Prenatal exome and genome sequencing for fetal structural abnormalities

Perinatal Outcomes of Cystic Hygroma: A Systematic Review and Meta-Analysis: Running Head: Systematic Review of Cystic Hygroma Outcomes

OBJECTIVES

The aim of this systematic review and meta-analysis was to describe the perinatal outcomes and modifiers of antenatally diagnosed cystic hygroma (CH).

DATA SOURCES

The PubMed, Embase and Web of Science Core Collection databases were searched from inception until March 18, 2024.

STUDY ELIGIBILITY CRITERIA

Full-text English-language observational cohort studies reporting any pregnancy and postnatal outcomes for fetuses with a CH diagnosed on prenatal ultrasound were included in this study.

METHODS

The primary outcome was the incidence of genetic diagnosis and incidence of major structural anomalies. Secondary outcomes included the incidence of perinatal loss, termination of pregnancy, CH resolution, live birth rate and normal postnatal outcomes. Stratified analyses were conducted of cases diagnosed in the first trimester as well as all cases with septations as part of diagnostic criteria. Pooled proportions were calculated for the different outcomes.

RESULTS

Fifty-seven studies met inclusion criteria (including 4693 cases of CH); these were cohort studies that included any of our primary search outcomes. The pooled prevalence of genetic diagnosis (56 studies, 3837 fetuses) was 55% (95% CI, 0.51-0.58). For specific aneuploidies, the pooled prevalence was 21% for Turner syndrome, 17% for Trisomy 21, 10% for Trisomy 18, 3% for Trisomy 13, and 5% for other genetic diagnoses. The overall pooled prevalence of major structural anomalies (30 studies, 1987 fetuses) was 42%; across 16 studies (1815 fetuses), 16% of fetuses with CH and an additional structural abnormality had no identified genetic diagnosis. Furthermore, 20% of all CH regressed or resolved during the pregnancy. The findings from the studies that that defined CH by the presence of septations, as well as those focusing solely on first trimester CH were consistent with the overall outcomes.

CONCLUSIONS

Our findings confirm that while CHs have a strong association with common trisomies and Turner syndrome, there is a proportion of cases with non-aneuploidy genetic diagnoses. Forty percent of cases are also associated with other structural anomalies that may be able to be elicited with a detailed first trimester anatomic ultrasound. Further studies should explore modifiers of CH outcomes to allow for more accurate and tailored patient counseling.

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.

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.

The fetal neurologist: Strategies to improve training, practice, and clinical care

Fetal neurology addresses counselling parents on the clinical significance of brain anomalies encountered in their fetus, including disruptive lesions (i.e. stroke, periventricular haemorrhagic infarction, and infection), and genetically based cortical (i.e. hemimegalencephaly, lissencephaly, cobblestone malformation, polymicrogyria, heterotopia) or posterior fossa anomalies (i.e. cerebellar agenesis and hypoplasia, rhombencephalosynapsis, Dandy-Walker syndrome, mega cisterna magna, Blake's pouch cyst). Unlike paediatric neurologists, fetal neurologists cannot examine the infant directly so they diagnose and prognosticate using imaging and other diagnostic studies. The integration of fetal neurologists into fetal multidisciplinary teams is essential for providing expert counselling and cohesive care. This review emphasizes the need for specialized training, multidisciplinary collaboration, and the development of comprehensive service designs to ensure consistent and effective care for families. Additionally, it emphasizes the critical role of fetal neurologists in identifying brain anomalies early and providing thorough counselling to parents, helping them to understand the prognosis, potential interventions, and long-term outcomes for their unborn child.

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.

Whole Exome Sequencing in a Population of Fetuses With Structural Anomalies

OBJECTIVE

To investigate the exome sequencing (ES) detection rate among fetuses with congenital anomalies and describe the rates in the setting of multiple versus isolated anomalies, perinatal autopsy, and family history of a previously affected child.

METHODS

A single-center retrospective chart review was conducted on 397 anomalous fetuses that underwent ES from May 2012 through December 2023. Medical record review included demographics, imaging, and genetic testing.

