Microarray and RASopathy-disorder testing in fetuses with increased nuchal translucency

Recurrent Increased Nuchal Translucency Led to the Identification of Novel NUP107 Variants

Five percent of fetuses presents increased fetal nuchal translucency. It is a well-known marker for aneuploidy (T21, Turner syndrome) and a variety of monogenic syndromes such as Noonan syndrome and certain skeletal dysplasias, as well as associated with structural malformations such as congenital heart disease. Current diagnostic algorithms for increased nuchal translucency include a rapid test for aneuploidy (fluorescence in situ hybridization, FISH, or quantitative PCR), a cytogenetic analysis (karyotype or chromosomal microarray, CMA) followed by or concurrent with targeted gene panel analysis for RASopathies/Noonan syndrome. Some centers now propose whole exome sequencing as an adjunct, but its usefulness in isolated increased nuchal translucency remains debated. We describe the recurrence of apparently isolated increased nuchal translucency in 2 euploid fetuses. Whole genome sequencing identified two compound heterozygous variants in the NUP107 gene in both fetuses. Biallelic variants in NUP107 are responsible for severe steroid-resistant nephrotic syndrome, either isolated or syndromic (Galloway-Mowat syndrome); in addition to the renal phenotype, the latter also includes intellectual deficiency and dysmorphic features. Pregnancy termination made it impossible to assess whether the NUP107 variants found would have resulted in isolated or syndromic steroid-resistant nephrotic syndrome. However, identifying the responsible gene improved the accuracy of the genetic counseling. This family is an example of the added benefit of introducing WES/WGS in standardized protocols for prenatal diagnosis of euploid fetuses in "isolated" increased nuchal translucency.

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.

Guideline No. 456: Prenatal Screening for Fetal Chromosomal Anomalies

OBJECTIVE

To review the available prenatal aneuploidy screening options and to provide updated clinical guidelines for reproductive care providers.

TARGET POPULATION

All pregnant persons receiving counselling and providing informed consent for prenatal screening.

BENEFITS, HARMS, AND COSTS

Implementation of the recommendations in this guideline should increase clinician competency to offer counselling for prenatal screening options and provide appropriate interventions. Given the variety of available options for prenatal screening with different performance, cost, and availability across Canada, appropriate counselling is of paramount importance to offer the best individual choice to Canadian pregnant persons. Prenatal screening may cause anxiety, and the decisions about prenatal diagnostic procedures are complex given the potential risk of fetal loss.

EVIDENCE

Published literature was retrieved through searches of Medline, PubMed, and the Cochrane Library in and prior to July 2023, using an appropriate controlled vocabulary (prenatal diagnosis, amniocentesis, chorionic villi sampling, non-invasive prenatal screening) and key words (prenatal screening, prenatal genetic counselling). Results were restricted to systematic reviews, randomized control trials/controlled clinical trials, and observational studies written in English and published from January 1995 to July 2023.

VALIDATION METHODS

The authors rated the quality of evidence and strength of recommendations using the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. See online Appendix A (Tables A1 for definitions and A2 for interpretations).

INTENDED AUDIENCE

Health care providers involved in prenatal screening, including general practitioners, obstetricians, midwives, maternal-fetal medicine specialists, geneticists, and radiologists.

SOCIAL MEDIA ABSTRACT

Non-invasive prenatal screening is the most accurate method for detecting major aneuploidies. It is not universally available in the public health system and has some limitations.

SUMMARY STATEMENTS

RECOMMENDATIONS.

Chromosomal Anomalies in Fetuses With Increased Nuchal Translucency: A Vietnamese Retrospective Study

Background Previously, fetuses with increased nuchal translucency (NT) were mainly tested for aneuploidy. Recent evidence has shown an incidence of other genetic disorders in euploidy fetuses with thickened NT. Chromosomal microarray analysis (CMA) and next-generation sequencing (NGS) can detect the incremental yield of microdeletions and microduplications (copy number variants (CNVs)) and provide useful information for prenatal counseling. This study aims to determine the frequency of pathogenic CNV (pCNV) and its associated factors in euploidy fetuses with increased NT. Methods This was a retrospective study of 491 fetuses with NT ≥ 3 mm that underwent chorionic villus sampling or amniocentesis and was tested either by CMA or CNV-seq at Tu Du Hospital between August 2020 and January 2022. Results A total of 491 cases with NT ≥ 3 mm were indicated for genetic testing. Among 397 euploidy fetuses, 36 (9.1%) were pCNV, 24 (6.0%) were submicroscopic pCNV (not visible by karyotyping), and 25 (6.3%) were variants of unknown significance (VUS). The most common pCNV were 22q11 duplication and 16p11.2-p12.2 deletion. The incidence of pCNV in fetuses with increased NT and other structural abnormalities was significantly higher than in fetuses with isolated increased NT in the first trimester (OR 3.75, 95% CI 1.79-7.86, p < 0.001). Maternal age and the thickness of NT were not associated with an increased risk of harboring pCNV. Conclusion CMA or CNV-seq can detect the incremental yield of pCNV in euploidy fetuses with increased NT to assist in more accurate prenatal counselling.

