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Liu L, Wang J, Liu X, Wang J, Chen L, Zhu H, Mai J, Hu T, Liu S. Prenatal prevalence and postnatal manifestations of 16p11.2 deletions: A new insights into neurodevelopmental disorders based on clinical investigations combined with multi-omics analysis. Clin Chim Acta 2024; 552:117671. [PMID: 37984529 DOI: 10.1016/j.cca.2023.117671] [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: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/22/2023]
Abstract
BACKGROUND The 16p11.2 deletion is one of the most common genetic aetiologies of neurodevelopmental disorders (NDDs). The prenatal phenotype of 16p11.2 deletion and the potential mechanism associated with postnatal clinical manifestations were largely unknow. We revealed the developmental trajectories of 16p11.2 deletion from the prenatal to postnatal periods and to identify key signaling pathways and candidate genes contributing to neurodevelopmental abnormalities. METHODS In this 5-y retrospective cohort study, women with singleton pregnancies who underwent amniocentesis for chromosomal abnormalities were included. Test of copy-number variations (CNVs) involved single nucleotide polymorphism-array and CNV-seq was performed to detected 16p11.2 deletion. For infants born carrying the 16p11.2 deletion, neurological and intellectual evaluations using the Chinese version of the Gesell Development Scale. For patients observed to have vertebral malformations, Sanger sequencing for T-C-A haplotype of TBX6 was performed. For those infants with clinical manifestations, whole-exome sequencing was consecutively performed in trios to rule out single-gene diseases, and transcriptomics combined with untargeted metabolomics were performed. RESULTS The prevalence of 16p11.2 deletion was 0.063% (55/86,035) in the prenatal period. Up to 80% (20/25) of the 16p11.2 deletions were proven de novo by parental confirmation. Approximately half of 16p11.2 deletions (28/55) were detected with prenatal abnormal ultrasound findings. Vertebral malformations were identified as the most distinctive structural malformations and were enriched in fetuses with 16p11.2 deletions compared with controls (90.9‰ [5/55] vs. 8.4‰ [72/85,980]; P < 0.001). All 5 fetuses with vertebral malformations were confirmed to have the TBX6 haplotype of T-C-A. Overall, 47.6% (10/21) infants birthed were diagnosed with NDDs of different degrees. Language impairment was the predominant manifestation (7/10; 70.0%), followed by motor delay (5/10; 50%). Multi-omics analysis indicated that MAPK3 was the central hub of the differentially expressed gene (DEG) network. We firstly reported that histidine-associated metabolism may be the core metabolic pathway related to the 16p11.2 deletion. CONCLUSION We demonstrated the prenatal presentation, incomplete penetrance and variable expressivity of the 16p11.2 deletion. We identified vertebral malformations were the most distinctive prenatal phenotypes, and language impairment was the predominant postnatal manifestation. Most of the 16p11.2 deletion was de novo. Meanwhile, we suggested that MAPK3 and histidine-associated metabolism may contribute to neurodevelopmental abnormalities of 16p11.2 deletion.
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Affiliation(s)
- Lan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Medical College, Tibet University, Lhasa, Tibet 850000, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xijing Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Lin Chen
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongmei Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Jingqun Mai
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China; Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan 610041, China; Department of Obstetrics and Gynecology, West China Second University Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
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Qian Y, Hu T, Zhang Z, Xiao L, Wang J, Hu R, Liao N, Liu Z, Wang H, Liu S. Prenatal diagnosis with chromosome microarray analysis and pregnancy outcomes of fetuses with umbilical cord cysts. J Matern Fetal Neonatal Med 2023; 36:2203793. [PMID: 37088564 DOI: 10.1080/14767058.2023.2203793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
OBJECTIVE To investigate the prenatal diagnostic value of chromosome microarray analysis (CMA) in fetuses with isolated or non-isolated umbilical cord cysts (UCCs) of various locations and numbers. METHODS Between November 2015 and November 2021, 45 pregnant women carrying fetuses with UCCs underwent amniocentesis and CMA. Fetal prognoses were followed from 6 months to 5 years. RESULTS Five cases (11.1%, 5/45) of chromosomal aberrations were detected. No significant difference in total chromosome abnormalities was found between fetuses with isolated and non-isolated UCCs (13.3% [2/15] vs 10% [3/30]; p > .999). No common autosomal aneuploidies were found in fetuses with isolated UCCs. At follow-up, among 45 fetuses, there were 11 (24.4%) pregnancy terminations, 26 (57.8%) live healthy births, 4 (8.9%) postnatal UCC-related surgeries, and 4 (8.9%) live births of fetuses with other diseases. The frequency of postnatal surgeries of the infants with UCCs located adjacent to the anterior abdominal wall was higher than those located adjacent to the fetal surface of the placenta (30.8% [4/13] vs 0% [0/22]; p = .014). All 26 live healthy neonates and 4 neonates that underwent postnatal surgery had an overall good prognosis. CONCLUSIONS For fetuses with isolated or non-isolated UCC, CMA could be a choice for parents after providing detailed information. Even when surgery was required, pregnancy outcomes and short- and long-term prognoses for fetuses with UCCs were favorable.
