Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis

Reanalysis of unsolved prenatal exome sequencing for structural defects: diagnostic yield and contribution of postnatal/postmortem features

In 30-40% of fetuses with structural defects, the causal variant remains undiagnosed after karyotype, chromosomal microarray, and exome sequencing. This study presents the results of a reanalysis of unsolved prenatal ES (pES) cases and investigates how postnatal/postmortem phenotyping contributes to identifying relevant variants. pES data was prospectively reanalyzed for unsolved cases enrolled in the AnDDI-Prénatome cohort study. Postnatal/postmortem data were included with prenatal features using Human Phenotype Ontology terms up to 3 years after pES. The reanalysis involved updating bioinformatic processing and querying raw data using a GREP query. We reanalyzed 58/94 (62%) unsolved pES cases, including 8 variants of unknown significance. Data for clinical examination at birth was available for all live newborns, and postmortem examination was available in 12 terminated fetuses. Additional features were identified at birth in 27/58 cases (44%): 9 terminated fetuses, 2 stillbirths, and 16 live newborns. One diagnosis (SNAPC4) was obtained through a periodic query following recent associations with human disease, and without additional clinical data. Three additional VUS were identified through reanalysis with the addition of new clinical features, illustrating the limited contribution of updated postnatal/postmortem phenotyping in identifying relevant variants after negative pES. In conclusion, the benefit of prospective reanalysis of unsolved pES is limited, even over time. Postnatal genome sequencing may be a more appropriate option than reanalysis with postnatal/postmortem phenotyping to establish a causal diagnosis.

Sonographic diagnosis of fetal eye anomalies and their association with syndromal diseases: A retrospective multicenter analysis of 264 cases

INTRODUCTION

This study aims to systematically describe eye malformations and correlate these with extraocular findings. Based on these findings, we propose a protocol for ultrasound evaluation of the fetal eye.

MATERIAL AND METHODS

In this multicentric retrospective cohort study, 264 fetuses with ocular malformations from two tertiary referral centers for prenatal medicine were analyzed. Anophthalmia, microphthalmia, exophthalmos, hyper- or hypotelorism, cataract, aphakia, cyclopia, and retinal detachment were assessed, and their association with extraocular findings and genetic changes was investigated.

RESULTS

The majority of the cases (99.2%) were non-isolated and presented further extraocular findings. Most commonly, the brain and central nervous system (65.9%), the limbs and the heart (46.6% each) and the cranial anatomy (41.2%) were affected. Significant associations were found between exophthalmos and anomalies of the fetal skeletal system (OR = 4.8, 95% CI 1.6-14) and cranial malformations (OR = 3.3, 95% CI 1.5-7.4). Hypotelorism showed an increased risk of cardiac anomalies (OR = 1.8, 95% CI 1.1-3.5) and brain malformations (OR = 2.16, 95% CI 1.2-4.1), with holoprosencephaly being the most common one. Fetuses with microphthalmia were more likely to have anomalies in the renal system (OR = 2.3, 95% CI 1.2-4.3). In 51.4% of the cases, a genetic aberration could be found, among them most frequently trisomy 13.

CONCLUSIONS

There is a significant association between specific fetal eye anomalies and certain extraocular anomalies, as well as genetic changes. Systematic evaluation of the eye using the proposed protocol is simple to learn and highly reproducible and could help to concentrate diagnosis on a certain group of malformations. Data from this study could help to develop targeted diagnostic molecular tools.

Sequential prenatal diagnosis of fetal skeletal dysplasia: A cohort study

INTRODUCTION

Genetic factors are considered to be the main factors leading to fetal skeletal dysplasia (SD), and chromosomal microarray analysis (CMA) has been used clinically for the detection of SD fetuses. At present, whole exome sequencing (WES) has been applied in SD fetuses, but there is still a lack of data accumulation. The aim of this study is to perform sequential prenatal diagnosis for fetuses with SD indicated by ultrasound and to explore the clinical value of CMA followed by WES.

MATERIAL AND METHODS

From January 2019 to May 2024, 147 fetuses with SD were detected by prenatal ultrasound screening. After the collection of amniotic fluid or abortive tissue, CMA was performed first, then WES was performed in the cases with a negative CMA result.

RESULTS

147 cases accepted the prenatal CMA test, and 23 cases were reported to have chromosomal abnormalities, including 9 cases of chromosomal aneuploidies, 11 cases of pathogenic copy number variants, and 3 cases of likely pathogenic copy number variants. The detection rate of chromosomal abnormalities by the prenatal CMA test was 15.6% (23/147). 58 cases with negative results of CMA underwent WES, and 21 genes with pathogenic/likely pathogenic variants were detected in 21 cases, including FGFR3, COL2A1, COL1A1, COL1A2, RUNX2, LMX1B, GLI3, SHOX, ALPL, and DYNC2H1. The rate of abnormal prenatal WES was 36.2% (21/58). In the subgroup analysis of the SD phenotype, the detection rate of chromosomal abnormalities in isolated SD fetuses was 7.7% (7/91), which was significantly lower than that in SD fetuses combined with other system abnormalities (28.6%, 16/56) (p = 0.001). The detection rate of monogenic abnormalities in short long bones with other skeletal abnormalities was 62.5% (10/16), which was higher than that in short long bones with non-skeletal abnormalities 10.5% (2/19), and the difference was statistically significant (p = 0.003).

CONCLUSIONS

SD is mostly caused by monogenic abnormalities, and prenatal WES has significantly improved the detection rate of SD fetuses. The prenatal WES can be used as an important molecular genetic testing method combined with CMA in the sequential prenatal diagnosis of SD fetuses.

Reclassifying a Novel POMT1 Variant by Integrating Functional Analysis and Bioinformatics: Implications for Preimplantation Genetic Testing

The advancement of next-generation sequencing has spurred the growing adoption of whole-exome sequencing (WES) for genetic screening. Preimplantation genetic testing for monogenic disorders (PGT-M) can effectively prevent the transmission of pathogenic variants. However, interpreting vast data volumes and ensuring precise genetic counseling, especially with variants of uncertain significance (VUS), remains challenging. In this study, we investigated a family with recurrent fetal malformations detected by prenatal ultrasound. WES identified compound heterozygous POMT1 variants, c.1052 + 1G > A and c.1483G > A in the proband; the latter was initially categorized as a VUS. Then our bioinformatics analysis revealed that c.1483G > A variant was located in a highly conserved domain essential for POMT1's enzymatic activity, potentially altering the protein's 3D structure. In vitro studies using HEK293T cells showed that the variant led to aberrant POMT1 mRNA and protein accumulation, impaired cell viability, and abnormal protein localization in the cytoplasm, indicating disruption of normal glycosylation processes. Combining bioinformatics analysis with in vitro experiments, we reclassified the c.1483G > A variant as likely pathogenic. Subsequently, the couple opted for PGT-M, culminating in the birth of a healthy child. Our findings underscore the pivotal role of genetic testing in recurrent fetal malformations and expand the spectrum of POMT1 variants. The successful reclassification of the variant by integrating in vitro experiments with bioinformatics provides substantial evidence for clinicians implementing PGT-M, offering a feasible strategy for counseling with VUS detected by WES.

Research trajectory of the mechanism of preeclampsia: a scientometric perspective

OBJECTIVE

This study aims to conduct a scientometric analysis on the research history and emerging trends of the pathogenesis of preeclampsia using CiteSpace and VOSviewer software. The goal is to provide guidance for future research and clinical practice.

METHODS

The core collection database of Web of Science was searched for research literature on the mechanism of preeclampsia from January 1980 to March 2024. CiteSpace6. 1. R6, 5. 7. R5 (64-bit), and VOSviewer1.6.19 software were used for visual analysis, including networks of keywords, countries, authors, institutions, funds, and fields.

RESULTS

A total of 4989 documents were analyzed in this study. The number of published articles has shown a consistent increase from 1990 to 2022, indicating that this topic remains a significant area of research. The countries, institutions, authors, journals, and fields that contributed the most articles include the USA, University of Mississippi, Lamarca, Babbette, Placenta, and the field of OBSTETRICS and GYNECOLOGY. Keyword clustering and emergence analysis identified 7 clusters, while clustering and emergence analysis of cited documents identified 14 clusters. These analyses revealed that current research on the mechanism of preeclampsia primarily focuses on placental ischemia and hypoxia, inflammatory response and immune disorders, angiogenic factor imbalance, abnormal epigenetic modifications, and intestinal flora imbalance.

CONCLUSIONS

Research on the mechanisms of preeclampsia is rapidly advancing. Given the presence of multiple mechanisms and pathways, further collaborative research is essential to guide clinical treatment effectively and enhance maternal and child outcomes.

