Low-Depth NIPT Finds Fetal DNA Clues

A large review looked at 86,012 pregnant people who used a low-depth NIPT method. The test focused on cell-free DNA that is enriched by size. This approach aimed to spot fetal copy number variants, or CNVs. A Hidden Markov Model helped flag possible CNVs. Positive cases were then checked with chromosome microarray analysis.

The enrichment process reached an average fetal fraction of 18.88%, with a spread of 5.82%. Researchers found 340 CNVs in 339 pregnant people. That gave an overall positive rate of 0.39%. The group included 249 deletions and 91 duplications. The total positive predictive value was 59.20%. In other words, about 119 of 201 flagged CNVs were confirmed.

Size and position checks also mattered. For 85.83% of CNVs, the size difference was under 25% compared with CMA. For 80.42% of breakpoints, the location was within 1 Mb. The 22q11.21 deletion showed up most often, making up 16.76% of detected CNVs. Its PPV was 40.00%. Higher fetal fraction improved breakpoint accuracy. This suggests that boosting fetal fraction can be a useful way to sharpen NIPT performance.

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