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Wang X, Sha J, Han Y, Pang M, Liu M, Liu M, Zhang B, Zhai J. Efficiency of copy number variation sequencing combined with karyotyping in fetuses with congenital heart disease and the following outcomes. Mol Cytogenet 2024; 17:12. [PMID: 38741090 DOI: 10.1186/s13039-024-00681-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 04/26/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND Both copy number variant-sequencing (CNV-seq) and karyotype analysis have been used as powerful tools in the genetic aetiology of fetuses with congenital heart diseases (CHD). However, CNV-seq brings clinicians more confusions to interpret the detection results related to CHD with or without extracardiac abnormalities. Hence, we conducted this study to investigate the clinical value of CNV-seq in fetuses with CHD. RESULTS A total of 167 patients with fetal CHD including 36 single CHD (sCHD), 41 compound CHD (cCHD) and 90 non-isolated CHD (niCHD) were recruited into the study. 28 cases (16.77%, 28/167) were revealed with chromosomal abnormalities at the level of karyotype. The pathogenic detection rate (DR) of CNV-seq (23.17%, 19/82) was higher than that of karyotyping (15.85%, 13/82) in 82 cases by CNV-seq and karyotyping simultaneously. The DR of pathogenic copy number variations (PCNVs) (31.43%) was higher in niCHD subgroup than that in sCHD and cCHD (9.52% and 23.08%). Conotruncal defect (CTD) was one of the most common heart malformations with the highest DR of PCNVs (50%) in 7 categories of CHD. In terms of all the pregnancy outcomes, 67 (40.12%) cases were terminated and 100 (59.88%) cases were live neonates. Only two among 34 cases with a pathogenic genetic result chose to continue the pregnancy. CONCLUSIONS CNV-seq combined with karyotyping is a reliable and accurate prenatal technique for identifying pathogenic chromosomal abnormalities associated with fetal CHD with or without extracardiac abnormalities, which can assist clinicians to perform detailed genetic counselling with regard to the etiology and related outcomes of CHD.
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Affiliation(s)
- Xuezhen Wang
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China
- Graduate School of Bengbu Medical University, Donghai Avenue No.2600, Bengbu, 233000, Anhui, China
| | - Jing Sha
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China
| | - Yu Han
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China
- Key Laboratory of Brain Diseases Bioinformation of Xuzhou Medical University, Tongshan Road No.209, Xuzhou, 221004, Jiangsu, China
| | - Min Pang
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China
| | - Min Liu
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China
| | - Mengna Liu
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China
| | - Bei Zhang
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China.
- Graduate School of Bengbu Medical University, Donghai Avenue No.2600, Bengbu, 233000, Anhui, China.
| | - Jingfang Zhai
- Department of Prenatal Diagnosis Medical Center, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Jiefang South Road No.199, Xuzhou, 221009, Jiangsu, China.
- Graduate School of Bengbu Medical University, Donghai Avenue No.2600, Bengbu, 233000, Anhui, China.
- Key Laboratory of Brain Diseases Bioinformation of Xuzhou Medical University, Tongshan Road No.209, Xuzhou, 221004, Jiangsu, China.
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Dai YF, Wu XQ, Huang HL, He SQ, Guo DH, Li Y, Lin N, Xu LP. Experience of copy number variation sequencing applied in spontaneous abortion. BMC Med Genomics 2024; 17:15. [PMID: 38191380 PMCID: PMC10775620 DOI: 10.1186/s12920-023-01699-1] [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: 10/09/2022] [Accepted: 10/13/2023] [Indexed: 01/10/2024] Open
Abstract
PURPOSE We evaluated the value of copy number variation sequencing (CNV-seq) and quantitative fluorescence (QF)-PCR for analyzing chromosomal abnormalities (CA) in spontaneous abortion specimens. METHODS A total of 650 products of conception (POCs) were collected from spontaneous abortion between April 2018 and May 2020. CNV-seq and QF-PCR were performed to determine the characteristics and frequencies of copy number variants (CNVs) with clinical significance. The clinical features of the patients were recorded. RESULTS Clinically significant chromosomal abnormalities were identified in 355 (54.6%) POCs, of which 217 (33.4%) were autosomal trisomies, 42(6.5%) were chromosomal monosomies and 40 (6.2%) were pathogenic CNVs (pCNVs). Chromosomal trisomy occurs mainly on chromosomes 15, 16, 18, 21and 22. Monosomy X was not associated with the maternal or gestational age. The frequency of chromosomal abnormalities in miscarriages from women with a normal live birth history was 55.3%; it was 54.4% from women without a normal live birth history (P > 0.05). There were no significant differences among women without, with 1, and with ≥ 2 previous miscarriages regarding the rate of chromosomal abnormalities (P > 0.05); CNVs were less frequently detected in women with advanced maternal age than in women aged ≤ 29 and 30-34 years (P < 0.05). CONCLUSION Chromosomal abnormalities are the most common cause of pregnancy loss, and maternal and gestational ages are strongly associated with fetal autosomal trisomy aberrations. Embryo chromosomal examination is recommended regardless of the gestational age, modes of conception or previous abortion status.
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Affiliation(s)
- Yi-Fang Dai
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Xiao-Qing Wu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Hai-Long Huang
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Shu-Qiong He
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Dan-Hua Guo
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Ying Li
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China.
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China.
| | - Liang-Pu Xu
- Medical Genetic Diagnosis and Therapy Center of Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, No.18 Daoshan Road, Fuzhou, Fujian, 350001, China.
- Fujian Provincial Key Laboratory for Prenatal diagnosis and Birth Defect, No.18 Daoshan Road, Fuzhou, 350001, Fujian, China.
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Lin S, Shi S, Lu J, He Z, Li D, Huang L, Huang X, Zhou Y, Luo Y. Contribution of genetic variants to congenital heart defects in both singleton and twin fetuses: a Chinese cohort study. Mol Cytogenet 2024; 17:2. [PMID: 38178226 PMCID: PMC10768341 DOI: 10.1186/s13039-023-00664-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/09/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The contribution of genetic variants to congenital heart defects (CHDs) has been investigated in many postnatal cohorts but described in few prenatal fetus cohorts. Overall, specific genetic variants especially copy number variants (CNVs) leading to CHDs are somewhat diverse among different prenatal cohort studies. In this study, a total of 1118 fetuses with confirmed CHDs were recruited from three units over a 5-year period, composing 961 of singleton pregnancies and 157 of twin pregnancies. We performed chromosomal microarray analysis on all cases to detect numerical chromosomal abnormalities (NCAs) and pathogenic/likely pathogenic CNVs (P/LP CNVs) and employed whole-exome sequencing for some cases without NCAs and P/LP CNVs to detect P/LP sequence variants (P/LP SVs). RESULTS Overall, NCAs and P/LP CNVs were identified in 17.6% (197/1118) of cases, with NCA accounting for 9.1% (102/1118) and P/LP CNV for 8.5% (95/1118). Nonisolated CHDs showed a significantly higher frequency of NCA than isolated CHD (27.3% vs. 4.4%, p < 0.001), but there was no significant difference in the frequency of P/LP CNVs between isolated and nonisolated CHD (11.7% vs. 7.7%). A total of 109 P/LP CNVs were identified in 95 fetuses, consisting of 97 (89.0%) de novo, 6 (5.5%) parental inherited and 6 (5.5%) with unavailable parental information. The 16p11.2 proximal BP4-BP5 deletion was detected in 0.9% (10/1118) of all cases, second only to the most common 22q11.21 proximal A-D deletion (2.1%, 23/1118). Most of the 16p11.2 deletions (8/10) detected were de novo, and were enriched in CHD cases compared with a control cohort from a previous study. Additionally, SV was identified in 12.9% (8/62) of cases without NCA and P/LP CNV, most of which were de novo with autosomal dominant inheritance. CONCLUSIONS Our cohort study provides a deep profile of the contribution of genetic variants to CHDs in both singleton and twin fetuses; NCA and P/LP CNV contribute to 9.1% and 8.5% of CHD in fetuses, respectively. We confirmed the 16p11.2 deletion as a CHD-associated hotspot CNV, second only to the 22q11.21 deletion in frequency. Most 16p11.2 deletions detected were de novo. Additionally, P/LP SV was identified in 12.9% (8/62) of fetuses without NCA or P/LP CNV.
