You are currently viewing a new version of our website. To view the old version click .
MDPIMDPI
Search all articles
Genes
Download PDF
  • Article
  • Open Access

21 April 2022

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

,
,
,
,
,
,
,
,
and
1
Department of Medical Genetics, Institute of Mother and Child, 01-211 Warsaw, Poland
2
Department of Obstetrics and Gynecology, Institute of Mother and Child, 01-211 Warsaw, Poland
3
Department of Gynecology Oncology and Obstetrics, Center of Postgraduate Medical Education, 01-809 Warsaw, Poland
4
Second Department of Obstetrics and Gynecology, Center of Postgraduate Medical Education, 01-809 Warsaw, Poland
Genes2022, 13(5), 724;https://doi.org/10.3390/genes13050724
This article belongs to the Special Issue Novel Insights into Prenatal Genetic Testing
Version Notes
Order Reprints

Abstract

Background: Despite advances in routine prenatal cytogenetic testing, most anomalous fetuses remain without a genetic diagnosis. Exome sequencing (ES) is a molecular technique that identifies sequence variants across protein-coding regions and is now increasingly used in clinical practice. Fetal phenotypes differ from postnatal and, therefore, prenatal ES interpretation requires a large amount of data deriving from prenatal testing. The aim of our study was to present initial results of the implementation of ES to prenatal diagnosis in Polish patients and to discuss its possible clinical impact on genetic counseling. Methods: In this study we performed a retrospective review of all fetal samples referred to our laboratory for ES from cooperating centers between January 2017 and June 2021. Results: During the study period 122 fetuses were subjected to ES at our institution. There were 52 abnormal ES results: 31 in the group of fetuses with a single organ system anomaly and 21 in the group of fetuses with multisystem anomalies. The difference between groups was not statistically significant. There were 57 different pathogenic or likely pathogenic variants reported in 33 different genes. The most common were missense variants. In 17 cases the molecular diagnosis had an actual clinical impact on subsequent pregnancies or other family members. Conclusions: Exome sequencing increases the detection rate in fetuses with structural anomalies and improves genetic counseling for both the affected couple and their relatives.

1. Introduction

Congenital anomalies, as defined by the World Health Organization (WHO), are structural or functional abnormalities that occur during the intrauterine life. They can be identified prenatally, at birth or any time after birth and occur in approximately 2–3% of live births and 20% of spontaneously aborted fetuses [,]. As the underlying etiology of congenital anomalies includes genetic and environmental factors, current guidelines recommend chromosomal microarray analysis (CMA) as a first-tier prenatal test for fetal anomalies []. Prenatal karyotyping can detect clinically relevant chromosomal aberrations in about 32% of fetuses with structural anomalies and CMA increases the diagnostic yield by at least 6% [,]. However, most of the anomalous fetuses remain without a genetic diagnosis. Exome sequencing (ES) is a powerful tool to identify sequence variants across the protein-coding regions and is increasingly used in postnatal patients. ES is also a promising method to detect the underlying genetic etiology in the fetuses with structural anomalies and normal results of routine testing []. The main advantage of this approach is the possibility of identification of pathogenic variants across the exome and not narrowed to only the selected genes. ES is a phenotype-driven test and interpretation of detected variants is performed with the use of existing molecular and clinical data. The American College of Medical Genetics and Genomics (ACMG) criteria for classifying sequence variants are correlated with a clinical presentation []. A detected variant can be classified as pathogenic/likely pathogenic or as benign/likely benign if a particular combination of evidence of pathogenicity or benign impact is present. The remaining variants not consistent with the abovementioned criteria are classified as variants of unknown significance (VUS). In this context, a precise distinction of different fetal phenotypes with the use of Human Phenotype Ontology (HPO) terminology is essential for establishing both the diagnosis in the clinical case and general indications for prenatal ES [,]. Each term in the HPO describes a phenotypic abnormality and can be used to classify the anomalies in a standardized manner. The semantic clarity is necessary for communication between clinicians and scientists and for integration of biomedical human data and model organism data. There are bioinformatics tools using HPO terms (e.g., Exomiser—a JAVA program) that prioritize variants according to user-defined criteria and find potential disease-causing variants []. However, differences between fetal and postnatal phenotypes and limited access to additional diagnostic tests in a fetus make the interpretation of prenatal ES challenging. Therefore, a large amount of data available in public repositories and scientific reports is required to implement ES in routine prenatal diagnosis. The aim of this paper is to present the results of the first 122 prenatal ES analyses performed in our genetic department and to discuss its possible clinical impact on genetic counseling.