Advancing precision care in pregnancy through a treatable fetal findings list

The use of genomic sequencing (GS) for prenatal diagnosis of fetuses with sonographic abnormalities has grown tremendously over the past decade. Fetal GS also offers an opportunity to identify incidental genomic variants that are unrelated to the fetal phenotype but may be relevant to fetal and newborn health. There are currently no guidelines for reporting incidental findings from fetal GS. In the United States, GS for adults and children is recommended to include a list of "secondary findings" genes (ACMG SF v.3.2) that are associated with disorders for which surveillance or treatment can reduce morbidity and mortality. The genes on ACMG SF v.3.2 predominantly cause adult-onset disorders. Importantly, many genetic disorders with fetal and infantile onset are treatable as well. A proposed solution is to create a "treatable fetal findings list," which can be offered to pregnant individuals undergoing fetal GS or, eventually, as a standalone cell-free fetal DNA screening test. In this integrative review, we propose criteria for a treatable fetal findings list, then identify genetic disorders with clinically available or emerging fetal interventions and those for which clinical detection and intervention in the first week of life might lead to improved outcomes. Finally, we synthesize the potential benefits, limitations, and risks of a treatable fetal findings list.

Amniocentesis in pregnancies at or beyond 24 weeks: an international multicenter study

BACKGROUND

Amniocentesis for genetic diagnosis is most commonly done between 15 and 22 weeks of gestation but can be performed at later gestational ages. The safety and genetic diagnostic accuracy of amniocentesis have been well-established through numerous large-scale multicenter studies for procedures before 24 weeks, but comprehensive data on late amniocentesis remain sparse.

OBJECTIVE

To evaluate the indications, diagnostic yield, safety, and maternal and fetal outcomes associated with amniocentesis performed at or beyond 24 weeks of gestation.

STUDY DESIGN

We conducted an international multicenter retrospective cohort study examining pregnant individuals who underwent amniocentesis for prenatal diagnostic testing at gestational ages between 24w0d and 36w6d. The study, spanning from 2011 to 2022, involved 9 referral centers. We included singleton or twin pregnancies with documented outcomes, excluding cases where other invasive procedures were performed during pregnancy or if amniocentesis was conducted for obstetric indications. We analyzed indications for late amniocentesis, types of genetic tests performed, their results, and the diagnostic yield, along with pregnancy outcomes and postprocedure complications.

RESULTS

Of the 752 pregnant individuals included in our study, late amniocentesis was primarily performed for the prenatal diagnosis of structural anomalies (91.6%), followed by suspected fetal infection (2.3%) and high-risk findings from cell-free DNA screening (1.9%). The median gestational age at the time of the procedure was 28w5d, and 98.3% of pregnant individuals received results of genetic testing before birth or pregnancy termination. The diagnostic yield was 22.9%, and a diagnosis was made 2.4 times more often for fetuses with anomalies in multiple organ systems (36.4%) compared to those with anomalies in a single organ system (15.3%). Additionally, the diagnostic yield varied depending on the specific organ system involved, with the highest yield for musculoskeletal anomalies (36.7%) and hydrops fetalis (36.4%) when a single organ system or entity was affected. The most prevalent genetic diagnoses were aneuploidies (46.8%), followed by copy number variants (26.3%) and monogenic disorders (22.2%). The median gestational age at delivery was 38w3d, with an average of 59 days between the procedure and delivery date. The overall complication rate within 2 weeks postprocedure was 1.2%. We found no significant difference in the rate of preterm delivery between pregnant individuals undergoing amniocentesis between 24 and 28 weeks and those between 28 and 32 weeks, reinforcing the procedure's safety across these gestational periods.

CONCLUSION

Late amniocentesis, at or after 24 weeks of gestation, especially for pregnancies complicated by multiple congenital anomalies, has a high diagnostic yield and a low complication rate, underscoring its clinical utility. It provides pregnant individuals and their providers with a comprehensive diagnostic evaluation and results before delivery, enabling informed counseling and optimized perinatal and neonatal care planning.

Fetal Corpus Callosum Anomalies: A Review of Underlying Genetic Disorders and Prenatal Testing Options

Anomalies of the corpus callosum (CC) are amongst the most common fetal Central Nervous System (CNS) anomalies detectable on ultrasound. Underlying genetic disease plays an important part in defining prognosis. Associations with aneuploidy and submicroscopic chromosomal deletions or duplications have been well demonstrated using chromosomal microarray analysis. Next-generation sequencing techniques such as exome sequencing, have revolutionized the ability to detect monogenic disease in these fetuses. In the context of important recent publications on exome sequencing in prenatal populations, an updated review of genetic testing options in CC anomalies is presented.

Increased nuchal translucency thickness and normal chromosomal microarray: Danish nationwide cohort study

OBJECTIVE

To assess the outcome of pregnancies with increased fetal nuchal translucency (NT) thickness and a normal result from chromosomal microarray (CMA) vs conventional karyotyping.

METHODS

This was a Danish nationwide registry-based cohort study of all singleton pregnancies seen for combined first-trimester screening between 2008 and 2018. Data on NT thickness and pregnancy outcome were retrieved from the Danish Fetal Medicine Database, whereas data on cytogenetic and molecular karyotypes were retrieved from the Danish Cytogenetic Central Register. Pregnancies were stratified according to NT thickness, and we computed the prevalence of chromosomal aberration, termination of pregnancy (due to non-genetic abnormal findings aside from increased NT), pregnancy loss, major congenital malformation and unaffected live birth (live birth ≥ 24 weeks' gestation with no chromosomal aberration or major congenital malformation diagnosed). The prevalence of the different outcomes was further estimated for pregnancies with increased NT (≥ 3.5 mm) and a normal CMA result. Finally, to assess the impact of CMA compared with conventional karyotyping for increased NT, we compared the prevalence of chromosomal aberrations and each pregnancy outcome between the periods 2008-2012 and 2014-2018 (during which < 3% and > 60%, respectively, of pregnancies with increased NT were examined using CMA).

RESULTS

We identified 557 896 pregnancies with a NT measurement for which outcome data were registered. Fetal NT was ≥ 3.5 mm in 3717 (0.7%) pregnancies, of which 3368 (91%) underwent genetic examination. The prevalence of chromosomal aberrations increased significantly with increasing NT thickness, from 21% in pregnancies with NT of 3.5-4.4 mm to 69% in pregnancies with NT ≥ 6.5 mm. Trisomies 21, 18 and 13 accounted for the majority of chromosomal aberrations diagnosed in all subgroups of increased NT (range, 61-87%). In pregnancies with increased NT and a normal CMA result, the prevalence of unaffected live birth decreased significantly from 87% for NT of 3.5-4.4 mm to 29% for NT ≥ 6.5 mm. Increased uptake of CMA during 2014-2018 compared with 2008-2012 slightly increased the detection of submicroscopic aberrations. However, a normal CMA result, compared with a normal result from conventional karyotyping, did not substantially improve the prognosis in pregnancies with increased NT.

CONCLUSIONS

Our study reaffirms the association between increased NT and chromosomal aberrations. Although CMA improves diagnostic resolution in pregnancies with increased NT, a normal test result does not substantially impact the prevalence of unaffected live births. This highlights the ongoing need for accurate clinical guidance and continued research, especially as whole-genome sequencing is increasingly adopted in prenatal care. © 2025 The Author(s). Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Insights and Experiences From the 'Gatekeepers': A Qualitative Study Exploring Clinician Perspectives on Providing Publicly Funded Prenatal Exome Sequencing

BACKGROUND

Genomics has improved etiological diagnosis for foetal structural anomalies. It is being increasingly utilised in prenatal investigation both in Australia and internationally. To date, literature reporting diagnostic yield according to indication has been available. There is limited literature around the challenges of implementation and other aspects of utility.

AIMS

We aimed to explore the experiences and perspectives of clinicians involved with the delivery of a state-wide public prenatal exome sequencing (pES) service in Australia.

MATERIALS AND METHODS

This qualitative study was developed using a pragmatism framework. A multidisciplinary cohort of clinicians across all tertiary foetal medicine units in Victoria was interviewed. Inductive content analysis was used to understand the experiences, impact, and utility of pES.

RESULTS

Eight clinician interviews were analysed. The impact of pES on clinicians included: increased pressure, higher emotional toll, and balancing the benefits with resource limitations. PES was most useful when it provided prognostic information. The clinicians felt that pES had the most utility for patients when the result informed their decision about whether or not to continue a pregnancy. Clinicians acknowledged their 'gatekeeper' role and valued a collaborative, multidisciplinary approach. The main perceived harm for patients was the anxiety associated with waiting times for results.

