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.
This document details the SurePrint G3 Human Comparative Genomic Hybridization (CGH) platform extended with Single Nucleotide Polymorphism (SNP) probes. This extension allows for the simultaneous, high-resolution detection of copy number variations and copy-neutral variations, eliminating the need for separate microarray experiments. The workflow utilizes the same straightforward Agilent CGH sample preparation and hybridization process.
The note explains how restriction digestion of genomic DNA enables genotyping of SNPs located at enzyme recognition sites. After labeling and hybridization, data is analyzed using Agilent's Genomic Workbench software. The document presents results demonstrating that high-quality, high-resolution copy number and LOH information can be obtained, including the detection of copy-neutral lack of heterozygosity (LOH), uniparental disomy (UPD), and other genetic abnormalities.
| Resolution for LOH detection | ~5-10 Mb |
|---|---|
| Total features (2x400K) | 420,288 |
| Total features (4x180K) | 180,880 |
| Distinct biological CGH probes (2x400K) | 292,097 |
| Distinct biological SNP probes (2x400K) | 118,955 |
| SNP probes span | variant Alul or Rsal restriction enzyme recognition sites |
The platform allows for the simultaneous detection of copy number and copy-neutral variations.
The genotypes measured by using two SNP probes per SNP result in approximately 5-10 Mb resolution for LOH detection.
CGH+SNP microarray data are analyzed using novel algorithms contained within Agilent's Genomic Workbench software.
In the experiment described, the SNP call accuracy was greater than 99%.