A Unique Cytogenetics Tool

Agilent Technologies, Inc introduced the SurePrint G3 Human CGH+SNP microarray platform, an innovative system for simultaneous analysis of chromosomal copy number changes and copy-neutral aberrations. The system allows researchers to study the genetic basis of developmental disorders as well as many cancers.

This is the only two-colour CGH platform that can detect loss of heterozygosity/uniparental disomy (LOH/UPD) with 5- to 10- megabase resolution.

“Finally, we have an array that has optimal copy number detection, including the potential for exon-by-exon coverage, that also has SNPs to detect absence of heterozygosity [AOH] caused by UPD or consanguinity,” said Dr Arthur Beaudet, Chairman of the Department of Molecular and Human Genetics at Baylor College of Medicine.

The Agilent SurePrint G3 CGH+SNP arrays are available in both catalogue and custom designs, similar to our current array formats. Custom microarrays can be readily designed in eArray, Agilent’s free Web-based application, or eArray XD, the desktop version.

Both the catalogue SurePrint CGH+SNP 4x180K and 2x400K microarrays measure approximately 60,000 SNPs, resulting in approximately 5- to 10-megabase resolution for LOH/UPD detection across the entire genome. The approximately 120,000 CGH probes on the catalog 4x180K arrays consist of the International Standards for Cytogenomic Arrays Consortium’s entire 8x60K version probe set and an additional 60,000 backbone probes. The approximately 300,000 CGH
probes on the catalogue 2x400K array are gene- and exon-biased, focusing coverage on the most important regions of the genome.

The SurePrint G3 CGH+SNP microarrays use the identical highthroughput workflow as the current CGH-only microarrays so they can be simply and efficiently incorporated into cytogenetic research. Agilent’s Genomic Workbench software compliments array analysis by employing novel algorithms to determine copy number changes using CGH probes, to measure allele-specific copy numbers of SNP probes, and to locate regions of LOH/UPD. The software enables concurrent analysis of CGH and SNP data alongside QC metrics for high-confidence data evaluation.