Reproducible results with a powerful in vitro diagnostic microarray platform

Microarrays are an ideal solution for copy number variation (CNV) analysis and molecular cytogenetic testing in your clinical laboratory. The Applied Biosystems CytoScan Dx microarray platform is an in vitro diagnostic solution that offers a reliable genome-wide approach for high-resolution DNA copy number analysis to study gains, losses, loss of heterozygosity (LOH)/absence of heterozygosity (AOH), copy-neutral loss of heterozygosity (cnLOH), regions identical-by-descent, and mosaicism.


Our robust microarray IVD platform is designed to provide reproducible results and save time and money, while delivering quality performance consistent with your laboratory requirements.


Thermo Fisher Scientific offers powerful IVD microarray solution for postnatal clinical applications to obtain consistent, reliable, and high-quality results. 


Our complete microarray IVD platform, the CytoScan Dx Cytogenetics Suite, includes CytoScan Dx arrays, automated and manual target preparation options, fully kitted reagents, the GeneChip System 3000Dx instrument for array processing, and Chromosome Analysis Suite (ChAS Dx) Software for data interpretation and reporting. The platform supports laboratories to help maximize operational time.

CytoScan Dx Assay

The CytoScan Dx Assay was the first whole-genome in vitro diagnostic test available in the US market that is also CE-marked. It supports the identification of the underlying genetic cause of developmental delay, intellectual disability, congenital anomalies, or dysmorphic features in children. It is the recommended standard in chromosomal microarray analysis. The assays's remarkable performance provides:

  • 2.67 million markers for copy number analysis, including 750,000 SNPs and 1.9 million nonpolymorphic probes

Exceptional coverage across entries in OMIM database, RefSeq, ClinGen, and DECIPHER/DDD constitutional regions


The CytoScan Dx Assay is a qualitative assay intended for the postnatal detection of CNVs in genomic DNA obtained from peripheral whole blood in patients referred for chromosomal testing based on clinical presentation. The assay should be processed using the GeneChip System 3000Dx intrument and the data should be analyzed using Chromosome Analysis Suite Dx (ChAS Dx) Software. It is not intended to be used for standalone diagnostic purposes, pre-implantation or prenatal testing or screening, population screening, or detection of or screening for acquired or somatic genetic aberrations.

GeneChip System 3000Dx v.2

 The GeneChip System 3000Dx (GCS 3000Dx) v.2 is the only microarray system for RNA- and DNA-based clinical tests that is available in the US and is compliant with the EU In Vitro Diagnostic Medical Devices Regulation 2017/746 (IVDR) as well.

Key highlights of GCS 3000Dx v.2:

  • Compact size for better space utilization
  • High-resolution scanning of 0.51–2.5 μm pixelations, automatically selected by array type
  • Optimal image uniformity and collection efficiency across entire scan area with proprietary Flying Objective lens technology
  • No laser drift and reduced scanner-to-scanner variability
  • Automatic adjustment of residual arc correction and x-linearity
  •  Compatibililty with the GeneChip AutoLoader Dx for complete walk-away scanning of up to 48 arrays at a time


The GCS 3000Dx v.2 comes with GeneChip Data Collection Dx (GCDC Dx) Software and runs on Microsoft Windows 64-bit operating systems. Software features include:

  • An updated user interface with remote monitoring capability
  • Simplified batch registration of arrays
  • Easy management of the client operating system, applications, and security for IT departments
  • Notifications for network path interruptions
  • Support of 14+ languages

Chromosome Analysis Suite Dx (ChAS Dx) Software

Designed for cytogenetic analysis, ChAS Dx Software is a stand-alone application for analysis and visualization of chromosomal aberrations across the genome that may include CN gain or loss or LOH.

ChAS Dx Software provides tools to:

  • Perform single-sample analysis of intensity data (.cel) files​
  • Analyze segment data at different levels of resolution​
  • View and export data that summarize chromosomal aberrations in table and graphical formats
  • Customize and load your own annotations and regions for focused analysis
  • ·Apply separate filters to the entire genome and user-specified regions of interest
  • Perform detailed sample comparisons​
  • Directly access external databases (e.g., NCBI, UCSC Genome Browser, Ensembl, OMIM)
  • Generate a results summary page containing copy number and LOH data

Product specifications

CytoScan Dx Assay

GeneChip System 3000Dx v.2

Applications Description
The benchmark in cytogenetics research with highest genome-wide resolution of CNVs for applications in postnatal research GeneChip array processing, scanning, and analysis
Sample types Product line
Blood GeneChip
Size of aberration* Dimensions

Losses: 25 kb

Gains: 50 kb


Mosaicism: >20% (approximately)

Fluidics station: 28 x 16 x 15.8 in. (71.1 x 41 x 40.2 cm)
Scanner with autoloader: 22.5 x 31 x 44.5 inches (57.2 x 78.7 x 113 cm)

Workstation monitor: 20.2 x 11 x 21 in. (52 x 28 x 54 cm)
Workstation tower: 6.7 x 18.5 x 17.7 in. (17 x 47 x 45 cm)

Input DNA Weight
250 ng

Fluidics station: 36 kg
Scanner with autoloader: 47.6 kg

Workstation monitor: 10 kg

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

Protocol time
4 days  

*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.

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