1
|
Jin P, Hong J, Xu Y, Qian Y, Han S, Dong M. Molecular diagnostic yield of exome sequencing in a Chinese cohort of 512 fetuses with anomalies. BMC Pregnancy Childbirth 2024; 24:591. [PMID: 39251974 PMCID: PMC11385820 DOI: 10.1186/s12884-024-06782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/26/2024] [Indexed: 09/11/2024] Open
Abstract
BACKGROUND Currently, whole exome sequencing has been performed as a helpful complement in the prenatal setting in case of fetal anomalies. However, data on its clinical utility remain limited in practice. Herein, we reported our data of fetal exome sequencing in a cohort of 512 trios to evaluate its diagnostic yield. METHODS In this retrospective cohort study, the couples performing prenatal exome sequencing were enrolled. Fetal phenotype was classified according to ultrasound and magnetic resonance imaging findings. Genetic variants were analyzed based on a phenotype-driven followed by genotype-driven approach in all trios. RESULTS A total of 97 diagnostic variants in 65 genes were identified in 69 fetuses, with an average detection rate of 13.48%. Skeletal and renal system were the most frequently affected organs referred for whole exome sequencing, with the highest diagnostic rates. Among them, short femur and kidney cyst were the most common phenotype. Fetal growth restriction was the most frequently observed phenotype with a low detection rate (4.3%). Exome sequencing had limited value in isolated increased nuchal translucency and chest anomalies. CONCLUSIONS This study provides our data on the detection rate of whole exome sequencing in fetal anomalies in a large cohort. It contributes to the expanding of phenotypic and genotypic spectrum.
Collapse
Affiliation(s)
- Pengzhen Jin
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiawei Hong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yuqing Xu
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Yeqing Qian
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China
| | - Shuning Han
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Minyue Dong
- Women's Hospital, School of Medicine, Zhejiang University, Hangzhou, China.
- Key Laboratory of Reproductive Genetics (Zhejiang University), Ministry of Education, Hangzhou, China.
| |
Collapse
|
2
|
Zamłyński M, Zhemela O, Olejek A. Isolated Fetal Ventriculomegaly: Diagnosis and Treatment in the Prenatal Period. CHILDREN (BASEL, SWITZERLAND) 2024; 11:957. [PMID: 39201892 PMCID: PMC11352226 DOI: 10.3390/children11080957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/31/2024] [Accepted: 08/07/2024] [Indexed: 09/03/2024]
Abstract
Fetal ventriculomegaly (VM) is a defect of the central nervous system, typically diagnosed during the second-trimester ultrasound in fetuses with an atrial diameter (AD) of >10 mm. Non-isolated ventriculomegaly (NIVM) is heterogeneous in nature, coexisting with additional intracranial and/or extracranial malformations and genetic syndromes, resulting in an unfavorable prognosis for the further development of the child. Both the pregnancy management and counseling are dependent on the findings of combined ultrasound/MRI, genetic testing, and gestational age at diagnosis. The purpose of this review is to propose a hypothesis that diagnostic advancements allow to define the process of identification of the isolated forms of VM (IVM). Based on the evidence presented in the literature, we consider whether prenatal decompression for severe isolated VM (ISVM) is supported by the experimental trials and whether it might be implemented in clinical practice. Also, we describe the evolution of the diagnostic methods and expert opinions about the previously used prenatal decompression techniques for ISVM. In conclusion, we introduce the idea that fetal surgery centers have either reached or nearly reached the necessary level of expertise to perform such procedures. Endoscopic cystoventriculostomy (ETV) appears to be the most promising, as it is associated with minimal perinatal complications and favorable neurological outcomes in the neonatal period. Randomized trials with long-term neurodevelopmental follow-up of children who underwent prenatal decompression due to ISVM are necessary.
Collapse
Affiliation(s)
- Mateusz Zamłyński
- Department of Gynecology, Obstetrics and Oncological Gynecology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Stefana Batorego 15, 41-902 Bytom, Poland;
| | - Olena Zhemela
- Department of Obstetrics and Gynecology, Danylo Halytsky Lviv National Medical University, 79010 Lviv, Ukraine;
| | - Anita Olejek
- Department of Gynecology, Obstetrics and Oncological Gynecology, Faculty of Medical Sciences in Zabrze, Medical University of Silesia, Stefana Batorego 15, 41-902 Bytom, Poland;
| |
Collapse
|
3
|
Smeekens SP, Timmermans R, Westra D, Gilissen C, Faas BHW. Detection of DNA Contamination in Prenatal Samples from Whole Exome Sequencing Data. Clin Chem 2024; 70:1056-1063. [PMID: 38863407 DOI: 10.1093/clinchem/hvae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 04/16/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND Maternal cell contamination (MCC) in prenatal samples poses a risk for misdiagnosis, and therefore, testing for contamination is necessary during genetic analysis of prenatal specimens. MCC testing is currently performed as a method separate from the diagnostic method. With the increasing application of whole exome sequencing (WES) in prenatal diagnosis, we sought to develop a method to estimate the level of contamination from WES data, aiming to eliminate the need for a separate MCC test. METHODS To investigate the impact of MCC on the distribution of the variant allele fraction in WES data, contamination was both simulated in silico and artificially induced. Subsequently, a bioinformatic WES contamination method was developed and validated by comparing its performance to that of the gold standard (short tandem repeat [STR]) MCC test, validated for detecting ≥5% contamination. Finally, post-implementation performance was monitored for a 15-month period. RESULTS During validation, 270 prenatal samples underwent analysis with both WES and the gold standard test. In 259 samples, the results were concordant (248 not contaminated, 11 contaminated with both tests). In 11 samples, contamination was only detected in WES data (2 of which contained ≥5% contamination with WES, which is above the detection limit of the gold standard test). The data of the post-implementation evaluation on 361 samples, of which 68 were contaminated, were in line with the validation data. CONCLUSIONS Contamination can reliably be detected in WES data, rendering a separate contamination test unnecessary for the majority of samples.
