Research on the effectiveness of CMA and WES results in pregnant females with US findings and normal karyotype results from conventional karyotype analysis

The use of fetal exome sequencing in prenatal diagnosis: a points to consider document of the American College of Medical Genetics and Genomics (ACMG)

In cases requiring fetal diagnostic testing, conventional karyotype analysis is initially preferred. However, quantitative fluorescent-polymerase chain reaction (QF-PCR) or fluorescent in situ hybridization methods are used alongside conventional karyotype analysis to obtain rapid results. If results cannot be obtained from conventional karyotype analysis, chromosomal microarray analysis (CMA) is a reasonable option in necessary cases. In this study, we analyzed the conventional karyotype and CMA results from pregnancies reported as having normal karyotypes by QF-PCR and assessed their correlation with ultrasound imaging results. Between 2020 and 2023, pregnant women with fetal structural anomalies detected by ultrasound and magnetic resonance imaging at the Eskişehir City Hospital, Clinic of Perinatology were referred to our prenatal diagnosis center. In samples obtained using appropriate diagnostic methods, QR-PCR and conventional karyotype analysis were performed initially. Pregnancies with chromosomal anomalies detected by QF-PCR were excluded from the study. For pregnancies with normal karyotypes, CMA was applied. In 203 pregnancies with a normal karyotype result from QF-PCR, 202 (99.5%) were reported as normal in conventional karyotype analysis, while 1 (0.5%) case showed deletion of chromosome 7. Among the remaining pregnancies, CMA examination revealed abnormal karyotype results in 25 (12.3%) cases. A relationship was found only between ventriculomegaly detected by ultrasound and CMA results. The prevalence of ventriculomegaly was higher in those with CMA abnormalities (16%) compared to those with normal CMA (4.5%), and this difference was statistically significant (p=0.045). The benefit of CMA analysis in detecting chromosomal anomalies such as copy number variations, especially in cases reported as having a normal karyotype by QF-PCR and karyotype analysis, is evident. To evaluate the relationship between ultrasound anomalies and CMA results, each community should assess its own results.

eP083: Chromosomal microarray analysis as a supplement to exome sequencing in pediatric patients with suspected inborn errors of immunity

Objectives To evaluate the clinical utility of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in foetuses with oligohydramnios. Methods In this retrospective study, 126 fetuses with oligohydramnios at our centre from 2018 to 2021 were reviewed. The results of CMA and WES were analysed. Results One hundred and twenty-four cases underwent CMA and 32 cases underwent WES. The detection rate of pathogenic/likely pathogenic (P/LP) copy number variant (CNV) by CMA was 1.6% (2/124). WES revealed P/LP variants in 21.8% (7/32) of the foetuses. Six (85.7%, 6/7) foetuses showed an autosomal recessive inheritance pattern. Three (42.9%, 3/7) variants were involved in the renin–angiotensin–aldosterone system (RAAS), which are the known genetic causes of autosomal recessive renal tubular dysgenesis (ARRTD). Conclusion CMA has low diagnostic utility for oligohydramnios, while WES offers obvious advantages in improving the detection rate. WES should be recommended for fetuses with oligohydramnios.

Objective: To explore the application value of chromosome karyotype analysis, chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in prenatal diagnosis of isolated corpus callosum abnormality (CCA) fetus. Methods: Fetuses diagnosed with isolated CCA by ultrasound and MRI and receiving invasive prenatal diagnosis in Guangzhou Women and Children's Medical Center and Qingyuan People's Hospital from January 2010 to April 2021 were selected. Karyotype analysis and/or CMA [or copy number variation sequencing (CNV-seq)] were performed on all fetal samples, and WES was performed on fetal samples and their parents whose karyotype analysis and/or CMA (or CNV-seq) results were not abnormal. Results: Among 65 fetuses with isolated CCA, 38 cases underwent karyotype analysis, and 3 cases were detected with abnormal karyotypes, with a detection rate of 8% (3/38). A total of 49 fetuses with isolated CCA underwent CMA (or CNV-seq) detection, and 6 cases of pathogenic CNV were detected, the detection rate was 12% (6/49). Among them, the karyotype analysis results were abnormal, and the detection rate of further CMA detection was 1/1. The karyotype results were normal, and the detection rate of further CMA (or CNV-seq) detection was 14% (3/21). The detection rate of CMA as the first-line detection technique was 7% (2/27). A total of 25 fetuses with isolated CCA with negative results of karyotyping and/or CMA were tested by WES, and 9 cases (36%, 9/25) were detected with pathogenic genes. The gradient genetic diagnosis of chromosomal karyotyping, CMA and WES resulted in a definite genetic diagnosis of 26% (17/65) of isolated CCA fetuses. Conclusions: Prenatal genetic diagnosis of isolated CCA fetuses is of great clinical significance. The detection rate of CMA is higher than that of traditional karyotyping. CMA detection could be used as a first-line detection technique for fetuses with isolated CCA. WES could increase the pathogenicity detection rate of fetuses with isolated CCA when karyotype analysis and/or CMA test results are negative.

