GeneChip System 3000Dx

Take the proven path to market

Microarray technology is the only IVD microarray system for molecular diagnostics

Microarrays have been used to discover an impressive number of clinically informative genomic and pharmacogenomic biomarkers. However, converting promising gene signatures into clinical diagnostic or prognostic tests can be an expensive endeavor with significant development and regulatory risks.

The Affymetrix GeneChip System 3000Dx v.2 is a robust system for clinical research and the only IVD and CE-marked microarray system for RNA- and DNA-based clinical tests. The GeneChip System 3000Dx v.2 is the foundation of the expanding Affymetrix Clinical Toolkit that includes the IVD and CE-marked Gene Profiling Reagents and the Gene Profiling Array cGMP U133 P2, the cGMP-manufactured version of the widely cited GeneChip Human Genome U133 Plus 2.0 Array. The Clinical Toolkit provides a proven path to market, enabling test developers to save time and money while helping to reduce regulatory risks.

GeneChip technology has been relied upon by thousands of researchers to obtain reproducible results for all their microarray applications.

Powered by Affymetrix™ Program
Enabling diagnostic development…with more applications on the way

The Powered by Affymetrix (PbA) Program provides outstanding design, development, and regulatory support for clinical researchers, entrepreneurs, and pharmaceutical companies interested in the development and commercialization of separately cleared molecular diagnostics.

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GCS 3000Dx v.2

GCS 3000Dx v.2 for:


  • Analyze or study precious human samples with confidence 

Diagnostic test development

  • Several FDA-cleared in vitro diagnostic and CE-IVD diagnostic tests have been developed and commercialized by Powered by Affymetrix™ partnersMany more molecular diagnostic tests are in development

Routine testing

  • One system, multiple applications 

One platform—multiple applications

GeneChip® System 3000Dx v.2 assay menu
Application area RUO* IVD**
3’ IVT expression analysis
Whole-transcript expression analysis
Genotyping/copy number  
Cytogenetic analysis  
Drug metabolism/pharmacogenomics
miRNA gene regulation  
Targeted resequencing  
Custom assays
* Each “Research Use Only” (RUO) array requires an array-specific Assay Software Module (ASM). A custom ASM can be developed for any GeneChip® Array.
A Data Transfer Server (DTS) is required to export .CEL files.
** FDA-cleared, IVD or CE-marked test developed by a third-party company on the Affymetrix® GCS 3000Dx platform.

GeneChip System 3000Dx v.2 microarray system for clinical research and molecular diagnostics

"In clinical research where irreplaceable human specimens are used, you do not have a second chance. Once you use the sample, it is gone. Thus, it is highly beneficial to use Affymetrix® IVD reagents and system with an established good analytical performance."

Catherine Dumur, PhD,
Director of the Molecular Morphology
Genomics Facility and Associate Professor at
Virginia Commonwealth University

"Affymetrix provides the tools to make it easy for Skyline to concentrate on diagnostic content. Building our AMLProfiler test on the FDA-cleared, CE-marked GCS 3000Dx v.2 microarray system using the FDA-cleared, CE-marked Gene Profiling Reagents greatly reduces our regulatory and operational risks, providing a faster path to market."

Henk Viëtor
CEO, Skyline Diagnostics BV

"The need for an FDA-cleared microarray platform was an important consideration in choosing the Affymetrix GCS 3000Dx system for Pathwork’s two FDA-cleared Tissue of Origin (TOO) tests, one that uses FFPE and the other frozen tumor samples. The Pathwork- Affymetrix PbA partnership continues to create value for both parties."

David Craford
Chief Commercial Officer,
Pathwork Diagnostics

GeneChip Scanner 3000Dx v.2 with AutoLoaderDx
Weight ~100 lb (45.4 kg)
Dimensions 13“ W x 22” D x 18” H (33 cm x 56 cm x 46 cm)
Loading clearance 36” (91.4 cm) above laboratory bench
Additional 18“ (46 cm) in clearance for AutoloaderDx
Power Voltage: 100–240 VAC; Current: 4–2A; Frequency: 50–60 Hz


GeneChip Fluidics Station 450Dx v.2
Weight ~80 lb (36.3 kg)

28“ W x 16 1/8” D x 15 13/16” H (71.1 cm x 41 cm x 40.2 cm)

Loading clearance

Additional 4“ (10.2 cm) at the back for ventilation

Power Voltage: 100–240 VAC; Current: 3A; Power: 300 Watts


Workstation with Affymetrix Molecular Diagnostics Software (AMDS) v1.0 and higher
Weight Computer monitor – 26 lb (11.8 kg)
Computer tower – 43 lb (19.5 kg)
Dimensions Computer monitor – 20 ¼“ W x 11” D x 21” H (52 cm x 28 cm x 54 cm)
Computer tower – 6 ¾” W x 18 ½“ D x 17 2/3“ H (17 cm x 47 cm x 45 cm)
Loading clearance 36” (91.4 cm) above laboratory bench
Additional 18“ (46 cm) in clearance for AutoloaderDx
Power Voltage: 100–240 VAC