Copy number variations and fetal ventriculomegaly

Role of Sonographic Second Trimester Soft Markers in the Era of Cell-Free DNA Screening Options: A Review

Soft markers are sonographic structural, nonspecific signs with little pathological significance, often transient, usually considered as normal variants. However, they may also be associated with chromosomal abnormalities. The most widely examined soft markers include absent or hypoplastic nasal bone (NB), intracardiac echogenic focus (IEF), ventriculomegaly (VM), thickened nuchal fold (NF), choroid plexus cyst (CPC), echogenic bowel, short long bones, and urinary tract dilation (UTD). Although the use of noninvasive prenatal testing (NIPT) has been spreading quickly in maternal–fetal medicine, it is not a diagnostic test and it still remains unavailable or cost-prohibitive for most of the population in many countries. After normal screening test results in the first trimester, there is no uniform consensus regarding the clinical significance of isolated soft markers for aneuploidy. Nowadays, the search for soft markers in an ultrasound is still part of clinical evaluation, and the interpretation of these findings is often a matter of debate. In the present review, we summarize the recent literature about the role of soft markers in the era of NIPT and propose an overview of the different clinical guidelines.

Genomic approaches to improve the clinical diagnosis and management of patients with congenital hydrocephalus

Congenital hydrocephalus (CH), characterized by incomplete clearance of CSF and subsequent enlargement of brain ventricles, is the most common congenital brain disorder. The lack of curative strategies for CH reflects a poor understanding of the underlying pathogenesis. Herein, the authors present an overview of recent findings in the pathogenesis of CH from human genetic studies and discuss the implications of these findings for treatment of CH. Findings from these omics data have the potential to reclassify CH according to a molecular nomenclature that may increase precision for genetic counseling, outcome prognostication, and treatment stratification. Beyond the immediate patient benefits, genomic data may also inform future clinical trials and catalyze the development of nonsurgical, molecularly targeted therapies. Therefore, the authors advocate for further application of genomic sequencing in clinical practice by the neurosurgical community as a diagnostic adjunct in the evaluation and management of patients diagnosed with CH.

Comprehensive Assessment of Fetal Bilateral Ventriculomegaly Based on Genetic Disorders, Cytomegalovirus Infection, Extra Prenatal Imaging and Pregnancy Outcomes in a Tertiary Referral Center

Objective

This retrospective study aimed to systematically evaluate the genetic disorders, cytomegalovirus (CMV) infection, extra ultrasound findings and outcomes of fetuses with bilateral ventriculomegaly (BVM).

Methods

Data from pregnancies with fetal BVM were obtained between 2014 and 2020. The cases were divided into groups of isolated bilateral ventriculomegaly (IBVM) and non-isolated bilateral ventriculomegaly (NIBVM) according to the presence of extra prenatal imaging. Subgroups of mild, moderate, and severe were determined according to lateral ventricle widths. The NIBVM group was further classified into pregnancies with soft markers, non-structural abnormalities, and structural abnormalities.

Results

A total of 353 pregnancies were enrolled, including 153 cases of IBVM and 200 cases of NIBVM. Conventional karyotyping was performed on 192 samples, and 15 cases of numerical abnormalities and 3 cases of unbalanced structural abnormalities were identified. Chromosomal microarray analysis (CMA) was concurrently performed on 108 of them and revealed additional 5 cases (4.7%) of copy number variants with clinical significance. CMV DNA testing was performed on 154 of the 192 cases that underwent invasive prenatal diagnosis, and a positive result was found in 2 (1.3%) cases. In the IBVM group, the percentage of favorable prognosis in the mild, moderate and severe pregnancies were 94.4%, 79.2%, and 4.8%, respectively, and the termination of pregnancy (TOP) rates were 4.6%, 20.8%, and 85.7%, respectively. In both the mild and moderate NIBVM, the TOP rates progressively increased and the favorable prognosis survival rates progressively decreased relative to the soft markers, non-structural abnormalities, and structural abnormalities, respectively. Approximately 94.1% of severe NIBVM ended in termination.

Conclusion

Genetic disorders and fetal infection are important etiology of BVM. CMA is highly recommended for genetic disorders’ evaluation. Pregnancies with severe BVM always ended in TOP, while in mild-to-moderate NIBVM, prenatal imaging by ultrasound and/or MRI plays important roles in the pregnancy outcomes.

