GeneChip System 3000Dx

Take the proven path to market

It is the only FDA-cleared, IVDR compliant microarray system for RNA and DNA based clinical tests

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 Genechip System 3000Dx v.2 is the foundation of the Applied Biosystems Clinical Toolkit, which includes cGMP-manufactured microarrays. 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.


GCS 3000Dx v.2 for:


  • Analyze or study precious human samples with confidence 

Diagnostic test development

  • Several FDA-cleared in vitro diagnostic and IVDR compliant diagnostic tests have been developed. 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 areaRUO*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 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 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 GCS 3000Dx system for Pathwork’s two FDA-cleared Tissue of Origin (TOO) tests, one that uses FFPE and the other frozen tumor samples."

David Craford
Chief Commercial Officer,
Pathwork Diagnostics

GeneChip Scanner 3000Dx v.2 with AutoLoaderDx
Weight~100 lb (45.4 kg)
Dimensions13“ W x 22” D x 18” H (33 cm x 56 cm x 46 cm)
Loading clearance36” (91.4 cm) above laboratory bench
Additional 18“ (46 cm) in clearance for AutoloaderDx
PowerVoltage: 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

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


Workstation with Affymetrix Molecular Diagnostics Software (AMDS) v1.0 and higher
WeightComputer monitor – 26 lb (11.8 kg)
Computer tower – 43 lb (19.5 kg)
DimensionsComputer 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 clearance36” (91.4 cm) above laboratory bench
Additional 18“ (46 cm) in clearance for AutoloaderDx
PowerVoltage: 100–240 VAC

For In Vitro Diagnostic Use.