Reproducible results with powerful microarray analysis

Copy number variations (CNVs) are well-recognized genomic structural variants associated with genetic disorders and chromosomal microarray analysis (CMA). CMA can successfully detect submicroscopic CNVs. The American College of Medical Genetics (ACMG) recommends CMA be used as a first-tier test for postnatal research of unexplained intellectual disability, developmental delay, autism spectrum disorders, and congenital abnormalities. 


Applied Biosystems CytoScan microarrays enable labs to advance postnatal clinical research with powerful CMA. All CytoScan arrays are hybrid-SNP chromosomal microarrays that contain large numbers of both SNP probes and non-polymorphic probes. Hybrid-SNP arrays, with more than 99% genotype accuracy, boost confidence in breakpoint determination and provide independent confirmation of copy number events throughout the entire genome. 


Our robust microarray research solutions are designed to provide reproducible results, save you time and money while delivering quality performance consistent with your laboratory requirements. 


Thermo Fisher Scientific offers powerful microarray solutions for postnatal clinical research that are powered with robust workflows that make it easy to obtain consistent, reliable, and high-quality results. 


Our complete microarray platform, the CytoScan Cytogenetics Suite, includes hybrid-SNP arrays, automated and manual target preparation options, fully kitted reagents, the GeneChip System 3000 instrument for array processing, and Chromosome Analysis Suite (ChAS) software for data interpretation and reporting. These tools support laboratories to help maximize operational time. 

Product overview

CytoScan HD Array

The benchmark in cytogenetics research with highest genome-wide resolution of CNVs for applications in postnatal research. Key highlights of CytoScan HD array are:

  • 2.67 million markers for copy number analysis, including 750,000 SNPs and 1.9 million nonpolymorphic probes
  • Superior coverage across entries in OMIM® database, RefSeq, ClinGen, DECIPHER/DDD constitutional regions, and the COSMIC Cancer Gene Census (CGC)
  • Advanced, proprietary manufacturing technology that produces highly reproducible arrays between batches, with no risk of probe dropout that occurs with bead array technology

CytoScan XON Array

Sensitive single exon-level copy number analysis with exceptional coverage within exons across the whole genome. Use as a stand-alone test or to confirm CNV findings with alternative technologies like next generation sequencing. With the CytoScan XON array, you can:

  • Comprehensively detect single-exon deletions and duplications in a cost-effective manner
  • Complement NGS mutation analysis with reliable exon-level deletion and duplication detection
  • Confirm CNV findings from alternative technologies
  • Simplify and streamline copy number variants analysis

Product specifications

CytoScan HD

CytoScan XON

Research applications
The benchmark in cryogenics research with highest genome-wide resolution of CNVs for applications in prenatal and postnatal research

Research Applications

 Sensitive single exon-level copy number analysis with superior coverage within exons across the whole genome. Use as a standalone test or to confirm CNV findings with alternative technologies like next generation sequencing.

Sample types
Blood, buccal swabs, saliva, uncultured or cultured cells, chorionic villi, amniocytes, POC. Blood and other sources of DNA can be used upon building a customized reference file
Size of aberration*

Losses: 25 kb

Gains: 50 kb


Mosaicism: >15% (approximately)

95% sensitivity for the detection of exon-level CNVs.

Design to cover the whole genome, with increased coverage in 7,000 clinically relevant genes

Input DNA
10-250 ng** 100 ng
Probe structure

2.67 million markers for whole genome coverage

1.95 million nonpolymorphic markers

-743,000 SNP probes for LOH/AOH analysis, duo-trio assessment, and sample tracking

6.85 million empirically selected probes for whole-genome coverage including:

6.5 million copy number probes

300,000 SNP probes for LOH analysis, due-trio assessment, and sample tracking

3-4 days 4 days

*Size of aberration—The size of the segment call depends on the average marker spacing in the region. Best performance can be achieved in regions with higher marker coverage. Mosaicism detection may depend on the size of the altered segment and the type of aberration involved.

**250 ng is optimal but users have reported success using as little as 10 ng starting DNA.

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