Collapse
Affiliation(s)
- Sanne P Smeekens
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Raoul Timmermans
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Dineke Westra
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
- Radboud Institute for Molecular Life Sciences, Radboud university medical center, Nijmegen, the Netherlands
| | - Brigitte H W Faas
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| |
Collapse
|
4
|
Lamsal R, Yeh EA, Pullenayegum E, Ungar WJ. A Systematic Review of Methods and Practice for Integrating Maternal, Fetal, and Child Health Outcomes, and Family Spillover Effects into Cost-Utility Analyses. PHARMACOECONOMICS 2024; 42:843-863. [PMID: 38819718 PMCID: PMC11249496 DOI: 10.1007/s40273-024-01397-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 05/12/2024] [Indexed: 06/01/2024]
Abstract
BACKGROUND Maternal-perinatal interventions delivered during pregnancy or childbirth have unique characteristics that impact the health-related quality of life (HRQoL) of the mother, fetus, and newborn child. However, maternal-perinatal cost-utility analyses (CUAs) often only consider either maternal or child health outcomes. Challenges include, but are not limited to, measuring fetal, newborn, and infant health outcomes, and assessing their impact on maternal HRQoL. It is also important to recognize the impact of maternal-perinatal health on family members' HRQoL (i.e., family spillover effects) and to incorporate these effects in maternal-perinatal CUAs. OBJECTIVE The aim was to systematically review the methods used to include health outcomes of pregnant women, fetuses, and children and to incorporate family spillover effects in maternal-perinatal CUAs. METHODS A literature search was conducted in Medline, Embase, EconLit, Cochrane Collection, Cumulative Index to Nursing and Allied Health Literature (CINAHL), International Network of Agencies for Health Technology Assessment (INAHTA), and the Pediatric Economic Database Evaluation (PEDE) databases from inception to 2020 to identify maternal-perinatal CUAs that included health outcomes for pregnant women, fetuses, and/or children. The search was updated to December 2022 using PEDE. Data describing how the health outcomes of mothers, fetuses, and children were measured, incorporated, and reported along with the data on family spillover effects were extracted. RESULTS Out of 174 maternal-perinatal CUAs identified, 62 considered the health outcomes of pregnant women, and children. Among the 54 quality-adjusted life year (QALY)-based CUAs, 12 included fetal health outcomes, the impact of fetal loss on mothers' HRQoL, and the impact of neonatal demise on mothers' HRQoL. Four studies considered fetal health outcomes and the effects of fetal loss on mothers' HRQoL. One study included fetal health outcomes and the impact of neonatal demise on maternal HRQoL. Furthermore, six studies considered the impact of neonatal demise on maternal HRQoL, while four included fetal health outcomes. One study included the impact of fetal loss on maternal HRQoL. The remaining 26 only included the health outcomes of pregnant women and children. Among the eight disability-adjusted life year (DALY)-based CUAs, two measured fetal health outcomes. Out of 174 studies, only one study included family spillover effects. The most common measurement approach was to measure the health outcomes of pregnant women and children separately. Various approaches were used to assess fetal losses in terms of QALYs or DALYs and their impact on HRQoL of mothers. The most common integration approach was to sum the QALYs or DALYs for pregnant women and children. Most studies reported combined QALYs and incremental QALYs, or DALYs and incremental DALYs, at the family level for pregnant women and children. CONCLUSIONS Approximately one-third of maternal-perinatal CUAs included the health outcomes of pregnant women, fetuses, and/or children. Future CUAs of maternal-perinatal interventions, conducted from a societal perspective, should aim to incorporate health outcomes for mothers, fetuses, and children when appropriate. The various approaches used within these CUAs highlight the need for standardized measurement and integration methods, potentially leading to rigorous and standardized inclusion practices, providing higher-quality evidence to better inform decision-makers about the costs and benefits of maternal-perinatal interventions. Health Technology Assessment agencies may consider providing guidance for interventions affecting future lives in future updates.
Collapse
Affiliation(s)
- Ramesh Lamsal
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada
| | - E Ann Yeh
- Division of Neurology, Department of Pediatrics, University of Toronto, Toronto, ON, Canada
- Neurosciences and Mental Health, SickKids Research Institute, Toronto, ON, Canada
| | - Eleanor Pullenayegum
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Wendy J Ungar
- Child Health Evaluative Sciences, The Hospital for Sick Children, Toronto, ON, Canada.
- Institute of Health Policy, Management and Evaluation, University of Toronto, Toronto, ON, Canada.
- The Hospital for Sick Children, Peter Gilgan Centre for Research and Learning, 686 Bay Street, 11th Floor, Toronto, ON, M5G 0A4, Canada.
| |
Collapse
|
5
|
Ma C, Huang R, Fu F, Zhou H, Wang Y, Yan S, Guo F, Chen H, Li L, Jing X, Li F, Han J, Li D, Li R, Liao C. Prenatal diagnosis and outcomes in fetuses with duplex kidney. Int J Gynaecol Obstet 2024; 166:353-359. [PMID: 38189110 DOI: 10.1002/ijgo.15344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/09/2024]
Abstract
OBJECTIVE Duplex kidney is a relatively frequent form of urinary system abnormality. This study aimed to elucidate the value of chromosomal microarray analysis (CMA) and whole exome sequencing (WES) for duplex kidney and the perinatal outcomes of duplex kidney fetuses. METHODS This retrospective cohort study included 63 patients with duplex kidney diagnosed using antenatal ultrasound between August 2013 and January 2023. We reviewed the clinical characteristics, genetic test results, and pregnancy outcomes of the patients. RESULTS Among the 63 cases based on the inclusion criteria, the CMA detected seven (11.1%) clinically significant variants and nine variants of uncertain significance (VUS), and the pathogenic/likely pathogenic (P/LP) copy number variations (CNVs) in the recurrent region that were associated with prenatal duplex kidney included 17q12, 17p13.3, and 22q11.2. No significant disparity was observed in the CMA detection rate between the unilateral and bilateral groups, or between the isolated and non-isolated groups. WES identified three (50%) P/LP single-gene variants in six fetuses with duplex kidney. We detected the following pathogenic genes in the duplex kidney fetuses: KMT2D, SMPD4, and FANCI. Pregnancy termination in cases where clinically significant variants were detected by genetic testing was different in statistical significance from that in cases with negative results (9/10, 90.0% vs 8/48, 16.7%, P < 0.001). CONCLUSION This study elucidated the value of CMA and WES for fetal duplex kidney, proving that CMA and WES may be useful tools in prenatal diagnosis and genetic counseling.