Selection of prenatal screening with nuchal translucency > 95th centile and below 99th centile: a 4-year observational study with real-world data

OBJECTIVE

We sought to analyze the genetic outcomes of fetuses with nuchal translucency (NT) > 95th centile, and determine whether prenatal genetic counseling, chromosomal microarray analysis (CMA) or non-invasive prenatal testing (NIPT) are truly beneficial for the outcomes of fetuses with increased NT > 95th centile and below 99th centile.

MATERIALS AND METHODS

A total of 535 pregnant women were included in this study, with a fetal NT > 95th centile at 11-13+6 weeks of gestation from January 2017 to December 2020. 324 pregnant women with fetal NT > 95th centile and below 99th centile combined with other risk factors and NT > 99th centile received prenatal diagnostic karyotype analysis and CMA, and 211 pregnant women with fetal isolated increased NT > 95th centile and below 99th centile were selected to carry out NIPT.

RESULTS

A total of 211 pregnant women who underwent NIPT were included in the study, NIPT results showed that 8 high-risk cases were confirmed by prenatal diagnosis. Overall, the detection rate of NIPT was 3.79%. A total of 324 pregnant women with fetal NT > 95th centile and below 99th centile, along with other risk factors, and those with fetal NT > 99th centile, received karyotype analysis and CMA for prenatal diagnosis. Among them, a total of 73 genetic abnormalities were detected, including 45 cases of chromosomal aneuploidy, 7 cases of structural abnormalities, and 21 cases of copy number variations (CNVs) with a size of less than 10 Mb. In addition, the 73 women with genetic abnormalities are divided into three groups based on the NT measurement (Group 1: Fetuses with NT > 95th centile and below 99th centile, Group 2: Fetuses with NT > 99th centile, and Group 3: Fetuses with NT > 99th centile). 13.11% (8/61) of pathogenic genetic abnormalities (6 chromosomal aneuploidy, 1 structural abnormality, and 1 likely pathogenic CNV) will be missed if genetic counseling and prenatal genetic testing were not conducted in fetuses with increased NT > 95th centile and below 99th centile combined with other risks. Pathogenic CNVs were the most common abnormalities in group 3, and one likely pathogenic CNV was detected in group 1 and group 3, respectively, and a total of 14 CNVs of unknown clinical significance (VOUS) were detected.

CONCLUSIONS

Through this study, we demonstrated that the critical value of NT > 95th centile for invasive detection or NIPT. Invasive testing combined with CMA may be recommended for fetuses with NT > 95th centile and below 99th centile and with other risks. But when isolated NT > 95th centile and below 99th centile, NIPT would be appropriate.

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.

Prenatal screening after preimplantation genetic testing for aneuploidy: time to evaluate old strategies

RESEARCH QUESTION

How does first-trimester aneuploidy screening perform in pregnancies achieved through IVF with preimplantation genetic testing for aneuploidy (PGT-A) in a medical setting?

DESIGN

This retrospective cohort study was undertaken in a single tertiary care centre between January 2013 and June 2022. In total, 20,237 women had prenatal follow-up at the study centre and were included in the study. The women were divided into three groups: singleton pregnancies conceived through the transfer of a PGT-A-screened euploid embryo (n = 510); singleton pregnancies conceived through IVF without PGT-A (n = 3291); and singleton pregnancies conceived naturally (n = 16,436).

RESULTS

The conventional combined screening test for pregnancies conceived through IVF with PGT-A had specificity of 91%; sensitivity could not be calculated as there were no cases of fetal aneuploidy in this group. In 89.1% of pregnancies conceived through IVF with PGT-A with high risk for trisomy 21, 18 or 13, the result was related to advanced maternal age (>35 years at time of screening).

CONCLUSIONS

The current screening strategy for trisomies 21, 18 and 13 can generate unnecessary tests in pregnancies achieved through IVF with PGT-A. A new protocol is needed for these patients, with greater weight given to ultrasound markers.

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.

Single gene non-invasive prenatal screening for autosomal dominant conditions in a high-risk cohort

PURPOSE

To determine the utility of single gene non-invasive prenatal screening (NIPS-SGD) in a high-risk reproductive genetics clinic.

METHODS

A clinical pilot for NIPS-SGD was conducted from March 2020 to November 2021. A NIPS-SGD panel assessing pathogenic variants in 30 genes was offered to pregnant individuals for the following indications: (1) advanced sperm age ≥40 years, (2) nuchal translucency (NT) ≥ 3.5 mm, (3) fetal anomaly, or (4) family history of a condition covered by the panel. Diagnostic testing was offered concurrently.

RESULTS

NIPS-SGD was ordered for 253 individuals: 88 (34.8%) for fetal anomalies, 96 (37.9%) for advanced sperm age, 37 (14.6%) for increased NT, and 5 (2.0%) for family history. Among 228 (90.1%) completed tests, 8 (3.5%) were positive. Diagnostic testing for 78 individuals revealed no false positive or negative results. Of 41 (25.9%) individuals who received a molecular diagnosis, 34 (82.9%) were outside the scope of NIPS-SGD. Positive NIPS-SGD altered medical management in five cases.

