Implementation of Exome Sequencing in Prenatal Diagnosis and Impact on Genetic Counseling: The Polish Experience

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.

Simultaneous CNV-seq and WES: An effective strategy for molecular diagnosis of unexplained fetal structural anomalies

Background

Fetal structural anomalies are detected by ultrasound in approximately 3 % of pregnancies. Numerous genetic diagnostic strategies have been widely applied to identify the genetic causes of prenatal abnormalities. We aimed to assess the value of simultaneous copy number variation sequencing (CNV-seq) and whole exome sequencing (WES) in diagnosing fetuses with structural anomalies.

Methods

Fetuses with structural anomalies detected by ultrasound were included for eligibility. After genetic counseling, WES and CNV-seq were performed on DNA samples of fetuses and their parents. All detected variants were evaluated for pathogenicity according to ACMG criteria, with the final diagnosis was determined based on ultrasound results and relevant family history.

Results

The diagnostic rate of 174 fetuses with prenatal ultrasound abnormalities was 26.44 %, higher than that achieved through either CNV or WES analysis alone. Furthermore, the highest diagnostic rate was observed in fetuses with multiple system anomalies, accounting for 50 % of the total diagnostic yield, followed by skeletal system anomalies at 45.45 %. Three cases with multiple system abnormalities were found to have a dual diagnosis of pathogenic CNVs and SNV variants, representing 1.72 % of the total cohort. 38 pregnant women in their third trimester of pregnancy (27 weeks+) participated in this study, and 23.68 % received a confirmed genetic diagnosis. Finally, 31 women (67.39 %) voluntarily terminated their pregnancy following the testing and extensive genetic counseling.

Conclusions

Our study demonstrated that the simultaneous CNV-seq and WES analyses are beneficial for the molecular diagnosis of underlying unexplained structural anomalies in fetuses. This strategy is more efficient in elucidating prenatal abnormalities with compound problems, such as dual diagnoses. Furthermore, the simultaneous strategy has a shorter turnaround time and is particularly suitable for families with structural anomalies found in the third trimester of pregnancy.

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.

The incremental yield of prenatal exome sequencing over chromosome microarray for congenital heart abnormalities: A systematic review and meta-analysis

OBJECTIVES

To determine the incremental yield of prenatal exome sequencing (PES) over standard testing in fetuses with an isolated congenital heart abnormality (CHA), CHA associated with extra-cardiac malformations (ECMs) and CHA dependent upon anatomical subclassification.

METHODS

A systematic review of the literature was performed using MEDLINE, EMBASE, Web of Science and grey literature January 2010-February 2023. Studies were selected if they included greater than 20 cases of prenatally diagnosed CHA when standard testing (QF-PCR/chromosome microarray/karyotype) was negative. Pooled incremental yield was determined. PROSPERO CRD 42022364747.

RESULTS

Overall, 21 studies, incorporating 1957 cases were included. The incremental yield of PES (causative pathogenic and likely pathogenic variants) over standard testing was 17.4% (95% CI, 13.5%-21.6%), 9.3% (95% CI, 6.6%-12.3%) and 35.9% (95% CI, 21.0%-52.3%) for all CHAs, isolated CHAs and CHAs associated with ECMs. The subgroup with the greatest yield was complex lesions/heterotaxy; 35.2% (95% CI 9.7%-65.3%). The most common syndrome was Kabuki syndrome (31/256, 12.1%) and most pathogenic variants occurred de novo and in autosomal dominant (monoallelic) disease causing genes (114/224, 50.9%).

CONCLUSION

The likelihood of a monogenic aetiology in fetuses with multi-system CHAs is high. Clinicians must consider the clinical utility of offering PES in selected isolated cardiac lesions.

RASopathies are the most common set of monogenic syndromes identified by exome sequencing for nonimmune hydrops fetalis: A systematic review and meta-analysis

