Chromosomal microarray analysis (CMA) is a leading method for detecting DNA gains and losses across the entire genome.
Results are reported as copy number variants (CNVs): duplicated or deleted segments of DNA of at least 1,000 base pairs (1 kb) compared with a reference genome.
What microarray can identify
1Aneuploidy
Extra or missing chromosomes across all 23 pairs.
2Microdeletions & duplications
Clinically relevant submicroscopic syndromes.
3Large structural changes
Unbalanced rearrangements of chromosomes.
4Triploidy & contamination
SNP-based arrays detect triploidy and maternal cell contamination.
CNV classification
| Class | Meaning |
|---|---|
| Pathogenic | CNVs of clinical significance, linked to about 15% of genetic disease burden. |
| Non-pathogenic | CNVs with no clinical significance. |
| VOUS | Variants of uncertain significance. |
Advantages of microarray
- No culture failures: uses DNA from uncultured samples, so dividing cells are not needed and results are usually faster than karyotyping.
- Higher resolution: about 10–400 kb, compared with roughly 5–10 Mb for karyotyping.
- Detects maternal contamination: SNP-based analysis identifies triploidy and maternal cell contamination, reducing false negatives.
- Higher diagnostic yield: finds additional significant abnormalities in about 4–6% of pregnancies with abnormal ultrasound but a normal karyotype.
- Accuracy: automation reduces variation between observers.
Limitations
Microarray cannot detect balanced rearrangements (inversions or translocations with no gain or loss of material) or low-level mosaicism (generally below 10–15% of cells). Your counsellor will advise whether karyotyping is also needed.
Microarray vs karyotype
| Microarray (CMA) | Karyotype | |
|---|---|---|
| Resolution | 10–400 kb | 5–10 Mb |
| Cell culture needed | No | Yes |
| Detects balanced translocations | No | Yes |
| Detects microdeletions | Yes | No |