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Affiliation(s)
- Shaobin Lin
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhong Shan Er Road, Guangzhou, 510080, Guangdong, China
| | - Shanshan Shi
- Fetal Medicine Center, The First Affiliated Hospital, Jinan University, No. 613 Huangpu West Road, Guangzhou, 510630, Guangdong, China
| | - Jian Lu
- Medical Genetic Center, Guangdong Women and Children Hospital, Guangzhou, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, No.521, Xingnan Road, Panyu District, Guangzhou, 511400, Guangdong, China
| | - Zhiming He
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhong Shan Er Road, Guangzhou, 510080, Guangdong, China
| | - Danlun Li
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhong Shan Er Road, Guangzhou, 510080, Guangdong, China
| | - Linhuan Huang
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhong Shan Er Road, Guangzhou, 510080, Guangdong, China
| | - Xuan Huang
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhong Shan Er Road, Guangzhou, 510080, Guangdong, China
| | - Yi Zhou
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhong Shan Er Road, Guangzhou, 510080, Guangdong, China.
| | - Yanmin Luo
- Prenatal Diagnosis Center, Department of Obstetrics and Gynecology, The First Affiliated Hospital, Sun Yat-Sen University, 58 Zhong Shan Er Road, Guangzhou, 510080, Guangdong, China.
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Yang X, Bian X, Shi X, Ding J, Tang H, Xu P, Deng D, Zeng W, Chen S, Qiao F, Feng L, Wu Y. Diagnostic yield of copy number variation sequencing in fetuses with increased nuchal translucency: a retrospective study. Arch Gynecol Obstet 2024; 309:139-144. [PMID: 36602560 DOI: 10.1007/s00404-022-06900-x] [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: 10/23/2022] [Accepted: 12/18/2022] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To assess the efficacy of copy number variation sequencing (CNV-seq) and karyotyping for prenatal detection of chromosomal abnormalities in fetuses with increased nuchal translucency. METHODS Amniotic fluid samples were extracted from 205 fetuses with increased nuchal translucency (NT ≥ 2.5 mm), diagnosed by ultrasound between gestational ages of 11 and 13 + 6 weeks. Karyotyping and CNV-seq were performed for detecting chromosomal abnormalities. RESULTS There are 40 fetuses (19.51%) showing increased NT detected with chromosomal abnormalities in karyotyping, and trisomy 21 was found to be the most common abnormalities. There are 50 fetuses (24.39%) identified with chromosomal abnormalities by CNV-seq. The detection of the applied techniques indicated that CNV-seq revealed higher chromosomal aberrations. The risk of chromosomal abnormalities was significantly increased with NT thickening, from 13.64% in the NT group of 2.5-3.4 mm, 38.64% in the NT group of 3.5-4.4 mm, and to 51.72% in the NT group of over 4.5 mm (P < 0.05). The investigated cases with increased NT with presence of soft markers in ultrasound or high risk in non-invasive prenatal testing presented chromosomal abnormalities in higher rates, comparing with those with isolated NT or low risk (P < 0.05). CONCLUSION The results indicated that the risk of chromosomal abnormalities was associated with the NT thickness, detected by karyotype or CNV-seq. The combination application of two analysis was efficient to reveal the possible genetic defects in prenatal diagnosis. The finding suggested that the detection should be considered with ultrasonographic soft markers, and the NT thickness of 2.5-3.4 mm could be a critical value for detecting chromosomal abnormalities to prevent the occurrence of missed diagnosis.
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Affiliation(s)
- Xiao Yang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinyi Bian
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xinwei Shi
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jianlin Ding
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hongju Tang
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Peng Xu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dongrui Deng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Wanjiang Zeng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Suhua Chen
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Fuyuan Qiao
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ling Feng
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yuanyuan Wu
- Department of Obstetrics and Gynecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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Wang H, Lin X, Lyu G, He S, Dong B, Yang Y. Chromosomal abnormalities in fetuses with congenital heart disease: a meta-analysis. Arch Gynecol Obstet 2023; 308:797-811. [PMID: 36609702 DOI: 10.1007/s00404-023-06910-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 01/01/2023] [Indexed: 01/09/2023]
Abstract
PURPOSE The aim of this meta-analysis was to evaluate the risk of chromosomal abnormalities in fetuses with congenital heart disease (CHD). METHODS Four literature databases were searched until 17th January 2022 using the relevant medical subject heading terms, word variants, and keywords for "congenital heart defect, fetal, and chromosomal abnormalities". The prevalence of overall chromosomal abnormality, aneuploidy, 22q11 deletion, other copy number variants (CNVs), and variants of unknown significance (VOUS) was analyzed. RESULTS 45 studies met the inclusion criteria for the analysis. The pooled proportion of overall chromosomal abnormalities, aneuploidy, 22q11 deletion, and other CNVs in fetuses with CHD was 23% (95% CI: 20-26%), 19% (95% CI, 16-22%), 2% (95% CI, 2-3%), and 4% (95% CI, 3-5%), respectively. The incidence of overall chromosomal abnormalities, aneuploidy, and other CNVs in non-isolated CHD was higher than in isolated CHD, with odds ratios of 3.08, 3.45, and 4.02, respectively. The incidence of overall chromosomal abnormalities in septal defects was higher than in conotruncal defects and other defects, with odds ratios of 1.60 and 3.61, respectively. In addition, the pooled proportion of VOUS in CHD was 4%. CONCLUSION CHD is commonly associated with chromosomal abnormalities. If karyotyping or fluorescence in situ hybridization is normal, chromosomal microarray should be performed to look for submicroscopic abnormalities, especially in fetuses with non-isolated CHD and septal defects.
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Affiliation(s)
- Huaming Wang
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Zhongshan Load, Quanzhou, Fujian, China
| | - Xi Lin
- Department of Diagnostic Radiology, Fujian Cancer Hospital of Fujian Medical University, Fuzhou, Fujian, China
| | - Guorong Lyu
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Zhongshan Load, Quanzhou, Fujian, China.
