Targeted gene panel sequencing prenatally detects two novel mutations of DYNC2H1 in a fetus with increased biparietal diameter and polyhydramnios

Genetic analysis and prenatal diagnosis of short-rib thoracic dysplasia 3 with or without polydactyly caused by compound heterozygous variants of DYNC2H1 gene in four Chinese families

Background: To describe the genetic variation of dynein cytoplasmic 2 heavy chain 1 (DYNC2H1) gene in four Chinese families affected with short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3), and to provide evidence for accurate prenatal diagnosis and genetic counseling.

Methods: The detailed clinical prenatal sonographic features of four fetuses with SRTD3 were carried out. Trio-whole exome sequencing (WES) and proband-WES sequencing was applied to filtrated causative variants in four families. The causative variants of each family were validated in by Sanger sequencing. Bioinformation analysis was applied to predict the harmfulness of these mutations and perform the protein-protein interaction network and Gene Ontology (GO) analysis. A vitro minigene splicing assay was conducted to assess the influence of the splice site variant.

Results: Typical characterization of the four fetuses included short long bones, short ribs, narrow chest, hand and foot posture abnormalities, femur short in diameter and slightly bowing, cardiac abnormalities, and so on. Moreover, eight compound heterozygous variants of DYNC2H1 (NM_001080463.2): c.3842A>C (p.Tyr1281Ser) and c.8833-1G>A, c.8617A>G (p.Met2873Val) and c.7053_7054del (p.Cys2351Ter), c.5984C>T (p.Ala1995Val) and c.10219C>T (p.Arg3407Ter), c.5256del (p.Ala1753GlnfsTer13) and c.9737C>T (p.Thr3246Ile), were identified. Among which, c.10219C>T (p.Arg3407Terp), c.5984C>T (p.Ala1995Val) and c.9737C>T (p.Thr3246Ile) were reported in ClinVar databases, and c.8617A>G (p.Met2873Val), c.10219C>T (p.Arg3407Ter), c.5984C>T (p.Ala1995Val) were found in HGMD databases. Four variants (c.3842A>C (p.Tyr1281Ser), c.8833-1G>A, c.7053_7054del (p.Cys2351Ter) and c.5256del (p.Ala1753GlnfsTer13) were first reported as novel mutations. According to the ACMG guidelines, c.8617A>G (p.Met2873Val), c.7053_7054del (p.Cys2351Ter), c.5984C>T (p.Ala1995Val), c.10219C>T (p.Arg3407Ter) and c.5256del (p.Ala1753GlnfsTer13) were rated as pathogenic or likely pathogenic variants, others variants were predicted to be variants of uncertain significance mutations. The minigene assay results indicated that c.8833-1G>A caused the skipping over exon 56, resulting in exon 56 loss.

Conclusion: In our study, we analyzed the genetic mutations in four fetuses with SRTD3 by whole exome sequencing and identified pathogenic variants causing SRTD3. Our results expand the mutation spectrum of DYNC2H1 in SRTD3, which is helpful for the accurate prenatal diagnosis of SRTD3 fetuses and provide useful strategies for genetic counseling.

Compound heterozygous variants in DYNC2H1 in a foetus with type III short rib-polydactyly syndrome and situs inversus totalis

Background

Short-rib thoracic dysplasia 3 with or without polydactyly (SRTD3, OMIM: 613091) is an autosomal recessive disorder. SRTD3 presents clinically with a narrow thorax, short ribs, shortened tubular bones, and acetabular roof abnormalities. Clinical signs of SRTD3 vary among individuals. Pathogenic variants of DYNC2H1 (OMIM: 603297) have been reported to cause SRTD3.

Methods

We performed a detailed clinical prenatal sonographic characterization of a foetus with SRTD3. Trio whole-exome sequencing was used to identify causative variants in the family. The identified variants in the families were validated by Sanger sequencing and mass spectrometry. Multiple computational tools were used to predict the harmfulness of the two variants. A minigene splicing assay was carried out to evaluate the impact of the splice-site variant.