CONCLUSIONS

NIPS-SGD in a high-risk population can lead to earlier prenatal diagnosis, enhanced surveillance, and targeted genetic analysis, but should not replace clinically indicated diagnostic testing. Potential incidental findings include parental diagnoses and misattributed parentage.

Fetal left ventricular myocardial performance index measured at 11-14 weeks of gestation in fetuses with an increased nuchal translucency

OBJECTIVE

This study aimed to evaluate the effect of an increase in nuchal translucency (NT) thickness on the myocardial performance index (MPI) in fetuses without cardiac anomaly in the first trimester and to determine whether a difference in MPI between those with and without trisomy 21 in these fetuses could be determined.

METHODS

The study group consisted of 53 pregnancies complicated with increased NT thickness without any associated structural anomalies. Forty-six gestational age-matched pregnant women whose fetuses had normal NT thickness were enrolled as the control group.

RESULTS

In the increased NT thickness group, the mean isovolumetric relaxation time (IRT) value (0.050 ± 0.011 s) was significantly higher and the mean ejection time (ET) value (0.149 ± 0.010 s) was significantly lower than those values in the normal NT thickness group (0.045 ± 0.005 and 0.155 ± 0.009 s, p = 0.023 and p = 0.009, respectively). We found a significantly higher mean left MPI value in the increased NT thickness group (0.574 ± 0.153) versus the normal NT thickness group (0.487 ± 0.107, p < 0.001). Within the increased NT thickness group, the mean left MPI value was similar in the fetuses with normal karyotype and those with trisomy 21 (p = 0.419).

CONCLUSION

We demonstrated a significantly greater mean MPI value in the increased NT thickness group than in the normal NT thickness group. Within the increased NT thickness group, no differences in the left MPI value in the fetuses with normal karyotype and the fetuses with trisomy 21 were found.

Prenatal Diagnosis of Euploid Increased Nuchal Translucency on Fetal Ultrasound (II): RASopathy Disorders - Prenatal Ultrasound Findings and Genotype-phenotype Correlations

Prenatal diagnosis of euploid increased nuchal translucency (NT) remains a challenge to obstetricians and genetic counselors, although increased euploid NT at prenatal diagnosis can be associated with a favorable outcome. Prenatal diagnosis of euploid increased NT should include a differential diagnosis of pathogenetic copy number variants and RASopathy disorders (RDs) including Noonan syndrome. Therefore, chromosomal microarray analysis, whole-exome sequencing, RASopathy-disorder testing, and protein-tyrosine phosphatase nonreceptor type 11 gene testing may be necessary under such a circumstance. In this report, a comprehensive review of RDs with its prenatal ultrasound findings and genotype-phenotype correlations is presented.

A Pain in the Neck: Lessons Learnt from Genetic Testing in Fetuses Detected with Nuchal Fluid Collections, Increased Nuchal Translucency versus Cystic Hygroma-Systematic Review of the Literature, Meta-Analysis and Case Series

Fetal Nuchal fluid collections can manifest with two distinct presentations attributable to the same phenotypic spectrum: increased nuchal translucency (iNT) and cystic hygroma. The prenatal detection of these findings should prompt an accurate assessment through genetic counseling and testing, including karyotype, chromosomal microarray analysis (CMA) and multigene RASopathy panel. We performed a systematic review of the literature and meta-analysis, to calculate diagnostic yields of genetic testing in fetuses with iNT and cystic hygroma. We compared the results with a cohort of 96 fetuses with these isolated findings. Fetuses with isolated NT ≥ 2.5 mm showed karyotype anomalies in 22.76% of cases and CMA presented an incremental detection rate of 2.35%. Fetuses with isolated NT ≥ 3 mm presented aneuploidies in 14.36% of cases and CMA had an incremental detection rate of 3.89%. When the isolated NT measured at least 3.5 mm the diagnostic yield of karyotyping was 34.35%, the incremental CMA detection rate was 4.1%, the incremental diagnostic rate of the RASopathy panel was 1.44% and it was 2.44% for exome sequencing. Interestingly, CMA presents a considerable diagnostic yield in the group of fetuses with NT ≥ 3.5 mm. Similarly, exome sequencing appears to show promising results and could be considered after a negative CMA result.

Cancer incidence and surveillance strategies in individuals with RASopathies

RASopathies are a set of clinical syndromes that have molecular and clinical overlap. Genetically, these syndromes are defined by germline pathogenic variants in RAS/MAPK pathway genes resulting in activation of this pathway. Clinically, their common molecular signature leads to comparable phenotypes, including cardiac anomalies, neurologic disorders and notably, elevated cancer risk. Cancer risk in individuals with RASopathies has been estimated from retrospective reviews and cohort studies. For example, in Costello syndrome, cancer incidence is significantly elevated over the general population, largely due to solid tumors. In some forms of Noonan syndrome, cancer risk is also elevated over the general population and is enriched for hematologic malignancies. Thus, cancer surveillance guidelines have been developed to monitor for the occurrence of such cancers in individuals with some RASopathies. These include abdominal ultrasound and urinalyses for individuals with Costello syndrome, while complete blood counts and splenic examination are recommended in Noonan syndrome. Improved cancer risk estimates and refinement of surveillance recommendations will improve the care of individuals with RASopathies.