- Collaborative Innovation Center of Maternal and Child Health Service Technology, Quanzhou Medical College, Quanzhou, China.
| | - Shaozheng He
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Zhongshan Load, Quanzhou, Fujian, China
| | - Bingtian Dong
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Zhongshan Load, Quanzhou, Fujian, China
| | - Yiru Yang
- Department of Ultrasound, The Second Affiliated Hospital of Fujian Medical University, Zhongshan Load, Quanzhou, Fujian, China
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Yue F, Yang X, Jiang Y, Li S, Liu R, Zhang H. Prenatal phenotypes and pregnancy outcomes of fetuses with recurrent 1q21.1 microdeletions and microduplications. Front Med (Lausanne) 2023; 10:1207891. [PMID: 37692779 PMCID: PMC10484100 DOI: 10.3389/fmed.2023.1207891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/19/2023] [Indexed: 09/12/2023] Open
Abstract
Objective Chromosomal 1q21.1 deletions and duplications are genomic disorders that are usually diagnosed postnatally. However, the genotype-phenotype correlations of 1q21.1 copy number variants (CNVs) during the prenatal period are still not clear. This study aimed to provide a systematic summary of prenatal phenotypes for such genomic disorders. Methods In total, 26 prenatal amniotic fluid samples diagnosed with 1q21.1 microdeletions/microduplications were obtained from pregnant women who opted for invasive prenatal testing. Karyotypic analysis and chromosomal microarray analysis (CMA) were performed for all cases simultaneously. The pregnancy outcomes and health conditions after birth in all cases were followed up. Meanwhile, prenatal cases with 1q21.1 microdeletions or microduplications in the literature were retrospectively collected. Results In total, 11 pregnancies (11/8,252, 0.13%) with 1q21.1 microdeletions and 15 (15/8,252, 0.18%) with 1q21.1 microduplications were identified. Among these 1q21.1 CNVs, 4 cases covered the thrombocytopenia-absent radius (TAR) region, 16 cases covered the 1q21.1 recurrent microdeletion/microduplication region, and 6 cases covered all regions mentioned above. The prenatal abnormal ultrasound findings were recorded in four participants with 1q21.1 deletions and seven participants with 1q21.1 duplications. Finally, three cases with 1q21.1 deletions and five with 1q21.1 duplications terminated their pregnancies. Conclusion In the prenatal setting, 1q21.1 microdeletions were associated with increased nuchal translucency (NT), anomalies of the urinary system, and cardiovascular abnormalities, while 1q21.1 microduplications were correlated with cardiovascular malformations, nasal bone dysplasia, and increased NT. In addition, cerebral ventriculomegaly might be correlated with 1q21.1 microduplications. Considering the variable expressivity and incomplete penetrance of 1q21.1 CNVs, long-term follow-up after birth should be carried out in these cases.
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Affiliation(s)
- Fagui Yue
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Xiao Yang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Yuting Jiang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States
| | - Ruizhi Liu
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
| | - Hongguo Zhang
- Center for Reproductive Medicine and Center for Prenatal Diagnosis, First Hospital, Jilin University, Changchun, China
- Jilin Engineering Research Center for Reproductive Medicine and Genetics, Jilin University, Changchun, China
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Chen L, Wang L, Zeng Y, Yin D, Tang F, Xie D, Zhu H, Liu H, Wang J. Defining the scope of extended NIPS in Western China: evidence from a large cohort of fetuses with normal ultrasound scans. BMC Pregnancy Childbirth 2023; 23:593. [PMID: 37598172 PMCID: PMC10439619 DOI: 10.1186/s12884-023-05921-x] [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: 03/10/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023] Open
Abstract
BACKGROUND Standard noninvasive prenatal screening(NIPS) is an accurate and reliable method to screen for common chromosome aneuploidies, such as trisomy 21, 18 and 13. Extended NIPS has been used in clinic for not only aneuploidies but also copy number variants(CNVs). Here we aim to define the range of chromosomal abnormalities that should be able to identify by NIPS in order to be an efficient extended screening test for chromosomal abnormalities. METHODS A prospective study was conducted, involving pregnant women without fetal sonographic structural abnormalities who underwent amniocentesis. Prenatal samples were analyzed using copy number variation sequencing(CNV-seq) to identify fetal chromosomal abnormalities. RESULTS Of 28,469 pregnancies included 1,022 (3.59%) were identified with clinically significant fetal chromosome abnormalities, including 587 aneuploidies (2.06%) and 435 (1.53%) pathogenic (P) / likely pathogenic (LP) CNVs. P/LP CNVs were found in all chromosomes, but the distribution was not uniform. Among them, P/LP CNVs in chromosomes 16, 22, and X exhibited the highest frequencies. In addition, P/LP CNVs were most common on distal ends of the chromosomes and in low copy repeat regions. Recurrent microdeletion/microduplication syndromes (MMS) accounted for 40.69% of total P/LP CNVs. The size of most P/LP CNVs (77.47%) was < 3 Mb. CONCLUSIONS In addition to aneuploidies, the scope of extended NIPS should include the currently known P/LP CNVs, especially the regions with recurrent MMS loci, distal ends of the chromosomes, and low copy repeat regions. To be effective detection should include CNVs of < 3 Mb. Meanwhile, sufficient preclinical validation is still needed to ensure the clinical effect of extended NIPS.
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Affiliation(s)
- Lin Chen
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Li Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Yang Zeng
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Daishu Yin
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Feng Tang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Dan Xie
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Hongmei Zhu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
| | - Hongqian Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, 610041, Chengdu, China
| | - Jing Wang
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, 610041, China.
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, 610041, Chengdu, China.
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Cai M, Guo N, Fu M, Chen Y, Liang B, Que Y, Ji Q, Huang H, Xu L, Lin N. Prenatal diagnosis of genetic aberrations in fetuses with pulmonary stenosis in southern China: a retrospective analysis. BMC Med Genomics 2023; 16:119. [PMID: 37248535 DOI: 10.1186/s12920-023-01548-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
BACKGROUND The genetic etiology of congenital pulmonary stenosis (PS) in fetuses remains inadequately studied. We used karyotype analysis and chromosomal microarray analysis (CMA) to investigate the genetic aberrations associated with PS in human fetuses. METHODS A retrospective analysis was performed on 84 fetuses with congenital PS in southern China. Fetal amniotic fluid and umbilical cord blood samples were obtained for chromosomal karyotype analysis and CMA. RESULTS The rate of pathogenic copy number variation (CNV) was 15.5% (13/84) after karyotyping and CMA. An abnormal karyotype was detected in five cases (6.0%, 5/84) via karyotyping, whereas pathogenic CNVs were detected in 13 cases (15.5%, 13/84) via CMA. In addition to the five abnormal karyotypes detected using karyotype analysis, eight additional chromosomal microduplications and microdeletions were detected using CMA, comprising three cases of 22q11.21 microdeletion; two cases of 16p11.2 microdeletion; one case of simultaneous 18q23 microdeletion and 22q13.33 microduplication; one case of 15q24.1q24.2 microdeletion; and one case of 1q21.1q21.2 microduplication. The rate of pathogenic CNV occurrence was 11.5% in fetuses with isolated PS and 17.2% in fetuses with PS combined with other ultrasound abnormalities. This difference between the two experimental groups was statistically significant. Among 84 fetuses with PS, 39 pregnancies were terminated, and five were lost to follow-up. CONCLUSIONS CMA was not only conducive to detect PS-related pathogenic genomic abnormalities but also to accurately evaluate fetal prognosis in genetic counseling. The early detection of PS and genomic abnormalities will exerta positive impact on fetal intervention and the related prognosis of PS in perinatal infants.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Nan Guo
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meimei Fu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuqing Chen
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Bin Liang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yanting Que
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Qingqiang Ji
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China.