CONCLUSIONS

This study provides insights into the delivery of a publicly funded pES program. Our findings highlight the importance of the multidisciplinary team in the successful implementation of genomic technologies in reproductive health.

The PreGen Research Program: Implementing Prenatal Genomic Testing in Australia-A Commentary

Prenatal genomic sequencing, which can provide a significantly increased diagnostic rate for fetal structural anomaly (FSA) compared with karyotype and microarray, is not available uniformly across Australia. PreGen, a 5-year translational research program, has identified significant barriers to implementation including access to funding, the availability of genomic testing, access to termination of pregnancy services and the availability of specialist genomic centres. A federal item number for prenatal genomic testing would increase equitable test availability and reduce delays to diagnoses by making them in pregnancy whilst removing the need for low-yield diagnostic interventions and enabling personalised patient management and family support.

Whole Genome Sequencing in Prenatal Diagnostics: The Danish Approach to Guideline Formation and Implementation Within Public Healthcare

OBJECTIVE

To describe the implementation of whole genome sequencing (WGS) in prenatal diagnostics and outline the national guideline system facilitating this.

METHODS

Clinical guidelines for WGS in prenatal diagnostics were developed and implemented by the Danish Fetal Medicine Society.

RESULTS

Guidelines were developed by expert consensus following a review of 75 studies. Diagnostic yield served as a key factor in prioritizing WGS for various phenotypes, improving diagnostic accuracy and informing clinical decisions. Phenotypes for WGS include nuchal translucency ≥ 6.0 mm, multiple anomalies, skeletal dysplasia, neuromuscular diseases, non-immune hydrops fetalis, central nervous system malformations, congenital diaphragmatic hernia and severe fetal growth restriction (< 3 SDs not explained by placental insufficiency). Small regional variations exist in indications, bioinformatics, and funding, but WGS is now routinely used nationwide for these indications.

CONCLUSION

The Danish Fetal Medicine Society's guideline development, emphasizing diagnostic yield and gradual implementation, has supported the relatively uniform integration of WGS into prenatal diagnostics.

The power of mouse models in the diagnostic odyssey of patients with rare congenital anomalies

Congenital anomalies are structural or functional abnormalities present at birth, which can be caused by genetic or environmental influences. The availability of genome sequencing has significantly increased our understanding of congenital anomalies, but linking variant identification to functional relevance and definitive diagnosis remains challenging. Many genes have unknown or poorly understood functions, and with a lack of clear genotype-to-phenotype correlations, it can be difficult to move from variant discovery to diagnosis. Thus, for most congenital anomalies, there still exists a "diagnostic odyssey" which presents a significant burden to patients, families and society. Animal models are essential in the gene discovery process because they allow researchers to validate candidate gene function and disease progression within intact organisms. However, use of advanced model systems continues to be limited due to the complexity of efficiently generating clinically relevant animals. Here we focus on the use of precisely engineered mice in variant-to-function studies for resolving molecular diagnoses and creating powerful preclinical models for congenital anomalies, covering advances in genomics, genome editing and phenotyping approaches as well as the necessity for future initiatives aligning animal modelling to deep patient multimodal datasets.

Use of Clinically Informed Strategies and Diagnostic Yields of Genetic Testing for Fetal Structural Anomalies Following a Non-Diagnostic Microarray Result: A Population-Based Cohort Study

OBJECTIVE

To investigate the performance of targeted gene sequencing, expanded gene panels, and selected exomes for prenatally identified fetal anomalies, after non-diagnostic microarray results.

METHOD

All fetal samples received for genetic testing for fetal structural anomalies in the Canadian Maritime Provinces (2014-2022) were identified. Utilization and results of NGS sequencing strategies after a non-diagnostic microarray were correlated with ultrasound findings and autopsy results.

RESULTS

Five hundred and ninety-three cases of fetal anomalies with non-diagnostic RAD results were identified, including 319 (54%) with isolated anomalies. Diagnostic yield from the microarray was 7.5%. Sequence-based testing for 131 cases gave an overall diagnostic yield of 38% (8.4% of initial cohort). For isolated anomalies, diagnostic yield was highest in the intracranial, renal, and musculoskeletal systems (44%, 60%, 64% respectively). Appropriate targeted gene sequencing provided a diagnostic yield of 40%. With clinically indicated criteria for exome analysis, diagnostic yields were higher than when clinical information prompted use of a selected gene panel (73% vs. 27%). Expanding to an exome after a non-diagnostic gene panel had an additional diagnostic yield of 13%.

CONCLUSION

Multidisciplinary review and comprehensive clinical information can inform the selection of strategies for expanded genetic testing after non-diagnostic microarray for fetal anomalies within a publicly funded health care system.

Approaches to Evaluate Whole Exome Sequencing Data That Incorporate Genetic Intolerance Scores for Congenital Anomalies, Including Intronic Regions Adjacent to Exons

BACKGROUND

Whole exome sequencing (WES) aids in diagnosing monogenic diseases, yet > 50% of all cases remain undiagnosed. We aimed to improve diagnostic precision by developing an effective WES-based strategy for detecting congenital anomalies.

METHODS

Initially, 128 probands with congenital anomalies were assessed using trio-WES and copy number variation analysis-variant interpretation was for exons and splice sites. Thereafter, we reanalyzed the sequence data for undiagnosed cases using the following methods. First, we performed trio-WES analysis, adding genetic intolerance scores annotation. Second, we analyzed all exons, splicing sites, and intron variants for cases with phenotypes suggestive of specific causative genes using SpliceAI. Lastly, using SpliceAI, we analyzed all exons, splicing sites, and intron variants in genetically constrained genes filtered with genetic intolerance scores.

RESULTS

Initial analysis diagnosed 51 of 128 cases (39.8%). In the reanalysis, first, we identified novel likely pathogenic variants in MED12 and CCDC22 associated with X-linked diseases. Second, a novel TMEM67 intron variant associated with Meckel syndrome was detected. Finally, a de novo hemizygous pathogenic intronic variant in CASK was identified in a case of intrauterine fetal death.

CONCLUSIONS

WES analysis, including intronic regions and utilizing genetic intolerance scores, has the potential to efficiently improve diagnostic yield.

Use of Prenatal Exome Sequencing: Opinion Statement of the French Federation of Human Genetics Working Group

OBJECTIVE

Prenatal whole exome sequencing (pES) is increasingly prescribed for fetuses with ultrasound anomalies. Starting from the local French prenatal medicine practice, healthcare system and legal landscape, we aimed to address the broad medical and ethical issues raised by the use of pES for women and couples as well as for prenatal care providers.

METHOD

The French Federation of Human Genetics established a working group composed of clinicians and biologists from all over France to discuss pES challenges. A literature review was also performed.

RESULTS

We emphasize the importance of non-directive information that helps couples make a decision that is consistent with their personal values and ideas. We address the difficulty of obtaining informed consent that respects the couple's autonomy, despite the complexity of the information and regardless of their level of education and cultural background. We address whether variants of uncertain significance and unsolicited results should be reported. We emphasize the need for national harmonization of access to pES and the need for multidisciplinary meetings in complex situations. We point out that the specific French context of healthcare financing and the French law have a major influence on medical care organization and support for couples. The outcome of the working group is the development of 12 proposals.

CONCLUSION

This opinion statement, dedicated to prenatal care providers worldwide although linked to the French context, will provide food for thought and assist them in understanding the complexity and implications of pES.

Prenatal exome sequencing for the morphologically normal fetus: Should we be doing it?

OBJECTIVE

We aimed to investigate the yield of prenatal exome sequencing (pES) in morphologically normal fetuses.

METHOD

This retrospective study analyzed 254 families with morphologically normal fetuses who underwent prenatal trio exome sequencing based on parental request between September 2020 and October 2023.

RESULTS

Overall, abnormal findings were detected in 8 families (3.1%, 8/254) by pES. Among these, 6 families (2.3%, 6/254) were found to have fetuses affected with monogenic disorders (2 autosomal recessive conditions and 4 autosomal dominant conditions), while 2 families (0.8%, 2/254) were incidentally found to be couples at risk of having a future pregnancy with a recessive condition. Among the six fetuses detected with monogenic disorders, two fetuses carried a de novo variant in OPA1 and NF1, which are known to cause Optic atrophy 1 and Neurofibromatosis, respectively. One fetus was detected with a maternally inherited variant in PKD2 related to polycystic kidney disease 2 (not known to the mother until then). One fetus was detected with a maternally inherited variant in SDHB associated with Pheochromocytoma. Two fetuses carried compound heterozygous variants in NAGLU and GJB2 associated with Mucopolysaccharidosis type IIIB and Deafness, respectively. In the 2 families where parents were found to be carriers but the fetuses were unaffected, heterozygous variants in the GJB2 and SERPINB7 genes were detected in the parents, respectively, which are associated with deafness and palmoplantar keratoderma.