2. Materials and Methods

2.1. General Information

The Polish Society of Obstetricians and Gynecologists recommends at least four sonographic evaluations during pregnancy, which is in line with the international guidelines []. Patients at risk for fetal abnormality (age at delivery ≥35 years, family history of genetic or structural anomalies or abnormal ultrasound findings in current pregnancy) are offered genetic counseling and testing in terms of the National Prenatal Screening Program (NPSP) []. The Human Genetics Department at the Mother and Child Institute is certified by the Cytogenetic External Quality Assessment Service (CEQAS) and Polish Society of Human Genetics (pol. PTGC) and performs genetic tests for over a dozen obstetric gynecology centers that provide prenatal care from all country regions. Routine prenatal genetic testing performed at our department comprises CMA supplemented by karyotyping based on a single flask cell culture.
We performed a retrospective analysis of the results of ES conducted at our laboratory between January 2017 and June 2021. Written informed consent for molecular testing was obtained from all individuals after appropriate genetic counseling. Clinical and family history was taken in all cases prior to testing. Participants were informed that fetal ES would be performed in terms of research; thus, only results relevant to fetal anomalies would be reported back to parents and incidental findings from the ACMG recommended list would not be evaluated nor reported []. All individuals consented to the use of their de-identified data for research purposes. The study design was approved by an internal bioethics committee. Indications for fetal exome testing, molecular type, reporting status and clinical significance of detected variants, mode of inheritance, genotype–phenotype correlation, pregnancy outcome and impact of the molecular diagnosis on post-test genetic counselling were analyzed. Each fetal anomaly was labeled according to HPO terminology with HP identifiers [,]. We arranged fetal phenotypes into 9 categories: as anomalies of the central nervous system (HP:0002011), face (HP:000271), cardiovascular system (HP:0001626), abdomen (HP:0001438), genitourinary system (HP:0000119), musculoskeletal system (HP:0033127), neural tube defects (HP:0045005), non-immune hydrops fetalis (HP:0001790) and multisystem anomalies (i.e., fetuses with anomalies of two or more categories).

2.2. Exome Sequencing Procedure

In all cases, prior to exome sequencing, a chromosomal microarray was performed using the oligonucleotide array platform CytoSure Constitutional v3 (8 × 60 k) (Oxford Gene Technology, Oxford, UK) with approximately 60.000 probes across the genome. Data were analyzed with the CytoSure Interpret Software (OGT) which provided an average resolution of 120 kb. Subsequently, DNA specimens isolated from fetal samples were sent to the external laboratory for sequencing (CeGaT, Tübingen, Germany). The sequencing procedure was performed on the NovaSeq6000 (Illumina, San Diego, CA, USA) using SureSelect Human All Exon v.6 (Agilent, Santa Clara, CA, USA) for exome capture and library preparation. The resulting raw sequence data (FASTQ format files) were post-processed on site. Short reads were mapped against the human genome reference sequence (GRCh38/hg38) using the Burrows–Wheeler Alignment (BWA) and stored as Binary Sequence Alignment Map (BAM) files. Following alignment, we used the Genome Analysis Toolkit (GATK) software for variant calling, ANNOVAR for variant annotation and the CoNIFER algorithm for CNV detection from the exome sequencing data.