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9
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Yu X, Tao Y, Liu X, Yu F, Jiang C, Xiao Y, Zhang H, He Y, Ye L, Wang Y, Zhou C, Wang J, Jiang Z, Hong H. The implication of chromosomal abnormalities in the surgical outcomes of Chinese pediatric patients with congenital heart disease. Front Cardiovasc Med 2023; 10:1164577. [PMID: 37293289 PMCID: PMC10244782 DOI: 10.3389/fcvm.2023.1164577] [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: 02/13/2023] [Accepted: 04/05/2023] [Indexed: 06/10/2023] Open
Abstract
Background Copy number variations (CNVs) have been shown to be overrepresented in children with congenital heart disease (CHD). Genetic evaluation of CHD is currently underperformed in China. We sought to determine the occurrence of CNVs in CNV regions with disease-causing potential among a large cohort of Chinese pediatric CHD patients and investigate whether these CNVs could be the important critical modifiers of surgical intervention. Methods CNVs screenings were performed in 1,762 Chinese children who underwent at least one cardiac surgery. CNV status at over 200 CNV locus with disease-causing potential was analyzed with a high-throughput ligation-dependent probe amplification (HLPA) assay. Results We found 378 out of 1,762 samples (21.45%) to have at least one CNV and 2.38% of them were carrying multiple CNVs. The detection rates of ppCNVs (pathogenic and likely pathogenic CNVs) were 9.19% (162/1,762), significantly higher than that of the healthy Han Chinese individuals from The Database of Genomic Variants archive (9.19% vs. 3.63%; P = 0.0012). CHD cases with ppCNVs had a significantly higher proportion of complex surgeries compared to CHD patients with no ppCNVs (62.35% vs. 37.63%, P < 0.001). Duration of cardiopulmonary bypass and aortic cross clamp procedures were significantly longer in CHD cases with ppCNVs (all P < 0.05), while no group differences were identified for complications of surgery and one-month mortality after surgery. The detection rate of ppCNVs in the atrioventricular septal defect (AVSD) subgroup was significantly higher than that in other subgroups (23.10% vs. 9.70%, P = 0.002). Conclusions CNV burden is an important contributor to Chinese children with CHD. Our study demonstrated the robustness and diagnostic efficiency of HLPA method in the genetic screening of CNVs in CHD patients.
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Affiliation(s)
- Xiafeng Yu
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yu Tao
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Xu Liu
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Feng Yu
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Chuan Jiang
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yingying Xiao
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Haibo Zhang
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yongrui He
- Institute of Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Lincai Ye
- Institute of Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Ying Wang
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Chunxia Zhou
- Department of Cardiothoracic Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Jian Wang
- Department of Medical Genetics and Molecular Diagnostic Laboratory, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Zhengwen Jiang
- Department of Genetics, Genesky Biotechnologies Inc., Shanghai, China
| | - Haifa Hong
- Institute of Pediatric Congenital Heart Disease, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
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Lü Y, Jiang Y, Zhou X, Hao N, Lü G, Guo X, Guo R, Liu W, Xu C, Chang J, Li M, Zhang H, Zhou J, Zhang W(V, Qi Q. Evaluation and Analysis of Absence of Homozygosity (AOH) Using Chromosome Analysis by Medium Coverage Whole Genome Sequencing (CMA-seq) in Prenatal Diagnosis. Diagnostics (Basel) 2023; 13:diagnostics13030560. [PMID: 36766665 PMCID: PMC9914714 DOI: 10.3390/diagnostics13030560] [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: 12/14/2022] [Revised: 01/29/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE Absence of homozygosity (AOH) is a genetic characteristic known to cause human diseases mainly through autosomal recessive or imprinting mechanisms. The importance and necessity of accurate AOH detection has become more clinically significant in recent years. However, it remains a challenging task for sequencing-based methods thus far. METHODS In this study, we developed and optimized a new bioinformatic algorithm based on the assessment of minimum sequencing coverage, optimal bin size, the Z-score threshold of four types of allele count and the frequency for accurate genotyping using 28 AOH negative samples, and redefined the AOH detection cutoff value. We showed the performance of chromosome analysis by five-fold coverage whole genome sequencing (CMA-seq) for AOH identification in 27 typical prenatal/postnatal AOH positive samples, which were previously confirmed by chromosomal microarray analysis with single nucleotide polymorphism array (CMA/SNP array). RESULTS The blinded study indicated that for all three forms of AOH, including whole genomic AOH, single chromosomal AOH and segmental AOH, and all kinds of sample types, including chorionic villus sampling, amniotic fluid, cord blood, peripheral blood and abortive tissue, CMA-seq showed equivalent detection power to that of routine CMA/SNP arrays (750K). The subtle difference between the two methods is that CMA-seq is prone to detect small inconsecutive AOHs, while CMA/SNP array reports it as a whole. CONCLUSION Based on our newly developed bioinformatic algorithm, it is feasible to detect clinically significant AOH using CMA-seq in prenatal diagnosis.
