Clinical Performance Evaluation of Size-Selective Placental Cell-Free DNA Enrichment for Non-Invasive Prenatal Testing of Fetal Copy Number Variants.

Objective

To evaluate the performance of low-depth non-invasive prenatal testing (NIPT) using cell-free DNA enrichment for detecting fetal copy number variations (CNVs) and to assess its clinical utility.

Methods

A retrospective analysis was conducted on 86,012 pregnant women who underwent NIPT with size-selective cell-free DNA enrichment. CNVs were detected using a Hidden Markov Model. Following prenatal diagnosis of positive cases through chromosome microarray analysis (CMA), positive predictive values (PPVs) were evaluated across different CNV sizes and fetal fractions, and the accuracy of CNV breakpoint validation was assessed.

Results

DNA enrichment achieved a mean fetal fraction of 18.88% ± 5.82%. A total of 340 CNVs were detected in 339 pregnant women, with an overall CNV positive rate of 0.39% [95% CI: 0.35%, 0.44%] (339/86, 012), including 249 deletions and 91 duplications. The total PPV for CNVs was 59.20% [95% CI: 52.05%, 66.00%] (119/201). For the accuracy of CNV size and position, 85.83% [95% CI: 78.01%, 91.29%] (103/120) of CNVs had size discrepancies < 25% compared to CMA, and 80.42% [95% CI: 74.71%, 85.13%] (193/240) of breakpoints were within 1 Mb. The 22q11.21 deletion was the most frequent CNV (16.76% [95% CI: 13.04%, 21.26%] (57/340)), with a PPV of 40.00% [95% CI: 25.28%, 56.61%] (16/40).

Conclusion

An elevated fetal fraction improves breakpoint accuracy. In addition to increasing sequencing depth, it represents a promising technical approach to optimizing the performance of NIPT.