Effect of Exogenous Progesterone on Fetal Nuchal Translucency: An Observational Study

Introduction Nuchal translucency is a reliable first trimester screening test for fetal structural and chromosomal defects. Neonates with increased nuchal thickness are at greater risk for anomalies. Exogenous progesterone supplementation may affect nuchal translucency and thus the first trimester anomaly screening. We aimed to study if there was a difference in nuchal thickness between women receiving progesterone in the first trimester compared to those who were not supplemented with progesterone. Material and methods Forty-seven women with documented progesterone intake in the first trimester for at least 10 continuous days before the day of the nuchal translucency scan served as the study group compared to 47 other women who did not receive progesterone. Nuchal translucency was measured between 11 and 13 weeks and six days of gestation. Results The mean nuchal translucency increased with increasing gestation in both groups. Maximum mean nuchal translucency was greatest in the age group 18-20 years (1.35 + 0.1 millimeters) in women receiving progesterone compared to 36-40 years (1.65 + 0.49 millimeters) in controls. The mean nuchal translucency in women receiving progesterone was 1.15 + 0.26 millimeters, and in those that did not receive progesterone, it was 1.23 + 0.35 millimeters (p = 0.314). Conclusions Nuchal translucency increased with increasing gestation in both groups, irrespective of progesterone supplementation. There was no significant difference in mean nuchal translucency in women supplemented with progesterone compared to those that did not receive progesterone in the first trimester.

Prenatal Diagnosis of Euploid Increased Nuchal Translucency on Fetal Ultrasound (I): Noonan Syndrome: Prenatal Diagnosis and Genetic Testing

Prenatal diagnosis of euploid increased nuchal translucency (NT) remains a challenge to obstetricians and genetic counselors although increased euploid NT at prenatal diagnosis can be associated with a favorable outcome. Prenatal diagnosis of euploid increased NT should include a differential diagnosis of pathogenetic copy number variants and RASopathy disorders (RDs) including Noonan syndrome (NS). Therefore, chromosomal microarray analysis, whole-exome sequencing, RD testing, and protein-tyrosine phosphatase, nonreceptor type 11 (PTPN11) gene testing may be necessary under such a circumstance. In this report, a comprehensive review of NS with its prenatal diagnosis and genetic testing is presented.

Exploring the diagnostic utility of genome sequencing for fetal congenital heart defects

OBJECTIVE

The diagnostic yield for congenital heart defects (CHD) with routine genetic testing is around 10-20% when considering the pathogenic CNVs or aneuploidies as positive findings. This is a pilot study to investigate the utility of genome sequencing (GS) for prenatal diagnosis of CHD.

METHODS

Genome sequencing (GS, 30X) was performed on 13 trios with CHD for which karyotyping and/or chromosomal microarray results were non-diagnostic.

RESULTS

Trio GS provided a diagnosis for 4/13 (30.8%) fetuses with complex CHDs and other structural anomalies. Findings included pathogenic or likely pathogenic variants in DNAH5, COL4A1, PTPN11, and KRAS. Of nine cases without a possibly genetic etiology by GS, we had follow-up on eight. For five of them (60%), the parents chose to keep the pregnancy. A balanced translocation [46,XX,t(14;22)(q32.33;q13.31)mat] was detected in a trio with biallelic DNAH5 mutations, which together explained the recurrent fetal situs inversus and dextrocardia that was presumably due to de novo Phelan-McDermid syndrome. A secondary finding of a BRCA2 variant and carrier status of HBB, USH2A, HBA1/HBA2 were detected in the trio.

CONCLUSIONS

GS expands the diagnostic scope of mutation types over conventional testing, revealing the genetic etiology for fetal heart anomalies. Patients without a known genetic abnormality indicated by GS likely opted to keep pregnancy especially if the heart issue could be repaired. We provide evidence to support the application of GS for fetuses with CHD. This article is protected by copyright. All rights reserved.

Extending the prenatal Noonan's phenotype by review of ultrasound and autopsy data

OBJECTIVES

The antenatal phenotypic spectrum of Noonan Syndrome (NS) requires better characterization.

METHODS

This multicenter retrospective observational included 16 fetuses with molecularly confirmed NS admitted for fetopathological examination between 2009 and 2016.