CONCLUSION

Our research indicated that pES can provide significant critical information for families with morphologically normal fetuses. Prenatal screening with exome sequencing requires careful management and detailed pre-test and post-test genetic counseling.

Fetal imaging, phenotyping, and genomic testing in modern prenatal diagnosis

Genetic tests available in the prenatal setting have expanded rapidly with next generation sequencing, and fetal imaging can detect a breadth of many structural and functional abnormalities. To identify a fetal genetic disease, deep phenotyping is increasingly important to generate a differential diagnosis, choose the most appropriate genetic tests, and inform the results of those tests. The Human Phenotype Ontology (HPO) organizes and defines the features of human disease to support deep phenotyping, and ongoing efforts are being made to improve the scope of the HPO to comprehensively include fetal phenotypes. There are important limitations of fetal phenotyping to understand, including ongoing structural development and limited knowledge of how many genetic diseases present uniquely in utero. This article provides an overview of the use of HPO terms and artificial intelligence in the approach to fetal phenotyping and genetic testing.

Integrating Prenatal Exome Sequencing and Ultrasonographic Fetal Phenotyping for Assessment of Congenital Malformations: High Molecular Diagnostic Yield and Novel Phenotypic Expansions in a Consanguineous Cohort

To evaluate the diagnostic yield of prenatal exome sequencing (pES) in fetuses with structural anomalies detected by prenatal ultrasound in a consanguineous population. This was a prospective study of 244 anomalous fetuses from unrelated consanguineous Egyptian families. Detailed phenotyping was performed throughout pregnancy and postnatally, and pES data analysis was conducted. Genetic variants were prioritized based on the correlation of their corresponding human phenotype ontology terms with the ultrasound findings. Analyses were carried out to determine the diagnostic efficiency of pES and its correlation to the organ systems involved. The largest clinical category of fetuses referred for pES was those manifesting multisystem anomalies (104/244, 42.6%). pES provided a definitive diagnosis explaining the fetal anomalies in 47.1% (115/244) of the cases, with the identification of 122 pathogenic or likely pathogenic variants completely fitting with the phenotype. Variants of uncertain significance associated with the fetal phenotypes were detected in 84 fetuses (34%), while 18.44% (45/244) had negative results. Positive consanguinity is associated with a high diagnostic yield of ES. The novel variants and new fetal manifestations, described in our cohort, further expand the mutational and phenotypic spectrum of a wide variety of genetic disorders presenting with congenital malformations.

Retrospective study on the utility of optical genome mapping as a follow-up method in genetic diagnostics

BACKGROUND

Current standard-of-care (SOC) methods for genetic testing are capable of resolving deletions and sequence variants, but they mostly fail to provide information on the breakpoints of duplications and balanced structural variants (SV). However, this information may be necessary for their clinical assessment, especially if the carrier's phenotype is difficult to assess and/or carrier analysis of relatives is not viable. A promising approach to solving such challenging cases arises with access to optical genome mapping (OGM) but has not been systematically explored as of yet.

METHODS

In this retrospective study, we evaluated diagnostic cases from a 1-year period (2023) in which an SV discovery by SOC methods (microarray, karyotyping and whole-exome sequencing) was followed up by OGM, with the objective to unlock clinically relevant information about the SV.

RESULTS

Seven cases were shown by SOC methods to bear potential pathogenic SVs and were consequently followed up by OGM. Of these, six were solved by the additional use of OGM alone. One case required sequencing after OGM analysis to further specify the SV's breakpoints. In all seven cases, OGM was crucial for determining the clinical relevance of the detected SV.

CONCLUSION

This study describes the use of OGM as a valuable method for characterising duplications and balanced SVs. Often, this additional information does not add to the quality of a clinical report. However, for a subset of patients, these data are critical, especially in the prenatal setting or when no familial analyses are possible.

The Clinician-reported Genetic Testing Utility Index (C-GUIDE) for Prenatal Care: Initial evidence of content and construct validity

PURPOSE

To develop and assess the face and construct validity of the Clinician-reported Genetic Testing Utility Index (C-GUIDE) for genetic testing in prenatal care.

METHODS

After a literature review and consultation with clinical experts, a preliminary draft of C-GUIDE Prenatal was developed. Its face and content validity were then assessed by 19 prenatal genetics' providers using interviews and surveys. Feedback informed further revisions. To test construct validity, 4 geneticist raters completed C-GUIDE on a retrospective sample of cases that received prenatal genetic testing and completed a concurrent global assessment of utility of these cases using an anchor item. A generalized estimating equations model was used to adjust for rater correlation and measure the association between C-GUIDE scores, global item scores, and potential clinical variables.

RESULTS

To develop C-GUIDE Prenatal, 7 items were removed, 10 items were modified, and 4 items were added. For 101 cases rated for validation, on average, a 1-point increase in the global item score was associated with an increase of 1.1 in the C-GUIDE score (P = .04). Compared with uninformative results, informative positive and informative negative results were associated with a mean increase of 10.7 (SE = 1.05) (P < .001) and 5.6 (SE = 1.85) (P < .001), respectively. As indications for testing, known/familial variants were associated with a mean increase in the C-GUIDE score of 4.7 (SE = 2.21) (P < .001) compared with ultrasound findings. C-GUIDE scores increased by a mean of 3.0 (SE = 0.23) among cases for whom pregnancies were ongoing compared with those for whom they were not (P < .01).

CONCLUSION

The significant positive associations between C-GUIDE total and the global item score and between C-GUIDE total, result type, indication for testing, and pregnancy status in the expected directions provide evidence of construct validity.

Beckwith-Wiedemann Syndrome Diagnosed in the Early Second Trimester in Two Fetuses with Isolated Omphalocele

Beckwith-Wiedemann syndrome (BWS) is an imprinting disorder caused by various genetic or epigenetic alterations involving growth regulatory genes located on chromosome 11p15.5 region. Conventionally, most cases of BWS are diagnosed during the neonatal period or early childhood. Early prenatal diagnosis is very important because it provides information regarding the prognosis, guidance of delivery preparation, and postnatal care plan. We report two cases of BWS diagnosed in utero using exome sequencing (ES) after the early identification of fetal omphalocele and normal findings of microarray and methylation analyses. Case 1 carried a de novo CDKN1C c.694C>T (p.Gln232*) variant. Case 2 carried a familial CDKN1C c.827_828delinsAA (p.Phe276*) variant; another member in the family presented with features of BWS. In both cases, no macrosomia and visceromegaly were demonstrated. Although fetal omphalocele was identified in the first trimester, invasive testing was delayed to the early second trimester for methylation in the two cases. Fetal omphalocele should not be regarded as just an abdominal wall defect. When a fetal omphalocele was identified, a detailed family history, especially with searching for the signs of BWS in familial members, should be undertaken. For an omphalocele, ES is an option for patients after normal microarray and methylation analyses.

Current Diagnostic, Counseling, and Treatment Options in Non-Severe and Severe Apparently Isolated Fetal Ventriculomegaly

The widening of the vestibular dimension of lateral ventricles > 10 mm should be considered a symptom rather than a definitive diagnosis. In fact, fetal ventriculomegaly (VM) is a defect with 'multifaceted' clinical consequences in the child's further neurodevelopment. Isolated fetal ventriculomegaly can cause neurological defects ranging from mild neurodevelopmental delay to severe complications in the form of ongoing palliative care to the death of patients at various developmental periods. The spectrum of compilations often depends on the severity of the ventriculomegaly. In the prenatal period, the combined diagnostic tools include the following: ultrasound/MRI and genetic, infectious tests that form the basis of reliable counseling. We hypothesize that advances in the diagnostic process allow the identification of 'probably' isolated forms of severe VM (ISVM). The review authors electronically searched MEDLINE, EMBASE, and the Cochrane Library databases, describing the evidence-based validity and option of prenatal decompression for ISVM. The purpose of this review is to present the evolution of diagnostic techniques and views indicating the possibility and limitations of implementing prenatal decompression in severe ISVM. In conclusion, after reviewing the available data, we want to introduce the idea that perinatal centers are close to or have reached the necessary capability, expertise, and competence to perform ISVM decompression procedures. Endoscopic ventriculostomy of the third ventricle (ETV) appears to be promising, as it seems to be associated with minimal perinatal complications and better neurological outcomes for the newborn. However, long-term follow-up results for the neurodevelopment of patients who underwent ETV have not been reported. Looking ahead, randomized trials with the long-term neurodevelopmental follow-up of children who underwent prenatal decompression due to ISVM are needed.

