains differs considerably from the number of targets needed to detect a single copy-number loss, and this difference appears to be platform-dependent.