RESULTS

Among 12 pathogenic variants (PV) in PTPN11 (80%), 5 (42%) fell between position c.179 and c.182. Ultrasound showed increased nuchal translucency (n=13/16, 93%), increased nuchal fold after 15 weeks of gestation (n=12/16, 75%), pleural effusions (n=11/16, 69%), polyhydramnios (n=9/16, 56%), hydrops (n=7/16, 44%), cardiovascular (n=6/16, 38%) and cerebral (n=4/16, 25%) anomalies. Fetopathological examination found dysmorphic features in all cases, cardiovascular anomalies (n=12/15, 80%), pulmonary hypoplasia (n=10/15, 67%), effusions (n=7/15, 47%) and neuropathological anomalies (n=5/15, 33%). Hydrops was significantly (p=0.02) more frequent in the four fetuses with RIT1, NRAS and RAF1 PV versus the 12 fetuses with PTPN11 PV.

CONCLUSIONS

Increased nuchal translucency and nuchal fold is common in NS. NS antenatal phenotype showed high in utero fetal death, hydrops, prenatal pleural effusion and pulmonary hypoplasia, although the inclusion of only deceased fetuses will have selected more severe phenotypes. Non-specific cardiovascular and neurological abnormalities should be added to NS antenatal phenotype. Next generation sequencing will help detect more genotypes, clarifying the prenatal phenotype and identifying genotype-phenotype correlations. This article is protected by copyright. All rights reserved.

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.

The 16-week sonographic findings in fetuses with increased nuchal translucency and a normal array

OBJECTIVE

The aim of this prospective study is to evaluate the performance of the intermediate 16-week ultrasound in fetuses with increased nuchal translucency (NT) and a normal chromosomal microarray analysis (CMA).

METHODS

During a one-year period, a detailed ultrasound was performed at 16 week' gestation for patients with an increased NT (≥3.5 mm) and normal CMA. Pregnancy work-up included a traditional 22-week ultrasound scan, an echocardiography, and the option of a 10-gene Rasopathy panel after a normal 16-week scan. Abnormal findings and pregnancy outcomes were collected and analyzed.

RESULTS

In 52 fetuses with an isolated increased NT and normal CMA, 14 (26.5%) were noted to have structural defects on the 16-week ultrasound. Intrauterine fetal death occurred in one (1.9%) case identified by the 16-week scan. Of the remaining 37 cases, six opted for a RASopathy panel. In this group, one case of Noonan syndrome was detected. One case of unilateral duplex kidney had not been found until the 22-week scan. One case of fetal growth restriction was identified in the third trimester. The remaining 34 cases proceeded with normal ultrasound to term.

CONCLUSION

The 16-week ultrasound scan performed on fetuses with increased NT and normal CMA could detect the majority of structural abnormalities that are expected to be identified traditionally at 20-24 weeks.

Different Cutoff Values for Increased Nuchal Translucency in First-Trimester Screening to Predict Fetal Chromosomal Abnormalities

INTRODUCTION

Increased nuchal translucency (NT) is closely related to an increased risk of chromosomal abnormalities. However, the criterion of increased NT for invasive prenatal diagnosis remains controversial, as the cutoff values are inconsistent among countries. This study was conducted to compare the various cutoff values of increased NT and calculate the incidence of chromosomal abnormalities to determine the predictive ability of these cutoff values in conventional chromosome analysis.

METHODS

A total of 3223 invasive samples with increased nuchal translucency (NT) or other non-ultrasound indications were collected from singleton pregnant women. Samples with isolated increased NT were divided into five groups based on the NT thickness: 909 samples in the NT ≥2.5 mm group, 819 samples in the NT ≥95th group, 547 samples in the NT ≥99th group, 527 samples in the NT ≥3.0 mm group, and 253 samples in the NT ≥3.5 mm group; 2301 samples with normal NT were considered as the control group. All five groups were karyotyped and the results were compared. The accuracy of the NT cutoff value for the screening of chromosomal abnormalities was assessed using receiver operating characteristic curve analysis.

RESULTS

Detection of all chromosomal aberrations and trisomy 21 showed that the sensitivity and false-positive rate decreased sequentially in the NT ≥2.5 mm, NT ≥95th, NT ≥3 mm, NT ≥99th, and NT ≥3.5 mm groups, whereas the specificity, positive predictive value, and false-negative rates increased sequentially. Comprehensive analysis of various factors, including sensitivity and specificity, revealed values equal to or higher than the calculated 95th percentile of NT distribution, which showed a sensitivity of 49.2% and specificity of 75.67% for detecting all aneuploidies and a sensitivity of 64% and specificity of 75.45% for trisomy 21, exhibiting the highest ability for the screening of chromosomal defects in first-trimester screening.

CONCLUSION

For different thresholds of NT thickness, values equal to or higher than the calculated 95th percentile of the NT distribution showed the highest ability for the screening of chromosomal defects in first-trimester screening.

