Synthetic cfDNA for Aneuploidy Detection: 14 Chromosomal Conditions, Unlimited Validation Samples
Aneuploidies - whole chromosome gains or losses - are the foundation of prenatal screening. Trisomy 21, 18, and 13 are the conditions every NIPT laboratory must reliably detect. But validation has always faced the same constraint: where do you find enough positive samples to prove your assay works?
At Eabha Genomics, we've built synthetic cfDNA that solves this problem. Our platform generates biologically accurate cell-free DNA for 14 aneuploidy conditions, each validated to produce the expected z-scores that clinical pipelines depend on.
The Conditions We Cover
Common Trisomies
Every NIPT assay starts here:
| Condition | Chromosome | Our z-score | Prevalence |
|---|---|---|---|
| Trisomy 21 (Down syndrome) | chr21 | 7.66 | 1 in 700 |
| Trisomy 18 (Edwards syndrome) | chr18 | 5.53 | 1 in 5,000 |
| Trisomy 13 (Patau syndrome) | chr13 | 7.48 | 1 in 16,000 |
These are the conditions NIPT was built to detect. Our synthetic samples produce z-scores well above clinical thresholds (typically >3), giving you clear positive controls for validation.
Sex Chromosome Aneuploidies
Increasingly included in expanded NIPT panels:
| Condition | Karyotype | Our z-score | Prevalence |
|---|---|---|---|
| Turner syndrome | 45,X | -6.46 | 1 in 2,500 |
| Klinefelter syndrome | 47,XXY | 2.68 | 1 in 660 |
| Triple X | 47,XXX | 5.89 | 1 in 1,000 |
| 47,XYY | 47,XYY | 9.47 | 1 in 1,000 |
| 48,XXYY | 48,XXYY | 2.69 | 1 in 18,000 |
Rare Autosomal Trisomies
Often seen in mosaic form or in miscarriage samples:
| Condition | Chromosome | Our z-score | Notes |
|---|---|---|---|
| Trisomy 8 | chr8 | 3.22 | Often mosaic |
| Trisomy 9 | chr9 | 8.36 | Rare viable cases |
| Trisomy 16 | chr16 | 6.98 | Most common trisomy in miscarriage |
| Trisomy 22 | chr22 | 4.12 | Rare autosomal trisomy |
| Triploidy | genome-wide | multi-chr | Complete extra haploid set |
Why Synthetic Matters for Aneuploidy Validation
The math problem: A laboratory validating a T21 assay needs positive controls. With T21 occurring in 1 in 700 pregnancies, sourcing sufficient positive samples requires massive clinical networks or expensive commercial reference materials.
The rare condition problem: For Trisomy 9 or 48,XXYY? There are no commercial reference materials. Most labs have never seen a true positive.
Our solution: Generate unlimited synthetic cfDNA with precise chromosomal imbalances. Each sample includes:
- Configurable fetal fraction (2-25%)
- Controlled fragment length distributions matching real cfDNA
- GC bias patterns that align with clinical samples
- z-scores that clear clinical detection thresholds
Technical Validation
Every aneuploidy condition in our database has been:
- Generated with reference-backed fragments from hg38
- Aligned using BWA-MEM against GRCh38, achieving >95% mapping rate
- Detected using standard z-score methodology with GC correction
- Validated to produce expected signal at 15% fetal fraction
Get Started
Our aneuploidy panel is available now. We can generate custom sample sets tailored to your validation needs.
Contact us to discuss your requirements, or explore our full conditions database.