Affymetrix CytoScan Optima Chip: An economical approach to the genome-wide study of microdeletion/duplication syndrome

Affymetrix CytoScan® Optima Chip: An Economical Approach to Genome-Wide Study of Microdeletion/Duplication Syndromes

Chromosomal Microarray Analysis (CMA) has become one of the most reliable tools for identifying genetic abnormalities, microdeletions, and microduplications in prenatal, pediatric, and postnatal cases. Among the different microarray platforms available worldwide, the Affymetrix CytoScan® Optima Chip offers a cost-effective yet clinically valuable option for genetic diagnostics in cost-sensitive markets like India.

What is the CytoScan Optima Chip?

According to Affymetrix, the CytoScan® Optima Suite was designed using feedback from the genomics community and Affymetrix’s own experience with high-resolution arrays.

• Covers 396 clinically relevant regions, making it especially suitable for prenatal diagnosis and miscarriage analysis (Products of Conception / POC samples).

• Utilizes advanced SNP and CNV markers for improved accuracy.

• Provides data on microdeletion/duplication syndromes, uniparental disomy (UPD), loss of heterozygosity (LOH/AOH), and mosaicism.

Applications of the Optima Chip

While Affymetrix positions the Optima chip for prenatal applications, it is particularly valuable in:

• Miscarriage and POC Analysis

• Detects chromosomal abnormalities responsible for pregnancy loss.

• Provides crucial information for recurrence risk counseling.

• Prenatal Genetic Testing

• Identifies submicroscopic abnormalities not detectable by karyotyping or FISH.

• Useful in pregnancies with abnormal ultrasound findings.

• Pediatric & Postnatal Cases

• Detects developmental delays, autism spectrum disorders, congenital anomalies, and intellectual disability.

• More economical compared to higher-resolution arrays, making it a practical choice in India.

Advantages Over Other Platforms

• Higher coverage than Illumina Cyto12 Chip

• Contains a larger number of SNP and CNV markers.

• Better marker spacing in clinically relevant regions.

• Single-sample processing

• Allows faster turnaround time for results.

• Affordable option for India

• In cost-sensitive markets, Optima serves as a practical entry point for adopting microarray technology.

Limitations

• Available only in selected Asian countries – not widely used in North America or Europe, where high-resolution arrays with broader coverage are standard and recommended by genetic associations.

• Lower resolution compared to premium chips, meaning that very small variants may still be missed.

Conclusion

The Affymetrix CytoScan Optima Chip offers a balanced solution between cost and diagnostic utility, making it especially valuable for:

• Prenatal screening in India

• Miscarriage (POC) analysis

• Pediatric and postnatal genetic cases

While higher-resolution arrays remain the gold standard in developed nations, the Optima chip provides clinically relevant information at an economical cost, helping doctors and patients in India access advanced genetic diagnostics more easily.

📧 To learn more about Microarray Testing using Affymetrix CytoScan Optima Chip in India, contact us at info@labassure.com

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