Evaluating the Implementation of the Rapid Prenatal Exome Sequencing Service in England

INTRODUCTION

In October 2020, a national rapid prenatal exome sequencing (pES) service was rolled out across the English National Health Service (NHS). This service is delivered by multiple clinical and two laboratory teams. While there was high level national guidance to support implementation, it was unclear how the service had been delivered in practice. This study evaluated pES service implementation across England, using the major system change (MSC) framework to explore links between implementation approaches and outcomes.

METHODS

We conducted a national mixed-methods multi-site study of 17 clinical genomics services, their linked fetal medicine services and two laboratories delivering the pES service. The MSC framework informed the study. Key documents, semi-structured interviews (eight national service developers, 55 staff), and surveys (n = 159 staff) were analysed using inductive and deductive thematic analysis and descriptive statistics. Findings were integrated.

RESULTS

Implementation was influenced by a range of factors including evidence of benefit, laboratory service reconfiguration, and stakeholder support. Local implementation approaches varied; seven models of service delivery were identified. Key differences between models included leadership, staffing, and multidisciplinary team approaches. Local staff factors (e.g., time, capacity, attitudes), pES service factors (e.g., communication/collaboration, logistics), and organisational factors (e.g., infrastructure and previous experience) influenced implementation.

CONCLUSION

We have identified multiple barriers and facilitators that are associated with implementing a major change to genomic services in a complex national healthcare system. This study highlights which models of pES may work in practice and why. Findings will inform future development of the pES service.

Going Back in Time: Prenatal Presentations of Postnatal Genetic Diagnoses Made in a Neonatal Intensive Care Unit

OBJECTIVES

Prenatal genetic diagnosis can impact care across the perinatal continuum; however, prenatal suspicion for genetic disorders may be complicated by incomplete knowledge of fetal rare-disease phenotypes. Here, we describe the prenatal presentations of a cohort of infants with rare genetic conditions who were diagnosed postnatally in a neonatal intensive care unit (NICU), to characterize prenatal presenting features and evaluate why the diagnosis was not identified prenatally.

METHODS

Retrospective cohort study of infants born over a 7 year period (2017-2023) who were admitted to a Level IV NICU and received a postnatal genetic diagnosis prior to 1 year of age. We identified which of these infants had been imaged prenatally at our Maternal Fetal Care Center (MFCC) as an opportunity for prenatal genetic diagnosis. Clinical data were abstracted from the medical records.

RESULTS

51 cases met the inclusion criteria. Nine of the 51 infants were not strongly suspected to have a genetic syndrome prenatally when seen at the MFCC, as evidenced by lack of prenatal genetic consultation and lack of documented suspicion for a genetic etiology. These cases largely had absent or uncertain prenatal phenotypes. In most cases (42/51, 82.4%), prenatal diagnostic testing was not pursued even if offered. Overall, postnatal diagnoses, of which there was one dual diagnosis, were made by karyotype/FISH (11/52, 21.1%), microarray (8/52, 15.4%), gene panel/targeted testing (17/52, 32.7%), or exome sequencing (16/52, 30.8%).

CONCLUSIONS

Our data illustrate the challenges in fetal phenotyping and support a broad approach to prenatal testing to facilitate early genetic diagnosis, which may meaningfully impact postnatal care.

Genome sequencing in the prenatal diagnosis of structural malformations in the fetus

Prenatal genetic diagnosis has undergone two pivotal paradigm shifts, initially with the introduction of chromosomal microarray and subsequently with the advent of next-generation sequencing technologies (NGS). NGS technology has given rise to a multitude of applications, with gene panels, exome sequencing (ES), and genome sequencing (GS) emerging as highly promising tests for prenatal genetic investigations. These advanced approaches have demonstrated superior diagnostic rates when compared to conventional testing methods, showcasing the evolution and enhancement of prenatal genetic screening and diagnostic capabilities. With these ground-breaking innovations, NGS technologies have the potential to replace current standard practice in prenatal diagnosis. With the increasing use of prenatal sequencing, the need for better education and guidance on their applications grows. This chapter aims to illustrate the detection scope and feasibility of various NGS-based methods that are currently used in prenatal diagnosis.

Fetal whole genome sequencing as a clinical diagnostic tool: Advantages, limitations and pitfalls

Genome-wide sequencing, which includes exome sequencing and genome sequencing, has revolutionized the diagnostics of genetic disorders in both postnatal and prenatal settings. Compared to exome sequencing, genome sequencing enables the detection of many additional types of genomic variants, although this depends on the bioinformatics pipelines used. Variant classification might vary among laboratories. In the prenatal setting, variant classification may change if new fetal phenotypic features emerge as the pregnancy progresses. There is still a need to evaluate the incremental diagnostic yield of genome sequencing compared to exome sequencing in the prenatal setting. This article reviews the advantages and limitations of genome sequencing, with an emphasis on fetal diagnostics.

Impact of prenatal genomics on clinical genetics practice

Genetic testing for prenatal diagnosis in the pre-genomic era primarily focused on detecting common fetal aneuploidies, using methods that combine maternal factors and imaging findings. The genomic era, ushered in by the emergence of new technologies like chromosomal microarray analysis and next-generation sequencing, has transformed prenatal diagnosis. These new tools enable screening and testing for a broad spectrum of genetic conditions, from chromosomal to monogenic disorders, and significantly enhance diagnostic precision and efficacy. This chapter reviews the transition from traditional karyotyping to comprehensive sequencing-based genomic analyses. We discuss both the clinical utility and the challenges of integrating prenatal exome and genome sequencing into prenatal care and underscore the need for ethical frameworks, improved prenatal phenotypic characterization, and global collaboration to further advance the field.

Implementation of a national rapid prenatal exome sequencing service in England: evaluation of service outcomes and factors associated with regional variation

Introduction

Prenatal exome sequencing (pES) can enhance genetic diagnosis of fetuses with structural anomalies and has recently been introduced as a national service in England. We aimed to examine service outcomes such as diagnostic yield (definite final diagnosis), referral rate, and sources of referral, and explore variation in outcomes of pES by individual or service level factors between 01 October 2021 and 30 June 2022.

Methods

pES testing results from the National Health Service laboratories performing testing were linked to National Congenital Anomaly and Rare Disease Registration Service data and the Maternity Services Data Set and descriptive statistics computed.

Results

There were 475,089 women who gave birth in England during the study period. The referral rate for pES was 8.6 (95% CI 7.8, 9.4) per 10,000 maternities. About 59% of those referred proceeded with pES testing and 35% of women who proceeded received a definite final diagnosis with a median turnaround time of 15 days. Of those who had pES testing, 64.6% had a live birth, 25.3% underwent termination of pregnancy (median gestational age at termination: 26 weeks), and 9.3% had a stillbirth. Among the 85 women who had a definite final diagnosis, 40% had a termination of pregnancy, 18% had a stillbirth, and 42% had a live birth. The corresponding figures among women without a definite final diagnosis were 18%, 5%, and 78%, respectively. Among women who had a termination of pregnancy, the median gestational age at final report was 24.9 weeks and 26.2 weeks at termination. Variation observed in some of the characteristics and outcomes between regional services were limited by small sample size.

Conclusion

This study showed that of those referred, pES testing provided a diagnosis for one in three pregnancies with a fetal anomaly across England during the study period when other tests had been non-informative. Women who opted for a termination of pregnancy underwent the procedure at relatively late gestations. Earlier referral for pES, streamlining pathways, and faster turnaround times may help results to be available at an earlier gestation to allow families more time to make decisions around continuing or terminating their pregnancy. The variation in service outcomes between regional services needs to be investigated further to understand the reasons for these differences.

Progress in managing children with achondroplasia

INTRODUCTION

Achondroplasia is a heritable disorder of the skeleton that affects approximately 300,000 individuals worldwide. Until recently, treatment for this condition has been purely symptomatic. Efficacious treatment options for children are now approved or are in clinical trials.

AREAS COVERED

This review discusses key advances in the therapeutic management of children with achondroplasia, including vosoritide, the first approved drug, and other emerging precision therapies. These include navepegritide, a long-acting form of C-type natriuretic peptide, and infigratinib, a tyrosine kinase receptor inhibitor, summarizing trial outcomes to date.

EXPERT OPINION

The advent of the first approved precision therapy for achondroplasia in vosoritide has been a paradigm shifting advance for children affected by this condition. In addition to changing their natural growth history, it is hoped that it will decrease their medical complications and enhance functionality. These new treatment options highlight the importance of prompt prenatal identification and subsequent testing of a suspected fetus with achondroplasia and counseling of families. It is hoped that, in the near future, families will have the option to consider a range of effective targeted therapies that best suit their child with achondroplasia, starting from birth should they choose.

