AFFYMETRIX Microarray Solutions

Affymetrix® microarray solutions include all necessary components for a successful microarray experiment, from arrays and reagents to instruments and software. Our complete range of solutions addresses diverse research needs, from RNA to DNA analysis, a few to thousands of samples, and targeted to genome-wide analysis.

DNA Analysis Solutions

  • Genome-Wide Genotyping for Human Disease Research
  • Targeted Genotyping Analysis for Human Disease Research
  • Agrigenomics Solutions
  • Model Organisms and Companion Animals
  • Molecular Cytogenetics
  • OncoScan® assays
  • Copy Number Analysis
  • DMET plus Solution
  • Resequencing Analysis

Molecular Cytogenetics Arrays

Join the resolution revolution. Get performance that exceeds industry guidelines for specificity, sensitivity, and resolution. Be confident in identifying chromosomal aberrations.



Cytoscan HD

Highest genomic coverage: relevant today and in the future 

CytoScan HD Solution provides the broadest coverage and highest performance for detecting human chromosomal aberrations. CytoScan HD Array has greater than 99% sensitivity and can reliably detect 25-50 kb copy number changes across the genome at high specificity with SNP (allelic) call corroboration. With more than 2.6 million copy number markers, CytoScan Array has been recognized for its industry-leading coverage of all OMIM® and RefSeq genes. On a single platform, CytoScan HD Solution offers high-density resolution of the entire genome, extending throughout promoter and miRNA regions, for relevant aberration detection and reporting. Surpassing the limitations of current database curations, the whole-genome array ensures that novel findings can be catalogued for future discoveries and annotations which are often missed by targeted designs.

High-density SNPs: gene-level heterozygosity determination

CytoScan HD Array includes 750,000 SNPs with over 99% accuracy to detect accurate breakpoint estimation, loss of heterozygosity (LOH) determination, regions identical-by-descent, maternal contamination, and low-level mosaicism. The allelic information provides a powerful visualization of added confidence behind CNV calls as well as information on sample heterogeneity, clonal diversity, and uniparental disomy (UPD).

Support the broadest range of sample types – including FFPE!

CytoScan HD Array supports several different sample types for cancer and constitutional cytogenetic research analysis, including blood, bone marrow, buccal, saliva, fresh and frozen tissues, direct/cultured cells, amniocytes, and FFPE samples.


CytoScan 750K

Whole-genome coverage: best value 

CytoScan® 750K Cytogenetics Solution from Affymetrix enables cytogenetic researchers to detect and analyze relevant chromosomal aberrations with confidence. CytoScan 750K Cytogenetics Solution provides high-resolution coverage of cancer and constitutional genes of interest, along with high-density SNP coverage for loss of heterozygosity (LOH) detection.

Affymetrix developed CytoScan 750K Cytogenetics Array to provide a cost-effective solution that delivers industry-leading performance. Like CytoScan® HD Cytogenetics Solution, CytoScan® 750K Array, reagents, and software were developed with input from the international cytogenetics community to deliver an intuitive platform for fast and reliable detection of chromosomal aberrations.

Optimized reagent kit: streamlined workflow

CytoScan 750K Solution is designed to save time and money and reduce operator error. The simplified and streamlined assay protocol is aligned with laboratory workflow requirements, making it easier to obtain consistent and high-quality results. The reagent kit includes all reagents required for the array (except ethanol and the Clontech TITANIUM™ DNA Amplification Kit, P/N 639243)* including magnetic beads. Each component passes strict quality control inspection by Affymetrix to ensure the highest reproducibility and performance with CytoScan 750K Arrays. The CytoScan® protocol can be accomplished in 2.5 days with just seven hours of hands–on time.

*Clontech TITANIUM® Taq (ordered separately)

Most genotype-able SNPs: gene-level heterozygosity determination

CytoScan 750K Array includes 200,000 gene-centric SNPs to enable confident breakpoint estimation, 5 Mb loss of heterozygosity (LOH) determination and detection of uniparental iso-disomy (UPD) and regions identical-by-descent.


CytoScan® Optima Suite

 Robust and streamlined analysis of prenatal and miscarriage samples for the reliable detection of chromosomal abnormalities, submicroscopic aberrations, loss/absence of heterozygosity (LOH/AOH), uniparental disomy (UPD), and mosaics.

Approximately 50% of miscarriages are caused by chromosomal abnormalities. Traditional cytogenetic techniques such as karyotyping and FISH are limited by cell culture failure and usually lack the appropriate sensitivity.

CytoScan® Optima Suite has been designed with input from the cytogenetics community worldwide and empirically optimized from CytoScan® HD Suite. CytoScan® Optima Array offers whole-genome coverage for accurate detection of chromosomal abnormalities with increased probe coverage targeting 396 relevant regions for prenatal and miscarriage applications.

CytoScan Optima Suite includes arrays, reagents, and easy-to-use data analysis software for a cost-effective and streamlined analysis of your prenatal and product of conception (POC) samples.

CytoScan Optima Suite provides

Whole-genome coverage and higher resolution in key genetic regions to enable the detection of the following:

Whole-chromosome aneuploidies and submicroscopic gains and losses. This POC sample shows a 46 MB duplication in blue followed by a submicroscopic 2.2 MB deletion in red.

Whole-chromosome aneuploidies and submicroscopic gains and losses

LOH/AOH. This sample shows three confirmed purple LOH/AOH segments of different sizes and locations.


Triploidy and maternal cell contamination.
This whole-genome view shows four lines in the allelic difference track concordant with a triploidy in this first trimester POC sample.

Triploidy and maternal cell contamination
Low-level mosaicism

Low-level mosaicism. An increase in the signal in chromosome 2 shows a ~20% mosaic trisomy in this chorionic villi (CVS) sample.







An intuitive and flexible workflow for accurate analysis 

Chromosome Analysis Suite (ChAS) was developed with input from leading experts and enables you to easily view and summarize chromosomal aberrations across the genome. ChAS also includes

  • A database to store your data
  • Trio tool analysis
  • Flexible reporting tools
  • Updated external annotations
  • A built-in reference from CVS, amniocytes, cultured cells, POC, and blood samples
An intuitive and flexible workflow for accurate analysis