SNP Genotyping & CNV analysis

Affymetrix, Agilent and Illuminaoffer solutions for SNP genotyping for genome-wide association studies and CNV analysis for analysis of structural variation. The core facility provides wet lab and data analysis services for each platform.

Affymetrix SNP Genotyping and CNV analysis

The Affymetrix Genome-Wide Human SNP Array 6.0 features 1.8 million genetic markers, including more than 906,600 single nucleotide polymorphisms (SNPs) and more than 946,000 probes for the detection of copy number variation.

The next-generation Affymetrix Cytogenetics Research Solution includes arrays, reagents, and analysis software for the detection of a broad range of chromosome aberrations affecting phenotypes. The high-resolution array offers 2.7 million markers across the entire genome, including 400,000 SNPs to detect small structural changes and regions of autozygosity.

Other Affymetrix arrays include the Genome-Wide Human SNP Array 5.0 and the Human Mapping 500K Array Set.


Genome-wide copy number is important when analyzing solid tumors, as copy number aberrations and loss of heterozygosity (LOH) have been described in a high number of cancer associated genes. Several copy number aberrations are diagnostic as well as prognostic.

A challenge is to analyze small amounts of DNA from degraded FFPE samples. The Oncoscan FFPE assay from Affymetrix is developed for copy number and LOH profiling of highly degraded FFPE samples.

The Oncoscan assay requires a sample input of 80 ng of FFPE-derived DNA. One assay results in whole-genome copy number, LOH, and key somatic mutation data. This enables high resolution copy number detection in approximately 900 cancer genes. The Oncoscan Nexus Express free software allows rapid analysis of multiple of samples.


Axiom genotyping solution involves pre-designed custom arrays covering a high number of populations with validated genomic content from the Affymetrix Axiom database.

Arrays combining GWAS, replication, and fine mapping in one study, can be used for discovery of human disease genes, drug response biomarkers, or for population genetics.

For the analysis, genomic DNA (200 ng) is amplified and randomly fragmented and hybridized to Axiom array plates. Following hybridization, each polymorphic nucleotide is queried via a multi-color ligation event carried out on the array surface. After ligation, the arrays are stained and imaged on the Gene Titan array scanner.

Axiom Genotyping solution for agrigenomics includes arrays with content from the Axiom database from multiple species. Genotype any species, genome size, or ploidy level with your own proprietary markers or markers from recent sequencing initiatives.

Agilent CGH + SNP arrays

A complete solution for CGH, CGH+SNP, and CNV microarray analysis is provided by the Agilent platform.

SurePrint CGH Microarrays are a high-resolution tool for genome-wide DNA copy number variation profiling. SurePrint CGH+SNP Microarrays detect copy number changes as well as copy neutral aberrations, such as loss of heterozygosity (LOH) and uniparental disomy (UPD). SurePrint G3 and HD CNV microarrays are designed to study the estimated 0.9-1.3% “normal” difference in copy number of the genomes of unrelated people. In addition to human CGH arrays Agilent offer access to 8 different species.

Illumina Infinium HD

Illumina's Infinium HD beadchips feature genomic content available for genotyping, copy number variation (CNV), and cytogenetic analysis. Profile the human genome with 300,000 to nearly 1.2 million markers with dense coverage.

The Infinium HD Assay contains a proven robust chemistry with the beadchip array technology. The flexible Infinium HD design offers a powerful solution for different genetic analysis applications from customized studies on targeted regions to large-scale genome-wide association studies.