This study aims to investigate the utility of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) in fetuses diagnosed with talipes equinovarus (TE), as well as to explore the genetic factors contributing to TE. The study reviewed a total of 241 fetuses with TE between January 2015 and December 2023, categorizing them into two groups based on the absence or presence of additional ultrasound anomalies: 163 cases (67.6%) in the isolated TE group and 78 cases (32.4%) in the syndromic TE group. Karyotyping and CMA were performed for all cases, with WES being performed for 18 cases that had normal karyotype and CMA results. The results indicated a total detection rate of 16.2% (39/241) using karyotyping and CMA. Furthermore, the detection rates of karyotyping and CMA in the isolated TE group and syndromic TE group were 10.4% (17/163) and 28.2% (22/78) respectively, showing a statistically significant difference (p < 0.05). WES was conducted on 18 fetuses with normal karyotyping and CMA results. A total of six cases, consisting of five cases with pathogenic single nucleotide variant (SNV) and one case of variants of uncertain significance (VUS), were identified, resulting in a detection rate of 33.3% (6/18). The identified SNVs was associated with the RIT1, GNPNAT1, PEX1, RYR1, ASCC1, and GDAP1 genes. The detection rates of WES in the isolated TE group and syndromic TE group were 25% (1/4) and 35.7% (5/14) respectively, with no statistically significant difference (p > 0.05). The overall diagnostic yield of genetic testing was 18.7% (45/241) in fetuses with TE. When prenatal ultrasound identifies fetal TE, chromosome karyotyping and CMA should be considered as the first-line diagnostic tests. Unlike previous studies, this study recommended WES in cases of normal CMA results for both isolated and syndromic fetal TE.

This study aimed to investigate the clinical application of genetic testing in the prenatal diagnosis of fetal agenesis of the corpus callosum (ACC). Fetuses with ACC confirmed by prenatal systematic ultrasound and fetal MRI imaging underwent invasive prenatal diagnostic procedures. Amniotic fluid samples from the fetuses were collected for karyotype analysis and/or chromosomal microarray analysis (CMA). For ACC fetuses with normal karyotype and/or CMA results, whole-exome sequencing (WES) was further performed. Among the 15 ACC fetuses, karyotype analysis was performed in 14 cases, with one case (7.14%, 1/14) showing an abnormal chromosomal karyotype. CMA was performed in 14 cases, with pathogenic or likely pathogenic copy number variations (CNVs) detected in 4 cases (28.57%, 4/14), including microdeletions at 13q32.2q34, 18q21.2q21.31, 16p13.3, and 16p12.2. Among the 8 ACC fetuses with normal karyotype analysis and/or CMA re-sults, WES was further performed on both the fetuses and their parents, revealing two likely pathogenic variants in two cases (25%, 2/8) involving the FOXG1 and B3GALNT2 genes. Prenatal genetic diagnosis is of significant importance for ACC fetuses. CMA demonstrates a higher detection rate than karyotyping. WES can provide additional genetic diagnostic insights for ACC fetuses with normal karyotype and/or CMA.

Objective To estimate the incremental yield of detecting pathogenic or likely pathogenic diagnostic genetic variants (DGV) by whole exome sequencing (WES) over standard karyotype and chromosomal microarray (CMA) analyses in fetuses with isolated increased nuchal translucency (NT) and normal fetal anatomy at the time of 11-14 weeks scan. Materials and Methods Medline and Embase databases were searched. Inclusion criteria were fetuses with NT >95th percentile, normal karyotype and CMA and no associated structural anomalies at the time of the 11-14 weeks scan. The primary outcome was to estimate the incremental yield of detecting pathogenic or likely pathogenic genetic variants by WES over standard karyotype and CMA analyses in fetuses with isolated increased nuchal translucency. The secondary outcomes were the detection of a genetic variant of unknown significance. Sub-analysis according to different NT cutoffs (between 3.0 and 5.5 mm and > 5.5 mm) and considering fetuses with isolated NT in which fetal anatomy was confirmed to be normal at the anomaly scan were also performed. Random effects model meta-analyses of proportion were used to analyze the data. Results Eight articles (324 fetuses) were included in the systematic review. Of the fetuses with negative standard karyotype and CMA analysis, the 8.07% (95% CI 5.4–11.3) had pathogenic or likely pathogenic genetic variants detected exclusively by WES. When stratifying the analysis according to NT cutoffs, genetic anomalies detected exclusively at WES analysis were found in 44.70% (95% CI 26.8–63.4) of fetuses with NT between 3.0 mm and 5.5 mm and 55.3% (95% CI 36.6–73.2) in those fetuses with NT >5.5 mm and positive WES results. The 7.84% (95% CI 1.6–18.2) had variants of unknown significance identified by WES. When considering fetuses with isolated increased NT and normal fetal anatomy at the anomaly scan, the rate of pathogenic or likely pathogenic genetic variants detected by WES was 3.87% (95% CI 1.6–7.1), while variants of unknown significance were detected in 4.27% (95% CI 2.2–7.0) of cases. Conclusions Pathogenic and likely pathogenic genetic variants detected by WES are present in a significant proportion of fetuses with increased NT but normal standard karyotype and CMA analysis, also when no anomalies are detected at the anomaly scan. Further large studies sharing objective protocols of imaging assessment are needed to confirm these findings and to elucidate which gene panels should be assessed in fetuses with isolated increased NT to rule out associated genetic anomalies, which may potentially impact post-natal outcomes.