Isolated Increased Nuchal Translucency in First Trimester Ultrasound Scan: Diagnostic Yield of Prenatal Microarray and Outcome of Pregnancy

Background: Increased nuchal translucency (NT) is associated with aneuploidy. When the karyotype is normal, fetuses are still at risk for structural anomalies and genetic syndromes. Our study researched the diagnostic yield of prenatal microarray in a cohort of fetuses with isolated increased NT (defined as NT ≥ 3.5 mm) and questioned whether prenatal microarray is a useful tool in determining the adverse outcomes of the pregnancy. Materials and Methods: A prospective study was performed, in which 166 women, pregnant with a fetus with isolated increased NT (ranging from 3.5 to 14.3 mm with a mean of 5.4 mm) were offered karyotyping and subsequent prenatal microarray when karyotype was normal. Additionally, all ongoing pregnancies of fetuses with normal karyotype were followed up with regard to postnatal outcome. The follow-up time after birth was maximally 4 years. Results: Totally, 149 of 166 women opted for prenatal testing. Seventy-seven fetuses showed normal karyotype (52%). Totally, 73 of 77 fetuses with normal karyotype did not show additional anomalies on an early first trimester ultrasound. Totally, 40 of 73 fetuses received prenatal microarray of whom 3 fetuses had an abnormal microarray result: two pathogenic findings (2/40) and one incidental carrier finding. In 73 fetuses with an isolated increased NT, 21 pregnancies showed abnormal postnatal outcome (21/73, 28.8%), 29 had a normal outcome (29/73, 40%), and 23 were lost to follow-up (23/73, 31.5%). Seven out of 73 live-born children showed an adverse outcome (9.6%). Conclusions: Prenatal microarray in fetuses with isolated increased NT had a 5% (2/40) increased diagnostic yield compared to conventional karyotyping. Even with a normal microarray, fetuses with an isolated increased NT had a 28.8% risk of either pregnancy loss or an affected child.

Application of expanded noninvasive prenatal test in prenatal diagnosis of fetuses with increased nuchal translucency

OBJECTIVES

To investigate the efficiency of the upgraded noninvasive prenatal test (NIPT-Plus) in fetuses with increased nuchal translucency (NT).

METHODS

Fetuses with an increased NT at or above 2.5 mm were selected for prenatal diagnosis. Amniotic fluid was collected from all cases for karyotype analysis and copy number variation sequencing (CNV-seq), and cell-free fetal DNA (cfDNA) in maternal blood was tested using Noninvasive Prenatal Test (NIPT-Plus) before amniocentesis in some cases. The results of amniocentesis with different NT thicknesses were analyzed and compared with those of NIPT-Plus.

RESULTS

A total of 125 eligible patients were divided into group A (2.5 mm ≤ NT < 3.0 mm) and group B (NT ≥ 3.0 mm). In group A, the detection rate of chromosomal aneuploidy and pathogenic copy number variation (CNV) was 10.6% and 6.4%, respectively. The total chromosome abnormality rate in group B (34.7%) was significantly higher than that in group A (17%). In 72 patients who underwent NIPT-Plus and amniocentesis, chromosomal aneuploidy accounted for 80.8% of the total chromosomal abnormalities. Among 21 cases of chromosomal aneuploidy, NIPT-Plus detected 20 cases. The sensitivity and specificity of NIPT-Plus toward aneuploidy detection were 95.2% and 100%, respectively. Among the five cases of pathogenic CNV, only two were detected using NIPT-Plus.

CONCLUSION

NIPT-plus is recommended as the first choice for fetal diagnosis in pregnant women with 2.5 mm ≤ NT < 3.0 mm who do not accept invasive prenatal diagnosis. When NT ≥ 3.0 mm and NIPT-Plus detects chromosomal aneuploidy, a rapid prenatal diagnosis can be performed through amniocentesis. In cases where NIPT-Plus yields negative results, amniocentesis still needs to be performed to detect chromosome microdeletions/duplications in order to avoid a missed diagnosis.

Fetal exome sequencing for isolated increased nuchal translucency: should we be doing it?

Objective

To evaluate the utility of prenatal exome sequencing (ES) for isolated increased nuchal translucency (NT) and to investigate factors that increase diagnostic yield.

Design

Retrospective analysis of data from two prospective cohort studies.

Setting

Fetal medicine centres in the UK and USA.

Population

Fetuses with increased NT ≥3.5 mm at 11–14 weeks of gestation recruited to the Prenatal Assessment of Genomes and Exomes (PAGE) and Columbia fetal whole exome sequencing studies (n = 213).

Methods

We grouped cases based on (1) the presence of additional structural abnormalities at presentation in the first trimester or later in pregnancy, and (2) NT measurement at presentation. We compared diagnostic rates between groups using Fisher exact test.

Main outcome measures

Detection of diagnostic genetic variants considered to have caused the observed fetal structural anomaly.

Results

Diagnostic variants were detected in 12 (22.2%) of 54 fetuses presenting with non‐isolated increased NT, 12 (32.4%) of 37 fetuses with isolated increased NT in the first trimester and additional abnormalities later in pregnancy, and 2 (1.8%) of 111 fetuses with isolated increased NT in the first trimester and no other abnormalities on subsequent scans. Diagnostic rate also increased with increasing size of NT.

