Extended genetic testing in fetuses with sonographic skeletal system abnormalities

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.

Incremental yield of prenatal exome sequencing in fetuses with skeletal system abnormalities: A systematic review and meta-analysis

INTRODUCTION

Fetal skeletal abnormalities can be caused by various factors and genetic cause plays an important role. Prenatal exome sequencing (ES) has been shown to be a powerful approach for accurate prenatal molecular diagnoses. Diagnostic yield of ES in fetal skeletal abnormalities varies significantly across studies. This study aimed to perform a systematic review of the literature and meta-analysis to assess the incremental yield of ES in fetuses with different kinds of skeletal abnormalities and a negative result on chromosome microarray or karyotyping.

MATERIAL AND METHODS

The PubMed, Embase, Web of Science, and Cochrane Library databases were systematically searched up to November 26, 2022. Relevant data were collected from observational studies containing five or more cases of skeletal abnormalities who underwent ES. The incremental yield of ES was evaluated by single proportion analysis and 95% confidence interval (CI), both according to the article features and individual phenotypes. This study was registered on PROSPERO as CRD42022382800.

RESULTS

Twenty-six studies including 524 individuals met the inclusion criteria. The pooled incremental yield was 60.2% (95% CI, 53.4%-66.9%) for all fetuses with skeletal abnormalities. In subgroup analysis, the additional diagnostic yield was 83.9% (95% CI, 76.4%-90.4%) in isolated dysplasia cases (group I), 52.0% (95% CI, 32.9%-70.9%) in dysplasia with non-skeletal abnormalities cases (group II), 33.3% (95% CI, 19.3%-48.6%) in isolate dysostoses cases (group III), 47.8% (95 % CI, 35.8%-60.0%) in dysostoses with non-skeletal abnormalities cases (group IV), 83.0% (95% CI, 63.7%-97.1%) in combination of the two phenotypes without non-skeletal abnormalities cases (group V), 74.5% (95% CI, 54.9%-90.9%) in combination of the two phenotypes with non-skeletal abnormalities cases (group VI). The origin of the pathogenic variations differed among the groups. Most causative variants were de novo in groups I (97/133, 72.9%), V (14/23, 60.9%), and VI (15/26, 57.7%). Meanwhile, pathogenic variations in III (18/25, 72.0%) and IV (37/67, 55.2%) were more often inherited from a parent.

CONCLUSIONS

ES had a favorable incremental yield in fetuses with skeletal abnormalities. The common pathogenic variations and genetic patterns of skeletal abnormalities vary among different subtypes. Interpreting this difference is beneficial for personalized clinical consultation.

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.

Fetal Phenotyping and Whole Exome Sequencing for 12 Egyptian Families With Serine Biosynthesis Defect: Novel Clinical and Allelic Findings With a Founder Effect

OBJECTIVE

The purpose of this study was to improve our understanding of severe serine biosynthesis defects through a comprehensive description of prenatal, and postnatal manifestations and the mutational spectrum in a new cohort of 12 unrelated Egyptian Families.

METHODS

Detailed fetal ultrasound examination, postnatal assessment, and whole exome sequencing (WES) were performed in a cohort of 12 fetuses with suspected Neu-Laxova syndrome (NLS), the most severe expression of serine biosynthesis defects. Additionally, a comprehensive review of the literature was conducted by merging the data from all the molecularly-confirmed cases with ours to gain a better understanding of the clinical variability of NLS.

RESULTS

Novel clinical manifestations including intrauterine convulsions, hemivertebrae, natal teeth, holoprosencephaly, and rhombencephalosynapsis were observed. Molecular analysis identified 7 and 2 likely disease-causing variants in the PSAT1 and PHGDH genes, respectively. Four of them were novel, including the c.734G>A missense variant in PSAT1, which has been proposed to be a founder variant among Egyptians.

CONCLUSION

The present cohort expands the spectrum of serine biosynthesis disorders. Moreover, it illuminates the role of prenatal exome sequencing in lethal conditions constituting the most severe end of already-known human diseases.

A De novo Mutation in the COL1A1 Gene Leading to Severe Osteogenesis Imperfecta: Case Report and Review of the Literature

Introduction  Osteogenesis imperfecta (OI) is the most common monogenic inherited skeletal dysplasia disorder. Mutations in the COL1A1/COL1A2 gene cause ∼85 to 90% of OI. Studies of cases have demonstrated that missense mutations are the primary cause of OI, with poor prognosis. Case Description  We report the case of a fetus with skeletal abnormalities and subcutaneous edema. Ultrasound imaging revealed suspected skeletal malformations, including hypoplastic long bones of all four limbs, poorly ossified calvarium, unrevealing nasal bones, and generalized subcutaneous edema. Whole-exome sequencing revealed a heterozygous mutation in COL1A1 (c.2174G > T/p.(G725V), NM_000088.3). According to the American College of Medical Genetics and Genomics guidelines, it was determined to be a pathogenic variant and identified as a de novo variant (PS2 + PP3_strong + PM2_supporting), which has not been reported in the HGMD, gnomAD, ClinVar, or other databases. This variation causes a glycine-to-valine substitution at position 725, located within the Gly-Xaa-Yaa repeat in the helical domain of the collagen molecule. Conclusion  The COL1A1 mutation (c.2174G > T/p.(G725V), NM_000088.3) is a novel pathogenic variant of severe OI. Our study expanded the OI COL1A1 gene variation profiles in the Chinese population and provided a theoretical foundation for prenatal diagnosis, genetic counseling, and obstetric management.