2.3. Exome Variant Interpretation

Filtering of variants was conducted as a semi-rigid strategy and not precluded to reconsider any of the disregarded variants. Initial filters looked for quality control and an allele frequency, either from the open database (gnomAD < 0.01) or in-house database (<0.05; approximately 1000 postnatal samples sequenced in the same platform and processed using the same pipeline). Subsequent filtration steps were based on the molecular impact of the variant, known gene–disease correlation considering allele zygosity and clinical significance based on variant databases (ClinVar, HGMD), in silico evaluation of pathogenicity (SIFT, Polyphen-2, MutationTaster, CADD) and review of the literature. The filtering strategy was supported by the Exomiser tool in parallel to manual searching []. Selected variants were classified in accordance with the ACMG classification system and judged if apparently relevant to an observed fetal phenotype []. In each case, interpretation of the variant was discussed in a panel group of at least four participants (clinical geneticist, fetal medicine specialist, laboratory scientist and bioinformatician). Expected pathogenic or likely pathogenic variants (ACMG class 5 or 4, respectively) were verified by Sanger sequencing of the fetal DNA. Parental origin was tracked by Sanger sequencing of DNA isolated from peripheral blood of both parents. Variants of unknown significance (VUS; ACMG class 3) were verified, tracked and reported if they were found in trans (on the other allele) with the pathogenic or likely pathogenic variant in an autosomal recessive condition that fit the fetal phenotype. After completion of the analysis, we obtained pathogenic or likely pathogenic variants that explained fetal phenotype; these variants were classified as diagnostic variants or abnormal ES results, and thus, they are referred to further in this paper. Subsequently, in cases with normal ES results we proceeded to the expanded analysis. In this step, we obtained variants in disease-related genes that potentially could explain observed fetal anomalies but did not achieve scores for pathogenic/likely pathogenic variants or variants with a strong in silico prediction of deleteriousness in genes with a limited level of evidence for disease association (also referred to as candidate genes). These variants are referred to VUS thereinafter. The turnaround time of ES was around 12 weeks in each case, excluding time for the tissue culture and Sanger variants verification.

2.4. Outcome and Clinical Impact

ES results and post-test counsel were conveyed directly to patients by clinical geneticists from our center or to the referring clinical geneticist. Information on outcome was collected and divided into three categories: termination of pregnancy (TOP), livebirth and stillbirth. The impact of molecular diagnosis was subdivided into two categories: expected impact, defined as genetic risk assessment, and actual clinical impact, defined as altered reproductive management or molecular diagnosis in other family members.

2.5. Statistics

Statistical analysis was performed using STATA 12 (StataCorp LP, College Station, TX, USA). Means, medians and percentages were used to present descriptive statistics. A chi-square test was used to assess the differences between categorical data. A p-value < 0.05 was considered statistically significant.

3. Results

3.1. Cohort Characteristics

During the study period, 122 fetuses were subjected to ES at our institution. The mean maternal and gestational age at diagnosis was 31 years (range: 21–41 years) and 19.5 weeks (range: 12–35 weeks), respectively. Family history was positive in seven cases (similarly affected previous fetus, an affected parent or consanguineous parents) but no molecular diagnosis had previously been given. No exposure to any recognized teratogens or harmful environmental factors was identified in any of the patients. A detailed ultrasound examination and an invasive procedure was performed in each case (amniocentesis 114/122; 93.5%, chorionic villus sampling 6/122; 4.9%, fetal blood sampling 2/122; 1.6%). The first 11 (9.0%) samples were analyzed as trio exomes (fetus–mother–father), whereas the next cases were analyzed as fetus-only ES with targeted Sanger sequencing for detected variants in both parents. All cases were referred due to structural anomalies or fetal hydrops. We divided all cases into two groups: fetuses with a single organ system anomaly (64/122; 52.5%) and fetuses with multisystem anomalies (58/122; 47.5%).

3.2. Results by Phenotype

Overall, there were 52 (42.6%) abnormal ES results: 31 in the group of fetuses with a single organ system anomaly (31/64; 48.4%) and 21 in the group of fetuses with multisystem anomalies (21/58; 36.2%) (Table 1 and Table 2). The difference between groups was not statistically significant X2 (1, n = 122) = 1.86, p = 0.17. In a univariate logistic regression, musculoskeletal anomalies increased the odds of an abnormal ES result by 2.5 fold (OR 2.5, 95% CI 1.2–5.4; p = 0.016) whereas cardiovascular defects decreased the odds of an abnormal ES result by 0.34 fold (OR 0.34, 95% CI 0.14–0.8; p = 0.014).
Table 1. Diagnostic variants and variants of unknown significance detected by exome sequencing in different phenotypic groups of fetuses.
Table 2. Sonographic findings in fetuses with abnormal exome sequencing—detailed information.