RESULTS

The overall ES diagnostic rate was 34.3%. The rate of diagnosis was 31.6% in fetuses with a single anomaly and 42.6% in fetuses with 4 or more major organ systems involved. Of the fetuses with a single anomaly, lymphatic, craniofacial, skeletal, and neurological anomalies had the highest diagnostic rate on ES. 38.6% of deceased fetuses who underwent autopsy had a genetic diagnosis. Additionally, families who had a previously affected child had a 45.5% diagnostic rate.

CONCLUSIONS

ES is an important tool that should be offered in pregnancies affected with congenital abnormalities or at the time of fetal demise or termination. The diagnostic rate of ES in the prenatal setting is also highly dependent on comprehensive phenotyping. With diagnostic ES results, reproductive technology and testing options are available in subsequent pregnancies.

Recurrent First-trimester Cystic Hygroma with Normal Chromosomes Identified in Two Cases with a Recessive Genetic Syndrome

First-trimester cystic hygroma (CH) was a frequent finding in a general obstetric screening program for fetal aneuploidy. Chromosomal abnormalities can be diagnosed in most cases with CH, especially common trisomies and Turner syndrome. For first-trimester CH with a normal array result, management choices are limited except for waiting for serial ultrasounds to detect structural anomalies. We report two cases with a recurrent diagnosis of fetal first-trimester CH in two subsequent pregnancies. In both cases, detailed anatomic surveys in the second trimester showed structural anomalies. After excluding chromosomal abnormalities, trio-exome sequencing (ES) revealed two pathogenic variants, P3H1:c.1032T >A and c.1927_1930delinsGCTT in Case 1, and two pathogenic variants, KIAA1109:c.5788del and c. 3055C >T in Case 2. These findings were associated with two recessive genetic syndromes, osteogenesis imperfecta type VIII and Alkuraya-Kucinskas syndrome, in the two cases, respectively. Our study showed that the recurrence of fetal CH with a normal karyotype strongly indicates the existence of an autosomal recessive type of genetic disorder. For such cases, health providers should be alerted to this possibility, and early application of ES should be considered before the presentation of fetal structural anomalies which are usually present in second-trimester anatomic scans.

Obstetrics and neonatal outcomes of binder phenotype with antenatal diagnosis: A case report and literature review

BACKGROUND

Binder phenotype (BP) is a term used to define a form of maxillo-nasal dysplasia defined by the presence of flattened nose, verticalized nasal bones, and retrusion of the maxilla (BP triad). This facial anomaly can be associated with other anomalies in both genetic and acquired conditions as well as in isolation. This systematic review aimed to summarize the antenatal findings, maternal and obstetrics characteristics as well as the obstetrics and neonatal outcomes of all cases of BP diagnosed in utero.

METHODS

According to the PRISMA statement, we conducted a systematic review of the literatures to identify all the Binder phenotype cases diagnosed antenatally. We extracted and summarized obstetrics and neonatal characteristics of each study, including our case report.

MAIN FINDINGS

We identified a total of 47 cases of BP. The median gestational age at diagnosis was 23 weeks. BP was associated with other skeletal or non-skeletal anomalies in all cases apart from six confirmed to be isolated. Respiratory distress syndrome was observed in 12 neonates and in 18 cases BP was one of the clinical findings of chondrodysplasia punctata X-linked.

CONCLUSION

BP is often associated with other fetal defects; however, when isolated, BP seems to have good obstetrics and neonatal outcomes. In fetuses with apparent isolated BP at midtrimester, genetic testing with fluorescence in situ hybridization (FISH) for ARSE deletion can be offered for CDPX1 diagnosis while exome sequencing may be more informative in cases where a syndromic condition is suspected. Lastly, BP per se is associated with a higher risk of respiratory distress syndrome and feeding difficulties.

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.

