Molecular cytogenetic technique evaluating the entire genome for copy number variations (CNVs), including microdeletions and microduplications.
Array Comparative Genomic Hybridization (aCGH): Co-hybridizes differentially labeled patient DNA (e.g., green fluorophore) and reference DNA (e.g., red fluorophore) onto a microarray grid.
Fluorescence ratio determines genomic status: 1:1 ratio indicates normal representation, excess green indicates duplication, and excess red indicates deletion.
Single Nucleotide Polymorphism (SNP) Arrays: Evaluates polymorphic variations, detecting regions of homozygosity, uniparental disomy, and areas of consanguinity.
Clinical Indications
First-tier diagnostic test for unexplained intellectual disability, global developmental delay, and autism spectrum disorder.
Multiple congenital anomalies lacking a specific syndromic pattern.
Unexplained seizure disorders, dysmorphic facial features, and short stature.
Advantages and Limitations
Parameter
Advantages
Limitations
Diagnostic yield
15-20% in complex developmental presentations, vastly superior to traditional karyotyping (3%).
Generates Variants of Uncertain Significance (VUS), requiring parental testing for interpretation.
Resolution
Up to 50-fold higher than conventional karyotyping; detects single-exon anomalies (10-50 kilobases).
Cannot detect single nucleotide variants or point mutations.
Structural detection
Does not require dividing cells or cell cultures, allowing faster turnaround.
Sanger Sequencing: Gold standard utilizing chain-terminating dideoxynucleotides during in vitro replication. Used for targeted testing of known precise single-gene mutations and cascade family screening.
Next-Generation Sequencing (NGS): Massively parallel sequencing of millions of short DNA fragments simultaneously.
Targeted Gene Panels: Interrogates specific sets of genes associated with overlapping phenotypes (e.g., epilepsy or neuromuscular panels).
Whole Exome Sequencing (WES): Targets protein-coding regions (1-2% of the genome) harboring ~85% of disease-causing mutations. Yields 25-40% diagnostic success in rare genetic disorders.
Whole Genome Sequencing (WGS): Sequences entire coding and non-coding (intronic/regulatory) regions, providing 3,000 times more data than microarray.
Clinical Indications
Extreme genetic or locus heterogeneity (multiple genes causing the same condition).
Indistinct, atypical, or dual phenotypes (e.g., undiagnosed inborn errors of metabolism).
Critically ill infants requiring rapid generation of data (Rapid WES/WGS) for time-sensitive management.
Best performed using a trio approach (testing proband and both biological parents) to filter benign familial variants and pinpoint de novo mutations.
Advantages and Limitations
Parameter
Advantages
Limitations
Scope
Simultaneous interrogation of thousands of genes with high cost-efficiency per gene.
Variable coverage depth, particularly in GC-rich regions.
Analysis
Detects single nucleotide variants, missense/nonsense mutations, and small insertions/deletions. Enables re-analysis of data over time.
WES may miss triplet repeats, methylation defects, and large structural deletions.
Interpretation
Identifies specific genotype allowing precision therapeutics.
High rate of VUS, complex bioinformatics, and potential for incidental secondary findings (e.g., cancer predisposition) requiring ethical counseling.
Comparative Diagnostic Utility
Feature
Chromosomal Microarray
Next-Generation Sequencing
Primary target
Copy number variations, microdeletions, microduplications.
Single nucleotide variants, small insertions/deletions.
First-tier indication
Unexplained intellectual disability, global developmental delay, autism, congenital anomalies.