Collapse
Affiliation(s)
- Chunling Ma
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ruibin Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Hang Zhou
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - You Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Shujuan Yan
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fei Guo
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Huanyi Chen
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Lushan Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fucheng Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jin Han
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, China
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
6
|
Fortin O, Mulkey SB, Fraser JL. Advancing fetal diagnosis and prognostication using comprehensive prenatal phenotyping and genetic testing. Pediatr Res 2024:10.1038/s41390-024-03343-9. [PMID: 38937640 DOI: 10.1038/s41390-024-03343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/14/2024] [Accepted: 06/04/2024] [Indexed: 06/29/2024]
Abstract
Prenatal diagnoses of congenital malformations have increased significantly in recent years with use of high-resolution prenatal imaging. Despite more precise radiological diagnoses, discussions with expectant parents remain challenging because congenital malformations are associated with a wide spectrum of outcomes. Comprehensive prenatal genetic testing has become an essential tool that improves the accuracy of prognostication. Testing strategies include chromosomal microarray, exome sequencing, and genome sequencing. The diagnostic yield varies depending on the specific malformations, severity of the abnormalities, and multi-organ involvement. The utility of prenatal genetic diagnosis includes increased diagnostic clarity for clinicians and families, informed pregnancy decision-making, neonatal care planning, and reproductive planning. Turnaround time for results of comprehensive genetic testing remains a barrier, especially for parents that are decision-making, although this has improved over time. Uncertainty inherent to many genetic testing results is a challenge. Appropriate genetic counseling is essential for parents to understand the diagnosis and prognosis and to make informed decisions. Recent research has investigated the yield of exome or genome sequencing in structurally normal fetuses, both with non-invasive screening methods and invasive diagnostic testing; the prenatal diagnostic community must evaluate and analyze the significant ethical considerations associated with this practice prior to generalizing its use. IMPACT: Reviews available genetic testing options during the prenatal period in detail. Discusses the impact of prenatal genetic testing on care using case-based examples. Consolidates the current literature on the yield of genetic testing for prenatal diagnosis of congenital malformations.
Collapse
Affiliation(s)
- Olivier Fortin
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
| | - Sarah B Mulkey
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA
- Department of Neurology and Rehabilitation Medicine, George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - Jamie L Fraser
- Zickler Family Prenatal Pediatrics Institute, Children's National Hospital, Washington, DC, USA.
- Rare Disease Institute, Children's National Hospital, Washington, DC, USA.
- Center for Genetic Medicine Research, Children's National Hospital, Washington, DC, USA.
- Department of Pediatrics, George Washington University School of Medicine and Health Sciences, Washington, DC, USA.
| |
Collapse
|
7
|
Westenius E, Conner P, Pettersson M, Sahlin E, Papadogiannakis N, Lindstrand A, Iwarsson E. Whole-genome sequencing in prenatally detected congenital malformations: prospective cohort study in clinical setting. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2024; 63:658-663. [PMID: 38268232 DOI: 10.1002/uog.27592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 12/26/2023] [Accepted: 01/16/2024] [Indexed: 01/26/2024]
Abstract
OBJECTIVE To investigate the diagnostic yield of trio whole-genome sequencing (WGS) in fetuses with various congenital malformations referred to a tertiary center for prenatal diagnosis. METHODS In this prospective study, 50 pregnancies with different congenital malformations, negative for trisomies and causative copy-number variants, were analyzed further with fetal-parental trio WGS analysis. Parents were eligible for inclusion if they accepted further investigation following the detection of isolated or multiple malformations on prenatal ultrasound. Cases with isolated increased nuchal translucency, gamete donation or multiple pregnancy were excluded. WGS with the Illumina Inc. 30× polymerase-chain-reaction-free short-read sequencing included analysis of single-nucleotide variants, insertions and deletions, structural variants, short tandem repeats and copy-number identification of SMN1 and SMN2 genes. RESULTS A molecular diagnosis was achieved in 13/50 (26%) cases. Causative sequence variants were identified in 12 genes: FGFR3 (n = 2), ACTA1 (n = 1), CDH2 (n = 1), COL1A2 (n = 1), DHCR7 (n = 1), EYA1 (n = 1), FBXO11 (n = 1), FRAS1 (n = 1), L1CAM (n = 1), OFD1 (n = 1), PDHA1 (n = 1) and SOX9 (n = 1). The phenotypes of the cases were divided into different groups, with the following diagnostic yields: skeletal malformation (4/9 (44%)), multisystem malformation (3/7 (43%)), central nervous system malformation (5/15 (33%)) and thoracic malformation (1/10 (10%)). Additionally, two cases carried variants that were considered potentially clinically relevant, even though they were assessed as variants of uncertain significance, according to the guidelines provided by the American College of Medical Genetics and Genomics. Overall, we identified a causative or potentially clinically relevant variant in 15/50 (30%) cases. CONCLUSIONS We demonstrate a diagnostic yield of 26% with clinical WGS in prenatally detected congenital malformations. This study emphasizes the benefits that WGS can bring to the diagnosis of fetal structural anomalies. It is important to note that causative chromosomal aberrations were excluded from our cohort before WGS. As chromosomal aberrations are a well-known cause of prenatally detected congenital malformations, future studies using WGS as a primary diagnostic test, including assessment of chromosomal aberrations, may show that the detection rate exceeds the diagnostic yield of this study. WGS can add clinically relevant information, explaining the underlying cause of the fetal anomaly, which will provide information concerning the specific prognosis of the condition, as well as estimate the risk of recurrence. A genetic diagnosis can also provide more reproductive choice for future pregnancies. © 2024 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
