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Related Concept Videos

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
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Updated: May 3, 2026

Semiconductor Sequencing for Preimplantation Genetic Testing for Aneuploidy
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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
PubMed
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.

Keywords:
Chromosomal microarray analysisCopy number variantsNon-invasive prenatal testingPrenatal diagnosisSNP Array

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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.