Conclusions

The diagnostic yield of prenatal ES is low for fetuses with isolated increased NT but significantly higher where there are additional structural anomalies. Prenatal ES may not be appropriate for truly isolated increased NT but timely, careful ultrasound scanning to identify other anomalies emerging later can direct testing to focus where there is a higher likelihood of diagnosis.

Prenatal ES has a low diagnostic rate (<2%) for isolated increased NT but is significantly more likely to yield a diagnosis where there are additional fetal structural anomalies.

Linked article This article is commented on by AN Talati and NL Vora, p. 61–62 in this issue. To view this mini commentary visit https://doi.org/10.1111/1471-0528.16942.

Increased nuchal translucency after low-risk noninvasive prenatal testing: What should we tell prospective parents?

Three decades ago, the observation that first trimester fetuses with excess fluid accumulation at the back of the neck were more likely to be aneuploid, gave rise to a new era of prenatal screening. The nuchal translucency (NT) measurement in combination with serum biomarkers and maternal age, resulted in the first trimester combined screening (FTCS) program. The introduction of noninvasive prenatal testing (NIPT) over the past decade has introduced the option for parents to receive highly sensitive and specific screening information for common trisomy from as early as 10 weeks gestation, altering the traditional pathway FTCS pathway. The retention of the 11-13-week NT ultrasound remains important in the detection of structural anomalies; however, the optimal management of pregnancies with a low-risk NIPT result and an isolated increased NT measurement in an era of advanced genomic testing options is a new dilemma for clinicians. For parents, the prolonged period between the initial diagnosis in first trimester, and prognostic information at each successive stage of investigations up to 22-24 weeks, can be emotionally challenging. This article addresses the common questions from parents and clinicians as they navigate the uncertainty of having a fetus diagnosed with an increased NT after a low-risk NIPT result and presents suggested approaches to management.

First prenatal case of Noonan syndrome with SOS2 mutation: Implications of early diagnosis for genetic counseling

RASopathies are a group of syndromes with partially overlapping clinical features caused by germline mutations of the RAS/MAPK signaling pathway genes. The most common disorder is Noonan syndrome (NS; MIM 163950). We report the first prenatal case of NS with SOS2 (NM_006939.4) mutation in a euploid fetus with a severe increase in nuchal translucency (NT > 12 mm). Trio-based custom next-generation sequencing detected a de novo heterozygous missense mutation in the SOS2 gene: c.800 T > A (p.Met267Lys). Owing to the marked variable expressivity of NS and the scarcity of SOS2 mutation-related NS cases reported in the literature, it is difficult to provide appropriate genetic counseling. Several issues such as the best management technique and optimal NT cutoff have been discussed. In addition, in general, the fine balance between the advantages of an early prenatal diagnosis and the challenge of determining if the detected gene variant is pathogenic and, primarily, the stress of the counselees when providing a genetic counseling with limited information on the prenatal phenotype have been discussed. A prenatal path comprising examinations and multidisciplinary counseling is essential to support couples in a shared decision-making process.

Simultaneous Detection of CNVs and SNVs Improves the Diagnostic Yield of Fetuses with Ultrasound Anomalies and Normal Karyotypes

The routine assessment to determine the genetic etiology for fetal ultrasound anomalies follows a sequential approach, which usually takes about 6–8 weeks turnaround time (TAT). We evaluated the clinical utility of simultaneous detection of copy number variations (CNVs) and single nucleotide variants (SNVs)/small insertion-deletions (indels) in fetuses with a normal karyotype with ultrasound anomalies. We performed CNV detection by chromosomal microarray analysis (CMA) or low pass CNV-sequencing (CNV-seq), and in parallel SNVs/indels detection by trio-based clinical exome sequencing (CES) or whole exome sequencing (WES). Eight-three singleton pregnancies with a normal fetal karyotype were enrolled in this prospective observational study. Pathogenic or likely pathogenic variations were identified in 30 cases (CNVs in 3 cases, SNVs/indels in 27 cases), indicating an overall molecular diagnostic rate of 36.1% (30/83). Two cases had both a CNV of uncertain significance (VOUS) and likely pathogenic SNV, and one case carried both a VOUS CNV and an SNV. We demonstrated that simultaneous analysis of CNVs and SNVs/indels can improve the diagnostic yield of prenatal diagnosis with shortened reporting time, namely, 2–3 weeks. Due to the relatively long TAT for sequential procedure for prenatal genetic diagnosis, as well as recent sequencing technology advancements, it is clinically necessary to consider the simultaneous evaluation of CNVs and SNVs/indels to enhance the diagnostic yield and timely TAT, especially for cases in the late second trimester or third trimester.

First-trimester absent nasal bone: is it a predictive factor for pathogenic CNVs in the low-risk population?

OBJECTIVE

To evaluate the association of first-trimester absent nasal bone (NB) and genetic abnormalities at G-banding karyotype and chromosomal microarray analysis (CMA) according to the nuchal translucency (NT) thickness.

