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Updated: May 11, 2026
09:16
Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Combined array CGH plus SNP genome analyses in a single assay for optimized clinical testing.
Joanna Wiszniewska1, Weimin Bi1, Chad Shaw1
1Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
European Journal of Human Genetics : EJHG
|May 23, 2013
Summary
A new Chromosomal Microarray Analysis (CMA-COMP) combines array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping. This comprehensive platform efficiently detects copy number variants (CNVs) and absence of heterozygosity (AOH) for genetic disease diagnosis.
Area of Science:
- Genomics and Personalized Medicine
- Clinical Diagnostics
- Molecular Genetics
Background:
- Array comparative genomic hybridization (array CGH) and single nucleotide polymorphism (SNP) genotyping are key genomic technologies for diagnosing developmental delay, congenital anomalies, and neuropsychiatric disorders.
- Clinicians face challenges in selecting the optimal platform due to differing abilities to detect specific genomic alterations.
- SNP arrays excel at detecting copy-neutral absence of heterozygosity (AOH) but have limitations in identifying single-exon copy number variants (CNVs).
Purpose of the Study:
- To develop and evaluate a comprehensive genomic testing platform integrating array CGH and SNP genotyping.
- To assess the platform's ability to detect both copy number variants (CNVs) and copy-neutral absence of heterozygosity (AOH) efficiently.
- To address the diagnostic limitations of individual array CGH and SNP genotyping platforms.
Main Methods:
- Development of a custom-designed, high-resolution oligonucleotide array (CMA-COMP) with exon-targeted coverage for 1860 genes and 60,000 SNP probes.
- Evaluation of the CMA-COMP array in 3240 clinical cases.
- Analysis of detected copy number variants (CNVs), including exonic events, and absence of heterozygosity (AOH) regions.
Main Results:
- Clinically significant CNVs were identified in 445 cases, including 21 with exonic events.
- Absence of heterozygosity (AOH) regions greater than 10 Mb were detected in 162 cases (5.0%).
- The CMA-COMP array demonstrated reliable detection of AOH events (>10 Mb) and exonic CNVs, overcoming limitations of SNP genotyping alone.
Conclusions:
- The integrated CMA-COMP platform provides comprehensive genetic screening for both CNVs and AOH.
- Combining SNP probes with exon-targeted array CGH on a single platform offers an efficient diagnostic solution.
- This approach enhances the ability to detect the underlying genetic causes of developmental disorders and other conditions.
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