Prenatal Ventriculomegaly - Diagnosis, Prognostication and Management

Fetal ventriculomegaly (VM) refers to the abnormal enlargement of one or more ventricles of the brain in-utero. The enlargement may or may not be related to ventricular obstruction and increased intracranial pressure; therefore, the term "hydrocephalus" is not used. VM is diagnosed usually in the mid-trimester when the atrial diameter (AD) of the lateral ventricle is more than 10 mm on one or both sides. A thorough workup is then required to identify the cause as the etiology is diverse. Fetal magnetic resonance imaging (MRI) may yield additional information. Serial ultrasound follow-up would be required to assess its progression with advancing gestation. The prognosis and long-term outcomes greatly depend upon the etiology, the severity at diagnosis, progression, and associations. This article reviews the definitions, diagnosis, and workup of fetal VM, discusses follow-up protocols and prognosis, and examines the role of fetal therapy, including fetoscopic surgery in its prenatal management.

Performance of Chromosomal Microarray Analysis for Detection of Copy Number Variations in Fetal Echogenic Bowel

BACKGROUND

Fetal echogenic bowel (FEB) is associated with an increased risk of poor pregnant outcomes; however, karyotyping fails to detect copy number variations (CNVs) in FEB. This study aimed to evaluate the performance of chromosomal microarray analysis (CMA) for detection of FEB.

METHODS

The medical records of 147 pregnant women with FEB recruited during December 2015 to December 2018 were retrospectively reviewed, and prenatal samples were collected for karyotyping and CMA. The detection of chromosomal abnormality was compared between karyotyping and CMA.

RESULTS

Karyotyping identified eight cases with abnormal karyotypes (5.44% prevalence), including four fetuses with pathogenic aneuploidy, three with chromosome polymorphism and one with balanced chromosome translocation. CMA identified 13 abnormal CNVs (8.84% prevalence), including 4 fetuses with pathogenic aneuploidy as detected by karyotyping and 9 additional CNVs with normal karyotypes; however, CMA failed to detect chromosome polymorphism and balanced chromosome translocation. In fetuses with isolated FEB, no cases presented pathogenic findings and CMA detected two cases with variants of uncertain significance (VOUS). In cases presenting FEB along with other ultrasound abnormalities, CMA detected three cases with pathogenic CNVs and four cases with VOUS in addition to four cases with aneuploidy. There was no significant difference in the detection of abnormal CNVs between the fetuses with echogenic bowel alone and along with other ultrasound abnormalities (10% vs 8.67%, P > 0.05). Except 9 fetuses lost to the follow-up, the other 138 fetuses with echogenic bowel were successfully followed up. Pregnancy was terminated in 5 fetuses with chromosomal abnormality, 2 with pathogenic CNVs and 1 with VOUS, and other 16 with normal karyotypes and CMA findings but showing ultrasound abnormalities or multiple malformations.

CONCLUSION

Isolated FEB is associated with a good prognosis, and a satisfactory pregnant outcome is expected for fetuses with echogenic bowel that are negative for chromosomal anomalies and other severe structure abnormalities. CMA shows an important value in the genetic diagnosis of FEB. As a supplement to karyotyping, CMA may improve the accuracy of prenatal diagnosis of fetal intestinal malformations in pregnant women with FEB.

Outcomes of Isolated Fetal Ventriculomegaly That Resolve In Utero

OBJECTIVE

Isolated fetal ventriculomegaly is often an incidental finding on antenatal ultrasound. It is benign in up to 90% of cases, although it can be associated with genetic, structural, and neurocognitive disorders. The literature suggests that over 40% of isolated mild ventriculomegaly will resolve in utero, but it is unclear if resolution decreases the associated risks.The aim of this study is to compare the fetal and neonatal genetic outcomes of ventriculomegaly that persists or resolves on subsequent ultrasound.

STUDY DESIGN

This is a retrospective cohort study of women diagnosed with isolated ventriculomegaly via fetal ultrasound at a tertiary referral center between 2011 and 2019. Patients were excluded if other structural anomalies were identified on ultrasound.

RESULTS

A total of 49 patients were included in the study, 19 in the resolved ventriculomegaly group and 30 in the persistent ventriculomegaly group. Women in the resolved ventriculomegaly group were more likely to be diagnosed earlier (24 vs. 28 weeks, p = 0.007). Additionally, they were more likely to have mild ventriculomegaly (63 vs. 84%, p = 0.15), and less likely to have structural neurological abnormalities diagnosed on postnatal imaging (5 vs. 17%, p = 0.384), although these were not statistically significant. Aneuploidy risk for resolved compared with persistent ventriculomegaly was similar (5 vs. 7%, p = 0.999).

CONCLUSION

This study suggests that resolution of isolated ventriculomegaly in utero may not eliminate the risk of genetic or chromosomal abnormalities in this population and may warrant inclusion as part of the counselling of these at-risk patients. Larger prospective studies are needed to confirm these findings.

