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Sonner S, Reilly K, Woolf AS, Chandler N, Kilby MD, Maher ER, Flanagan C, McKnight AJ, Mone F. When should we offer antenatal sequencing for urinary tract malformations? A systematic review, cohort study and meta-analysis. Prenat Diagn 2024; 44:187-195. [PMID: 38056891 DOI: 10.1002/pd.6479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 12/08/2023]
Abstract
OBJECTIVE Determine the incremental yield of prenatal exome sequencing (PES) over chromosome microarray (CMA) and/or karyotype for urinary tract malformations (UTMs). METHOD A prospective cohort study encompassing data from the English Genomic Medicine Service North Thames Laboratory Hub for fetuses with bilateral echogenic kidneys (BEKs) was combined with data from a systematic review. MEDLINE, EMBASE, Web of Science, MedRxiv and GreyLit were searched from 01/2010-02/2023 for studies reporting on the yield of PES over CMA or karyotype in fetuses with UTMs. Pooled incremental yield was determined using a random effects model. PROSPERO CRD42023364544. RESULTS Fourteen studies (410 cases) were included. The incremental yield for multisystem UTMs, any isolated UTMs, and BEKs was 31% [95% CI, 18%-46%; I2 = 78%], 16% [95% CI, 6%-26%; I2 = 80%] and 51% [95% CI, 27%-75%; I2 = 34%]. The most common clinical diseases and syndromes identified, based on the variant genes detected, were Bardet-Biedl syndrome (BBS genes), dominant and recessive polycystic kidney diseases (PKD1, PKD2 and PKHD1) and renal cysts and diabetes syndrome (HNF1B). CONCLUSION There was a notable incremental genetic diagnostic yield when PES was applied to multisystem UTMs and BEKs. There was a modest incremental yield when this technique was used for UTMs other than BEKs.
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Affiliation(s)
- Sarah Sonner
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Kelly Reilly
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Adrian S Woolf
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, The University of Manchester, Manchester, UK
| | - Natalie Chandler
- North Thames Genomic Laboratory Hub, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Mark D Kilby
- Fetal Medicine Centre, Birmingham Women's & Children's Foundation Trust, Birmingham, UK
- College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
- Medical Genomics Research Group, Illumina, Cambridge, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, UK
| | - Cheryl Flanagan
- Institute of Pathology, Belfast Health and Social Care Trust, Belfast, UK
| | | | - Fionnuala Mone
- Centre for Public Health, Queen's University Belfast, Belfast, UK
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Huang Z, Shen Q, Wu B, Wang H, Dong X, Lu Y, Cheng G, Wang L, Lu W, Chen L, Kang W, Li L, Pan X, Wei Q, Zhuang D, Chen D, Yin Z, Yang L, Ni Q, Liu R, Li G, Zhang P, Qian Y, Peng X, Wang Y, Cao Y, Xu H, Hu L, Yang L, Zhou W. Genetic Spectrum of Congenital Anomalies of the Kidney and Urinary Tract in Chinese Newborn Genome Project. Kidney Int Rep 2023; 8:2376-2384. [PMID: 38025242 PMCID: PMC10658258 DOI: 10.1016/j.ekir.2023.08.005] [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: 07/21/2023] [Accepted: 08/07/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction Congenital anomalies of the kidney and urinary tract (CAKUT) corresponds to a spectrum of defects. Several large-cohort studies have used high-throughput sequencing to investigate the genetic risk of CAKUT during antenatal, childhood, and adulthood period. However, our knowledge of newborns with CAKUT is limited. Methods This multicenter retrospective cohort study explored the genetic spectrum of CAKUT in a Chinese neonatal cohort. Clinical data and whole exome sequencing (WES) data of 330 newborns clinically diagnosed with CAKUT were collected. WES data were analyzed for putative deleterious single nucleotide variants (SNVs) and potential disease-associated copy number variants (CNVs). Results In this study, pathogenic variants were identified in 61 newborns (18.5%, 61/330), including 35 patients (57.4%) with SNVs, 25 patients (41%) with CNVs, and 1 patient with both an SNV and a CNV. Genetic diagnosis rates were significantly higher in patients with extrarenal manifestations (P<0.001), especially in those with cardiovascular malformations (P<0.05). SNVs in genes related to syndromic disorders (CAKUT with extrarenal manifestations) were common, affecting 20 patients (57.1%, 20/35). KMT2D was the most common gene (5 patients) and 17q12 deletion was the most common CNV (4 patients). Patient 110 was detected with both a CNV (17q12 deletion) and an SNV (a homozygous variant of SLC25A13). Among the newborns with positive genetic results, 22 (36.1%, 22/61) patients may benefit from a molecular diagnosis and change in clinical management (including early multidisciplinary treatment, disease-specific follow-up, and familial genetic counseling). Conclusion This study shows the heterogeneous genetic etiologies in a Chinese CAKUT neonatal cohort by using WES. Patients with CAKUT who have extrarenal manifestations are more likely to harbor genetic diagnoses. Kabuki syndrome and 17q12 deletion syndrome were the most common genetic findings. Approximately 36.1% of the patients may benefit from molecular diagnoses and a change in clinical management.