Genetic correlation between fetal nuchal translucency thickening and cystic hygroma and exploration of pregnancy outcome

Chromosome microarray analysis (CMA) and whole exome sequencing (WES) are increasingly utilized in prenatal diagnosis of abnormal ultrasound findings, but studies on correlation between pathogenic copy number variations (pCNVs) and single-gene mutations in fetuses with nuchal translucency (NT) thickening/cystic hygroma (CH), and pregnancy outcomes, are rare. This study aimed to investigate clinical value of CMA and WES for NT thickening/CH in fetuses, explore genetic correlation between fetal NT thickening and CH, and analyze pregnancy outcomes. We retrospectively selected 215 pregnant women diagnosed with fetal NT thickening (NT > 95th)/CH who underwent invasive prenatal diagnosis at our hospital from January 2020 to June 2022. With negative chromosomal karyotype analysis (KA) and CMA results, patients voluntarily underwent WES. Patients were grouped by NT thickening/CH, and application value of KA, CMA, and WES examined. Ultrasound findings, pregnancy outcomes, and fetal growth post-birth were followed during mid/late pregnancy and post-delivery. Abnormalities in chromosomal number were detected in 28 of 215 samples, with a detection rate of 13.0%, and pCNVs were detected in 12 cases, with a detection rate of 5.6%. The most common abnormality in fetuses from both groups suggested by CMA was 22q11.21 microdeletion-microduplication syndrome. 35 patients with negative KA and CMA results underwent WES, and single gene variants were detected in 12 fetuses, with an abnormality rate of 34.3%. The incidence of adverse pregnancy outcomes was 28.2% in the NT thickening group and 82.9% in the CH group (P < 0.05). Overall, fetal NT thickening/CH was associated with genetic abnormalities, WES further improved the diagnosis of abnormal fetuses after negative KA and CMA results in both groups, and the incidence of adverse pregnancy outcomes was lower in the NT thickening group than in the CH group. The management of pregnancy outcomes could guide clinical genetic counselling.

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.

Chromosomal Microarray Analysis in Fetuses with Ultrasound Abnormalities

Objective

To explore and evaluate the value of chromosomal microarray analysis (CMA) in prenatal diagnosis of fetuses with ultrasound abnormalities.

Methods

A retrospective analysis was performed on 370 fetuses with ultrasound abnormalities received invasive prenatal diagnosis at Meizhou People's Hospital from October 2022 to December 2023. Fetal specimens were analyzed by CMA, and the detection rates of aneuploidy and pathogenic (P)/likely pathogenic (LP) copy number variations (CNVs) in ultrasound structural abnormalities (malformations of fetal anatomy) and non-structural abnormalities (abnormalities of fetal nonanatomical structure) were analyzed.

Results

There were 114 (30.8%) cases with isolated ultrasound structural abnormalities, 226 (61.1%) cases with isolated non-structural abnormalities (182 isolated ultrasound soft markers abnormalities, 30 isolated fetal growth restriction (FGR), and 8 isolated abnormalities of amniotic fluid volume), and 30 (8.1%) cases with both structural and non-structural abnormalities. The overall detection rate of aneuploidy and P/LP CNVs in isolated ultrasonic structural abnormalities was 5.3%, among which cardiovascular system abnormalities were the highest. In addition, the largest number of fetuses with non-structural abnormalities was nuchal translucency (NT) thickening (n = 81), followed by ventriculomegaly (n = 29), and nasal bone dysplasia (n = 24). The detection rate of chromosomal abnormalities of fetuses with abnormal ultrasound soft markers was 9.9%, and the detection rate in single abnormal ultrasound soft marker, and multiple ultrasound soft markers abnormalities was 9.7% (16/165) and 11.8% (2/17), respectively. Moreover, the detection rate of chromosomal abnormalities of fetuses with FGR and structural abnormalities combined with non-structural abnormalities was 6.7% (2/30), and 13.3% (4/30), respectively.

Conclusion

The incidence of chromosomal abnormalities (aneuploidy and P/LP CNVs) varies among different fetal ultrasound abnormalities.

Population-based surveillance of congenital anomalies over 40 years (1981-2020): Results from the Paris Registry of Congenital Malformations (remaPAR)

INTRODUCTION

Registries of congenital anomalies (CAs) play a key role in the epidemiological surveillance of CAs. The objective was to estimate the prevalence of CAs and proportions of prenatal diagnosis, terminations of pregnancy for fetal anomaly (TOPFA) and infant mortality in the Paris Registry of Congenital Malformations (remaPAR) over 40 years, from 1981 to 2020.