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Affiliation(s)
- Yanping Qian
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Zhu Zhang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Like Xiao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Jiamin Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Rui Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Na Liao
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Zhushu Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - He Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
| | - Shanling Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Ministry of Education, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), China
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Zhao Q, Xiang Q, Tan Y, Xiao X, Xie H, Wang H, Yang M, Liu S. A novel CLCNKB variant in a Chinese family with classic Bartter syndrome and prenatal genetic diagnosis. Mol Genet Genomic Med 2022; 10:e2027. [PMID: 35913199 PMCID: PMC9544217 DOI: 10.1002/mgg3.2027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 05/10/2022] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Background Type III Bartter syndrome (BS), often known as classic Bartter syndrome is caused by variants in CLCNKB gene, which encoding the basolateral chloride channel protein ClC‐Kb, and is characterized by renal salt wasting, hypokalemia, metabolic alkalosis, increased renin, and aldosterone levels. Methods A 2‐year‐old boy presented severe malnutrition, severe metabolic alkalosis and severe hypokalemia and was clinically diagnosed with BS. The trio exome sequencing (ES) was performed to discover the genetic cause of this patient, followed by validation using Sanger sequencing and quantitative polymerase chain reaction subsequently. Results The genetic analysis indicated that this patient with a compound heterozygous variants of CLCNKB gene including a novel nonsense variant c.876 T > A and a whole‐gene deletion. The two variants were inherited from his parents, respectively. Subsequently, target sequencing of CLCNKB gene was performed for next pregnancy, and prenatal genetic diagnosis was provided for the family. Conclusions The results of current study identified the compound heterozygous variants in a patient with classic BS. The novel variant expands the spectrum of CLCNKB variants in BS. Our study also indicates that ES is an alternative tool to simultaneously detect single‐nucleotide variants and copy‐number variants.
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Affiliation(s)
- Qianying Zhao
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Qinqin Xiang
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Yu Tan
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Xiao Xiao
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Hanbing Xie
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - He Wang
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Mei Yang
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
| | - Shanling Liu
- Department of Obstetrics & Gynecology, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, China
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Yang M, Liu Y, Lin Z, Sun H, Hu T. A novel de novo missense mutation in EFTUD2 identified by whole-exome sequencing in mandibulofacial dysostosis with microcephaly. J Clin Lab Anal 2022; 36:e24440. [PMID: 35435265 PMCID: PMC9102503 DOI: 10.1002/jcla.24440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/10/2022] [Accepted: 04/05/2022] [Indexed: 11/08/2022] Open
Abstract
Background Mandibulofacial dysostosis with microcephaly (MFDM) is a rare multiple malformation syndrome characterized by malar and mandibular hypoplasia and congenital‐ or postnatal‐onset microcephaly induced by haploinsufficiency of (elongation factor Tu GTP‐binding domain‐containing 2) EFTUD2. Methods We report the case of a 16‐month‐old boy with MFDM symptoms, including malar and mandibular hypoplasia, microcephaly, micrognathia, midline cleft palate, microtia, auditory canal atresia, severe sensorineural hearing loss, and developmental delay. Whole‐exome sequencing (WES) analysis of the patient's family was performed to identify the genetic etiology responsible for this phenotype. Results We identified a novel de novo missense mutation (c.671G>T, p.Gly224Val) in the EFTUD2. According to the American College of Medical Genetics and Genomics (ACMG) 2015 guidelines, the c.671G>T mutation was classified as likely pathogenic (PS2, PM1, PM2, and PP3). Based on our findings, prenatal diagnosis was performed on the second baby of the proband's parents to exclude the mutation and it was confirmed that the baby did not have the MFDM phenotype after 14 months of follow‐up. Furthermore, the zebrafish model confirmed that the EFTUD2 c.671G>T mutation caused a loss of gene function in EFTUD2, and the pathogenicity of the EFTUD2 c.671G>T mutation was classified as pathogenic (PS2, PS3, PM1, and PM2). Conclusion Our results indicate that WES is a useful tool for identifying potentially pathogenic mutations, particularly in rare disorders, and is advantageous for genetic counseling and subsequent prenatal diagnosis. Moreover, the importance of functional assays cannot be underestimated, which could further confirm the pathogenicity of the genetic variants.
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Affiliation(s)
- Mei Yang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Yanyan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
| | - Ziyuan Lin
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.,SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Huaqin Sun
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China.,SCU-CUHK Joint Laboratory for Reproductive Medicine, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, China
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