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Affiliation(s)
- Zhelan Huang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Qian Shen
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
| | - Bingbing Wu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Huijun Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Xinran Dong
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yulan Lu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Guoqiang Cheng
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
| | - Laishuan Wang
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Wei Lu
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Liping Chen
- Jiangxi Provincial Children’s Hospital, Nanchang, China
| | - Wenqing Kang
- Children’s Hospital Affiliated to Zhengzhou University, Zhengzhou, China
| | - Long Li
- Department of Neonatology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xinnian Pan
- Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Qiufen Wei
- Maternal and Child Health Care Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | | | - Dongmei Chen
- Quanzhou Women and Children’s Hospital, Quanzhou, China
| | | | - Ling Yang
- Hainan Women and Children’s Medical Center, Haikou, China
| | - Qi Ni
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Renchao Liu
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Gang Li
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Ping Zhang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yanyan Qian
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Xiaomin Peng
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yao Wang
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Hong Xu
- Department of Nephrology, Children’s Hospital of Fudan University, Shanghai, China
| | - Liyuan Hu
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
| | - Lin Yang
- Department of Endocrinology and Inherited Metabolic Diseases, Children’s Hospital of Fudan University, Shanghai, China
| | - Wenhao Zhou
- Center for Molecular Medicine, Children’s Hospital of Fudan University, Shanghai, China
- Division of Neonatology, Children’s Hospital of Fudan University, Shanghai, China
- Key Laboratory of Birth Defects, Children’s Hospital of Fudan University, Shanghai, China
- Xiamen Children’s Hospital, Xiamen, China
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Liu W, Cao J, Shi X, Li Y, Qiao F, Wu Y. Genetic testing and diagnostic strategies of fetal skeletal dysplasia: a preliminary study in Wuhan, China. Orphanet J Rare Dis 2023; 18:336. [PMID: 37875969 PMCID: PMC10599061 DOI: 10.1186/s13023-023-02955-4] [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: 10/31/2022] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
BACKGROUND Fetal skeletal dysplasia is a diverse group of degenerative diseases of bone and cartilage disorders that can lead to movement disorder and even death. This study aims to evaluate the diagnostic yield of sonographic examination and genetic testing for fetal skeletal dysplasia. METHODS From September 2015 to April 2021, the study investigated 24 cases with suspected short-limb fetuses, which were obtained from Tongji Hospital affiliated to Tongji Medical College of Huazhong University of Science and Technology. To identify the causative gene, multiple approaches (including karyotype analysis, copy number variations and whole exome sequencing) were performed on these fetuses. And further segregation analysis of the candidate variant was performed in parents by using Sanger sequencing. RESULTS ① Out of 24 cases, likely pathogenic variants in FGFR3, FBN2, COL1A2, CUL7 and DYNC2H1 were detected in 6 cases; pathogenic variants in FGFR3, IMPAD1 and GORAB were identified in other 6 cases; and variants in WNT1, FBN1, OBSL1, COL1A1, DYNC2H1 and NEK1, known as Variant of Undetermined Significance, were found in 4 cases. There were no variants detected in the rest 8 cases by the whole exome sequencing. ② Of 24 cases, 12 (50%) were found to carry variants (pathogenic or likely pathogenic) in seven genes with 12 variants. Four fetuses (16.7%) had variants of uncertain significance. CONCLUSION Genetic testing combining with ultrasound scanning enhances the accurate diagnosis of fatal skeletal dysplasia in utero, and then provides appropriate genetic counseling.
