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Affymetrix GeneChip SNP

AffymetrixoneClickGCH, CGH Fusion and cnTrack are fully Affymetrix-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 by the infoQuant copy number analysis suite:

  • CytoScan HD
  • Cytogenetics Whole-Genome 2.7m Array
  • Genome-Wide Human SNP Array 6.0
  • Genome-Wide Human SNP Array 5.0
  • Human Mapping 500K
  • Human Mapping 100K
  • Human Mapping 10K

Cytogeneticists using Affymetrix platform can benefit from ISCN-compliant reporting module built into infoQuant software. oneClickCGH can be used to obtain full cytogenetic overview of a particular case at hands within minutes utilizing benefits of ultra-high resolution of Affymetrix arrays. CGH Fusion on the other hand allows its users to compare results across batches of samples and facilitates comparison of Affymetrix data with data generated by other array platforms, if necessary.

infoQuant's reliable aberration detection module based on a robust implementation of the industry standard  CBS approach can be used to make copy number calls on imported log-ratio data. 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 DNA anomaly calls. Visualization of both types of measurements makes chromosome 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.

Clinical users will find genome-wide data visualization and alteration reporting modules of oneClickCGH irreplaceable for diagnostic procedures.  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.

Larger laboratories can benefit from infoQuant’s data management solution cnTrack. cnTrack can be used to streamline array data operations in a multi-user environment. By integration with infoQuant’s Copy Number analytics suite and incorporation of various types of patient information into SNP array workflow cnTrack establishes itself as an end-to-end software solution for a high-throughput Cytogenetic laboratory.