Collapse
Affiliation(s)
- E Westenius
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - P Conner
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Center for Fetal Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - M Pettersson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - E Sahlin
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - N Papadogiannakis
- Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Pathology, Karolinska University Hospital, Stockholm, Sweden
| | - A Lindstrand
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| | - E Iwarsson
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics and Genomics, Karolinska University Hospital, Stockholm, Sweden
| |
Collapse
|
8
|
Wang Y, Hu L, Chai Y, Liu X. An unusual case of trisomy 8 mosaicism complicated by coexistence of phenylketonuria. Clin Chim Acta 2024; 555:117794. [PMID: 38341017 DOI: 10.1016/j.cca.2024.117794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 01/05/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024]
Abstract
Trisomy 8 syndrome, also known as " Warkany syndrome type 2 ", was first reported in 1971. Complete trisomy 8 are mostly aborted spontaneouslyinthe first trimester. Trisomy 8 mosaicism (T8M), predominated in the current cases reported. Itisahighlyheterogeneous Chromosome disorder. We know little about its effects on fertility. In this case, a patient with T8M combined with phenylketonuria was diagnosed. She's mentally retarded. After evaluating the anatomy and function of the reproductive system, the patient conceived through preimplantationgenetictesting-intracytoplasmicsperminjection-embryotransfer (PGT-ICSI-ET) and obtained a healthy fetus, which is the first report. The study focuses on the maintenance of fertility in patients with T8M, the effects of phenylketonuria and genetic counseling.
Collapse
Affiliation(s)
- Yanan Wang
- Medical Genetics/Prenatal Diagnostic Department, Luoyang Maternal and Child Health Hospital, Luoyang 471000, China.
| | - Lina Hu
- Medical Genetics/Prenatal Diagnostic Department, Luoyang Maternal and Child Health Hospital, Luoyang 471000, China
| | - Yuqiong Chai
- Medical Genetics/Prenatal Diagnostic Department, Luoyang Maternal and Child Health Hospital, Luoyang 471000, China
| | - Xiaofei Liu
- Medical Genetics/Prenatal Diagnostic Department, Luoyang Maternal and Child Health Hospital, Luoyang 471000, China
| |
Collapse
|
9
|
Hong Z, He X, Duan J, Yu F, Liu H, Lu D, Wang M, Zhang Y. Prenatal diagnostic approaches diagnosed craniosynostosis and identified a novel nonsense variant in SMAD6 in a Chinese fetus. Gene 2024; 896:147994. [PMID: 37977316 DOI: 10.1016/j.gene.2023.147994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 10/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
Craniosynostosis is one of the most common congenital craniofacial birth defects. The genetic etiology is complex, involving syndromic developmental diseases, chromosomal abnormalities, and monogenic non-syndromic diseases. Herein, we presented a proband of craniosynostosis, who firstly displayed structural abnormalities. This research conducted dynamic ultrasound monitoring a fetus with gradually developing intrauterine growth retardation (IUGR). A novel de novo variant c.41G > A: p.W14* in SMAD6 was identified by pedigree analysis and genetic examination approaches. Recombinant plasmid carrying wild-type sequence and mutant that carries c.41G > A in SMAD6 were constructed and transfected into HEK293T cells. mRNA and protein expression of SMAD6 were reduced in SMAD6 mutants compared to the wild type. Cycloheximide (CHX) treatment and si-UPF1 transfection rescued the SMAD6 mRNA expression in the mutant construct, indicating that c.41G > A: p.W14* in SMAD6 triggered nonsense-mediated mRNA degradation (NMD) process and thus led to haploinsufficiency of the protein product. Our study demonstrated that whole-exome sequencing (WES) was a powerful tool for further diagnosis and etiological identification once fetal malformation was detected by ultrasound. Novel de novo c.41G > A: p.W14* in SMAD6 is pathogenic and potentially leads to craniosynostosis via NMD process.
Collapse
Affiliation(s)
- Zhidan Hong
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Xuanyi He
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Jie Duan
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China; Department of Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Fang Yu
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China; Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Huanyu Liu
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Dan Lu
- Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China; Department of Ultrasound, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China
| | - Mei Wang
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China
| | - Yuanzhen Zhang
- Center for Reproductive Medicine, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, PR China; Clinical Medicine Research Center of Prenatal Diagnosis and Birth Health in Hubei Province, Wuhan, Hubei, PR China; Wuhan Clinical Research Center for Reproductive Science and Birth Health, Wuhan, Hubei, PR China.
| |
Collapse
|
10
|
Coghlan S, Gyngell C, Vears DF. Ethics of artificial intelligence in prenatal and pediatric genomic medicine. J Community Genet 2024; 15:13-24. [PMID: 37796364 PMCID: PMC10857992 DOI: 10.1007/s12687-023-00678-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 10/06/2023] Open
Abstract
This paper examines the ethics of introducing emerging forms of artificial intelligence (AI) into prenatal and pediatric genomic medicine. Application of genomic AI to these early life settings has not received much attention in the ethics literature. We focus on three contexts: (1) prenatal genomic sequencing for possible fetal abnormalities, (2) rapid genomic sequencing for critically ill children, and (3) reanalysis of genomic data obtained from children for diagnostic purposes. The paper identifies and discusses various ethical issues in the possible application of genomic AI in these settings, especially as they relate to concepts of beneficence, nonmaleficence, respect for autonomy, justice, transparency, accountability, privacy, and trust. The examination will inform the ethically sound introduction of genomic AI in early human life.