3.3. Results by Molecular Diagnosis

There were 57 different pathogenic or likely pathogenic variants reported in 33 different genes. The most common were missense variants (28/57; 49.1%), followed by frameshift variants (13/57; 22.8%), nonsense variants (12/57; 21.1%) and splicing variants (4/57; 7.0%); 34 variants were novel (34/57; 59.6%), whereas the remaining 23 were previously reported (23/57; 40.4%). The molecular mechanism of pathogenicity in the majority of novel variants was the same as previously reported for specific genes (31/34; 83.8%). The mechanism of pathogenicity in the three remaining novel variants was different than frequently reported, but the fetal phenotype was consistent with the literature data (Table 2 ID 10, 23 and 45). Variants of unknown significance were detected in 39 out of 70 fetuses without definite genetic diagnosis (55.7%; 1–5 VUS per fetus); 77 different variants were identified in 73 genes. Four genes were present twice (COL2A1, EVC2, GLI3 and KMT2C, presented in Table 3 with ID 63, 91, 66, 81, 76, 83, 62 and 84, respectively). The mode of inheritance was autosomal dominant (AD) in 31 cases of abnormal results (31/52; 59.6%), autosomal recessive (AR) in 18 cases (18/52; 34.6%) and X-linked (XL) in 3 cases (3/52; 5.8%). In 24 cases, based on sonographic findings, the referring clinician suggested a specific genetic diagnosis (19.7%; 24/122), which was confirmed by ES in 15 cases (62.5%; 15/24).
Table 3. Sonographic findings in fetuses with VUSs detected in exome sequencing—detailed information.

3.4. Outcome and Clinical Impact

The outcome of the pregnancy was known in 107 cases (87.7%; 107/122): in 54 cases the pregnancy was terminated upon parental request, because of fetal major anomalies, after appropriate counseling (TOP), 47 pregnancies ended in livebirth and 6 fetuses were stillborn. (Table 2, Table 3 and Table 4). In all 52 families with abnormal fetal ES results, the genetic risk was estimated based on the molecular diagnosis causing expected impact on individuals. Actual clinical impact was observed in 17 cases (13.9%). Reproductive management was altered in 13 families either by using highly effective contraception (n = 2) or by altered medical management in the subsequent pregnancy (n = 11), such as in vitro fertilization with preimplantation genetic diagnosis and embryo selection, CVS with targeted molecular diagnosis, ultrasound and prenatal care in the reference center. In four families, molecular diagnosis was established not only in the fetus, but also in other affected relatives.
Table 4. Sonographic findings in fetuses with normal ES detected in exome sequencing—detailed information.

4. Discussion

4.1. Diagnostic Yield of Prenatal ES

Previous studies report a wide range of the added value of prenatal ES, ranging between 6 and 80% [,]. The discrepancy between various studies is most probably due to different study populations, inclusion criteria and sample size. Two large prospective studies on 610 and 234 fetuses with various sonographic anomalies, including isolated, increased NT, indicated a diagnostic yield of ES of 8.5% and 10%, respectively [,]. In contrast, Fu et al. reported a diagnostic yield of ES of 24% in a group of 191 fetuses with structural malformations; however, they excluded fetuses with isolated, large NT or cystic hygroma []. In our cohort, the added value of ES was even higher and reached 42.6%, similar to 39.4% reported by He et al. []. This may be due to a relatively high proportion of cases with skeletal anomalies included and can be considered as selection bias. We found a high diagnostic rate of 62,1% in fetuses with musculoskeletal system abnormalities, which is consistent with the data from other authors [,,,,,]. Interestingly, in our cohort cardiac defects significantly decreased the odds of an abnormal ES result. The proportion of detected pathogenic or likely pathogenic variants in fetuses with isolated cardiac defects was 16.7%, slightly higher than 11.5% reported in a large prospective cohort study and systematic review []. The diagnostic yield in both isolated, specific anomalies and recognizable multisystem sets of anomalies is probably more valuable for clinical practice than the overall diagnostic yield in heterogenous cohorts.