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Affiliation(s)
- Yan Lü
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Yulin Jiang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Xiya Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Na Hao
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Guizhen Lü
- AmCare Genomics Lab, Guangzhou 510335, China
| | | | - Ruidong Guo
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Wenjie Liu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Chenlu Xu
- AmCare Genomics Lab, Guangzhou 510335, China
| | - Jiazhen Chang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Mengmeng Li
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Hanzhe Zhang
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Jing Zhou
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
| | | | - Qingwei Qi
- Department of Obstetrics and Gynecology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Beijing 100730, China
- Correspondence: ; Tel.: +86-1851-066-6066
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11
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Vedel C, Hjortshøj TD, Jørgensen DS, Tabor A, Rode L, Sundberg K, Ekelund CK, Petersen OB. Prevalence of chromosomal disorders in cases with congenital heart defect: registry-based study from Denmark between 2008 and 2018. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2023; 61:40-48. [PMID: 36099538 PMCID: PMC10107356 DOI: 10.1002/uog.26075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 08/08/2022] [Accepted: 09/02/2022] [Indexed: 05/27/2023]
Abstract
OBJECTIVE To estimate the prevalence of chromosomal conditions in all fetuses and children with major congenital heart defect (CHD) in Denmark between 2008 and 2018. METHODS This was a national registry-based study including all singleton pregnancies with a prenatally or postnatally diagnosed major CHD usually requiring surgery within the first year after birth and a due date between July 2008 and December 2018 in Denmark. Data were retrieved from the Danish Fetal Medicine Database (DFMD) and the Danish Cytogenetic Central Register (DCCR) in October 2020. The DCCR contains information on all prenatal and postnatal genetic analyses, including karyotyping, chromosomal microarray, polymerase chain reaction, multiplex ligation-dependent probe amplification and fluorescence in-situ hybridization. All cases were reviewed by a clinical geneticist, and genetic changes were classified as pathogenic, likely pathogenic, variant of uncertain significance, likely benign or benign. Pathogenic and likely pathogenic variants were considered to be abnormal. Cases with CHD without any registered chromosomal analysis reported were considered genetically normal. Isolated CHD was defined as a case with major CHD without any other structural malformations detected prenatally or postnatally. Results are given as n (%). Comparisons between isolated and non-isolated cases were performed using logistic regression analysis, and data are presented as odds ratios (ORs) with 95% CIs. RESULTS A total of 8482 cases with any cardiovascular diagnosis were retrieved from the DFMD. Twins (n = 112) and minor CHD cases (n = 6921) were excluded, resulting in 1449 cases with major CHD. Of the included cases, 918 (63.4%) underwent chromosomal analysis. An abnormal test result was found in 187 cases, giving a prevalence of a chromosomal condition of 12.9% (95% CI, 11.2-14.7%) among all cases with major CHD. The highest prevalence of a chromosomal condition was found in cases with pulmonary atresia with intact ventricular septum and those with truncus arteriosus (both 28.6%), while the lowest prevalence was found in cases with transposition of the great arteries (2.2%) and congenitally corrected transposition of the great arteries (0%). In isolated cases of transposition of the great arteries, the prevalence of a chromosomal condition was 0.6%. The overall OR for a chromosomal condition in non-isolated cases compared with isolated cases was 2.72 (95% CI, 1.90-3.88). CONCLUSIONS We found an overall prevalence of a chromosomal condition of 12.9% among cases with major CHD in a national cohort with a high participation rate in first- and second-trimester screening, without employing whole genome and whole exome sequencing. The prevalence of a chromosomal condition varied considerably according to CHD diagnosis and presence of associated extracardiac malformations. These findings are important for prenatal counseling. © 2022 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- C. Vedel
- Department of Obstetrics, Center of Fetal Medicine and PregnancyCopenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - T. D. Hjortshøj
- Department of Clinical GeneticsCopenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - D. S. Jørgensen
- Department of Obstetrics, Center of Fetal Medicine and PregnancyCopenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - A. Tabor
- Department of Obstetrics, Center of Fetal Medicine and PregnancyCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Department of Clinical MedicineCopenhagen UniversityCopenhagenDenmark
| | - L. Rode
- Department of Clinical BiochemistryCopenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - K. Sundberg
- Department of Obstetrics, Center of Fetal Medicine and PregnancyCopenhagen University Hospital RigshospitaletCopenhagenDenmark
| | - C. K. Ekelund
- Department of Obstetrics, Center of Fetal Medicine and PregnancyCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Department of Clinical MedicineCopenhagen UniversityCopenhagenDenmark
| | - O. B. Petersen
- Department of Obstetrics, Center of Fetal Medicine and PregnancyCopenhagen University Hospital RigshospitaletCopenhagenDenmark
- Department of Clinical MedicineCopenhagen UniversityCopenhagenDenmark
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12
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Yi T, Hao X, Sun H, Zhang Y, Han J, Gu X, Sun L, Liu X, Zhao Y, Guo Y, Zhou X, He Y. Genetic aetiology distribution of 398 foetuses with congenital heart disease in the prenatal setting. ESC Heart Fail 2022; 10:917-930. [PMID: 36478645 PMCID: PMC10053168 DOI: 10.1002/ehf2.14209] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/24/2022] [Accepted: 10/02/2022] [Indexed: 12/12/2022] Open
Abstract
AIMS Copy number variant-sequencing (CNV-seq) and exome sequencing (ES) have been used as powerful tools in understanding the role of genetic variants in congenital heart diseases (CHDs). A few previous large cohort studies have utilized CNV-seq and ES to investigate prenatally diagnosed CHD. Here, we sought to determine the value of CNV-seq and ES for genetic evaluation of foetal CHDs. METHODS AND RESULTS We recruited 398 pregnant women diagnosed with CHDs between 8 January 2017 and 30 November 2020. CNV-seq and ES were performed on foetal and parent samples. CHD cases were classified following the guidelines of the International Paediatric and Congenital Cardiac Code and the Tenth and Eleventh Revisions of the International Classification of Diseases. Data on aneuploids (AUP), pathogenic CNVs (pCNVs), and single nucleotide variants (SNVs) were collected and compared, following appropriate procedures. We identified genetic abnormalities in 129 (32.41%) foetuses. These abnormalities included AUP (10.80%), pCNVs (13.32%), and SNVs (8.04%). ES analysis yielded higher SNVs in cases without AUP or pCNVs. Non-isolated CHDs were associated with higher genetic abnormalities than isolated CHDs, mainly due to AUP differences between the two groups. The prevalence of genetic defects was the highest in foetuses with atrioventricular septal defects (AVSD), left ventricular outflow tract obstruction (LVOTO), and conotruncal defects (CTD). AVSD and anomalies of atrioventricular junctions and valves were associated with AUP abnormalities. CTD, anomalies of extrapericardial arterial trunks, and anomalies of the ventricular outflow tracts were the most common CHD categories diagnosed using CNVs. The most common CHDs associated with single ventricle (SV) abnormalities were heterotaxy (Hex) (14.89%), LVOTO (14.58%), and ventricular septal defect (VSD) (26.67%, 4/15). Although the ES yields were higher than CNV-seq for VSD (44.4%, 4/9), LVOTO (20%, 7/35), Hex (14.89%, 7/47), and CTD (9.1%, 11/121), its diagnostic yield did not increase for SV (6.7%, 1/15), AVSD (3.8%, 1/26), or right ventricular obstruction defects (2.6%, 1/38). The most common mutations were observed in KMT2D, CHD7, and NOTCH1. CONCLUSIONS To our knowledge, this is the largest cohort study to investigate the incidence of SNVs using ES in foetal CHD. CNV-seq and ES identified genetic abnormalities in nearly 1/3 of foetal CHD cases. Thus, CNV-seq and ES can provide clinically relevant information for pregnancy management.