Collapse
Affiliation(s)
- Simon Coghlan
- School of Computing and Information Systems (CIS), Centre for AI and Digital Ethics (CAIDE), The University of Melbourne, Grattan St, Melbourne, Victoria, 3010, Australia.
- Australian Research Council Centre of Excellence for Automated Decision Making and Society (ADM+S), Melbourne, Victoria, Australia.
| | - Christopher Gyngell
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Rd, Parkville, Victoria, 3052, Australia
- University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Danya F Vears
- Biomedical Ethics Research Group, Murdoch Children's Research Institute, The Royal Children's Hospital, 50 Flemington Rd, Parkville, Victoria, 3052, Australia
- University of Melbourne, Parkville, Victoria, 3052, Australia
- Centre for Biomedical Ethics and Law, KU Leuven, Kapucijnenvoer 35, 3000, Leuven, Belgium
| |
Collapse
|
11
|
Huang Q, Zhang Y, Jing X, Li F, Qin J, Li F, Li D, Li R, Liao C. Association of prenatal thoracic ultrasound abnormalities with copy number variants at a single Chinese tertiary center. Int J Gynaecol Obstet 2024; 164:770-777. [PMID: 37565521 DOI: 10.1002/ijgo.15040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Revised: 07/19/2023] [Accepted: 07/25/2023] [Indexed: 08/12/2023]
Abstract
OBJECTIVE To systematically evaluate the association of prenatal thoracic ultrasound abnormalities with copy number variants (CNVs). METHODS Chromosomal microarray (CMA) data and clinical characteristics from fetuses with thoracic ultrasound abnormalities were retrieved and analyzed. RESULTS Thoracic ultrasound findings were mainly isolated except for fetal pleural effusion (FPE) and pulmonary hypoplasia. The diagnostic yield of CMA for thoracic anomaly was 9.66%, and FPE (17/68, 25%), pulmonary hypoplasia (1/8, 12.5%), and congenital diaphragmatic hernia (CDH) (6/79, 7.59%) indicated relatively high pathogenic/likely pathogenic (P/LP) CNV findings. The detection rate for P/LP CNVs was obviously increased in non-isolated thoracic anomalies (27.91% vs. 1.96%, P < 0.0001), non-isolated FPE (37.78% vs. 0%, P = 0.0007) and non-isolated congenital pulmonary airway malformation (CPAM) (27.27% vs. 0%, P < 0.0001), and significantly different among thoracic anomalies. Additionally, the rate of termination of pregnancy in cases with non-isolated thoracic anomalies (58.49% vs. 12.34%, P < 0.0001) and P/LP CNVs (85.71% vs. 24.15%, P < 0.0001) was obviously increased. CONCLUSION The present study expanded phenotype spectrums for particular recurrent CNVs. FPE, CDH, and pulmonary hypoplasia indicated relatively high P/LP CNV findings among common thoracic ultrasound abnormalities, CPAM associated with other ultrasound abnormalities increased the incidence of diagnostic CNVs, while bronchopulmonary sequestration might not be associated with positive CNVs. The present data recommended CMA application for cases with prenatal thoracic ultrasound abnormalities, especially non-isolated FPE, non-isolated CPAM, CDH, and pulmonary hypoplasia.
Collapse
Affiliation(s)
- Qiong Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Yongling Zhang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Xiangyi Jing
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fucheng Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Jiachun Qin
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Fatao Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| | - Can Liao
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
12
|
Wang Y, Yin F, Chai Y, Jin J, Zhang P, Tan Q, Chen Z. Prenatal diagnosis of fetuses with ultrasound anomalies by whole-exome sequencing in Luoyang city, China. Front Genet 2024; 14:1301439. [PMID: 38318287 PMCID: PMC10838985 DOI: 10.3389/fgene.2023.1301439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 12/20/2023] [Indexed: 02/07/2024] Open
Abstract
Background: There is a great obstacle in prenatal diagnosis of fetal anomalies due to their considerable genetic and clinical heterogeneity. Whole-exome sequencing (WES) has been confirmed as a successful option for genetic diagnosis in pediatrics, but its clinical utility for prenatal diagnosis remains to be limited. Methods: A total of 60 fetuses with abnormal ultrasound findings underwent karyotyping or chromosomal microarray analysis (CMA), and those with negative results were further subjected to WES. The identified variants were classified as pathogenic or likely pathogenic (P/LP) and the variant of uncertain significance (VUS). Pregnancy outcomes were obtained through a telephone follow-up. Results: Twelve (20%, 12/60) fetuses were diagnosed to have chromosomal abnormalities using karyotyping or CMA. Of the remaining 48 cases that underwent WES, P/LP variants were identified in 14 cases (29.2%), giving an additional diagnostic yield of 23.3% (14/60). The most frequently affected organ referred for prenatal WES was the head or neck system (40%), followed by the skeletal system (39.1%). In terms of pathogenic genes, FGFR3 was the most common diagnostic gene in this cohort. For the first time, we discovered five P/LP variants involved in SEC24D, FIG4, CTNNA3, EPG5, and PKD2. In addition, we identified three VUSes that had been reported previously. Outcomes of pregnancy were available for 54 cases, of which 24 cases were terminated. Conclusion: The results confirmed that WES is a powerful tool in prenatal diagnosis, especially for fetuses with ultrasonographic anomalies that cannot be diagnosed using conventional prenatal methods. Additionally, newly identified variants will expand the phenotypic spectrum of monogenic disorders and greatly enrich the prenatal diagnostic database.