Deciphering the pathogenic role of rare RAF1 heterozygous missense mutation in the late-presenting DDH

Background

Developmental Dysplasia of the Hip (DDH) is a skeletal disorder where late-presenting forms often escape early diagnosis, leading to limb and pain in adults. The genetic basis of DDH is not fully understood despite known genetic predispositions.

Methods

We employed Whole Genome Sequencing (WGS) to explore the genetic factors in late-presenting DDH in two unrelated families, supported by phenotypic analyses and in vitro validation.

Results

In both cases, a novel de novo heterozygous missense mutation in RAF1 (c.193A>G [p.Lys65Glu]) was identified. This mutation impacted RAF1 protein structure and function, altering downstream signaling in the Ras/ERK pathway, as demonstrated by bioinformatics, molecular dynamics simulations, and in vitro validations.

Conclusion

This study contributes to our understanding of the genetic factors involved in DDH by identifying a novel mutation in RAF1. The identification of the RAF1 mutation suggests a possible involvement of the Ras/ERK pathway in the pathogenesis of late-presenting DDH, indicating its potential role in skeletal development.

Prenatal diagnosis of fetuses with ultrasound anomalies by whole-exome sequencing in Luoyang city, China

Background: There is a great obstacle in prenatal diagnosis of fetal anomalies due to their considerable genetic and clinical heterogeneity. Whole-exome sequencing (WES) has been confirmed as a successful option for genetic diagnosis in pediatrics, but its clinical utility for prenatal diagnosis remains to be limited. Methods: A total of 60 fetuses with abnormal ultrasound findings underwent karyotyping or chromosomal microarray analysis (CMA), and those with negative results were further subjected to WES. The identified variants were classified as pathogenic or likely pathogenic (P/LP) and the variant of uncertain significance (VUS). Pregnancy outcomes were obtained through a telephone follow-up. Results: Twelve (20%, 12/60) fetuses were diagnosed to have chromosomal abnormalities using karyotyping or CMA. Of the remaining 48 cases that underwent WES, P/LP variants were identified in 14 cases (29.2%), giving an additional diagnostic yield of 23.3% (14/60). The most frequently affected organ referred for prenatal WES was the head or neck system (40%), followed by the skeletal system (39.1%). In terms of pathogenic genes, FGFR3 was the most common diagnostic gene in this cohort. For the first time, we discovered five P/LP variants involved in SEC24D, FIG4, CTNNA3, EPG5, and PKD2. In addition, we identified three VUSes that had been reported previously. Outcomes of pregnancy were available for 54 cases, of which 24 cases were terminated. Conclusion: The results confirmed that WES is a powerful tool in prenatal diagnosis, especially for fetuses with ultrasonographic anomalies that cannot be diagnosed using conventional prenatal methods. Additionally, newly identified variants will expand the phenotypic spectrum of monogenic disorders and greatly enrich the prenatal diagnostic database.

Using MRI-derived observed-to-expected total fetal lung volume to predict lethality in fetal skeletal dysplasia

BACKGROUND

Pulmonary hypoplasia is the primary cause of perinatal death in lethal skeletal dysplasias. The antenatal ultrasound correlates for lethality are indirect, measuring the thorax (thoracic circumference, TC) or femur compared to the abdomen (TC/AC, FL/AC). A single study has correlated lethality with the observed-to-expected total lung volume (O/E-TFLV) on fetal MRI in 23 patients.

OBJECTIVE

Our aim was to define a cutoff value to predict lethality more specifically using MRI-derived O/E-TFLV.

MATERIALS AND METHODS

Two large fetal center databases were searched for fetuses with skeletal dysplasia and MRI; O/E-TFLV was calculated. Ultrasound measures were included when available. Each was evaluated as a continuous variable against lethality (stillbirth or death in the first month of life). Logistic regression and receiver operating characteristic (ROC) curve analyses evaluated the prediction ability. AUC, sensitivity, and specificity were calculated. P < 0.05 was considered statistically significant.