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Affiliation(s)
- Tong Yi
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Xiaoyan Hao
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Hairui Sun
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Ye Zhang
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Jiancheng Han
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Xiaoyan Gu
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Lin Sun
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Xiaowei Liu
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Ying Zhao
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Yong Guo
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Xiaoxue Zhou
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
| | - Yihua He
- Beijing Key Laboratory of Maternal‐Fetal Medicine and Fetal Heart Disease Capital Medical University Affiliated Anzhen Hospital Beijing China
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Zhang S, Xu Y, Lu D, Fu D, Zhao Y. Combined use of karyotyping and copy number variation sequencing technology in prenatal diagnosis. PeerJ 2022; 10:e14400. [PMID: 36523456 PMCID: PMC9745786 DOI: 10.7717/peerj.14400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 10/25/2022] [Indexed: 12/12/2022] Open
Abstract
Background Karyotyping and genome copy number variation sequencing (CNV-seq) are two techniques frequently used in prenatal diagnosis. This study aimed to explore the diagnostic potential of using a combination of these two methods in order to provide a more accurate clinical basis for prenatal diagnosis. Methods We selected 822 pregnant women undergoing amniocentesis and separated them into six groups according to different risk indicators. Karyotyping and CNV-seq were performed simultaneously to compare the diagnostic performance of the two methods. Results Among the different amniocentesis indicators, abnormal fetal ultrasounds accounted for 39.29% of the total number of examinees and made up the largest group. The abnormal detection rate of non-invasive prenatal testing (NIPT) high risk was 37.93% and significantly higher than the other five groups (P < 0.05). The abnormal detection rate of mixed indicators was significantly higher than the history of the adverse reproductive outcomes group (P = 0.0151). The two methods combined found a total of 119 abnormal cases (14.48%). Karyotyping detected 57 cases (6.93%) of abnormal karyotypes, 30 numerical aberrations, and 27 structural aberrations. CNV-seq identified 99 cases (12.04%) with altered CNVs, 30 cases of chromosome aneuploidies, and 69 structural aberrations (28 pathogenic, eight that were likely pathogenic, and 33 microdeletion/duplication variants of uncertain significance (VUS)). Thirty-seven cases were found abnormal by both methods, 20 cases were detected abnormally by karyotyping (mainly mutual translocation and mostly balanced), and 62 cases of microdeletion/duplication were detected by CNV-seq. Steroid sulfatase gene (STS) deletion was identified at chromosome Xp22.31 in three cases. Postnatal follow-up confirmed that babies manifested skin abnormalities one week after birth. Six fetuses had Xp22.31 duplications ranging from 1.5 Kb to 1.7 Mb that were detected by CNV-seq. Follow-up showed that five babies presented no abnormalities during follow-up, except for one terminated pregnancy due to a history of adverse reproductive outcomes. Conclusion The combination of using CNV-seq and karyotyping significantly improved the detection rate of fetal pathogenic chromosomal abnormalities. CNV-seq is an effective complement to karyotyping and improves the accuracy of prenatal diagnosis.
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Affiliation(s)
- Suhua Zhang
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Yuexin Xu
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Dan Lu
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Dan Fu
- Department of Gynaecology and Obstetrics, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
| | - Yan Zhao
- Medical Research Center, Clinical Medical College of Yangzhou University, Northern Jiangsu People’s Hospital, Yang Zhou, Jiangsu Province, China
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Wójtowicz A, Madetko-Talowska A, Wójtowicz W, Szewczyk K, Huras H, Bik-Multanowski M. Cardiovascular Anomalies among 1005 Fetuses Referred to Invasive Prenatal Testing-A Comprehensive Cohort Study of Associated Chromosomal Aberrations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10019. [PMID: 36011653 PMCID: PMC9408756 DOI: 10.3390/ijerph191610019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/06/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
This retrospective cohort study comprehensively evaluates cardiovascular anomalies (CVAs) and associated extracardiac structural malformations (ECMs) among 1005 fetuses undergoing invasive prenatal testing at a single tertiary Polish center in the context of chromosomal aberrations detected in them by array comparative genomic hybridization (aCGH) and G-band karyotyping. The results of our study show that CVAs are among the most common malformations detected in fetuses undergoing invasive prenatal testing, as they affected 20% of all cases seen in our department. Septal defects predominated among fetuses with numerical aberrations, while conotruncal defects were the most common findings among fetuses with pathogenic copy number variants (CNVs). In 61% of cases, CVAs were associated with ECMs (the diagnosis was confirmed postnatally or in cases of pregnancy termination by means of autopsy). The most common ECMs were anomalies of the face and neck, followed by skeletal defects. In total, pathogenic chromosomal aberrations were found in 47.5% of CVAs cases, including 38.6% with numerical chromosomal aberrations. Pathogenic CNVs accounted for 14.5% of cases with CVAs and normal karyotype. Thus, our study highlights the importance of assessing the anatomy of the fetus, and of the genetic testing (preferably aCGH) that should be offered in all CVA and ECM cases.
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Affiliation(s)
- Anna Wójtowicz
- Department of Obstetrics & Perinatology, Jagiellonian University Medical College, 31-501 Kraków, Poland
| | - Anna Madetko-Talowska
- Department of Medical Genetics, Jagiellonian University Medical College, 30-663 Kraków, Poland
| | - Wojciech Wójtowicz
- Information Technology Systems Department, Faculty of Management and Social Communication, Jagiellonian University, 30-348 Kraków, Poland
| | - Katarzyna Szewczyk
- Department of Medical Genetics, Jagiellonian University Medical College, 30-663 Kraków, Poland
| | - Hubert Huras
- Department of Obstetrics & Perinatology, Jagiellonian University Medical College, 31-501 Kraków, Poland
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15
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Cao J, Chen A, Tian L, Yan L, Li H, Zhou B. Application of whole exome sequencing in fetal cases with skeletal abnormalities. Heliyon 2022; 8:e09819. [PMID: 35855989 PMCID: PMC9287157 DOI: 10.1016/j.heliyon.2022.e09819] [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: 10/17/2021] [Revised: 01/11/2022] [Accepted: 06/24/2022] [Indexed: 11/18/2022] Open
Abstract
Objectives To investigate the role of whole exome sequencing (WES) technology in fetuses with skeletal abnormalities (SKA) for establishing an appropriate clinical diagnosis and treatment path. Methods From April 2019 to August 2020, eight special families were enrolled into the study. Their fetuses showed abnormal SKA by ultrasonic testing during pregnancy, but it is inconsistent with the normal results identified by chromosomal microarray analysis (CMA) of amniotic fluid or abortion. For further diagnosis, WES was performed to detect the causative genes mutations followed by Sanger sequencing. Results Among of these eight fetuses with SKA, we found more than half of pathogenic mutations were in COL1A1/2 gene, except for a known hotspot mutation in FGFR3 gene (c.1138G>A). Three heterozygous mutations of COL1A1 gene, c.2885G>A p (Gly962Asp), c.994G>A p (Gly332Arg) and c.1002 + 5G>T, were de novo mutations. The c.1002 + 5G>T mutation in COL1A1 was firstly reported. In addition, one fetus carried a novel heterozygous mutation of COL1A1 c.644G>A p (Gly215Asp), which was inherited from the mother. Another novel heterozygous mutation c.2482G>T p (Val828Phe) in the COL1A2 gene was identified in another fetus and was inherited from the father. Among of these COL1A1 mutations, these results might involve in two novel splicing mutations. Conclusion Our study reported several novel heterozygous mutations which expands the COL1A1/2 mutation spectrum for prenatal diagnosis of SKA. Most importantly, WES technology is necessary as a routine step of the SKA diagnosis before or during pregnancy, combining with the detection of chromosome level.