Collapse
Affiliation(s)
- Yanan Wang
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Fan Yin
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| | - Yuqiong Chai
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Jiapei Jin
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Pai Zhang
- Department of Genetics and Prenatal Diagnosis, Luoyang Maternal and Child Health Hospital, Luoyang, China
| | - Qianqian Tan
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| | - Zhigang Chen
- Puluo (Wuhan) Medical Biotechnology Co., LTD., Wuhan, China
| |
Collapse
|
13
|
Hadjipanteli A, Theodosiou A, Papaevripidou I, Evangelidou P, Alexandrou A, Salameh N, Kallikas I, Kakoullis K, Frakala S, Oxinou C, Marnerides A, Kousoulidou L, Anastasiadou VC, Sismani C. Sodium Channel Gene Variants in Fetuses with Abnormal Sonographic Findings: Expanding the Prenatal Phenotypic Spectrum of Sodium Channelopathies. Genes (Basel) 2024; 15:119. [PMID: 38255008 PMCID: PMC10815715 DOI: 10.3390/genes15010119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 01/08/2024] [Accepted: 01/17/2024] [Indexed: 01/24/2024] Open
Abstract
Voltage-gated sodium channels (VGSCs) are responsible for the initiation and propagation of action potentials in the brain and muscle. Pathogenic variants in genes encoding VGSCs have been associated with severe disorders including epileptic encephalopathies and congenital myopathies. In this study, we identified pathogenic variants in genes encoding the α subunit of VGSCs in the fetuses of two unrelated families with the use of trio-based whole exome sequencing, as part of a larger cohort study. Sanger sequencing was performed for variant confirmation as well as parental phasing. The fetus of the first family carried a known de novo heterozygous missense variant in the SCN2A gene (NM_001040143.2:c.751G>A p.(Val251Ile)) and presented intrauterine growth retardation, hand clenching and ventriculomegaly. Neonatally, the proband also exhibited refractory epilepsy, spasms and MRI abnormalities. The fetus of the second family was a compound heterozygote for two parentally inherited novel missense variants in the SCN4A gene (NM_000334.4:c.4340T>C, p.(Phe1447Ser), NM_000334.4:c.3798G>C, p.(Glu1266Asp)) and presented a severe prenatal phenotype including talipes, fetal hypokinesia, hypoplastic lungs, polyhydramnios, ear abnormalities and others. Both probands died soon after birth. In a subsequent pregnancy of the latter family, the fetus was also a compound heterozygote for the same parentally inherited variants. This pregnancy was terminated due to multiple ultrasound abnormalities similar to the first pregnancy. Our results suggest a potentially crucial role of the VGSC gene family in fetal development and early lethality.
Collapse
Affiliation(s)
- Andrea Hadjipanteli
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Athina Theodosiou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Ioannis Papaevripidou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Paola Evangelidou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Angelos Alexandrou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | - Nicole Salameh
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | | | | | | | - Christina Oxinou
- Christina Oxinou Histopathology/Cytology Laboratory, 1065 Nicosia, Cyprus
| | | | - Ludmila Kousoulidou
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| | | | - Carolina Sismani
- The Cyprus Institute of Neurology and Genetics, Cytogenetics and Genomics, 2371 Nicosia, Cyprus; (A.H.)
| |
Collapse
|
14
|
Waddington SN, Peranteau WH, Rahim AA, Boyle AK, Kurian MA, Gissen P, Chan JKY, David AL. Fetal gene therapy. J Inherit Metab Dis 2024; 47:192-210. [PMID: 37470194 PMCID: PMC10799196 DOI: 10.1002/jimd.12659] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Fetal gene therapy was first proposed toward the end of the 1990s when the field of gene therapy was, to quote the Gartner hype cycle, at its "peak of inflated expectations." Gene therapy was still an immature field but over the ensuing decade, it matured and is now a clinical and market reality. The trajectory of treatment for several genetic diseases is toward earlier intervention. The ability, capacity, and the will to diagnose genetic disease early-in utero-improves day by day. A confluence of clinical trials now signposts a trajectory toward fetal gene therapy. In this review, we recount the history of fetal gene therapy in the context of the broader field, discuss advances in fetal surgery and diagnosis, and explore the full ambit of preclinical gene therapy for inherited metabolic disease.
