What is SNP Array Analysis?
SNP Array analysis uses Illumina genotyping microarray technology to simultaneously examine hundreds of thousands of single-nucleotide polymorphisms (SNPs) across the genome. Unlike standard karyotyping, which can only detect large chromosomal changes, this approach reveals copy number variations (CNVs) — microdeletions and microduplications — as well as regions of homozygosity (ROH), all from a single test. We don't just count chromosomes.
High Resolution
Detects very small chromosomal copy number variations (CNVs) invisible to standard karyotyping.
Homozygosity (ROH) Analysis
Unlike classic aCGH, SNP Array can identify homozygous regions, critical for consanguineous families and recessive disease diagnosis.
Precision Genotyping
Uses SNP probes alongside copy number probes to maximize accuracy and eliminate false positives.
Who Should Take This Test?
Prenatal Testing
Amniotic fluid or CVS. Recommended for:
- Increased NT (≥ 3.5mm) on ultrasound
- Structural anomalies on anomaly scan
- Previous pregnancy with unexplained chromosomal abnormalities
- High-risk result in NIPT / cell-free DNA screening
Postnatal Testing
Peripheral blood (EDTA). Recommended for:
- Developmental and motor delay
- Intellectual disability
- Autism spectrum disorders
- Multiple congenital anomalies and dysmorphic features
- Unexplained short stature or treatment-resistant seizures
Oncology & Research
SNP Array technology is also applied in tumor profiling and translational research, where it can detect:
- Somatic copy number alterations (amplifications and deletions) in tumor samples
- Loss of heterozygosity (LOH) relevant to tumor biology
- Genome-wide structural changes to support research studies
Platform Details
| Platform | Illumina Global Screening Array v3 (GSA v3), run on the Illumina iScan™ system |
|---|---|
| Total Markers | > 654,000 markers |
| CNV Resolution | High resolution in targeted regions for microdeletion / microduplication detection |
| Call Rate | > 99.8% |
| Reference Genome | GRCh37 / GRCh38 |
| Disease Coverage | Dense coverage for rare disease variants, GWAS, and pharmacogenomics |
| PGx Content | Includes key markers for drug-gene interaction analysis |
From Result to Clinical Decision
SNP Array results give clinicians concrete, actionable information. Two examples illustrate how findings translate into clinical decisions.
Microdeletion Syndromes
A deletion detected at chromosome 22q11.2 is consistent with DiGeorge syndrome, prompting specific clinical evaluation for cardiac, immune, and endocrine involvement — a diagnosis that structural karyotyping alone would likely miss.
Regions of Homozygosity (ROH)
Extended runs of homozygosity can indicate consanguinity and raise the likelihood of autosomal recessive conditions, helping guide targeted follow-up testing and genetic counseling for the family.
See SNP Array Results in Action
Explore a sample report and download our brochure to learn more about SNP Array testing.
Frequently Asked Questions
What is SNP Array testing?
SNP Array testing is a genome-wide genotyping technique that examines hundreds of thousands of single-nucleotide polymorphisms (SNPs) simultaneously, allowing detection of copy number variations (CNVs) and regions of homozygosity (ROH) in a single assay.
What is the difference between SNP Array and karyotyping?
Conventional karyotyping visualizes chromosomes under a microscope and can only detect relatively large structural changes. SNP Array uses molecular probes to detect much smaller copy number changes, and can also identify regions of homozygosity that karyotyping cannot detect at all.
What sample types are accepted?
For prenatal testing, amniotic fluid or chorionic villus sampling (CVS) is accepted. For postnatal testing, a peripheral blood sample collected in an EDTA tube is used.
How long does testing take?
Turnaround time depends on sample type and clinical urgency. Contact our team for current processing times.
Who should consider this test?
Prenatal candidates include pregnancies with increased nuchal translucency, structural anomalies on ultrasound, a prior unexplained chromosomal abnormality, or a high-risk NIPT result. Postnatal candidates include individuals with developmental delay, intellectual disability, autism spectrum disorder, multiple congenital anomalies, or unexplained short stature or seizures.
Can SNP Array detect all genetic conditions?
No single test detects everything. SNP Array identifies copy number variations and regions of homozygosity, but it does not detect balanced chromosomal rearrangements (such as balanced translocations or inversions) or single-gene point mutations and small insertions/deletions — these require complementary tests such as karyotyping or sequencing-based analysis.
What is a region of homozygosity (ROH) and why does it matter?
An ROH is a stretch of DNA where both inherited copies are identical, often a sign of shared ancestry between parents (consanguinity). Extended ROH can raise the likelihood of autosomal recessive conditions, making this information valuable for genetic counseling.