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Affiliation(s)
- Wanlu Liu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Jing Cao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Xinwei Shi
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Yuqi Li
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Fuyuan Qiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
| | - Yuanyuan Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030 China
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Mitrovic K, Zivotic I, Kolic I, Djordjevic A, Zakula J, Filipovic Trickovic J, Zivkovic M, Stankovic A, Jovanovic I. Identification and functional interpretation of miRNAs affected by rare CNVs in CAKUT. Sci Rep 2022; 12:17746. [PMID: 36273030 PMCID: PMC9587983 DOI: 10.1038/s41598-022-22749-1] [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: 02/10/2022] [Accepted: 10/19/2022] [Indexed: 01/18/2023] Open
Abstract
Rare copy number variants (CNVs) are among the most common genomic disorders underlying CAKUT. miRNAs located in rare CNVs represent well-founded functional variants for human CAKUT research. The study aimed to identify and functionally interpret miRNAs most frequently affected by rare CNVs in CAKUT and to estimate the overall burden of rare CNVs on miRNA genes in CAKUT. The additional aim of this study was to experimentally confirm the effect of a rare CNV in CAKUT on candidate miRNA's expression and the subsequent change in mRNA levels of selected target genes. A database of CAKUT-associated rare CNV regions, created by literature mining, was used for mapping of the miRNA precursors. miRNAs and miRNA families, most frequently affected by rare CAKUT-associated CNVs, have been subjected to bioinformatic analysis. CNV burden analysis was performed to identify chromosomes with over/underrepresentation of miRNA genes in rare CNVs associated with CAKUT. A functional study was performed on HEK293 MIR484+/- KO and HEK293 WT cell lines, followed by the analysis of relative miRNA and mRNA target gene levels. 80% of CAKUT patients with underlying rare CNV had at least one miRNA gene overlapping the identified CNV. Network analysis of the most frequently affected miRNAs has revealed the dominant regulation of the two miRNAs, hsa-miR-484 and hsa-miR-185-5p. Additionally, miR-548 family members have shown substantial enrichment in rare CNVs in CAKUT. An over/underrepresentation of miRNA genes in rare CNVs associated with CAKUT was observed in multiple chromosomes, such as chr16, chr20, and chr21. A significant 0.37 fold downregulation of hsa-miR-484, followed by a notable upregulation of MDM2 and APAF1 and downregulation of NOTCH3 was detected in HEK293 MIR484+/- KO compared to HEK293 WT cell lines, supporting the study hypothesis. miRNA genes are frequently affected by rare CNVs in CAKUT patients. Understanding the potential of CNV-affected miRNAs to participate in CAKUT as genetic drivers represent a crucial implication for the development of novel therapeutic approaches.
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Affiliation(s)
- Kristina Mitrovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivan Zivotic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivana Kolic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ana Djordjevic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jelena Zakula
- grid.7149.b0000 0001 2166 9385Department of Molecular Biology and Endocrinology, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Jelena Filipovic Trickovic
- grid.7149.b0000 0001 2166 9385Department of Physical Chemistry, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Maja Zivkovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Aleksandra Stankovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
| | - Ivan Jovanovic
- grid.7149.b0000 0001 2166 9385Department of Radiobiology and Molecular Genetics, “Vinča” Institute of Nuclear Sciences, National Institute of the Republic of Serbia, University of Belgrade, Belgrade, Serbia
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