Copy Number Analysis with Microarrays

Microarrays are the platform of choice for detecting DNA structural variants (SV) such as chromosome insertions, duplications and deletions. In addition to these copy number variations (CNVs), whole-genome arrays that cover not-only polymorphic (SNP) but also non polymorphic regions can additionally detect chromosomal imbalances and allelic imbalance indicative of absence of heterozygosity (AOH), loss of heterozygosity (LOH), or long contiguous stretches of homozygosity (LCSH). 

Microarray based assays advantages:

  • Whole-genome coverage covering genes established as significant today as well as those with emerging evidence
  • High detection sensitivity: for low-level mosaics elucidating patterns of clonal evolution, heterogeneous samples, structural inconsistencies, and gDNA or cellular contamination
  • Flexible workflow: for processing from few to thousands of samples cost-effectively, manually or automated.
  • High quality, reproducible data that can be easily integrated on compared to public repositories and collaborators’ sources.
  • Fast turnaround time from sample to results, including data analysis, in 2- to 3-days

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Application areas

Reproductive Health

Compromising on genomic coverage, content, or resolution by using traditional methods such as karyotyping, fluorescent in situ hybridization (FISH), and low-resolution arrays leads to significant aberrations being missed, which necessitates further analysis, delaying results and increasing costs. Whole-genome microarrays that cover both polymorphic (SNPs) and non-polymorphic regions of the genome can be used to assess DNA copy number alterations at a much higher resolution than those older conventional methods.

Neurodevelopmental and Genetics Research

Most CNVs found in the human genome do not cause an effect in human health, however, hundreds of CNVs have been associated to neurological disorders such as schizophrenia, autism, attention deficit hyperactivity disorder (ADHD), intellectual disability and bipolar disorder.  Several well known studies using high resolution whole-genome microarrays reported that CNVs in the same genes might be implicated across these neurodevelopmental disorders.


Chromosomal abnormalities and genomic instability are one of the most important aberrations in cancer. Fully maximize cancer discoveries with whole genome coverage to simultaneously detect CNVs, LOH, cnLOH, low level mosaicism, ploidy, and sample heterogeneity.

Custom High-Throughput Applications

Create your own high throughput 96- or 384-panel with the most relevant markers for your own custom applications as well as genome-wide association, replication, fine mapping, and candidate gene studies combined with the capability of CNV elucidation.

Instruments and software

Low- to Medium-Throughput Instrument

The GeneChip™ Instrument System is a fully integrated platform for conducting your research using GeneChip-brand cartridge arrays. We offer three versions of this system and accessories for low- to medium-throughput array processing.

High-Throughput Instrument

GeneTitan Multi-Channel (MC) Instrument automates array processing from target hybridization to data generation by combining a hybridization oven, fluidics processing, and state-of-the art imaging device into a single bench-top instrument. GeneTitan MC Instrument allows unattended, overnight processing of large numbers of samples in parallel using 16-, 24-, 96- and 384-array layouts.


Chromosome Analysis Suite (ChAS) provides a free-of-charge intuitive and flexible workflow for accurate analysis. ChAS was developed with input from leading experts and is tailored for copy number and cytogenetics research analysis and reporting. ChAS enables you to view and summarize chromosomal aberrations across the genome. Chromosomal aberrations may include copy number gain or loss, mosaicism, or loss/absence of heterozygosity (LOH/AOH). The latest ChAS 3.1 includes the addition of a powerful database and the unique automatic diploid-centering algorithm for oncology applications.

CytoScan HD suite

Coverage without compromise

The CytoScan™ array was designed by empirically selecting probes from a pool of over 20 million probes and then further screening them with over 3,000 samples to choose those that performed best for whole-genome Copy Number applications.

The design is optimized for balanced whole-genome coverage, enabling high-resolution DNA copy number analysis with precise breakpoint accuracy, as well as high-density SNP coverage for LOH/AOH and LCSH that can lead to uniparental disomy (UPD) detection.

Our proprietary manufacturing technology produces arrays that are highly reproducible between each batch.

  • Exceptional performance: high specificity, sensitivity, dynamic range, and resolution across the genome
  • Designed to evolve with your applications: covers all 36,000 RefSeq genes, including 14,000 OMIM, all ClinGen (formerly ICCG and ISCA) and Decipher constitutional regions, and Sanger cancer genes.
  • High-density SNPs with >99% genotype accuracy: enables low-level mosaicism visualization, AOH and acquired UPD (aUPD) detection, copy number change confirmation, triploidy detection, allelic imbalance pattern visualization, genomic contamination identification, and parent-of-origin analysis
  • Complete solution helps save time and money: Simple and robust manual or automated protocols, easy-to-use software, and self-paced or laboratory-based training
  • Streamlined data analysis: Chromosome Analysis Suite (ChAS) is a software offering enhanced analysis features, including the ability to view and summarize chromosomal aberrations (CNVs, mosaicism, and LOH), duo-trio consistency tools, database building capabilities, and flexible results export options.
  • Robust across the broadest range of sample types: blood, bone marrow, buccal swabs, saliva, fresh and frozen tissues, uncultured or cultured cells, and many more