Table 1 Array-based comparative genomic hybridization versus single nucleotide polymorphism array

Probes

Traditionally, the probes are long oligonucleotides (50 to 70 bases) solely designed for copy number analysis. Newer platforms have added SNP-based probes for limited regions of the genome mainly to detect UPD (for example, Agilent CGH + SNP arrays)

SNP-based oligonucleotides designed for SNP genotyping. Copy number can be inferred by additional analysis. Newer platforms have added long oligonucleotides designed solely for copy number analysis to improve resolution (for example, Affymetrix SNP 6.0, Illumina 1M)

Experimentation

Genomic DNA from the patient and a control are labeled with different fluorophores and hybridized to the same array. The differences in signal intensity between the patient and control samples, which is converted to a log₂ ratio, indicates a difference of copy number

In SNP-arrays the patient sample is hybridized to the microarray by itself. Copy number is determined by comparing the signal intensity data obtained from the patient sample with a collection of controls previously analyzed and incorporated into the analysis software

Resolution

Probes can be tiled to provide very high resolution. More flexibility and customization of probe content and density. Single exon resolution possible

The placement of probes is dependent on location of SNPs limiting resolution. Less flexibility in way of customization of probe content

Applications

Can only be used for copy number analysis. Will not detect UPD or consanguinity unless SNP probes are specifically added. Will also detect low-level mosaicism of CNVs

Will detect UPD, consanguinity, as well as copy number variations. Will also detect low-level mosaicism of CNVs