Chromosomal Microarray for Prenatal and Neurodevelopmental Diagnosis

Microarray as a First-Tier Test

Chromosomal Microarray (CMA) has revolutionized genetic diagnostics by enabling high-resolution genome-wide detection of copy number variations (CNVs). It has replaced conventional karyotyping as the first-tier genetic test in multiple clinical scenarios, particularly for prenatal diagnosis and neurodevelopmental disorders.

The American College of Medical Genetics (ACMG) and American College of Obstetricians and Gynecologists (ACOG) strongly recommend CMA over karyotyping in cases of :

Unexplained fetal anomalies detected by ultrasound.
Stillbirth or recurrent pregnancy loss.
Intellectual disability, developmental delay, autism spectrum disorder (ASD), or multiple congenital anomalies in postnatal cases.

Key Applications

Key Applications of Microarray in Clinical Practice

Prenatal Diagnosis :

CMA is recommended for all cases of fetal structural anomalies detected on ultrasound, as it increases the detection rate of pathogenic CNVs by 6-10% beyond karyotyping.

Fetal anomalies on ultrasound (e.g., congenital heart defects, brain malformations, diaphragmatic hernia).
Recurrent pregnancy loss or stillbirth (CMA has a 6-15% higher yield over karyotyping in cases of IUFD).
Normal karyotype but high-risk NIPT (CMA can detect cryptic deletions/duplications missed in karyotyping).
Advanced maternal age or abnormal serum screening results.

Prenatal CMA detects microdeletion/microduplication syndromes such as :

22q11.2 deletion syndrome (DiGeorge syndrome)

1p36 deletion
syndrome

Williams-Beuren syndrome (7q11.23 deletion)

Cri-du-chat syndrome
(5p deletion)

Postnatal Diagnosis

CMA is the gold standard for detecting genomic imbalances in children with:

Developmental delay/intellectual disability (~15-20% diagnostic yield).
Autism spectrum disorder (ASD) (~10-15% yield).
Multiple congenital anomalies (~15-20% yield).
Unexplained epilepsy/seizures.

CMA can also detect uniparental disomy (UPD) in disorders such as Prader-Willi and Angelman syndromes.

Pregnancy Loss and Stillbirth

CMA has a much higher detection rate (6–15%) than traditional karyotyping in identifying genetic causes of:

Recurrent pregnancy loss
Second/third-trimester fetal demise
Miscarriages with abnormal fetal phenotype

Microarray vs. Karyotyping

Microarray vs. Karyotyping: Why is CMA Superior?

Feature	Karyotyping	Microarray
Resolution	~5-10 Mb	~100-200 Kb
CNV Detection	Large chromosomal changes	Submicroscopic deletions & duplications
Detection of Uniparental Disomy (UPD)	No	Yes
Mosaicism Detection	Limited	Mosaicism Detection Limited Moderate (if >20%)
Turnaround Time	14+ days	~7 days

Microarray increases diagnostic yield by 6-10% beyond karyotyping in structurally normal fetuses with abnormal ultrasound findings.

Platform & Methodology

Microarray Testing Platform & Methodology

Suraksha Genomics utilizes Affymetrix Cytoscan Optima & Cytoscan 750K microarray platforms, ensuring:

Whole-genome coverage with exon-level resolution.
High signal-to-noise ratio, ensuring accurate CNV detection.
Interpretation based on ACMG, ClinGen, and Decipher standards.

Technology Details :

Probe density : 750,000 oligonucleotide and SNP probes.
Data analysis pipeline : Uses state-of-the-art bioinformatics algorithms to detect CNVs, loss of heterozygosity (LOH), and UPD.

Precision & Progress

Sample Requirements & Processing

Prenatal (Amniotic Fluid)

10-15 ml AF in sterile tube

Prenatal (CVS)

5 mg placental tissue in sterile medium

Postnatal (Peripheral Blood)

2-5 ml EDTA blood

Pregnancy Loss (POC Tissue)

20 mg tissue in sterile saline

Shipping Conditions : Room temperature or cold pack (depending on sample type).

Clinical Guidelines

Key Clinical Guidelines Supporting Microarray Use

Prenatal Testing Guidelines :

ACMG (2023) : CMA is the first-tier test for fetuses with structural anomalies.
ACOG/SMFM (2020) : CMA should be offered when prenatal ultrasound detects anomalies.

Postnatal Testing Guidelines :

American Academy of Pediatrics (AAP) : CMA is first-line for developmental delay, ASD, and congenital anomalies.
ISCA Consortium : CMA should replace karyotyping in postnatal cases.

Pregnancy Loss Guidelines :

ACOG (2013) : CMA should be offered for stillbirth evaluation.
ISPD (2018) : CMA increases detection rate in recurrent pregnancy loss.

Your results

Understanding Microarray Test Results

Result Type	Clinical Significance	Next Steps
Pathogenic CNV	Confirmed association with disease	Genetic counseling, further testing
Likely Pathogenic CNV	High probability of being disease-causing	Parental testing, further investigation
Variant of Uncertain Significance (VUS)	Unknown clinical impact	Requires parental CMA & follow-up
Benign CNV	No known clinical relevance	No action needed

How to Interpret a VUS?

Parental Testing

Determines whether the CNV is inherited or de novo.

Clinical Correlation

Compare with patient phenotype.

Database Comparison

Referencing ClinGen, Decipher and ExAC databases.

Why Refer Your Patients to Us?

Expertise : State-of-the-art technology backed by experience.
High Sensitivity & Accuracy : Uses Cytoscan Optima & 750K.
Comprehensive Reporting : ClinGen & ACMG guideline-based interpretations.
Genetic Counseling Support : Dedicated experts to guide clinicians.
Rapid Turnaround Time : Reports in 7-10 days.

Consult our experts

Chromosomal Microarray - For Doctors