Collapse
Affiliation(s)
- Simon N Waddington
- EGA Institute for Women's Health, University College London, London, UK
- Faculty of Health Sciences, Wits/SAMRC Antiviral Gene Therapy Research Unit, Johannesburg, South Africa
| | - William H Peranteau
- The Center for Fetal Research, Division of General, Thoracic, and Fetal Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Ahad A Rahim
- UCL School of Pharmacy, University College London, London, UK
| | - Ashley K Boyle
- EGA Institute for Women's Health, University College London, London, UK
| | - Manju A Kurian
- Developmental Neurosciences, Zayed Centre for Research into Rare Disease in Children, GOS-Institute of Child Health, University College London, London, UK
- Department of Neurology, Great Ormond Street Hospital for Children, London, UK
| | - Paul Gissen
- Great Ormond Street Institute of Child Health, University College London, London, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- National Institute of Health Research Great Ormond Street Biomedical Research Centre, London, UK
| | - Jerry K Y Chan
- Department of Reproductive Medicine, KK Women's and Children's Hospital, Singapore, Singapore
- Academic Clinical Program in Obstetrics and Gynaecology, Duke-NUS Medical School, Singapore, Singapore
- Experimental Fetal Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Anna L David
- EGA Institute for Women's Health, University College London, London, UK
| |
Collapse
|
15
|
Deutsche Gesellschaft für Humangenetik e.V. (GfH). MED GENET-BERLIN 2023; 35:307-311. [PMID: 38841554 PMCID: PMC11006311 DOI: 10.1515/medgen-2023-2059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2024]
|
16
|
Wang Y, Liu L, Fu F, Li R, Lei T, Huang R, Li D, Liao C. Chromosome Microarray Analysis and Exome Sequencing: Implementation in Prenatal Diagnosis of Fetuses with Digestive System Malformations. Genes (Basel) 2023; 14:1872. [PMID: 37895220 PMCID: PMC10606699 DOI: 10.3390/genes14101872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
(1) Purpose: Retrospective back-to-back comparisons were performed to evaluate the accuracy, effectiveness, and incremental yield of chromosome microarray analysis (CMA) and exome sequencing (ES) analysis in fetuses with digestive system malformations (DSMs). (2) Methods: In total, 595 women with fetal DSMs who underwent prenatal diagnosis were enrolled. We analyzed the diagnostic yields of CMA and ES and evaluated pregnancy outcomes. Copy number variants (CNVs) were classified according to the American College of Medical Genetics and Genomics guidelines. (3) Results: Pathogenic CNVs were detected in 11/517 (2.12%) fetuses, and variants of unknown significance (VUS) were identified in 69 (13.35%) fetuses using CMA. ES detected 29 pathogenic/likely pathogenic variants in 23/143 (16.08%) fetuses and 26/143 (18.2%) VUS. In those with other ultrasound abnormalities, the detection rate of multiple system structural malformations was 41.2%, followed by skeletal (33.3%), cardiovascular (25.4%), and central nervous system (18.6%) malformations. Of the 391 surviving children, 40 (10.2%) exhibited varying degrees of mental retardation. (4) Conclusion: A correlation exists between DSMs and chromosomal abnormalities. When combined with other systemic abnormalities, the incidence of chromosomal abnormalities increases significantly. Patients with congenital DSM are at risk of developing neurodevelopmental disorders. Combined CMA and ES detection of fetal DSM has good clinical application potential.
Collapse
Affiliation(s)
- You Wang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; (Y.W.); (L.L.)
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Liyuan Liu
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; (Y.W.); (L.L.)
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Fang Fu
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Ru Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Tingying Lei
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Ruibin Huang
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Dongzhi Li
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| | - Can Liao
- The First School of Clinical Medicine, Southern Medical University, Guangzhou 510515, China; (Y.W.); (L.L.)
- Department of Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangzhou 510620, China; (F.F.); (R.L.); (T.L.); (R.H.); (D.L.)
| |
Collapse
|
17
|
Yang W, Zu S, Jin Q, Liu Y, Wang C, Shen H, Wang R, Zhang H, Liu M. Fetal hyperechoic kidney cohort study and a meta-analysis. Front Genet 2023; 14:1237912. [PMID: 37662847 PMCID: PMC10469696 DOI: 10.3389/fgene.2023.1237912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 08/04/2023] [Indexed: 09/05/2023] Open
Abstract
Objective: To investigate the positive rate of chromosomal and monogenic etiologies and pregnancy outcomes in fetuses with hyperechoic kidney, and to provide more information for genetic counseling and prognosis evaluation. Methods: We performed a retrospective analysis of 25 cases of hyperechoic kidney diagnosed prenatal in the Second Affiliated Hospital of Harbin Medical University and Harbin Red Cross Central Hospital (January 2017-December 2022). Furthermore, we conducted a meta-analysis of a series of hyperechoic kidneys (HEK) in the literature to assess the incidence of chromosomal and monogenic etiologies, mortality, and pooled odds ratio (OR) estimates of the association between the incidence of these outcomes and other associated ultrasound abnormalities. Results: 25 fetuses of HEK were enrolled in the cohort study, including 14 with isolated hyperechoic kidney (IHK) and 11 with non-isolated hyperechoic kidney (NIHK). Chromosomal aneuploidies were detected in 4 of 20 patients (20%). The detection rate of pathogenic or suspected pathogenic copy number variations (CNVs) was 29% (4/14) for IHK and 37% (4/11) for NIHK. Whole exome sequencing (WES) was performed in 5 fetuses, and pathogenic genes were detected in all of them. The rate of termination of pregnancy was 56% in HEK. 21 studies including 1,178 fetuses were included in the meta-analysis. No case of abnormal chromosome karyotype or (intrauterine death)IUD was reported in fetuses with IHK. In contrast, the positive rate of karyotype in NIHK was 22% and that in HEK was 20%, with the ORs of 0.28 (95% CI 0.16-0.51) and 0.25, (95% CI 0.14-0.44), respectively. The positive rate of (chromosome microarray analysis) CMA in IHK was 59% and that in NIHK was 32%, with the ORs of 1.46 (95% CI 1.33-1.62) and 0.48 (95% CI, 0.28-0.85), respectively. The positive rate of monogenic etiologies in IHK was 31%, with the OR of 0.80 (95% CI 0.25-2.63). In IHK, the termination rate was 21% and neonatal mortality was 13%, with the ORs of 0.26 (95% CI, 0.17-0.40), 1.72 (95% CI, 1.59-1.86), and that in NIHK was 63%, 0.15 (95% CI, 0.10-0.24); 11%, 0.12 (95% CI, 0.06-0.26), respectively. The intrauterine mortality in NIHK group was 2%, with the OR of 0.02 (95% CI, 0.01-0.05). HNF1B variant has the highest incidence (26%) in IHK. Conclusion: The positive rate of karyotype was 20% in HEK and 22% in NIHK. The positive rate of CMA was 32% in NIHK and 59% in IHK. The positive rate of IHK monogenic etiologies was 31%. HNF1B gene variation is the most common cause of IHK. The overall fetal mortality rate of NIHK is significantly higher than that of IHK. The amount of amniotic fluid, kidney size and the degree of corticomedullary differentiation have a great impact on the prognosis, these indicators should be taken into consideration to guide clinical consultation and decision-making.
