The CGI offers cytoSNP array services to enable high-resolution genome-wide analysis of copy number variation (CNV) and loss of heterozygosity (LOH) for research and clinical-adjacent applications. Utilizing the Illumina high-density SNP array platform, the core supports studies in cytogenetics, cancer genomics, developmental disorders, and population genetics. Services include project consultation, DNA quality assessment, array processing, and standardized data generation, with optional downstream analysis to aid interpretation. Experienced core staff work closely with investigators to ensure appropriate platform selection, robust data quality, and reproducible results, providing a reliable and cost-effective solution for genome-wide structural variation analysis.
Human Cytogenomics
The CGI offers the Illumina Infinium CytoSNP 850K BeadChip to support genome integrity screens in human samples/cell lines. The Infinium CytoSNP BeadChip consists of ~850K SNPs with 15X redundancy across the human karyotype, and enriched coverage for 3,262 cytogenetically relevant and dosage-sensitive genes.
Offering the ability to detect abnormalities as small as 1kb (theoretical detection based on genes with the highest probe density), the Infinium CytoSNP BeadChip can detect low level mosaicism, Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Chromosomal abnormalities, Copy number variants (CNVs), and absence of heterozygosity (AOH).
Each array supports up to 8 samples and arrays are scanned either on the Illumina NextSeq 550 or Illumina iScan system. Data is processed through BlueFuse Multi Software, with a report generated for the user detailing abnormalities, if detected. The Center for Genome Innovation reports all genomic abnormalities on a Research Use Only (RUO) basis and adheres to the following minimum reporting requirements across the genome:
Call Minimums:
Gains/Losses: 400Kb
LOH: 5Mb
If there are specific region/regions in your samples that you would like us to examine in more detail, we will make note of any findings with (*) if these abnormalities appear to be real but do not meet the minimum reporting requirements.
Additional array configurations and targets are available from Illumina. You can explore the current offering of Illumina arrays here. Please contact us if you are interested in any of these options. We can work with you and Illumina to determine the best solution for your research and whether we can accommodate your needs.
Non-human Cytogenomics and Region-specific screening
Illumina offers several options for non-human cytogenomic screening. Currently, they offer Bovine BeadChips and custom array solutions. You can explore the current offering of Illumina arrays here.