Results

We evaluated prenatal sonographic images of the foetus with SRTD3, including abnormal rib curvature, narrow thorax, bilateral hypoplastic lungs, bilateral polydactyly, syndactyly, and foetal visceral situs inversus with mirror-image dextrocardia. We revealed novel compound variants of DYNC2H1 (NM_001377.3:c.11483T > G (p.Ile3828Arg) and c.2106 + 3A > T). Various statistical methods predicted that the variants would cause harmful effects on genes or gene products. The minigene assay findings suggested that c.2106 + 3A > T caused the skipping over exon 14, producing an exon 14 loss in the protein.

Conclusion

This study identified a foetus with SRTD3 with situs inversus totalis with mirror-image dextrocardia in a Chinese family, revealing two novel compound heterozygous dynein cytoplasmic 2 heavy chain 1 (DYNC2H1) variants, expanding the phenotypic spectrum of SRTD3. The minigene study of c.2106 + 3A > T was predicted to cause an inframe exclusion of exon 14, which was predicted to have important molecular functions. Our findings strongly supported the use of WES in prenatal diagnosis and helped to understand the correlation of genotype and phenotypes of DYNC2H1. The specific sonographic findings and the molecular diagnosis helped add experience to further our expertise in prenatal counselling for SRTD3.

The effect of polyhydramnios degree on chromosomal microarray results: a retrospective cohort analysis of 742 singleton pregnancies

PURPOSE

To analyze the risk for clinically significant microarray aberrations in pregnancies with polyhydramnios.

METHODS

Data from all chromosomal microarray analyses (CMA) performed due to polyhydramnios between January 2013 and December 2019 were retrospectively obtained from the Ministry of Health Database. The rate of clinically significant (pathogenic and likely pathogenic) CMA findings in isolated and non-isolated polyhydramnios cohorts was compared to a local control group of 5541 fetuses with normal ultrasound, in which 78 (1.4%) abnormal results were demonstrated. Subgroup analyses were performed by the degree of polyhydramnios, week of diagnosis, maternal age, and the presence of additional sonographic anomalies.

RESULTS

In the isolated polyhydramnios cohort, 19/623 (3.1%) clinically significant CMA aberrations were noted, a significantly higher rate compared to the control population. However, the risk for abnormal CMA results in the 158 cases with mild polyhydramnios (AFI 25-29.9, or maximal vertical pocket 8-11.9 cm) did not significantly differ from pregnancies with normal ultrasound. Of 119 cases of non-isolated polyhydramnios (most frequently associated with cardiovascular (26.1%) and brain (15.1%) anomalies), 8 (6.7%) abnormal CMA findings were noted, mainly karyotype-detectable.

CONCLUSION

Mild polyhydramnios was not associated with an increased rate of clinically significant microarray results, compared to pregnancies with normal ultrasound. An extensive anatomical sonographic survey should be performed in pregnancies with polyhydramnios, with consideration of fetal echocardiography.

Prenatal diagnosis of micrognathia in 41 fetuses: Retrospective analysis of outcome and genetic etiologies

Fetal micrognathia can be detected early in pregnancy. Prognosis of micrognathia depends on the risk of respiratory distress at birth and on the long-term risk of intellectual disability. The purpose of this study was to evaluate the long-term prognosis of fetuses with prenatal diagnosis of micrognathia by estimating the prevalence and the severity of confirmed genetic diagnosis in our cohort. Our retrospective study included 41 fetuses with prenatal diagnosis of micrognathia referred to the multidisciplinary centers for prenatal diagnosis in Nice and Marseille, France, between 2006 and 2016. Fetal micrognathia was associated with cleft palate in 27 cases. A genetic cause was confirmed in 21 cases (67%). A chromosomal abnormality was present in 12 cases, including three copy-number variations diagnosed by array CGH. Monogenic disorders were identified in nine cases, most often after birth. Fetuses with family history of micrognathia or Pierre Robin sequence had a favorable outcome. Prognosis was good for the fetuses without associated findings and normal chromosomal analysis, with the exception of one case with a postnatal diagnosis of mandibulofacial dysostosis with microcephaly. Prognostic was poor for the fetuses with additional ultrasound anomalies, as only 5 out of 28 children had a good outcome. Prenatal diagnosis of micrognathia is an indicator of a possible fetal pathology justifying multidisciplinary management. Our study confirms the necessity of performing prenatal array CGH. Use of high-throughput gene sequencing in prenatal period could improve diagnostic performance, prenatal counseling, and adequate postnatal care.