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Affiliation(s)
- Juan Cao
- Ningbo Women and Children Healthcare Center, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315-12, China
| | - An'er Chen
- Ningbo Women and Children Healthcare Center, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315-12, China
| | - Liyun Tian
- Ningbo Women and Children Healthcare Center, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315-12, China
| | - Lulu Yan
- Ningbo Women and Children Healthcare Center, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315-12, China
| | - Haibo Li
- Ningbo Women and Children Healthcare Center, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315-12, China
| | - Bihua Zhou
- Ningbo Women and Children Healthcare Center, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, 315-12, China
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16
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Hsiao CH, Chen JS, Shiao YM, Chen YJ, Chen CH, Chu WC, Wu YC. Prenatal Diagnosis Using Chromosomal Microarray Analysis in High-Risk Pregnancies. J Clin Med 2022; 11:jcm11133624. [PMID: 35806909 PMCID: PMC9267905 DOI: 10.3390/jcm11133624] [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: 05/13/2022] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 12/03/2022] Open
Abstract
Background: To assess the value of chromosomal microarray analysis (CMA) during the prenatal diagnosis of high-risk pregnancies. Methods: Between January 2016 and November 2021, we included 178 chorionic villi and 859 amniocentesis samples from consecutive cases at a multiple tertiary hospital. Each of these high-risk singleton pregnancies had at least one of the following indications: (1) advanced maternal age (AMA; ≥35 years; 546, 52.7%); (2) fetal structural abnormality on ultrasound (197, 19.0%); (3) high-risk first- or second-trimester Down syndrome screen (189, 18.2%), including increased nuchal translucency (≥3.5 mm; 90, 8.7%); or (4) previous pregnancy, child, or family history (105, 10.1%) affected by chromosomal abnormality or genetic disorder. Both G-banding karyotype analysis and CMA were performed. DNA was extracted directly and examined with oligonucleotide array-based comparative genomic hybridization. Results: Aneuploidies were detected by both G-banding karyotyping and CMA in 42/1037 (4.05%) cases. Among the 979 cases with normal karyotypes, 110 (10.6%) cases had copy number variants (CNVs) in CMA, including 30 (2.9%) cases with reported pathogenic and likely pathogenic CNVs ≥ 400 kb, 37 (3.6%) with nonreported VOUS, benign, or likely benign CNVs ≥ 400 kb, and 43 (4.1%) with nonreported CNVs < 400 kb. Of the 58 (5.6%) cases with aneuploidy rearrangements, 42 (4.1%) were diagnosed by both G-banding karyotyping and CMA; four inversions, six balanced translocations, and six low mosaic rates were not detected with CMA. Conclusions: CMA is an effective first step for the prenatal diagnosis of high-risk pregnancies with fetal structural anomalies found in ultrasonography or upon positive findings.
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Affiliation(s)
- Ching-Hua Hsiao
- Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-C.C.); (Y.-C.W.)
- Department of Obstetrics and Gynecology, Taipei City Hospital, Women and Children Campus, Taipei 100, Taiwan;
- Correspondence: or ; Tel.: +886-2-28267025; Fax: +886-2-28210847
| | - Jia-Shing Chen
- School of Medicine for International Students, I-Shou University, Kaohsiung 840, Taiwan;
| | - Yu-Ming Shiao
- Department of Bioscience Technology, Chung Yuan Christian University, Taoyuan 320, Taiwan;
- Union Clinical Laboratory, Taipei 106, Taiwan
| | - Yann-Jang Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang Ming Chiao Tung University, Taipei 112, Taiwan;
| | - Ching-Hsuan Chen
- Department of Obstetrics and Gynecology, Taipei City Hospital, Women and Children Campus, Taipei 100, Taiwan;
| | - Woei-Chyn Chu
- Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-C.C.); (Y.-C.W.)
| | - Yi-Cheng Wu
- Department of Biomedical Engineering, National Yang Ming Chiao Tung University, Taipei 112, Taiwan; (W.-C.C.); (Y.-C.W.)
- Department of Obstetrics and Gynecology, Ultrasound Center of Taiwan IVF Group, Ton-Yen General Hospital, Zhubei 302, Taiwan
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17
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Mastromoro G, Khaleghi Hashemian N, Guadagnolo D, Giuffrida MG, Torres B, Bernardini L, Ventriglia F, Piacentini G, Pizzuti A. Chromosomal Microarray Analysis in Fetuses Detected with Isolated Cardiovascular Malformation: A Multicenter Study, Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:diagnostics12061328. [PMID: 35741137 PMCID: PMC9221891 DOI: 10.3390/diagnostics12061328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 12/10/2022] Open
Abstract
Cardiovascular malformations (CVM) represent the most common structural anomalies, occurring in 0.7% of live births. The CVM prenatal suspicion should prompt an accurate investigation with fetal echocardiography and the assessment through genetic counseling and testing. In particular, chromosomal microarray analysis (CMA) allows the identification of copy number variations. We performed a systematic review and meta-analysis of the literature, studying the incremental diagnostic yield of CMA in fetal isolated CVM, scoring yields for each category of heart disease, with the aim of guiding genetic counseling and prenatal management. At the same time, we report 59 fetuses with isolated CVM with normal karyotype who underwent CMA. The incremental CMA diagnostic yield in fetuses with isolated CVM was 5.79% (CI 5.54–6.04), with conotruncal malformations showing the higher detection rate (15.93%). The yields for ventricular septal defects and aberrant right subclavian artery were the lowest (2.64% and 0.66%). Other CVM ranged from 4.42% to 6.67%. In the retrospective cohort, the diagnostic yield was consistent with literature data, with an overall CMA diagnostic yield of 3.38%. CMA in the prenatal setting was confirmed as a valuable tool for investigating the causes of fetal cardiovascular malformations.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (N.K.H.); (D.G.); (A.P.)
- Correspondence:
| | - Nader Khaleghi Hashemian
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (N.K.H.); (D.G.); (A.P.)
| | - Daniele Guadagnolo
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (N.K.H.); (D.G.); (A.P.)
| | - Maria Grazia Giuffrida
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, 71013 San Giovanni Rotondo, Italy; (M.G.G.); (B.T.); (L.B.)
| | - Barbara Torres
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, 71013 San Giovanni Rotondo, Italy; (M.G.G.); (B.T.); (L.B.)
| | - Laura Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, 71013 San Giovanni Rotondo, Italy; (M.G.G.); (B.T.); (L.B.)
| | - Flavia Ventriglia
- Department of Pediatrics, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy;
- Santa Maria Goretti Hospital, 04100 Latina, Italy
| | - Gerardo Piacentini
- Fetal and Pediatric Cardiology Unit, “San Giovanni Calibita” Fatebenefratelli Isola Tiberina Hospital, 00186 Rome, Italy;
- Neonatology and Neonatal Intensive Care Unit, “San Giovanni Calibita” Fatebenefratelli Isola Tiberina Hospital, 00186 Rome, Italy
| | - Antonio Pizzuti
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (N.K.H.); (D.G.); (A.P.)
