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Background

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.

Objective

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.

Study design

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.

Results

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.

Conclusion

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.

Background

Heterozygous pathogenic variants in HNRNPK cause Au-Kline syndrome (AUKS), a neurodevelopmental disorder characterized by congenital anomalies and developmental delay. Prenatal diagnosis of AUKS remains challenging due to nonspecific ultrasound findings, such as increased nuchal translucency (NT) and nuchal fold (NF), which overlap with other genetic conditions.

Methods

Whole-exome sequencing (WES) was performed on a fetus exhibiting increased NT and NF thickening, alongside parental samples. Identified variants were validated by Sanger sequencing, with structural and functional impacts predicted using bioinformatic tools.

Results

WES revealed a de novo heterozygous frameshift variant in HNRNPK (NM_031263.4: c.504_507del) in exon nine of 17, which has been deposited in the ClinVar database with accession number VCV003899365 and classified as pathogenic (P). This variant results in a truncated protein (p.Lys168AsnfsTer35): bioinformatic predictions indicate the resulting mRNA is likely subject to nonsense-mediated mRNA decay (NMD), and any escaping mRNA would produce a severely truncated protein lacking critical functional domains, rendering it nonfunctional. Sanger sequencing confirmed the variant was absent in both parental genomes. Ultrasound findings aligned with AUKS-associated nonspecific prenatal anomalies, and post-induction gross examination confirmed subtle AUKS-related craniofacial features, expanding the known prenatal phenotype of AUKS and providing phenotypic severity context.

Conclusion

Structural and functional analyses provide mechanistic insights into the variant's pathogenicity, highlighting HNRNPK's role in fetal development. These findings advocate for integrating genomic and phenotypic data to improve prenatal diagnosis of rare genetic syndromes.

Background

Primary autosomal recessive microcephaly and Seckel syndrome spectrum (MCPH-SCKS) disorders are a group of autosomal recessive conditions characterized by severe growth retardation and neurodevelopmental impairment. CEP152 variants are established causes of both microcephaly and Seckel syndrome phenotypes, but the pathogenicity of different variant combinations and their clinical recurrence patterns require further verification with additional cases.

Methods

Clinical and genetic analyses were performed for two consecutive pregnancies of a non-consanguineous Chinese couple. Fetal phenotypes were evaluated by ultrasound and fetal MRI sequentially; copy number variation sequencing (CNV-seq) was used to detect large genomic variants, whole-exome sequencing (WES) to screen for point variants, and minigene splicing assays to characterize the functional impact of key variants.

Results

Fetuses in both pregnancies were diagnosed with MCPH-SCKS and harbored identical compound heterozygous CEP152 variants: a paternally inherited splice-site variant c.3346-5T>C and a maternally inherited 129.6 kb chromosomal deletion localized to 15q21.1, encompassing the entire CEP152 gene. Minigene assays confirmed that the c.3346-5T>C variant caused aberrant splicing via intron retention and exon skipping, clarifying its pathogenicity. The second pregnancy in 2024 independently verified the pathogenicity of this variant combination and disease recurrence.

Conclusion

This study represents the first report of identical compound heterozygous CEP152 variants causing MCPH-SCKS in two consecutive pregnancies. The independent occurrence in the second pregnancy not only confirms the pathogenicity of this variant combination but also provides clinical evidence for the 25% recurrence risk of autosomal recessive disorders. Furthermore, this report underscores the critical importance of comprehensive genetic testing, including CNV analysis, for the prenatal diagnosis of MCPH-SCKS, offering valuable guidance for genetic counseling and prenatal intervention in similar families.