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Updated: Aug 7, 2025
Array Comparative Genomic Hybridization Array CGH for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
The Clinical Diagnostic Utility of Array CGH in Children with Syndromic Microcephaly
Manisha Goyal1, Mohammed Faruq2, Ashok Gupta1
1Department of Pediatrics, Centre of Rare Diseases, SMS Medical College, Jaipur, Rajasthan, India.
Insights
Array comparative genomic hybridization (CGH) identified copy number variations in 33.3% of children with syndromic microcephaly. This highlights the role of submicroscopic chromosomal changes in causing this condition.
Area of Science:
- Genetics
- Pediatrics
- Medical Diagnostics
Background:
- Syndromic microcephaly is a complex condition often associated with developmental delays and congenital anomalies.
- Identifying the genetic underpinnings of microcephaly is crucial for diagnosis and management.
Purpose of the Study:
- To identify copy number variations (CNVs) causative of microcephaly using chromosomal array comparative genomic hybridization (CGH).
- To investigate the contribution of submicroscopic chromosomal alterations to syndromic microcephaly.
Main Methods:
- A prospective study was conducted on 60 children diagnosed with syndromic microcephaly at a tertiary pediatric healthcare center in India.
- Array CGH was employed to analyze the genomes of children, excluding those with known genetic or acquired causes of microcephaly.
- Potentially pathogenic copy number variants (CNVs) were identified and analyzed for their clinical relevance.
Main Results:
- Clinically relevant pathogenic or likely pathogenic CNVs were detected in 20 out of 60 (33.3%) patients.
- Deletions were the most common type of pathogenic CNV (12 cases), followed by duplications (5 cases) and complex chromosomal rearrangements (3 cases).
- Twelve cases with pathogenic CNVs involved genes known to be implicated in the etiology of microcephaly.
Conclusions:
- Submicroscopic chromosomal changes significantly contribute to the etiology of syndromic microcephaly.
- Array CGH analysis is beneficial in diagnosing patients with syndromic microcephaly, revealing underlying genetic causes.
Background:
A prospective study using array CGH in children with Syndromic microcephaly from a tertiary pediatric healthcare centre in India.
Aim:
To identify the copy number variations causative of microcephaly detected through chromosomal array CGH.
Patients And Methods:
Of the 60 patients, 33 (55%) males and 27 (45%) females who consulted the Rare Disease Clinic at Department of Pediatrics, SMS Medical College, Jaipur, with developmental delay/facial dysmorphism/congenital anomalies in combination with microcephaly were included.
Exclusion Criteria:
Children with acquired or non-genetic causes of microcephaly, craniosynostosis, metabolic diseases, known chromosomal aneuploidy such as trisomy 21, 13, and 18 and abnormal karyotype were excluded. The cohort was analyzed by array CGH in order to identify potentially pathogenic copy number variants (CNVs).
Results:
Clinically relevant pathogenic or likely pathogenic copy number variations (CNVs) were identified in 20/60 (33.3%) patients, variant of uncertain significance (VOUS) in 4/60 (6.6%) cases and benign CNVs in 3/60 (5%) of total cases. Out of 20 cases with pathogenic CNVs, 12 (60%) patients detected with a deletion, five (25%) patients with duplication and three (15%) patients resulted with a complex chromosomal rearrangement. Twelve cases present CNVs containing genes known to be implicated in microcephaly etiology.
Conclusion:
This research highlights the contribution of submicroscopic chromosomal changes in the etiology of microcephaly in combination with developmental delay/facial dysmorphism/congenital anomalies (syndromic microcephaly). Our studies provide more insights into the benefits derived by using array CGH analysis in patients with syndromic microcephaly.
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