Contribution of Genomic Imbalance in Prenatal Congenital Anomalies of the Kidney and Urinary Tract: A Multi-Center Cohort Study

OBJECTIVES

To investigate the diagnostic utility of copy-number variant (CNV) detection by chromosomal microarray analysis (CMA) and genotype-phenotype associations in prenatal congenital anomalies of the kidney and urinary tract (CAKUT).

METHODS

This is a retrospective multi-center study of CNV analysis in 457 fetuses with ultrasound-detected CAKUT and normal karyotypes. Cohorts from published studies were included for further pooled analyses (N = 2746). A literature review of single-nucleotide variant (SNV) and small insertions and deletions (Indel) analysis by whole-exome sequencing was performed to investigate monogenic causes.

RESULTS

In our multi-center cohort, 5.3% (24/457) of fetuses had pathogenic CNVs (pCNV); 3.9% (14/359) and 10.2% (10/98) in isolated and non-isolated CAKUT, respectively. Fetuses with isolated hyperechogenic kidneys (HEK) had the highest incidence of having pCNVs. In the literature review, 6.6% (180/2746) of fetuses carried pCNVs; 6.1% and 7.5% in isolated and non-isolated CAKUT, respectively. SNV/Indel analysis provided at least 16.5% (63/381) additional diagnostic yield beyond CNV analysis; 12.8% and 23.8% in isolated and non-isolated CAKUT, respectively.

CONCLUSION

pCNVs comprise a significant proportion of genetic diagnostic findings in prenatal CAKUT, most commonly detected in fetuses with isolated HEK, MCDK, renal agenesis, and non-isolated CAKUT. Monogenic causes should be considered when karyotyping and CMA are nondiagnostic.

Idiopathic polyhydramnios and postnatal outcomes of children: The role of exome sequencing

OBJECTIVES

The objective of our study was to evaluate the long-term outcome of children born from a pregnancy complicated by idiopathic polyhydramnios. The secondary objective was to investigate factors associated with adverse outcomes.

METHODS

We conducted a retrospective study in two prenatal diagnosis centers between January 1, 2009 and December 31, 2020. Inclusion criteria were pregnancies with a diagnosis of idiopathic polyhydramnios, defined by a deepest pocket greater than 8 cm, no detectable abnormality at ultrasound and a negative amniotic fluid assessment including karyotype, chromosomal microarray, biochemical assays (electrolytes and digestive enzymes), and viruses (parvovirus B19 and cytomegalovirus). One-year outcomes of these children were collected. The primary endpoint was adverse postnatal outcome, defined by at least one of the following criteria: stillbirth, neonatal death, or serious and incurable condition diagnosed in the first year of life.

RESULTS

Of the 245 women referred for isolated polyhydramnios, 73 were diagnosed with idiopathic polyhydramnios after prenatal investigations. The mean age at follow-up of children was 28 months (95% CI 20-36). An adverse outcome occurred in 25% of cases (18/73), with one stillbirth, two neonatal deaths, and 15 severe conditions diagnosed postnatally, including a rate of monogenic disorders of 8.2% (6/73). Pediatric follow-up was normal for 75% of the children (55/73), including a rate of 9% (5/55) of curable conditions. Repeated amnioreduction was independently associated with an adverse outcome.

CONCLUSION

Pregnant women with polyhydramnios should be informed of the increased risk of 25% of perinatal mortality and serious conditions diagnosed after birth.

Extending the new era of genomic testing into pregnancy management: A proposed model for Australian prenatal services

BACKGROUND

Trio exome sequencing can be used to investigate congenital abnormalities identified on pregnancy ultrasound, but its use in an Australian context has not been assessed.

AIMS

Assess clinical outcomes and changes in management after expedited genomic testing in the prenatal period to guide the development of a model for widespread implementation.

MATERIALS AND METHODS

Forty-three prospective referrals for whole exome sequencing, including 40 trios (parents and pregnancy), two singletons and one duo were assessed in a tertiary hospital setting with access to a state-wide pathology laboratory. Diagnostic yield, turn-around time (TAT), gestational age at reporting, pregnancy outcome, change in management and future pregnancy status were assessed for each family.

RESULTS

A clinically significant genomic diagnosis was made in 15/43 pregnancies (35%), with an average TAT of 12 days. Gestational age at time of report ranged from 16 + 5 to 31 + 6 weeks (median 21 + 3 weeks). Molecular diagnoses included neuromuscular and skeletal disorders, RASopathies and a range of other rare Mendelian disorders. The majority of families actively used the results in pregnancy decision making as well as in management of future pregnancies.

CONCLUSIONS

Rapid second trimester prenatal genomic testing can be successfully delivered to investigate structural abnormalities in pregnancy, providing crucial guidance for current and future pregnancy management. The time-sensitive nature of this testing requires close laboratory and clinical collaboration to ensure appropriate referral and result communication. We found the establishment of a prenatal coordinator role and dedicated reporting team to be important facilitators. We propose this as a model for genomic testing in other prenatal services.

Application of Whole-Exome Sequencing in the Prenatal Diagnosis of Foetuses With Central Nervous System Abnormalities

OBJECTIVE

To investigate the clinical value of whole-exome sequencing (WES) in the diagnosis of foetuses with central nervous system (CNS) abnormalities but having a normal karyotyping and chromosomal microarray result.

METHOD

During the period of 2016-2022, there were a total of 149 foetuses with CNS abnormalities but having negative karyotyping and chromosomal microarray analysis results; WES was performed on these foetuses and their parents. Variants were classified according to ACMG guidelines, and the association of pathogenic variants with specific types of CNS abnormalities was explored.

RESULTS

Among these 149 foetuses, three categories of abnormalities, namely, single CNS abnormality, multiple CNS abnormalities, CNS abnormalities along with other organ system abnormalities were identified, for which the detection rate of P/LP variants is 17.4% (12/69), 28.6% (14/49) and 54.8% (17/31), respectively.

CONCLUSION

WES brought about an increase of 28.9% in diagnostic yield in the prenatal evaluation of foetuses with CNS abnormalities but having negative karyotyping and chromosome array results. WES may also be of benefit for the diagnosis of foetuses with isolated CNS abnormalities, as well as for making more informed interpretations of imaging findings and for providing better genetic counselling.

Diagnostic yield of prenatal exome sequencing in the genetic screening of fetuses with brain anomalies detected by MRI and ultrasonography: A systematic review and meta-analysis

BACKGROUND

Brain anomalies (BAs) have been the focus of research, as they have a high impact on fetal health but therapeutic and diagnostic approaches are limited.

OBJECTIVES

In this study, the application and efficiency of exome sequencing (ES) in detecting different cases of BAs in fetuses were evaluated and compared with chromosomal microarray analysis (CMA).

SEARCH STRATEGY

To conduct this study, three databases including PubMed, Web of Science and Embase were utilised with the keywords 'prenatal', 'diagnoses', 'brain anomalies' and 'exome sequencing'.

SELECTION CRITERIA

Studies were included based on the STARD checklist, for which the ES and CMA diagnostic yields were calculated.

DATA COLLECTION AND ANALYSIS

Meta-analysis was performed on the included studies using a random-effects model and subgroup analysis to define the risk difference between them.

MAIN RESULTS

We included 11 studies representing 779 fetuses that implemented ES along with imaging techniques. The pooled ES diagnostic yield in fetuses with BAs detected through magnetic resonance imaging (MRI) and ultrasonography was 26.53%, compared with 3.46% for CMA. The risk difference between ES and CMA for complex BAs was 0.36 [95% confidence interval (CI) 0.24-0.47], which was higher than for single BAs (0.22; 95% CI 0.18-0.25].

CONCLUSIONS

ES is a useful method with a significantly higher diagnostic yield than CMA for genetic assessment of fetuses with complex BAs detected by imaging techniques. Moreover, ES could be applied to suspected fetuses with related family histories to predict congenital diseases with high efficiency.

Molecular diagnostic yield of exome sequencing in a Chinese cohort of 512 fetuses with anomalies

BACKGROUND

Currently, whole exome sequencing has been performed as a helpful complement in the prenatal setting in case of fetal anomalies. However, data on its clinical utility remain limited in practice. Herein, we reported our data of fetal exome sequencing in a cohort of 512 trios to evaluate its diagnostic yield.

METHODS

In this retrospective cohort study, the couples performing prenatal exome sequencing were enrolled. Fetal phenotype was classified according to ultrasound and magnetic resonance imaging findings. Genetic variants were analyzed based on a phenotype-driven followed by genotype-driven approach in all trios.

RESULTS

A total of 97 diagnostic variants in 65 genes were identified in 69 fetuses, with an average detection rate of 13.48%. Skeletal and renal system were the most frequently affected organs referred for whole exome sequencing, with the highest diagnostic rates. Among them, short femur and kidney cyst were the most common phenotype. Fetal growth restriction was the most frequently observed phenotype with a low detection rate (4.3%). Exome sequencing had limited value in isolated increased nuchal translucency and chest anomalies.