KEY POINTS

· Ventriculomegaly is known to be associated with genetic and chromosomal abnormalities.. · Resolution of the ventriculomegaly in utero may not eliminate those risks.. · Patients with resolved ventriculomegaly should be offered aneuploidy screening or testing..

Correlation between mild fetal ventriculomegaly, chromosomal abnormalities, and copy number variations

BACKGROUND

Lateral ventriculomegaly is the most common abnormality of the fetal nervous system. This study investigated the incidence of chromosomal abnormalities and copy number variations (CNVs) in fetuses with mild ventriculomegaly (MV) based on various ultrasonic manifestations, identifying their corresponding features via ultrasound examination.

METHODS

A retrospective analysis was performed on ultrasound and neurosonogram (NSG) manifestations and genetic profiles of 334 cases with MV and invasive prenatal diagnosis.

RESULTS

Three hundred thirty-four cases with fetal MV were assessed via karyotyping. Further chromosomal microarray analysis (CMA) was performed in 182 cases with normal chromosome karyotypes; pathogenic chromosomal copy number variations (CNVs) were found in eight cases with a prevalence of 4.4% (8/182). In this study, the incidence rate of pathogenic abnormalities of chromosomes and CNVs was 5.7% (19/334). Based on whether lateral ventriculomegaly was complicated with other ultrasonic features, the 334 patients were divided into two groups: (1) 175 cases exhibited isolated ventriculomegaly (IVM; 52.4%, 175/334 group A) including two (1.1%, 2/175) with pathogenic chromosomal karyotype abnormalities-both trisomy 21; (2) 159 cases exhibited non-isolated ventriculomegaly (N-IVM; 47.6%, 159/334) with pathogenic chromosomal abnormalities and CNVs detected in17 cases (10.7%, 17/159). The N-IVM group was further divided into two groups: 105 cases exhibited MV with undetermined ultrasonic abnormalities (31.4%, 105/334, group B) with pathogenic chromosomal abnormalities and CNVs detected in eight cases (7.6%, 8/105); 54 cases exhibited MV with structural malformations (16.2%, 54/334, group C) of which nine cases (16.7%, 9/54) presented both pathogenic chromosomal abnormalities and CNVs, and five cases (55.6%, 5/9) were diagnosed with various cortical malformations. The pathogenicity rates of the IVM and N-IVM groups were statistically different (χ ²=14.159, p = 0.000). There were significant differences (χ²=7.992, p = 0.005) among groups A, B, and C.

CONCLUSIONS

Combinations of various ultrasonic abnormalities significantly affect the risk of pathogenic chromosomal abnormalities and CNVs in fetuses with MV. Cases involving cortical malformations require particular attention to the occurrence of pathogenic genetic abnormalities. When fetal MV is detected, a comprehensive ultrasound examination focusing on undetermined ultrasonic abnormalities is critical. Fetal NSG should be conducted to detect potential cerebral cortical malformation easily missed by routine ultrasound.

Prenatal diagnosis of chromosomal aberrations by chromosomal microarray analysis in foetuses with ventriculomegaly

Ventriculomegaly is considered to be linked to abnormal neurodevelopment outcome. The aim of this retrospective study was to investigate the current applications of chromosomal microarray analysis (CMA) in foetuses with ventriculomegaly. A total of 548 foetuses with ventriculomegaly detected by prenatal ultrasound underwent single nucleotide polymorphism (SNP) array testing and were subjected to long-term follow-up. The overall prevalence of chromosomal aberrations was 7.30% (40/548), including 4.20% (23/548) with pathogenic/likely pathogenic copy number variants. The incidence of chromosomal aberrations was significantly higher in foetuses with bilateral ventriculomegaly than in those with unilateral ventriculomegaly (10.56% vs. 5.71%, P = 0.040), in foetuses with non-isolated ventriculomegaly than in those with isolated ventriculomegaly (12.99% vs. 2.38%, P < 0.0001), and in foetuses with severe ventriculomegaly than in those with mild-to-moderate ventriculomegaly (23.08% vs. 6.51%, P = 0.005). The outcome in foetuses with mild ventriculomegaly was significantly better than in those with moderate ventriculomegaly (95.60% vs. 84.00%, P = 0.003). Thus, CMA should be regarded as the first-tier test for prenatal diagnosis of foetal ventriculomegaly, especially in foetuses with bilateral or non-isolated ventriculomegaly. The outcome of foetuses with mild ventriculomegaly is favourable; however, there is an increased risk of neurodevelopmental disabilities in foetuses with moderate ventriculomegaly.

