Chen Songchang, Xu Wenqiu, Zhang Li, Luan Xiaorui, Liu Mengdi, You Hong, Shi Weihui, Zhou Xuanyou, Yang Zhen, Yang Yun, Xu Chenming
Institute of Reproduction and Development, Shanghai Key Laboratory of Reproduction and Development, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China; Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China.
Clin Lab, Shanghai, China.
Am J Obstet Gynecol. 2025 Jun 21. doi: 10.1016/j.ajog.2025.06.043.
Noninvasive prenatal screening for single-gene disorders is an emerging tool that might complement traditional aneuploidy screening by providing earlier, safer insights to invasive diagnostic methods, such as amniocentesis and chorionic villus sampling. However, previous studies were limited by small gene panels and incomplete follow-up data, hindering the accurate assessment of screening performance.
This study aimed to demonstrate the technical feasibility and evaluate the potential clinical performance of noninvasive prenatal screening for 202 dominant single-gene disorders using an expanded 155-gene panel in high-risk pregnancies, while also addressing limitations of prior studies, particularly in the calculation of positive predictive value and negative predictive value.
We conducted noninvasive prenatal screening for 202 dominant single-gene disorders on 750 maternal plasma samples from pregnant women with definitive ultrasound abnormalities. Unique molecular identifiers were used for sequencing error correction. All participants underwent confirmatory prenatal diagnostic testing via whole genome sequencing or whole exome sequencing of amniotic fluid samples. Variants identified through noninvasive prenatal screening for single-gene disorders were classified based on allele frequencies, and performance metrics (sensitivity, specificity, positive predictive value, and negative predictive value) were calculated to evaluate the efficacy of the screening approach.
Among 750 high-risk pregnancies, noninvasive prenatal screening for 202 dominant single-gene disorders identified 32 positive cases. Subsequent prenatal diagnosis confirmed one false positive and no false negatives, yielding a sensitivity of 100.0% (95% confidence interval, 100.0% to 100.0%) and a specificity of 99.9% (95% confidence interval, 99.6% to 100.1%). The positive predictive value and negative predictive value were 96.9% and 100.0%, respectively. Notably, 7 (22.6%) confirmed positive cases involved genes not covered in previous screening panels. Variant with a variant allele frequency >20% required maternal carrier verification to rule out potential false-positive results. A negative case initially classified as a variant of uncertain significance was reclassified as likely pathogenic following trio whole genome sequencing/whole exome sequencing analysis.
This study demonstrated the technical feasibility and clinical performance of an expanded noninvasive prenatal screening for 202 dominant single-gene disorders in the high-risk cohort. However, this screening panel does not replace the need for invasive diagnostic procedures, particularly for high variant allele frequency variants, and confirmatory trio whole genome sequencing/whole exome sequencing enhanced variant interpretation. Further studies in low-risk populations are needed to assess the clinical utility of this screening and to guide its appropriate integration with existing prenatal screening strategies.
单基因疾病的无创产前筛查是一种新兴工具，它可以通过提供更早、更安全的侵入性诊断方法（如羊膜穿刺术和绒毛取样）的信息来补充传统的非整倍体筛查。然而，先前的研究受到小基因面板和不完整随访数据的限制，阻碍了对筛查性能的准确评估。
本研究旨在证明使用扩展的155个基因面板对高危妊娠中的202种显性单基因疾病进行无创产前筛查的技术可行性，并评估其潜在的临床性能，同时解决先前研究的局限性，特别是在计算阳性预测值和阴性预测值方面。
我们对750例有明确超声异常的孕妇的母血样本进行了202种显性单基因疾病的无创产前筛查。使用独特的分子标识符进行测序错误校正。所有参与者通过羊水样本的全基因组测序或全外显子组测序进行确诊性产前诊断测试。通过单基因疾病无创产前筛查鉴定出的变异根据等位基因频率进行分类，并计算性能指标（敏感性、特异性、阳性预测值和阴性预测值）以评估筛查方法的有效性。
在750例高危妊娠中，对202种显性单基因疾病的无创产前筛查鉴定出32例阳性病例。随后的产前诊断确认了1例假阳性，无假阴性，敏感性为100.0%（95%置信区间，100.0%至100.0%），特异性为99.9%（95%置信区间，99.6%至100.1%）。阳性预测值和阴性预测值分别为96.9%和100.0%。值得注意的是，7例（22.6%）确诊阳性病例涉及先前筛查面板未涵盖的基因。变异等位基因频率>20%的变异需要对母亲携带者进行验证，以排除潜在的假阳性结果。一例最初分类为意义未明的变异在三联体全基因组测序/全外显子组测序分析后重新分类为可能致病。
本研究证明了在高危队列中对202种显性单基因疾病进行扩展无创产前筛查的技术可行性和临床性能。然而，该筛查面板并不能取代侵入性诊断程序的需求，特别是对于高变异等位基因频率的变异，并且确诊性三联体全基因组测序/全外显子组测序增强了变异解读。需要在低风险人群中进行进一步研究，以评估该筛查的临床效用，并指导其与现有产前筛查策略的适当整合。