CONCLUSIONS

This study provides our data on the detection rate of whole exome sequencing in fetal anomalies in a large cohort. It contributes to the expanding of phenotypic and genotypic spectrum.

Genetic analysis of pregnancy loss and fetal structural anomalies by whole exome sequencing

BACKGROUND

Whole exome sequencing (WES) has been recommended to investigate the genetic cause of fetal structural anomalies. In this retrospective study, we aimed to evaluate the diagnostic yield of WES in our cohort of families with pregnancy loss or termination of pregnancy due to structural anomalies.

METHODS

As aneuploidy, triploidy and copy number variations (CNVs) could be detected by exome-based CNV analysis, only WES is performed in this study. And the results of 375 cases assessed by WES were analyzed.

RESULTS

The overall detection rate was 32.3% (121/375), including aneuploidy and triploidy (7.5%, 28/375), CNVs (5.1%, 19/375) and single-nucleotide variants (SNVs) /insertions or deletions (Indels) (19.7%, 74/375). Among these, the diagnostic yield for likely pathogenic (LP) or pathogenic (P) CNVs is 4.8% (18/375), and the diagnostic yield for LP or P SNVs/Indels is 15.2% (57/375). And an additional 4.8% (18/375) of cases had CNVs or SNVs/Indels classified as variants of uncertain significance (VUS) with potential clinical significance.

CONCLUSIONS

Our findings expand the known mutation spectrum of genetic variants related to fetal abnormalities, increase our understanding of prenatal phenotypes, and enable more accurate counseling of recurrence risk for future pregnancies.

A Practical, Systematic Approach to Genetic Diagnosis in a Fetus or Neonate with Congenital Anomalies

Congenital anomalies contribute significantly to perinatal, neonatal, and infant morbidity and mortality. The causes of these anomalies vary, ranging from teratogen exposure to genetic disorders. A high suspicion for a genetic condition is especially important because a genetic diagnosis carries a risk of recurrence in future pregnancies. Various methods are available for genetic testing, and each plays a role in establishing a genetic diagnosis. This review summarizes a practical, systematic approach to a fetus or neonate with congenital anomalies.

Prenatal exome sequencing, a powerful tool for improving the description of prenatal features associated with genetic disorders

OBJECTIVE

Prenatal exome sequencing (pES) is now commonly used in clinical practice. It can be used to identifiy an additional diagnosis in around 30% of fetuses with structural defects and normal chromosomal microarray analysis (CMA). However, interpretation remains challenging due to the limited prenatal data for genetic disorders.

METHOD

We conducted an ancillary study including fetuses with pathogenic/likely pathogenic variants identified by trio-pES from the "AnDDI-Prenatome" study. The prenatal phenotype of each patient was categorized as typical, uncommon, or unreported based on the comparison of the prenatal findings with documented findings in the literature and public phenotype-genotype databases (ClinVar, HGMD, OMIM, and Decipher).

RESULTS

Prenatal phenotypes were typical for 38/56 fetuses (67.9%). For the others, genotype-phenotype associations were challenging due to uncommon prenatal features (absence of recurrent hallmark, rare, or unreported). We report the first prenatal features associated with LINS1 and PGM1 variants. In addition, a double diagnosis was identified in three fetuses.

CONCLUSION

Standardizing the description of prenatal features, implementing longitudinal prenatal follow-up, and large-scale collection of prenatal features are essential steps to improving pES data interpretation.

Molecular autopsy for fetal structural anomaly: diagnostic and clinical utility of multidisciplinary team approach

OBJECTIVE

In the West Midlands regional genetics service, cases of perinatal death with a possible genetic diagnosis are evaluated by the perinatal pathology genetic multidisciplinary team (MDT). The MDT assesses autopsy findings and suggests appropriate genomic assessment. The objective of this retrospective service evaluation was to determine the clinical utility of the MDT in assessing perinatal deaths associated with structural anomaly. This is the first evaluation since the introduction of whole-genome and whole-exome sequencing in routine clinical care.

METHODS

This was a retrospective service evaluation including all cases of perinatal death with an associated structural anomaly and suspected genetic etiology that underwent perinatal MDT assessment between January and December 2021. All cases received a full or partial postmortem examination and at least a chromosomal microarray analysis. Demographic characteristics, phenotype, genotype, MDT recommendations, diagnoses, outcomes and impact of postmortem analysis and genetic testing data were collected from patient case notes.

RESULTS

Overall, 123 cases were discussed at the MDT meetings in 2021. Genetic evaluation was recommended in 84 cases and accepted in 64 cases. A range of genetic tests were requested according to indication and availability. Thirty diagnoses were made in 29 cases from 26 unrelated families. The diagnostic yield was 24% (29/123) in all cases or 45% (29/64) in cases with a suspected genetic diagnosis who underwent genetic testing. Postmortem examination provided clinically actionable phenotypic data in 79% of cases. A genetic diagnosis enabled accurate recurrence risk counseling and provision of appropriate follow-up, including prenatal testing and preimplantation diagnosis for patients with inherited conditions.

CONCLUSIONS

Genomic testing was a clinically useful addition to (but not a substitute for) postmortem examination in cases of perinatal death associated with structural anomaly. The MDT approach helped assess cases and plan appropriate follow-up. Expedited whole-genome sequencing or panel-agnostic analysis were most appropriate for heterogeneous presentations. This broad approach can also expand knowledge of prenatal phenotypes and detect novel disease genes, and should be a priority in future research. © 2024 International Society of Ultrasound in Obstetrics and Gynecology.

Isolated Fetal Ventriculomegaly: Diagnosis and Treatment in the Prenatal Period

Fetal ventriculomegaly (VM) is a defect of the central nervous system, typically diagnosed during the second-trimester ultrasound in fetuses with an atrial diameter (AD) of >10 mm. Non-isolated ventriculomegaly (NIVM) is heterogeneous in nature, coexisting with additional intracranial and/or extracranial malformations and genetic syndromes, resulting in an unfavorable prognosis for the further development of the child. Both the pregnancy management and counseling are dependent on the findings of combined ultrasound/MRI, genetic testing, and gestational age at diagnosis. The purpose of this review is to propose a hypothesis that diagnostic advancements allow to define the process of identification of the isolated forms of VM (IVM). Based on the evidence presented in the literature, we consider whether prenatal decompression for severe isolated VM (ISVM) is supported by the experimental trials and whether it might be implemented in clinical practice. Also, we describe the evolution of the diagnostic methods and expert opinions about the previously used prenatal decompression techniques for ISVM. In conclusion, we introduce the idea that fetal surgery centers have either reached or nearly reached the necessary level of expertise to perform such procedures. Endoscopic cystoventriculostomy (ETV) appears to be the most promising, as it is associated with minimal perinatal complications and favorable neurological outcomes in the neonatal period. Randomized trials with long-term neurodevelopmental follow-up of children who underwent prenatal decompression due to ISVM are necessary.

Experience of the first adult-focussed undiagnosed disease program in Australia (AHA-UDP): solving rare and puzzling genetic disorders is ageless

BACKGROUND

Significant recent efforts have facilitated increased access to clinical genetics assessment and genomic sequencing for children with rare diseases in many centres, but there remains a service gap for adults. The Austin Health Adult Undiagnosed Disease Program (AHA-UDP) was designed to complement existing UDP programs that focus on paediatric rare diseases and address an area of unmet diagnostic need for adults with undiagnosed rare conditions in Victoria, Australia. It was conducted at a large Victorian hospital to demonstrate the benefits of bringing genomic techniques currently used predominantly in a research setting into hospital clinical practice, and identify the benefits of enrolling adults with undiagnosed rare diseases into a UDP program. The main objectives were to identify the causal mutation for a variety of diseases of individuals and families enrolled, and to discover novel disease genes.

METHODS

Unsolved patients in whom standard genomic diagnostic techniques such as targeted gene panel, exome-wide next generation sequencing, and/or chromosomal microarray, had already been performed were recruited. Genome sequencing and enhanced genomic analysis from the research setting were applied to aid novel gene discovery.

RESULTS

In total, 16/50 (32%) families/cases were solved. One or more candidate variants of uncertain significance were detected in 18/50 (36%) families. No candidate variants were identified in 16/50 (32%) families. Two novel disease genes (TOP3B, PRKACB) and two novel genotype-phenotype correlations (NARS, and KMT2C genes) were identified. Three out of eight patients with suspected mosaic tuberous sclerosis complex had their diagnosis confirmed which provided reproductive options for two patients. The utility of confirming diagnoses for patients with mosaic conditions (using high read depth sequencing and ddPCR) was not specifically envisaged at the onset of the project, but the flexibility to offer recruitment and analyses on an as-needed basis proved to be a strength of the AHA-UDP.