RESULTS

A total of 80 fetuses met inclusion criteria. O/E-TFLV < 0.49 was a significant risk factor in predicting lethality, with sensitivity and specificity of 0.63 and 0.93, respectively, and an AUC of 0.81 (P < 0.001). FL/AC < 0.129 was also a strong variable with sensitivity, specificity, and AUC of 0.73, 0.88, and 0.78, respectively (P < 0.001). TC/AC and TC percentile were not significant risk factors for lethality. An O/E-TFLV of < 0.38 defines a specificity for lethality at 1.00.

CONCLUSION

MRI-derived O/E-TFLV and US-derived FL/AC are significant predictors of lethality in fetuses with skeletal dysplasia. When prognosis is uncertain after ultrasound, calculation of MRI-derived O/E-TFLV may provide additional useful information for prognosis and delivery planning.

Prenatal exome sequencing and impact on perinatal outcome: cohort study

OBJECTIVES

First, to determine the uptake of prenatal exome sequencing (pES) and the diagnostic yield of pathogenic (causative) variants in a UK tertiary fetal medicine unit following the introduction of the NHS England Rapid Exome Sequencing Service for fetal anomalies testing (R21 pathway). Second, to identify how the decision to proceed with pES and identification of a causative variant affect perinatal outcomes, specifically late termination of pregnancy (TOP) at or beyond 22 weeks' gestation.

METHODS

This was a retrospective cohort study of anomalous fetuses referred to the Liverpool Women's Hospital Fetal Medicine Unit between 1 March 2021 and 28 February 2022. pES was performed as part of the R21 pathway. Trio exome sequencing was performed using an Illumina next-generation sequencing platform assessing coding and splice regions of a panel of 974 prenatally relevant genes and 231 expert reviewed genes. Data on demographics, phenotype, pES result and perinatal outcome were extracted and compared. Descriptive statistics and the χ-square or Fisher's exact test were performed using IBM SPSS version 28.0.1.0.

RESULTS

In total, 72 cases were identified and two-thirds of eligible women (n = 48) consented to trio pES. pES was not feasible in one case owing to a low DNA yield and, therefore, was performed in 47 cases. In one-third of cases (n = 24), pES was not proposed or agreed. In 58.3% (14/24) of these cases, this was because invasive testing was declined and, in 41.7% (10/24) of cases, women opted for testing and underwent chromosomal microarray analysis only. The diagnostic yield of pES was 23.4% (11/47). There was no overall difference in the proportion of women who decided to have late TOP in the group in which pES was agreed compared with the group in which pES was not proposed or agreed (25.0% (12/48) vs 25.0% (6/24); P = 1.0). However, the decision to have late TOP was significantly more frequent when a causative variant was detected compared with when pES was uninformative (63.6% (7/11) vs 13.9% (5/36); P < 0.0009). The median turnaround time for results was longer in cases in which a causative variant was identified than in those in which pES was uninformative (22 days (interquartile range (IQR), 19-34) days vs 14 days (IQR, 10-15 days); P < 0.0001).

CONCLUSIONS

This study demonstrates the potential impact of identification of a causative variant by pES on decision to have late TOP. As the R21 pathway continues to evolve, we urge clinicians and policymakers to consider introducing earlier screening for anomalies, developing robust guidance for late TOP and ensuring optimized support for couples. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Next Generation Sequencing after Invasive Prenatal Testing in Fetuses with Congenital Malformations: Prenatal or Neonatal Investigation

Congenital malformations diagnosed by ultrasound screening complicate 3–5% of pregnancies and many of these have an underlying genetic cause. Approximately 40% of prenatally diagnosed fetal malformations are associated with aneuploidy or copy number variants, detected by conventional karyotyping, QF-PCR and microarray techniques, however monogenic disorders are not diagnosed by these tests. Next generation sequencing as a secondary prenatal genetic test offers additional diagnostic yield for congenital abnormalities deemed to be potentially associated with an underlying genetic aetiology, as demonstrated by two large cohorts: the ‘Prenatal assessment of genomes and exomes’ (PAGE) study and ‘Whole-exome sequencing in the evaluation of fetal structural anomalies: a prospective cohort study’ performed at Columbia University in the US. These were large and prospective studies but relatively ‘unselected’ congenital malformations, with little Clinical Genetics input to the pre-test selection process. This review focuses on the incremental yield of next generation sequencing in single system congenital malformations, using evidence from the PAGE, Columbia and subsequent cohorts, with particularly high yields in those fetuses with cardiac and neurological anomalies, large nuchal translucency and non-immune fetal hydrops (of unknown aetiology). The total additional yield gained by exome sequencing in congenital heart disease was 12.7%, for neurological malformations 13.8%, 13.1% in increased nuchal translucency and 29% in non-immune fetal hydrops. This demonstrates significant incremental yield with exome sequencing in single-system anomalies and supports next generation sequencing as a secondary genetic test in routine clinical care of fetuses with congenital abnormalities.

Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis

Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.