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Prenatal SNP-array chromosomal microarray analysis in 3,549 pregnancies: indication-specific yields and clinical
Yilun Tao1,2, Yuefeng Wei3, Zerong Yao3
1Medical Genetic Center, Changzhi Maternal and Child Health Care Hospital, 38 Weiyuanmen Road, Changzhi, Shanxi, 046000, China. yltao21@163.com.
BMC Pregnancy and Childbirth
|May 1, 2026
Summary
SNP-based chromosomal microarray analysis (CMA) offers a 10.9% diagnostic yield in prenatal testing, with higher rates for NIPT high-risk referrals. This supports an indication-based approach for genomic testing in pregnancy.
Area of Science:
- Genetics
- Genomics
- Prenatal Diagnostics
Background:
- SNP-based chromosomal microarray analysis (CMA) is a key tool in invasive prenatal diagnosis.
- Its real-world performance in the era of non-invasive prenatal testing (NIPT) requires further characterization.
Purpose of the Study:
- To evaluate the diagnostic yield of SNP-array CMA across various prenatal referral pathways.
- To assess the impact of referral indications and ultrasound findings on diagnostic yield and variant of uncertain significance (VOUS) detection.
Main Methods:
- Retrospective analysis of 3,549 prenatal invasive samples tested using SNP-array.
- Evaluation of diagnostic yield stratified by referral indication (NIPT high-risk, ultrasound, advanced maternal age, serum screening) and ultrasound phenotype.
Main Results:
- Overall diagnostic yield was 10.9% (398 pathogenic/likely pathogenic variants in 386 fetuses), including 223 aneuploidies and 175 pathogenic copy number variations (CNVs).
- Variants of uncertain significance (VOUS) were found in 12.0% of cases, with stable rates across indications.
- Diagnostic yield was highest for NIPT high-risk referrals (38.9%) and ultrasound cases (~11%), significantly lower for advanced maternal age (4.2%) and serum screening (~5-6%).
- Multisystem anomalies (27.3%) and increased nuchal translucency (NT) were strong predictors of pathogenic findings.
Conclusions:
- SNP-array CMA identified clinically actionable findings in 10.9% of prenatal cases.
- NIPT serves as an effective triage for aneuploidy, enhancing diagnostic yields for high-risk populations.
- An indication-based genomic testing strategy, utilizing NIPT and CMA, is supported, alongside improved VOUS counseling.
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