4.2. Interpretation of Detected Variants

The process of reaching the ES result is based on discarding variants that are unlikely to be responsible for the disease and leaving a variant or variants correlated with the phenotype. In our research, Exomiser was helpful in the detection of likely causative variants, but the final decision relied on man. The interpretation of VUS in a prenatal setting presented a particular challenge [,]. In three cases of limb-body wall complex (LBWC), the condition where severe anomalies are not compatible with postnatal life, the significance of variants detected in CEP120, FLNB and COL2A1 genes was unknown (Table 3 ID 89, 90 and 91). Complexity of the disorder, lack of the specified HPO term for LBWC and absence of postnatal patients with LBWC caused problems in sequence variants interpretation. Potential risks of both overdiagnosing the variant as pathogenic and misdiagnosing as a benign finding should be considered. Therefore, in selected cases, a consensus decision made in a multidisciplinary panel hastened the diagnosis. Lefebvre et al. described a blind to phenotype, genotype-first approach that we do not consider appropriate—without knowing the phenotype, the variants cannot be interpreted [].

4.3. Molecular Mechanism, Inheritance Mode and Their Clinical Impact

The most common molecular changes in our cohort were missense variants, which is in line with other studies [,,,]. In the majority of cases, the mechanism of pathogenicity was in accordance with previous reports. In three cases, however, the mechanism was different and a detailed sonographic description enabled a correct diagnosis (Table 2 ID 10, 23 and 45). For instance, two novel heterozygous variants (missense and frameshift) in the NEK9 gene were found in a fetus, which presented with micrognathia, akinesia, an abnormally shaped abdomen and an increased level of free β-hCG (14.1 MoM) at 12 weeks of gestation (Table 2 ID 45). Pathogenic missense variants in the NEK9 gene have previously been reported in individuals with arthrogryposis, avascular necrosis of the femoral head and cardiac defects, which was not consistent with the anomalies detected in our case. However, a literature review revealed a report of two related families, in which five offspring were homozygous for a nonsense variant in NEK9 exactly phenotypically matching our case []. To our knowledge, this is the first report of the lethal congenital contracture syndrome (OMIM # 617022) caused by the NEK9 variant and diagnosed in the first trimester.
The mode of inheritance in our cohort was similar to that described in other studies [,,,,,,,,]. The majority of diagnostic variants were de novo autosomal dominant, most fetuses with autosomal recessive variants were compound heterozygotes and X-linked inheritance was the least common.
By having information on a detected diagnostic variant and its inheritance trait, we were able to estimate the recurrence risk in affected couples. Furthermore, we observed that 13 families benefited from the exome results to act according to their beliefs and make conscious decisions. As noticed by several authors, the introduction of prenatal ES is important in a wide context of genetic counseling [,,,,,]. It can offer considerable advantages for both the couple of the affected fetus and other family members. The turnaround time in our study was around 12 weeks; thus, the results did not have a direct impact on clinical management in current pregnancies. However, by gaining experience the turnaround time can be reduced, which is essential for the decision making in ongoing pregnancies.

5. Conclusions

To conclude, exome sequencing increases the detection rate in fetuses with structural anomalies and improves genetic counseling. Establishing a molecular diagnosis has clinical impact on subsequent pregnancies, as well as other family members.

Author Contributions

Conceptualization: A.K.-C., T.R. and B.N.; methodology: A.K.-C.; software: M.G.; formal analysis: A.K.-C.; resources: A.K.-C., M.G., T.R., J.B., D.M., H.C., I.P.-C., A.B., E.O., A.K.-K., P.W. (Paweł Własienko), M.K.-W., P.W. (Piotr Węgrzyn), L.D., W.K. and M.R.-K.; data curation: M.G.; writing—original draft preparation: A.K.-C.; writing—review and editing: J.B., D.M. and M.C.; supervision: B.N.; funding acquisition: J.B. and D.M. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Ministry of Health, granted to the Center of Postgraduate Medical Education, Poland, grant number Minigrant-501-1-106-44-20/MG4 to J.B., and by the National Science Centre, Poland, grant number Miniatura 2—Dec2018/02/X/NZ2/00709 to D.M.

Institutional Review Board Statement

The study was conducted in accordance with the Declaration of Helsinki, and approved by the Institutional Ethics Committee of the Center of Postgraduate Medical Education, PB/126/2018; date of approval: 12 December 2018, and by the Institutional Ethics Committee of the Center of Postgraduate Medical Education, 80/PB/2020; date of approval: 15 June 2020.