CONCLUSION

AHA-UDP demonstrates the utility of a UDP approach applying genome sequencing approaches in diagnosing adults with rare diseases who have had uninformative conventional genetic analysis, informing clinical management, recurrence risk, and recommendations for relatives.

Phenotypic and genotypic analysis of 11 fetal cases with Bardet-Biedl syndrome

OBJECTIVE

To present the prenatal sonographic features and genomic spectrum of pregnancies with fetal Bardet-Biedl syndrome (BBS).

METHODS

This was a retrospective study of 11 cases with BBS diagnosed by prenatal ultrasound and confirmed by genetic testing. Clinical and laboratory data were collected and reviewed for these cases, including maternal demographics, prenatal sonographic findings, molecular testing sequencing results, and pregnancy outcomes.

RESULTS

All cases had unremarkable first-trimester ultrasound scans without reporting limb malformations. All had second-trimester abnormal ultrasounds: postaxial polydactyly in nine cases (9/11), renal abnormalities in seven (7/11), reduced amniotic fluid volume in two (2/11), central nervous system anomalies in two (2/11), and ascites in three (3/11). Ten fetuses presented with at least two-system anomalies, and one (Case 11) presented with only postaxial polydactyly. Variants were detected in five genes, including BBS2, ARL6/BBS3, BBS7, CEP290/BBS14 and IFT74/BBS22. Ten pregnancies were terminated in the second trimester, while one continued to term.

CONCLUSION

Enlarged hyperechogenic kidneys and postaxial polydactyly are the two most common sonographic features of fetal BBS. Prenatal diagnosis of BBS can be done with ultrasound and genetic testing although the diagnosis may be made in the second trimester.

Guidelines for NGS procedures applied to prenatal diagnosis by the Spanish Society of Gynecology and Obstetrics and the Spanish Association of Prenatal Diagnosis

OBJECTIVE

This document addresses the clinical application of next-generation sequencing (NGS) technologies for prenatal genetic diagnosis and aims to establish clinical practice recommendations in Spain to ensure uniformity in implementing these technologies into prenatal care.

METHODS

A joint committee of expert obstetricians and geneticists was created to review the existing literature on fetal NGS for genetic diagnosis and to make recommendations for Spanish healthcare professionals.

RESULTS

This guideline summarises technical aspects of NGS technologies, clinical indications in prenatal setting, considerations regarding findings to be reported, genetic counselling considerations as well as data storage and protection policies.

CONCLUSIONS

This document provides updated recommendations for the use of NGS diagnostic tests in prenatal diagnosis. These recommendations should be periodically reviewed as our knowledge of the clinical utility of NGS technologies, applied during pregnancy, may advance.

A systematic review to assess the utility of genomic autopsy using exome or genome sequencing in cases of congenital anomalies and perinatal death

PURPOSE

Exome or genome sequencing (ES or GS) can identify genetic causes of otherwise unexplained congenital anomaly and perinatal death (PND) but is not routine practice. The evidence base for "genomic autopsy" after termination of pregnancy for fetal anomaly (TOPFA) and PND has been synthesized to determine the value of this investigation.

METHODS

We conducted a systematic review and meta-analysis of studies meeting prespecified inclusion criteria and containing ≥10 cases of TOPFA or PND (with or without major congenital abnormality), in which ES or GS was conducted. We determined test performance, including diagnostic yield, accuracy, and reliability. We also reported outcomes associated with clinical utility and harms, where described.

RESULTS

From 2245 potentially eligible studies, 32 publications were eligible and had data extracted, representing 2120 cases that could be meta-analyzed. No diagnostic accuracy or comparative studies were identified, although some analysis of concordance between different ES/GS methodologies could be performed. Studies reporting parent-related outcomes or long-term follow-up did not do so in a systematic or quantifiable manner.

CONCLUSION

Evidence suggests that approximately one-fourth to one-third of fetal losses associated with TOPFA or unexplained PND are associated with a genetic cause identifiable on ES or GS-albeit this estimate varies depending on phenotypic and background risk factors. Despite the large body of evidence on ES and GS, little research has attempted to validate the accuracy of testing, nor measure the clinical or societal outcomes in families that follow the diagnostic investigation in this context.

Prenatal Genome-Wide Sequencing analysis (Exome or Genome) in detecting pathogenic Single Nucleotide Variants in fetal Central Nervous System Anomalies: systematic review and meta-analysis

Prenatal Exome (pES) or Genome (pGS) Sequencing analysis showed a significant incremental diagnostic yield over karyotype and chromosomal microarray analysis (CMA) in fetal structural anomalies. Optimized indications and detection rates in different fetal anomalies are still under investigation. The aim of this study was to assess the incremental diagnostic yield in prenatally diagnosed Central Nervous System (CNS) anomalies. A systematic review on antenatal CNS anomalies was performed according to PRISMA guidelines, including n = 12 paper, accounting for 428 fetuses. Results were pooled in a meta-analysis fitting a logistic random mixed-effect model. The effect of interest was the incremental diagnostic rate of pES over karyotype/CMA in detecting likely pathogenic/pathogenic Single Nucleotide Variants (SNVs). A further meta-analysis adding the available pGS studies (including diagnostic coding SNVs only) and submeta-analysis on three CNS subcategories were also performed. The pooled incremental diagnostic yield estimate of pES studies was 38% (95% C.I.: [29%;47%]) and 36% (95% C.I.: [28%;45%]) when including diagnostic SNVs of pGS studies. The point estimate of the effect resulted 22% (95% C.I.: [15%;31%]) in apparently isolated anomalies, 33% (95% C.I.: [22%;46%]) in CNS-only related anomalies (≥1) and 46% (95% C.I.: [38%;55%]) in non-isolated anomalies (either ≥ 2 anomalies in CNS, or CNS and extra-CNS). Meta-analysis showed a substantial diagnostic improvement in performing Prenatal Genome-Wide Sequencing analysis (Exome or Genome) over karyotype and CMA in CNS anomalies.

Advancing fetal diagnosis and prognostication using comprehensive prenatal phenotyping and genetic testing

Prenatal diagnoses of congenital malformations have increased significantly in recent years with use of high-resolution prenatal imaging. Despite more precise radiological diagnoses, discussions with expectant parents remain challenging because congenital malformations are associated with a wide spectrum of outcomes. Comprehensive prenatal genetic testing has become an essential tool that improves the accuracy of prognostication. Testing strategies include chromosomal microarray, exome sequencing, and genome sequencing. The diagnostic yield varies depending on the specific malformations, severity of the abnormalities, and multi-organ involvement. The utility of prenatal genetic diagnosis includes increased diagnostic clarity for clinicians and families, informed pregnancy decision-making, neonatal care planning, and reproductive planning. Turnaround time for results of comprehensive genetic testing remains a barrier, especially for parents that are decision-making, although this has improved over time. Uncertainty inherent to many genetic testing results is a challenge. Appropriate genetic counseling is essential for parents to understand the diagnosis and prognosis and to make informed decisions. Recent research has investigated the yield of exome or genome sequencing in structurally normal fetuses, both with non-invasive screening methods and invasive diagnostic testing; the prenatal diagnostic community must evaluate and analyze the significant ethical considerations associated with this practice prior to generalizing its use. IMPACT: Reviews available genetic testing options during the prenatal period in detail. Discusses the impact of prenatal genetic testing on care using case-based examples. Consolidates the current literature on the yield of genetic testing for prenatal diagnosis of congenital malformations.

Embryo and fetal gene editing: Technical challenges and progress toward clinical applications

Gene modification therapies (GMTs) are slowly but steadily making progress toward clinical application. As the majority of rare diseases have an identified genetic cause, and as rare diseases collectively affect 5% of the global population, it is increasingly important to devise gene correction strategies to address the root causes of the most devastating of these diseases and to provide access to these novel therapies to the most affected populations. The main barriers to providing greater access to GMTs continue to be the prohibitive cost of developing these novel drugs at clinically relevant doses, subtherapeutic effects, and toxicity related to the specific agents or high doses required. In vivo strategy and treating younger patients at an earlier course of their disease could lower these barriers. Although currently regarded as niche specialties, prenatal and preconception GMTs offer a robust solution to some of these barriers. Indeed, treating either the fetus or embryo benefits from economy of scale, targeting pre-pathological tissues in the fetus prior to full pathogenesis, or increasing the likelihood of complete tissue targeting by correcting pluripotent embryonic cells. Here, we review advances in embryo and fetal GMTs and discuss requirements for clinical application.