Affymetrix GeneChip SNP

oneClickGCH and CGH Fusion are GeneChip-compatible solutions. Log-ratios and allele-specific measurements can be easily imported into infoQuant software from .CYCHP or .CNCHP files generated using Affymetrix Chromosome Analysis Suite or Genotyping Console respectively. The following chip types are supported:

• Genome-wide Cyto Chip 2.7m
• Genome-wide Human SNP Array 6.0
• Genome-wide Human SNP Array 5.0
• Human Mapping 500K
• Human Mapping 100K
• Human Mapping 10K

infoQuant’s reliable aberration detection module based on the CBS approach can be used to make copy number calls on imported log-ratio data, including X chromosome. Alternatively, results of copy number analysis performed by Affymetrix Chromosome Analysis Suite or Genotyping Console can be imported with the data and utilized in both oneClickCGH and CGH Fusion.

Affymetrix users can also benefit from infoQuant's reliable procedure of LOH region detection. Our software combines log-ratio and allele-specific information in order to deliver robust LOH calls. Visualization of both types of measurements makes alteration analysis even more comprehensive.

Analysis of very large sets of samples for common Copy Number and/or LOH patterns is one of infoQuant's strongest areas of expertise. The memory- and CPU-efficient cross-sample analysis pipeline of CGH Fusion ensures that high resolution SNP datasets can be quickly processed on an average PC.

Cytogeneticists will find genome-wide data visualization and alteration reporting modules of oneClickCGH irreplaceable for diagnostic procedures. For ultra-high resolution chips infoQuant products provide unique benefits if you are looking to process array data on an average PC. Both oneClickCGH and CGH Fusion provide fast and memory-efficient yet fully interactive analysis and visualization of array data. Intelligent integration of gene annotations, known CNVs and other useful information simplifies clinical interpretation of detected aberrations. probe-level plots integrated into cytogenetic views preserve the high resolution of acquired data and make Copy Number/LOH reporting procedure more reliable.