Data Availability Statement

Data supporting reported results can be found in tables.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

References

  1. Centers for Disease Control and Prevention. Update on Overall Prevalence of Major Birth Defects–Atlanta, Georgia, 1978–2005. MMWR Morb. Mortal. Wkly. Rep. 2008, 57, 1–5. [Google Scholar]
  2. Shepard, T.H.; Fantel, A.G.; Fitzsimmons, J. Congenital defect rates among spontaneous abortuses: Twenty years of monitoring. Teratology 1989, 39, 325–331. [Google Scholar] [CrossRef]
  3. Society for Maternal-Fetal Medicine. Committee Opinion No. 682 Summary: Microarrays and Next-Generation Sequencing Technology: The Use of Advanced Genetic Diagnostic Tools in Obstetrics and Gynecology. Obstet. Gynecol. 2016, 128, 1462–1463. [Google Scholar] [CrossRef] [PubMed]
  4. Wapner, R.J.; Martin, C.L.; Levy, B.; Ballif, B.C.; Eng, C.M.; Zachary, J.M.; Savage, M.; Platt, L.D.; Saltzman, D.; Grobman, W.A.; et al. Chromosomal Microarray versus Karyotyping for Prenatal Diagnosis. N. Engl. J. Med. 2012, 367, 2175–2184. [Google Scholar] [CrossRef] [Green Version]
  5. Bijok, J.; Kucińska–Chahwan, A.; Massalska, D.; Ilnicka, A.; Panek, G.; Roszkowski, T. In-house genetic counseling increases the detection of abnormal karyotypes—A 26-year experience in prenatal diagnosis in a single tertiary referral hospital in Poland. J. Assist. Reprod. Genet. 2020, 37, 1999–2006. [Google Scholar] [CrossRef] [PubMed]
  6. International Society for Prenatal Diagnosis, Society for Maternal and Fetal Medicine, Perinatal Quality Foundation. Joint Position Statement from the International Society for Prenatal Diagnosis (ISPD), the Society for Maternal Fetal Medicine (SMFM), and the Perinatal Quality Foundation (PQF) on the use of genome-wide sequencing for fetal diagnosis. Prenat. Diagn. 2018, 38, 6–9. [Google Scholar] [CrossRef]
  7. Richards, S.; Aziz, N.; Bale, S.; Bick, D.; Das, S.; Gastier-Foster, J.; Grody, W.W.; Hegde, M.; Lyon, E.; Spector, E.; et al. Standards and guidelines for the interpretation of sequence variants: A joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015, 17, 405–424. [Google Scholar] [CrossRef] [Green Version]
  8. Köhler, S.; Schulz, M.H.; Krawitz, P.; Bauer, S.; Dölken, S.; Ott, C.E.; Mundlos, C.; Horn, D.; Mundlos, S.; Robinson, P.N. Clinical diagnostics in human genetics with semantic similarity searches in ontologies. Am. J. Hum. Genet. 2009, 85, 457–464. [Google Scholar] [CrossRef] [Green Version]
  9. Köhler, S.; Gargano, M.; Matentzoglu, N.; Carmody, L.C.; Lewis-Smith, D.; Vasilevsky, N.A.; Danis, D.; Balagura, G.; Baynam, G.; Brower, A.M.; et al. The Human Phenotype Ontology in 2021. Nucleic Acids Res. 2020, 49, D1207–D1217. [Google Scholar] [CrossRef]
  10. Robinson, P.N.; Köhler, S.; Oellrich, A.; Wang, K.; Mungall, C.J.; Lewis, S.E.; Washington, N.; Bauer, S.; Seelow, D.; Krawitz, P.; et al. Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res. 2013, 24, 340–348. [Google Scholar] [CrossRef] [Green Version]
  11. Borowski, D.; Pietryga, M.; Basta, P.; Cnota, W.; Czuba, B.; Dubiel, M.; Fuchs, T.; Huras, H.; Iciek, R.; Jaczynska, R.; et al. Practice guidelines of the Polish Society of Gynecologists and Obstetricians—Ultrasound Section for ultrasound screening in uncomplicated pregnancy—2020. Ginekol. Polska 2020, 91, 490–501. [Google Scholar] [CrossRef] [PubMed]