Collapse
Affiliation(s)
- Wei Yang
- Department of Obstetrics and Gynecology, The Second Affliliated Hospital of Harbin Medical University, Harbin, China
- Department of Prenatal Diagnosis, Harbin Red Cross Central Hospital, Harbin, China
| | - Shujing Zu
- Department of Prenatal Diagnosis, Harbin Red Cross Central Hospital, Harbin, China
| | - Qiu Jin
- Department of Obstetrics and Gynecology, The Second Affliliated Hospital of Harbin Medical University, Harbin, China
| | - Yu Liu
- Department of Obstetrics and Gynecology, The Second Affliliated Hospital of Harbin Medical University, Harbin, China
| | - Chao Wang
- Department of Obstetrics and Gynecology, The Second Affliliated Hospital of Harbin Medical University, Harbin, China
| | - Huimin Shen
- Department of Obstetrics and Gynecology, The Second Affliliated Hospital of Harbin Medical University, Harbin, China
| | - Ruijing Wang
- Department of Obstetrics and Gynecology, The Second Affliliated Hospital of Harbin Medical University, Harbin, China
| | - Hui Zhang
- Department of Prenatal Diagnosis, Harbin Red Cross Central Hospital, Harbin, China
| | - Meimei Liu
- Department of Obstetrics and Gynecology, The Second Affliliated Hospital of Harbin Medical University, Harbin, China
| |
Collapse
|
18
|
Huang R, Fu F, Zhou H, Zhang L, Lei T, Cheng K, Yan S, Guo F, Wang Y, Ma C, Li R, Yu Q, Deng Q, Li L, Yang X, Han J, Li D, Liao C. Prenatal diagnosis in the fetal hyperechogenic kidneys: assessment using chromosomal microarray analysis and exome sequencing. Hum Genet 2023; 142:835-847. [PMID: 37095353 DOI: 10.1007/s00439-023-02545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/13/2023] [Indexed: 04/26/2023]
Abstract
Fetal hyperechogenic kidneys (HEK) is etiologically a heterogeneous disorder. The aim of this study was to identify the genetic causes of HEK using prenatal chromosomal microarray analysis (CMA) and exome sequencing (ES). From June 2014 to September 2022, we identified 92 HEK fetuses detected by ultrasound. We reviewed and documented other ultrasound anomalies, microscopic and submicroscopic chromosomal abnormalities, and single gene disorders. We also analyzed the diagnostic yield of CMA and ES and the clinical impact the diagnosis had on pregnancy management. In our cohort, CMA detected 27 pathogenic copy number variations (CNVs) in 25 (25/92, 27.2%) fetuses, with the most common CNV being 17q12 microdeletion syndrome. Among the 26 fetuses who underwent further ES testing, we identified 7 pathogenic/likely pathogenic variants and 8 variants of uncertain significance in 9 genes in 12 fetuses. Four novel variants were first reported herein, expanding the mutational spectra for HEK-related genes. Following counseling, 52 families chose to continue the pregnancy, and in 23 of them, postnatal ultrasound showed no detectable renal abnormalities. Of these 23 cases, 15 had isolated HEK on prenatal ultrasound. Taken together, our study showed a high rate of detectable genetic etiologies in cases with fetal HEK at the levels of chromosomal (aneuploidy), sub-chromosomal (microdeletions/microduplications), and single gene (point mutations). Therefore, we speculate that combined CMA and ES testing for fetal HEK is feasible and has good clinical utility. When no genetic abnormalities are identified, the findings can be transient, especially in the isolated HEK group.
Collapse
Affiliation(s)
- Ruibin Huang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Hang Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Lu Zhang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Tingying Lei
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Ken Cheng
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
- School of Medicine, South China University of Technology, Guangzhou, 510641, Guangdong, China
| | - Shujuan Yan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Fei Guo
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - You Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Chunling Ma
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
- The First Clinical Medical College, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Qiuxia Yu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Qiong Deng
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Lushan Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510620, Guangdong, China.
| |
Collapse
|
19
|
Xie MJ, Cromie GA, Owens K, Timour MS, Tang M, Kutz JN, El-Hattab AW, McLaughlin RN, Dudley AM. Predicting the functional effect of compound heterozygous genotypes from large scale variant effect maps. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.11.523651. [PMID: 36711904 PMCID: PMC9882023 DOI: 10.1101/2023.01.11.523651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Background Pathogenic variants in PHGDH, PSAT1 , and PSPH cause a set of rare, autosomal recessive diseases known as serine biosynthesis defects. Serine biosynthesis defects present in a broad phenotypic spectrum that includes, at the severe end, Neu-Laxova syndrome, a lethal multiple congenital anomaly disease, intermediately in the form of infantile serine biosynthesis defects with severe neurological manifestations and growth deficiency, and at the mild end, as childhood disease with intellectual disability. However, because L-serine supplementation, especially if started early, can ameliorate and in some cases even prevent symptoms, knowledge of pathogenic variants is highly actionable. Methods Recently, our laboratory established a yeast-based assay for human PSAT1 function. We have now applied it at scale to assay the functional impact of 1,914 SNV-accessible amino acid substitutions. In addition to assaying the functional impact of individual variants in yeast haploid cells, we can assay pairwise combinations of PSAT1 alleles that recapitulate human genotypes, including compound heterozygotes, in yeast diploids. Results Results of our assays of individual variants (in haploid yeast cells) agree well with clinical interpretations and protein structure-function relationships, supporting the use of our data as functional evidence under the ACMG interpretation guidelines. Results from our diploid assay successfully distinguish patient genotypes from those of healthy carriers and agree well with disease severity. Finally, we present a linear model that uses individual allele measurements (in haploid yeast cells) to accurately predict the biallelic function (in diploid yeast cells) of ~ 1.8 million allele combinations corresponding to potential human genotypes. Conclusions Taken together, our work provides an example of how large-scale functional assays in model systems can be powerfully applied to the study of a rare disease.
Collapse
|