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.

To evaluate the clinical utility of genetic testing via karyotyping, chromosomal microarray analysis (CMA), and exome sequencing in cases with corpus callosum abnormalities (CCA). Here, 65 prenatal and 12 postnatal cases diagnosed with CCA via ultrasound and magnetic resonance imaging examination were enrolled. All cases were divided into two groups: 21 (27.3%) isolated and 56 (72.7%) non-isolated CCA groups. Karyotyping and CMA were first performed in parallel, then followed by whole exome sequencing (WES) after negative karyotype and CMA results. Clinical outcomes were also followed up. Karyotype abnormalities were identified in 7 cases (9.1%, 7/77). Karyotype abnormality rates in the isolated and non-isolated CCA groups were 8.0% and 9.6%, respectively (p > 0.05). Pathogenic/likely pathogenic (P/LP) CNVs were identified in 11 cases (14.3%, 11/77), including 2(9.5%, 2/21) and 9(16.1%, 9/56) cases in the isolated and non-isolated CCA groups, respectively (p > 0.05). WES identified P/LP diagnostic genetic variants in 8 (47.1%, 8/17) cases, including 2 and 6 cases in the isolated and non-isolated CCA groups, respectively. Additionally, 3 cases with variants of unknown significance were identified. Of the 65 prenatal cases with CCA, 31 (47.7%) were terminated, 1 (1.5%) was a miscarriage, 33 (50.8%) yielded live born babies; of these, 4(12.1%, 4/33) yielded babies with neurodevelopment disorders (NDDs). Of the 12 postnatal cases with CCA, all presented NDDs. Genetic causes of CCA are highly variable. Prenatal brain magnetic resonance imaging and systemic ultrasound examination should be performed to examine other anomalies when CCAs are detected via ultrasound. WES is also recommended following negative karyotype and CMA results.

To evaluate the genetic etiology of fetal dextrocardia, associated ultrasound anomalies, and perinatal outcomes, we investigated the utility of whole exome sequencing (WES) for prenatal diagnosis of dextrocardia. Fetuses with dextrocardia were prospectively collected between January 2016 and December 2022. Trio-WES was performed on fetuses with dextrocardia, following normal karyotyping and/or chromosomal microarray analysis (CMA) results. A total of 29 fetuses with dextrocardia were collected, including 27 (93.1%) diagnosed with situs inversus totalis and 2 (6.9%) with situs inversus partialis. Cardiac malformations were present in nine cases, extra-cardiac anomalies were found in seven cases, and both cardiac and extra-cardiac malformations were identified in one case. The fetal karyotypes and CMA results of 29 cases were normal. Of the 29 cases with dextrocardia, 15 underwent WES, and the other 14 cases refused. Of the 15 cases that underwent WES, clinically relevant variants were identified in 5/15 (33.3%) cases, including the diagnostic variants DNAH5, DNAH11, LRRC56, PEX10, and ZIC3, which were verified by Sanger sequencing. Of the 10 cases with non-diagnostic results via WES, eight (80%) chose to continue the pregnancies. Of the 29 fetuses with dextrocardia, 10 were terminated during pregnancy, and 19 were live born. Fetal dextrocardia is often accompanied by cardiac and extra-cardiac anomalies, and fetal dextrocardia accompanied by situs inversus is associated with a high risk of primary ciliary dyskinesia. Trio-WES is recommended following normal karyotyping and CMA results because it can improve the diagnostic utility of genetic variants of fetal dextrocardia, accurately predict fetal prognosis, and guide perinatal management and the reproductive decisions of affected families.