RASopathies are a group of malformation syndromes known to lead to nonimmune hydrops fetalis (NIHF) in severe presentations. Pathogenic variants can be de novo or parentally inherited. Despite being a known frequent presentation, the fraction of monogenic NIHF cases due to RASopathies is limited in the literature. Also, the specific parental contribution of RASopathies to NIHF is not well described. Our objective was to review pooled exome sequencing (ES) diagnostic yield of RASopathies for NIHF and to determine the parental contribution of RASopathy to NIHF. We performed a systematic review of prenatal ES studies from January 1, 2000 to August 1, 2022. Thirty-six studies met inclusion criteria. Cases with RASopathy gene variants were reviewed. NIHF cases were further classified as isolated or non-isolated. Thirty-six ES studies including 46 pregnancies with NIHF and a diagnosed RASopathy were reviewed. Forty-four diagnostic variants and 2 variants of uncertain significance in 12 RASopathy genes were identified. Expanding on what was previously published, a total of 506 NIHF cases were extracted with 191 cases yielding a positive diagnosis by ES. The overall rate of RASopathy diagnosis in clinically diagnosed NIHF cases was 9% (44/506). The rate of RASopathy diagnosis among NIHF cases with positive genetic diagnosis by ES was 23% (44/191). Of the 46 cases identified, 13 (28%) variants were parentally inherited; specifically, 5/13 (38%) maternal, 3/13 (23%) paternal, 2/13 (15%) biparental, and 3/13 (23%) unspecified. Majority of NIHF cases 29/46 (63%) were isolated. Among NIHF cases with positive ES diagnoses, RASopathy diagnostic yield by ES was 23%. NIHF secondary to RASopathies was parentally inherited in 28% of cases. Most cases of NIHF due to RASopathy were isolated, with no prenatal detection of associated anomalies.

When should we offer antenatal sequencing for urinary tract malformations? A systematic review, cohort study and meta-analysis

OBJECTIVE

Determine the incremental yield of prenatal exome sequencing (PES) over chromosome microarray (CMA) and/or karyotype for urinary tract malformations (UTMs).

METHOD

A prospective cohort study encompassing data from the English Genomic Medicine Service North Thames Laboratory Hub for fetuses with bilateral echogenic kidneys (BEKs) was combined with data from a systematic review. MEDLINE, EMBASE, Web of Science, MedRxiv and GreyLit were searched from 01/2010-02/2023 for studies reporting on the yield of PES over CMA or karyotype in fetuses with UTMs. Pooled incremental yield was determined using a random effects model. PROSPERO CRD42023364544.

RESULTS

Fourteen studies (410 cases) were included. The incremental yield for multisystem UTMs, any isolated UTMs, and BEKs was 31% [95% CI, 18%-46%; I2  = 78%], 16% [95% CI, 6%-26%; I2  = 80%] and 51% [95% CI, 27%-75%; I2  = 34%]. The most common clinical diseases and syndromes identified, based on the variant genes detected, were Bardet-Biedl syndrome (BBS genes), dominant and recessive polycystic kidney diseases (PKD1, PKD2 and PKHD1) and renal cysts and diabetes syndrome (HNF1B).

CONCLUSION

There was a notable incremental genetic diagnostic yield when PES was applied to multisystem UTMs and BEKs. There was a modest incremental yield when this technique was used for UTMs other than BEKs.

Prenatal whole-exome sequencing in fetuses with increased nuchal translucency

BACKGROUND

Increased nuchal translucency (NT) is associated with an increased risk for genetic disorders. The aim of this study was to investigate the value of whole-exome sequencing (WES) in detecting genetic abnormalities for fetuses with isolated first-trimester increased NT.

METHODS

After the exclusion of aneuploidies and pathogenic copy number variants (CNVs) by quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray analysis (CMA), WES was performed on 63 fetuses with isolated first-trimester increased NT (≥3.5 mm).

RESULTS

Overall, WES yielded a 4.8% (3/63) diagnostic rate for fetuses with isolated increased NT. Pathogenic variants were identified in 37.5% (3/8) fetuses that developed additional structural anomalies later in gestation, and no pathogenic variants were detected in increased NT that resolved or remained isolated throughout the pregnancy.

CONCLUSION

This study provides powerful evidence to offer prenatal WES for increased NT only when additional abnormalities are present. Early detailed ultrasound to detect emerging anomalies can help physicians offer prenatal WES to fetuses with a greater likelihood of diagnosis.

The Successful Management of Primary Amenorrhea in Woodhouse-Sakati Syndrome: A Case Report and a Literature Review

BACKGROUND

Woodhouse-Sakati syndrome (WSS) is a rare multisystemic disease resulting from an autosomal recessive gene mutation characterized by distinctive facial appearance, alopecia, impaired HbA1c, and hypogonadism.

PURPOSE

To present the successful management of primary amenorrhea in a WSS patient.

CASE PRESENTATION

We report a 19-year-old Saudi female referred to the gynecology clinic at the age of 16 as a case of primary amenorrhea. The patient underwent a genetic analysis, which revealed mutations in the DCAF17 gene, confirming the diagnosis of WSS. Treatment includes hormonal replacement therapy for the induction of puberty.

CONCLUSIONS

Careful and detailed medical and physical examination led to appropriate testing confirming the WSS diagnosis. Genetic tests for family members and the offspring of the patient are strongly recommended. Treatment timing and dosage are determined by the patient's individual needs, which take into consideration the patient's potential for growth, the family's readiness, and any comorbidities.