Novel and recurrent variants identified in fetuses with central nervous system abnormalities by trios-medical exome sequencing

BACKGROUND

Fetal central nervous system abnormalities often associated with infant death or severe disability. The etiology in fetuses with CNS abnormalities who have normal karyotypes and copy number variants (CNVs) remains unclear, which increases the difficulty in following management and the assessment of prognosis.

METHOD

11 unrelated fetuses with CNS abnormalities and their parents were enrolled. Genomic DNA was obtained and then trios-medical exome sequencing (trios-MES) including 4000 genes (fetuses and their parents) was performed after both karyotyping and chromosome microarray showed negative results.

RESULTS

Pathogenic and likely pathogenic variants were identified in five of 11 cases (5/11, 45.5%), including five novel mutations and two recurrent mutations in ISPD, L1CAM, and GRIN2B genes. Most cases (4/5, 80%) carried one or two recessive mutations, indicating a high recurrent risk.

CONCLUSION

Exome sequencing should be considered for fetuses with CNS abnormalities following negative results of karyotyping and chromosome array. Trios-MES as one of exome sequencing is a potential method for the diagnosis of these fetuses.

Prenatal genetic considerations in congenital ventriculomegaly and hydrocephalus

BACKGROUND

Fetal ventriculomegaly (VM) is a frequent finding in prenatal ultrasound. Rather than a proper diagnosis, VM is a sonographic sign, making prenatal counseling a complex and challenging undertaking. VM can range from severe pathologic processes leading to severe neurodevelopmental delay to normal variants.

DISCUSSION

A growing number of genetic conditions with different pathophysiological mechanisms, inheritance patterns, and long-term prognosis have been associated both to isolated and complex fetal VM. These include chromosomal abnormalities, copy number variants, and several single gene diseases. In this review, we describe some of the most common genetic conditions associated with fetal VM and provide a simplified diagnostic workflow for the clinician.

Prenatal detection of 1p36 deletion syndrome: ultrasound findings and microarray testing results

OBJECTIVE

Only a small number of reports have been made on the prenatal ultrasound findings observed in 1p36 deletion syndrome. We explored prenatal diagnosis of 1p36 deletion by ultrasound as well as chromosomal microarray (CMA), and delineated the fetal presentation of this syndrome.

STUDY DESIGN

This was a retrospective analysis of 10 new prenatal cases of 1p36 deletion identified by CMA at a single Chinese medical center. Clinical data were reviewed for these cases, including maternal demographics, indications for invasive testing, sonographic findings, CMA results and pregnancy outcomes.

RESULTS

One case was diagnosed because of a positive cell-free DNA (cfDNA) testing result for terminal 1p deletion, and the remaining nine cases were identified because of an abnormal ultrasound findings, including early miscarriage, structural abnormalities and fetal growth restriction. CMA revealed 1p36 deletions to be terminal in six cases, and interstitial in four cases. Deletion sizes ranged from 1.7 to 42.7 Mb.

CONCLUSIONS

Prenatal findings such as cardiac malformations, especially Ebstein anomaly, and fetal growth retardation should warrant the diagnosis of 1p36 deletion and invasive genetic testing using CMA.

The application of chromosomal microarray analysis to the prenatal diagnosis of isolated mild ventriculomegaly

OBJECTIVE

To investigate the clinical value of chromosomal microarray analysis (CMA) in the prenatal diagnosis of genetic abnormalities in fetal isolated mild ventriculomegaly.

MATERIALS AND METHODS

This retrospective study reviewed 101 fetuses with isolated mild ventriculomegaly who had undergone invasive prenatal diagnosis at our hospital. CMA was performed in all cases to detect chromosomal aneuploidy as well as copy number variations (CNVs) that are too small to be detected by conventional karyotyping. Real time quantitative PCR (qPCR) or multiplex ligation dependent probe amplification (MLPA) was used to confirm all fetal CNVs <400 Kb.

RESULTS

Except for three cases of chromosomal aneuploidy, CMA revealed pathogenic copy number variations (CNVs) in 3.0% (3/101) of the fetuses; these cases demonstrated involvement in the chromosomal regions 15q11.2, 1q21.1 and Xq27.3q28. Furthermore, we detected three likely pathogenic (3.0%) and two variants of uncertain significance (2.0%) among 101 fetuses diagnosed as isolated mild ventriculomegaly on ultrasound examination.

CONCLUSION

Our study suggests that CNVs could aid in the risk assessment and genetic counseling in fetuses with isolated ventriculomegaly.