MATERIAL AND METHODS

remaPAR records all births (live births, stillbirths ≥22 weeks of gestation and TOPFA at any gestational age) with CAs detected prenatally until the early neonatal period. We estimated the prevalence of CAs and proportions of prenatal diagnosis, TOPFA and infant mortality, overall and for a selected group of CAs in 3-year intervals.

RESULTS

The prevalence of CAs remained stable during the study period: 2.9 % of total births and 2.1 % of live births. Genetic anomalies were the most frequent subgroup (about 23 %), followed by congenital heart defects (about 22 %) and limb defects (about 20 %). Among non-genetic anomalies, the prevalence per 10,000 births was the highest for hypospadias (about 18 %) and the lowest for bilateral renal agenesis (about 1 %). Prenatal diagnoses increased from about 17 % in the 1980s to approximately 70 % in the most recent period (2018-2020), whereas the proportion of early TOPFA <16 weeks of gestation increased from 0.4 % to 14 %. Infant mortality ranged from 0 % for transverse limb reduction defects to 86 % for hypoplastic left heart syndrome.

CONCLUSION

The overall prevalence of CAs was fairly stable in Paris from 1981 to 2020. Prenatal diagnoses substantially increased, accompanied by much smaller increases in TOPFA.

First-Trimester Ultrasound Screening in Routine Obstetric Practice

Technologic advances and ultrasonographer-physician experience in fetal imaging have led to significant improvements in our ability to distinguish between normal and abnormal fetal structural development in the latter part of the first trimester. As a critical component of pregnancy care, assessment of fetal anatomy at the end of the first trimester with a standardized imaging protocol should be offered to all pregnant patients regardless of aneuploidy screening results because it has been demonstrated to identify approximately half of fetal structural malformations. Early identification of abnormalities allows focused genetic counseling, timely diagnostic testing, and subspecialist consultation. In addition, a normal ultrasound examination result offers some degree of reassurance to most patients. Use of cell-free DNA alone for aneuploidy screening while foregoing an accompanying early anatomic evaluation of the fetus will result in many anomalies that are typically detected in the first trimester not being identified until later in pregnancy, thus potentially diminishing the quality of obstetric care for pregnant individuals and possibly limiting their reproductive options, including pregnancy termination.

The Evolving Role of Genetic Evaluation in the Prenatal Diagnosis and Management of Congenital Heart Disease

Congenital heart disease (CHD) is increasingly diagnosed prenatally and the ability to screen and diagnose the genetic factors involved in CHD have greatly improved. The presence of a genetic abnormality in the setting of prenatally diagnosed CHD impacts prenatal counseling and ensures that families and providers have as much information as possible surrounding perinatal management and what to expect in the future. This review will discuss the genetic evaluation that can occur prior to birth, what different genetic testing methods are available, and what to think about in the setting of various CHD diagnoses.

Access to prenatal exome sequencing for fetal malformations: A qualitative landscape analysis in the US

OBJECTIVE

There is increasing evidence supporting the clinical utility of next generation sequencing for identifying fetal genetic disorders. However, there are limited data on the demand for and accessibility of these tests, as well as payer coverage in the prenatal context. We sought to identify clinician perspectives on the utility of prenatal exome sequencing (ES) and on equitable access to genomic technologies for the care of pregnancies complicated by fetal structural anomalies.

METHOD

We conducted two focus group discussions and six interviews with a total of 13 clinicians (11 genetic counselors; 2 Maternal Fetal Medicine/Geneticists) from U.S. academic centers and community clinics.

RESULTS

Participants strongly supported ES for prenatal diagnostic testing in pregnancies with fetal structural anomalies. Participants emphasized the value of prenatal ES as an opportunity for a continuum of care before, during, and after a pregnancy, not solely as informing decisions about abortions. Cost and coverage of the test was the main access barrier, and research was the main pathway to access ES in academic centers.

CONCLUSION

Further integrating the perspectives of additional key stakeholders are important for understanding clinical utility, developing policies and practices to address access barriers, and assuring equitable provision of prenatal diagnostic testing.