  12. Republic of Poland, Journal of Laws No. 210, Item 2135, Dated 27 August 2004. Available online: https://isap.sejm.gov.pl/isap.nsf/DocDetails.xsp?id=wdu20042102135 (accessed on 18 April 2022).
  13. Kalia, S.S.; Adelman, K.; Bale, S.J.; Chung, W.K.; Eng, C.; Evans, J.P.; Herman, G.E.; Hufnagel, S.B.; Klein, T.E.; Korf, B.R.; et al. Recommendations for reporting of secondary findings in clinical exome and genome sequencing, 2016 update (ACMG SF v2.0): A policy statement of the American College of Medical Genetics and Genomics. Genet. Med. 2017, 19, 249–255. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  14. Best, S.; Wou, K.; Vora, N.; Van der Veyver, I.B.; Wapner, R.; Chitty, L.S. Promises, pitfalls and practicalities of prenatal whole exome sequencing. Prenat. Diagn. 2018, 38, 10–19. [Google Scholar] [CrossRef] [PubMed]
  15. Mellis, R.; Oprych, K.; Scotchman, E.; Hill, M.; Chitty, L.S. Diagnostic yield of exome sequencing for prenatal diagnosis of fetal structural anomalies: A systematic review and meta-analysis. Prenat. Diagn. 2022. [Google Scholar] [CrossRef] [PubMed]
  16. Lord, J.; McMullan, D.J.; Eberhardt, R.Y.; Rinck, G.; Hamilton, S.J.; Quinlan-Jones, E.; Prigmore, E.; Keelagher, R.; Best, S.K.; Carey, G.K.; et al. Prenatal exome sequencing analysis in fetal structural anomalies detected by ultrasonography (PAGE): A cohort study. Lancet 2019, 393, 747–757. [Google Scholar] [CrossRef] [Green Version]
  17. Petrovski, S.; Aggarwal, V.; Giordano, J.L.; Stosic, M.; Wou, K.; Bier, L.; Spiegel, E.; Brennan, K.; Stong, N.; Jobanputra, V.; et al. Whole-exome sequencing in the evaluation of fetal structural anomalies: A prospective cohort study. Lancet 2019, 393, 758–767. [Google Scholar] [CrossRef]
  18. Fu, F.; Li, R.; Li, Y.; Nie, Z.-Q.; Lei, T.; Wang, D.; Yang, X.; Han, J.; Pan, M.; Zhen, L.; et al. Whole exome sequencing as a diagnostic adjunct to clinical testing in fetuses with structural abnormalities. Ultrasound Obstet. Gynecol. 2018, 51, 493–502. [Google Scholar] [CrossRef] [Green Version]
  19. He, M.; Du, L.; Xie, H.; Zhang, L.; Gu, Y.; Lei, T.; Zheng, J.; Chen, D. The Added Value of Whole-Exome Sequencing for Anomalous Fetuses with Detailed Prenatal Ultrasound and Postnatal Phenotype. Front. Genet. 2021, 12, 627204. [Google Scholar] [CrossRef]
  20. Zhang, L.; Pan, L.; Teng, Y.; Liang, D.; Li, Z.; Wu, L. Molecular diagnosis for 55 fetuses with skeletal dysplasias by whole-exome sequencing: A retrospective cohort study. Clin. Genet. 2021, 100, 219–226. [Google Scholar] [CrossRef]
  21. Peng, Y.; Yang, S.; Huang, X.; Pang, J.; Liu, J.; Hu, J.; Shen, X.; Tang, C.; Wang, H. Whole Exome Sequencing Analysis in Fetal Skeletal Dysplasia Detected by Ultrasonography: An Analysis of 38 Cases. Front. Genet. 2021, 12, 728544. [Google Scholar] [CrossRef]
  22. Mone, F.; Eberhardt, R.Y.; Morris, R.K.; Hurles, M.E.; McMullan, D.J.; Maher, E.R.; Lord, J.; Chitty, L.S.; Giordano, J.L.; Wapner, R.J.; et al. COngenital heart disease and the Diagnostic yield with Exome sequencing (CODE) study: Prospective cohort study and systematic review. Ultrasound Obstet. Gynecol. 2021, 57, 43–51. [Google Scholar] [CrossRef] [PubMed]