To evaluate the diagnostic yield of prenatal whole exome sequencing (WES) for monogenic disorders in fetuses with structural malformations and normal results on cytogenetic testing, and to describe information on pathogenic variants that is provided by WES. Karyotyping, chromosomal microarray analysis (CMA) and WES were performed sequentially on stored samples from a cohort of 3949 pregnancies with fetal structural abnormalities detected on ultrasound and/or magnetic resonance imaging, referred between January 2011 and December 2015. Diagnostic rates of the three techniques were investigated overall, for phenotypic subgroups and for proband-only vs fetus-mother-father samples. Information on pathogenic variants was identified by WES. Overall, 18.2% (720/3949) of fetuses had an abnormal karyotype. Pathogenic copy number variants were detected on CMA in 8.2% (138/1680) of fetuses that had a normal karyotype result. WES performed on a subgroup of 196 fetuses with normal CMA and karyotype results revealed the putative genetic variants responsible for the abnormal phenotypes in 47 cases (24%). The molecular diagnosis rates for fetus-mother-father and proband-only samples were 26.5% (13/49) and 23.1% (34/147), respectively. Variants of uncertain significance were detected in 12.8% (25/196) of fetuses, of which 22 were identified in the fetal proband-only group (15%; 22/147) and three in the fetus-mother-father group (6.1%; 3/49). The incidental finding rate was 6.1% (12/196). WES is a promising method for the identification of genetic variants that cause structural abnormalities in fetuses with normal results on karyotyping and CMA. This enhanced diagnostic yield has the potential to improve the clinical management of pregnancies and to inform better the reproductive decisions of affected families. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.

Aim: This study aimed to investigate the predictive value of prenatal ultrasonography (USG) findings in detecting chromosomal abnormalities identified through chromosomal microarray analysis (CMA) in high-risk pregnancies. Material and Methods: A retrospective analysis was conducted on 122 singleton high-risk pregnancies undergoing CMA between 2021 and 2022. High-risk status was based on advanced maternal age, abnormal screening results, USG anomalies, or relevant family history. A scoring system was applied to USG findings, assigning one point for each fetal system with an anomaly. CMA was performed as a first-tier test via amniocentesis. Maternal demographics, USG scores, CMA results, and pregnancy outcomes were recorded and analyzed. Results: Abnormal CMA results were detected in 34 (27.9%) cases. Maternal age was significantly higher in the abnormal CMA group (median 32 years vs. 29 years, p=0.030). Among pregnancies with abnormal CMA results, the rates of continuation and termination were equal at 44.1% (n=15). USG anomalies were significantly more prevalent in patients with abnormal CMA results, particularly in the abdominal (OR=2.84, 95% CI=1.01-7.96, p=0.041) and skin (OR=5.85, 95% CI=1.63-21.03, p=0.006) systems. Higher USG scores were significantly associated with abnormal CMA results (p&amp;lt;0.001). The most common chromosomal abnormalities were deletions (n=20, 58.8%) and duplications (n=10, 29.4%). Conclusion: USG findings, especially system-specific anomalies and elevated USG scores, are significantly associated with abnormal CMA results. Advanced maternal age is also a predictive factor. Integrating USG scoring with CMA may enhance the diagnostic value in prenatal genetic assessment. Multicenter prospective studies are needed to validate these findings and improve clinical application.

Should prenatal chromosomal microarray analysis be offered for isolated fetal growth restriction? A French multicenter study

Skeletal dysplasias are a group of diseases characterized by bone and joint abnormalities, which can be detected during prenatal ultrasound. Next-generation sequencing has rapidly revolutionized molecular diagnostic approaches in fetuses with structural anomalies. This review studies the additional diagnostic yield of prenatal exome sequencing in fetuses with prenatal sonographic features of skeletal dysplasias. This was a systematic review by searching PubMed for studies published between 2013 and July 2022 that identified the diagnostic yield of exome sequencing after normal karyotype or chromosomal microarray analysis (CMA) for cases with suspected fetal skeletal dysplasias based on prenatal ultrasound. We identified 10 out of 85 studies representing 226 fetuses. The pooled additional diagnostic yield was 69.0%. The majority of the molecular diagnoses involved de novo variants (72%), while 8.7% of cases were due to inherited variants. The incremental diagnostic yield of exome sequencing over CMA was 67.4% for isolated short long bones and 77.2% for non-isolated cases. Among phenotypic subgroup analyses, features with the highest additional diagnostic yield were an abnormal skull (83.3%) and a small chest (82.5%). Prenatal exome sequencing should be considered for cases with suspected fetal skeletal dysplasias with or without a negative karyotype or CMA results. Certain sonographic features, including an abnormal skull and small chest, may indicate a potentially higher diagnostic yield.