Affymetrix CytoScan Optima Chip: An economical approach to the Genome wide study of micro deletion/duplication syndrome

According to the Affymetrix’s website, the CytoScan® Optima Suite is designed on the basis of the inputs received from the genomics community and Affymetrix’s own experience with higher resolution arrays. Optima Array chips are designed to provide enhanced coverage of 396 relevant regions for prenatal and miscarriage applications.

Microarray technology uses specially designed chips to study the DNA from various sample types such as Blood, Amniotic Fluid, Tissue etc. The design of the chip has a very significant bearing on the quality of results and detection rates for various disorders.

While the company’s website provides a variety of information about the chip, the basis of shortlisting the relevant regions is not very clear. Nevertheless, there is enough information available to help us compare the various chips offered by Affymetrix and other providers such as Illumina.

Although, Affymetrix has positioned the chip for prenatal applications, we believe that it is most suited for detection of chromosomal abnormalities in cases of miscarriage or POC (Products of Conception) samples. This chip can help detect chromosomal abnormalities, micro-deletion/duplication syndromes, uniparental disomy (UPD), loss or absence of hetrozygosity (LOH/AOH) and mosaicism which is not possible through alternate technologies such as FISH (Fluorescence In Situ Hybridization) or Karyotyping or BAC on Beads.

The Affymetrix Optima chip can also offer an economical option in Paediatric and Post Natal cases especially for the current users of Illumina Cyto12 chip. The Optima chip has higher number of bio markers (SNP, CNV) and better marker spacing in the region of interest.


The Affymetrix Microarray system allows for processing of single samples, thereby improving the turnaround time.

chip is available only in selected countries in Asia. The countries in North America and Europe are mainly using the high resolution chips which offer significantly higher coverage and are accepted by the various genetic associations and communities. However, in cost sensitive markets like India, the Optima chip can provide a good starting point for the use of microarray, leading to improved diagnostics.