METHODS

This is a retrospective cohort study of fetuses that underwent the first-trimester scan for the combined test at 11⁺⁰ to 13⁺⁶ weeks' gestation. Invasive test with G-banding karyotype and/or CMA was performed based on the result of the combined test or if fetal defects were detected or for patient's choice, after genetic counseling. All cases with absent NB in the first and second trimester underwent a detailed anomaly scan with echocardiography in the second trimester, had a longitudinal ultrasound, and postnatal follow-up up to at least 1 year.

RESULTS

Between 2013 and 2018, 7228 women underwent the first-trimester scan at 11⁺⁰ to 13⁺⁶ weeks. Overall prevalence of absent NB was 1.3% (96/7228). Of those, in 86 pregnancies (1.2%), the absence of NB was confirmed also in the second trimester: 0.58% (40/6909) in the group with NT <95th centile; 6%(14/233) in the group with NT between 95 and 99th centile; and 37.2% (32/86) in the group with NT >99th centile, respectively. CMA pathogenic variants were found only in the group with NT >99th centile with a diagnostic yield of 9.4%. Fetuses with absent NB and NT between 95 and 99th centile had in 57% (8/14) a major chromosomal anomaly, while in the NT <95 centile group, there were 5% (2/40) of chromosomal abnormalities (one inherited from the father).

CONCLUSION

In the first trimester, the risk for genetic syndromes detectable by CMA is related mainly to the NT thickness rather than to the absence of NB per se. In fetuses with absent NB and NT >99th centile, CMA should be performed after karyotype analysis, while for NT between 95 and 99th centile, a karyotype should be proposed as first-line procedure. Data provided by our study may be helpful in counseling women/couples when an absent NB is identified in the first trimester.

Exome sequencing improves genetic diagnosis of fetal increased nuchal translucency

OBJECTIVE

The aim of this retrospective study is to determine the monogenic syndromes in fetuses with isolated first-trimester increased nuchal translucency (NT) in order to provide more accurate parental counseling.

METHODS

Medical trio exome sequencing (ES) was performed on DNA extracted from chorionic villi in 73 fetuses with isolated first-trimester increased NT (≥3.5 mm) and normal chromosomal microarray analysis (CMA). This testing targets coding exons for 4200 clinically relevant disease-causing genes. The interpretation of variants was performed according to the American College of Medical Genetics guidelines.

RESULTS

Pathogenic variants were detected in four cases in which phenotypes and genotypes correlate well. Medical trio ES offered a 5.5% (4/73) increase in diagnostic rate over CMA in cases with isolated increased NT. Three of four cases with pathogenic variants developed structural anomalies on ultrasound at mid pregnancy, leading to the pregnancy termination. Only one case with a pathogenic variant demonstrated normal ultrasound throughout pregnancy.

CONCLUSION

Our results indicate that after a normal CMA, fetuses with isolated first-trimester increased NT have a 1.4% (1/73) risk of significant childhood genetic syndromes caused by known disease-causing variants, which will not be detectable on prenatal ultrasound. This information may be useful in parental counseling.

Prenatal Diagnosis of Fetuses With Increased Nuchal Translucency by Genome Sequencing Analysis

Background: Increased nuchal translucency (NT) is an important biomarker associated with increased risk of fetal structural anomalies. It is known to be contributed by a wide range of genetic etiologies from single-nucleotide variants to those affecting millions of base pairs. Currently, prenatal diagnosis is routinely performed by karyotyping and chromosomal microarray analysis (CMA); however, both of them have limited resolution. The diversity of the genetic etiologies warrants an integrated assay such as genome sequencing (GS) for comprehensive detection of genomic variants. Herein, we aim to evaluate the feasibility of applying GS in prenatal diagnosis for the fetuses with increased NT.

Methods: We retrospectively applied GS (> 30-fold) for fetuses with increased NT (≥3.5 mm) who underwent routine prenatal diagnosis. Detection of single-nucleotide variants, copy number variants, and structural rearrangements was performed simultaneously, and the results were integrated for interpretation in accordance with the guidelines of the American College of Medical Genetics and Genomics. Pathogenic or likely pathogenic (P/LP) variants were selected for validation and parental confirmation, when available.

Results: Overall, 50 fetuses were enrolled, including 34 cases with isolated increased NT and 16 cases with other fetal structural malformations. Routine CMA and karyotyping reported eight P/LP CNVs, yielding a diagnostic rate of 16.0% (8/50). In comparison, GS provided a twofold increase in diagnostic yield (32.0%, 16/50), including one mosaic turner syndrome, eight cases with microdeletions/microduplications, and seven cases with P/LP point mutations. Moreover, GS identified two cryptic insertions and two inversions. Follow-up study further demonstrated the potential pathogenicity of an apparently balanced insertion that disrupted an OMIM autosomal dominant disease-causing gene at the insertion site.

Conclusions: Our study demonstrates that applying GS in fetuses with increased NT can comprehensively detect and delineate the various genomic variants that are causative to the diseases. Importantly, prenatal diagnosis by GS doubled the diagnostic yield compared with routine protocols. Given a comparable turnaround time and less DNA required, our study provides strong evidence to facilitate GS in prenatal diagnosis, particularly in fetuses with increased NT.