Simultaneous Detection of Copy Number and Copy-Neutral LOH Using a Single Microarray

The current SurePrint G3 Human Comparative Genomic Hybridization (CGH) platform has been extended to include a set of Single Nucleotide Polymorphism (SNP) probes on the same microarray. This allows for the simultaneous, high-resolution detection of copy number and copy-neutral variations and eliminates the need to run two separate microarray experiments.

The same straightforward Agilent CGH workflow is used to prepare the samples for hybridization to the new SurePrint G3 Human CGH+SNP microarrays. Restriction digestion of genomic DNA allows genotyping of SNPs located in the enzymes’ recognition sites. After labeling and hybridization, CGH+SNP microarray data are analyzed using novel algorithms contained within Agilent’s Genomic Workbench software. In this application note, we measure SNP genotypes to discover copy-neutral lack or loss of heterozygosity (LOH), as well as copy number variations, to discover cytogenetic abnormalities associated with examples of known syndromes. We conclude that simultaneous high-quality, highresolution copy number and LOH information can be obtained with the new SurePrint G3 Human CGH+SNP microarrays, available in various catalog and custom formats.