  23. Marangoni, M.; Smits, G.; Ceysens, G.; Costa, E.; Coulon, R.; Daelemans, C.; De Coninck, C.; Derisbourg, S.; Gajewska, K.; Garofalo, G.; et al. Implementation of fetal clinical exome sequencing: Comparing prospective and retrospective cohorts. Genet Med. 2022, 24, 344–363. [Google Scholar] [CrossRef] [PubMed]
  24. Basel-Salmon, L.; Sukenik-Halevy, R. Challenges in variant interpretation in prenatal exome sequencing. Eur. J. Med. Genet. 2021, 65, 104410. [Google Scholar] [CrossRef]
  25. Lefebvre, M.; Bruel, A.L.; Tisserant, E.; Bourgon, N.; Duffourd, Y.; Collardeau-Frachon, S.; Attie-Bitach, T.; Kuentz, P.; Assoum, M.; Schaefer, E.; et al. Genotype-first in a cohort of 95 fetuses with multiple congenital abnormalities: When exome sequencing reveals unexpected fetal pheno-type-genotype correlations. J. Med. Genet. 2021, 58, 400–413. [Google Scholar] [CrossRef]
  26. Normand, E.A.; Braxton, A.; Nassef, S.; Ward, P.A.; Vetrini, F.; He, W.; Patel, V.; Qu, C.; Westerfield, L.E.; Stover, S.; et al. Clinical exome sequencing for fetuses with ultrasound abnormalities and a suspected Mendelian disorder. Genome Med. 2018, 10, 74. [Google Scholar] [CrossRef] [PubMed]
  27. Casey, J.P.; Brennan, K.; Scheidel, N.; McGettigan, P.; Lavin, P.T.; Carter, S.; Ennis, S.; Dorkins, H.; Ghali, N.; Blacque, O.E.; et al. Recessive NEK9 mutation causes a lethal skeletal dysplasia with evidence of cell cycle and ciliary defects. Hum. Mol. Genet. 2016, 25, 1824–1835. [Google Scholar] [CrossRef] [Green Version]
  28. Mone, F.; Abu Subieh, H.; Doyle, S.; Hamilton, S.; McMullan, D.J.; Allen, S.; Marton, T.; Williams, D.; Kilby, M.D. Evolving fetal phenotypes and clinical impact of progressive prenatal exome sequencing pathways: Cohort study. Ultrasound Obstet. Gynecol. 2021. [Google Scholar] [CrossRef]
  29. Talati, A.N.; Gilmore, K.L.; Hardisty, E.E.; Lyerly, A.D.; Rini, C.; Vora, N.L. Parental motivations for and adaptation to trio-exome sequencing in a prospective prenatal testing cohort: Beyond the diagnosis. Prenat. Diagn. 2022, 1, 8. [Google Scholar] [CrossRef]
  30. Talati, A.N.; Gilmore, K.L.; Hardisty, E.; Vora, N.L. How can prenatal exome sequencing inform future pregnancies? Am. J. Obstet. Gynecol. 2022. [Google Scholar] [CrossRef]
  31. Gabriel, H.; Korinth, D.; Ritthaler, M.; Schulte, B.; Battke, F.; von Kaisenberg, C.; Wüstemann, M.; Schulze, B.; Friedrich-Freksa, A.; Pfeiffer, L.; et al. Trio exome sequencing is highly relevant in prenatal diagnostics. Prenat. Diagn. 2021, 1, 7. [Google Scholar] [CrossRef]
  32. Becher, N.; Andreasen, L.; Sandager, P.; Lou, S.; Petersen, O.B.; Christensen, R.; Vogel, I. Implementation of exome sequencing in fetal diagnostics—Data and experiences from a tertiary center in Denmark. Acta Obstet. Gynecol. Scand. 2020, 99, 783–790. [Google Scholar] [CrossRef] [PubMed]
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Article Metrics

Citations

Article Access Statistics

Journal Statistics
Multiple requests from the same IP address are counted as one view.
Download PDF
Epigenetic Regulation Mechanisms of the Cofilin-1 Gene in the Development and Differentiation of Bovine Primary Myoblasts
Previous
Severe Infantile Axonal Neuropathy with Respiratory Failure Caused by Novel Mutation in X-Linked LAS1L Gene
Next