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18
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Mastromoro G, Guadagnolo D, Khaleghi Hashemian N, Marchionni E, Traversa A, Pizzuti A. Molecular Approaches in Fetal Malformations, Dynamic Anomalies and Soft Markers: Diagnostic Rates and Challenges-Systematic Review of the Literature and Meta-Analysis. Diagnostics (Basel) 2022; 12:575. [PMID: 35328129 PMCID: PMC8947110 DOI: 10.3390/diagnostics12030575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Fetal malformations occur in 2-3% of pregnancies. They require invasive procedures for cytogenetics and molecular testing. "Structural anomalies" include non-transient anatomic alterations. "Soft markers" are often transient minor ultrasound findings. Anomalies not fitting these definitions are categorized as "dynamic". This meta-analysis aims to evaluate the diagnostic yield and the rates of variants of uncertain significance (VUSs) in fetuses undergoing molecular testing (chromosomal microarray (CMA), exome sequencing (ES), genome sequencing (WGS)) due to ultrasound findings. The CMA diagnostic yield was 2.15% in single soft markers (vs. 0.79% baseline risk), 3.44% in multiple soft markers, 3.66% in single structural anomalies and 8.57% in multiple structural anomalies. Rates for specific subcategories vary significantly. ES showed a diagnostic rate of 19.47%, reaching 27.47% in multiple structural anomalies. WGS data did not allow meta-analysis. In fetal structural anomalies, CMA is a first-tier test, but should be integrated with karyotype and parental segregations. In this class of fetuses, ES presents a very high incremental yield, with a significant VUSs burden, so we encourage its use in selected cases. Soft markers present heterogeneous CMA results from each other, some of them with risks comparable to structural anomalies, and would benefit from molecular analysis. The diagnostic rate of multiple soft markers poses a solid indication to CMA.
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Affiliation(s)
- Gioia Mastromoro
- Department of Experimental Medicine, Policlinico Umberto I Hospital, Sapienza University of Rome, 00161 Rome, Italy; (D.G.); (N.K.H.); (E.M.); (A.T.); (A.P.)
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19
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Salzer-Sheelo L, Polak U, Barg A, Kahana S, Yacobson S, Agmon-Fishman I, Klein C, Matar R, Rurman-Shahar N, Sagi-Dain L, Basel-Salmon L, Maya I, Sukenik-Halevy R. Prenatal and postnatal chromosomal microarray analysis in 885 cases of various congenital heart defects. Arch Gynecol Obstet 2022; 306:1007-1013. [PMID: 35083553 DOI: 10.1007/s00404-021-06366-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
PURPOSE This study aimed to evaluate the prevalence of clinically significant (pathogenic and likely pathogenic) variants detected by chromosomal microarray (CMA) tests performed for prenatally and postnatally detected congenital heart defects. METHODS A retrospective evaluation of CMA analyses over a period of four years in a single tertiary medical center was performed. Detection rate of clinically significant variants was calculated in the whole cohort, prenatal vs. postnatal cases, and isolated vs. non-isolated CHD. This rate was compared to previously published control cohorts, and to a theoretical detection rate of noninvasive prenatal testing (NIPS; 5 chromosomes). RESULTS Of the 885 cases of CHD, 111 (12.5%) clinically significant variants were detected, with no significant difference between the 498 prenatal and the 387 postnatal cases (10.8% vs. 14.7%, p = 0.08). In both groups, the detection rate was significantly higher for non-isolated vs. isolated CHD (76/339 = 22.4% vs. 35/546 = 6.4%, respectively, p < 0.05). The detection rate was higher than the background risk in both groups, including cases of postnatal isolated CHD. 44% of abnormal findings in the prenatal setting would be detectable by NIPS. CONCLUSION CMA should be performed for both prenatally and postnatally detected CHD, including postnatal cases of isolated CHD, while NIPS can be considered in specific scenarios.
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Affiliation(s)
- Liat Salzer-Sheelo
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel. .,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Uri Polak
- Pediatric Cardiac Critical Care Unit, Hadassah University Medical Center, Ein Kerem, Jerusalem, Israel.,Pediatric Cardiology, Hadassah University Medical Center, Ein Kerem, Jerusalem, Israel.,The Hebrew University Hadassah Medical School, Jerusalem, Israel
| | | | - Sarit Kahana
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel
| | - Shiri Yacobson
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel
| | - Ifaat Agmon-Fishman
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel
| | - Cochava Klein
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel
| | - Reut Matar
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel
| | - Noa Rurman-Shahar
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel
| | - Lena Sagi-Dain
- Genetics Institute, Carmel Medical Center, Affiliated To the Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa, Israel
| | - Lina Basel-Salmon
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel.,Pediatric Genetics Unit, Schneider Children's Medical Center, Petah Tikva, Israel
| | - Idit Maya
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Rivka Sukenik-Halevy
- The Raphael Recanati Genetic Institute, Rabin Medical Center, 49100, Petah Tikva, Israel.,Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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20
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Zhang T, Yuan H, Zhu H, Ying Y, Ding J, Ding H, Shi X, He Y, Pan H, Zhong Y. Fetal Congenital Heart Disease Caused by Compound Heterozygous Mutations in the DNAH9 Gene: A Case Report. Front Genet 2022; 12:771756. [PMID: 35116053 PMCID: PMC8804278 DOI: 10.3389/fgene.2021.771756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 12/20/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Fetal congenital heart disease (CHD) is the most common congenital defect, with an incidence of 0.6–0.8%, accounting for 30–50% of infant congenital disease deaths. The pathogenesis of CHD is still unclear, so an active and effective prenatal diagnosis is very important for the prevention and control of CHD. Herein, a Chinese CHD patient with rare compound heterozygous mutations in the DNAH9 gene was reported, and the 3D structure and functional changes of DNAH9 protein were predicted.Case presentation: A 23-year-old pregnant woman came to our hospital for prenatal diagnosis at 27 weeks of gestation. Both she and her partner were unaffected. Fetal CHD was detected by ultrasound screening. Copy number variation sequencing (CNV-seq) revealed an 81 kb deletion at chr17p12 (11,486,795–11,568,385), including exons 1–15 of DNAH9 gene, which plays a key role in cardiac development. Then, whole exome sequencing (WES) was used and identified a nonsense mutation (c.10975C>T) in DNAH9, which resulted in the mutation of amino acid 3,659 from glutamine to termination. The 3D mutant protein structures were predicted using SWISS-MODEL and showed structural changes from functional β-sheet and α-helix to termination, respectively.Conclusion: We describe a case of fetal CHD caused by DNAH9 mutations and provide an effective diagnostic technique for identifying intragenic deletions. This diagnostic process can be implicated in prenatal diagnosis of CHD.
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Affiliation(s)
- Tao Zhang
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Hua Yuan
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Hongdan Zhu
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yuyi Ying
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Jinlong Ding
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Haigang Ding
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Xiaoliang Shi
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Yao He
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
| | - Haitao Pan
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
- *Correspondence: Haitao Pan, ; Yongxing Zhong,
| | - Yongxing Zhong
- Shaoxing Maternity and Child Health Care Hospital, Shaoxing, China
- Obstetrics and Gynecology Hospital of Shaoxing University, Shaoxing, China
- *Correspondence: Haitao Pan, ; Yongxing Zhong,
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21
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Zhang Z, Hu T, Wang J, Hu R, Li Q, Xiao L, Liao N, Liu Z, Wang H, Liu S. Pregnancy outcomes of fetuses with congenital heart disease after a prenatal diagnosis with chromosome microarray. Prenat Diagn 2021; 42:79-86. [PMID: 34918366 DOI: 10.1002/pd.6078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 12/30/2022]
Abstract
OBJECTIVE To evaluate the pregnancy outcomes of fetuses with congenital heart disease (CHD) after chromosome microarray (CMA)-based prenatal diagnosis. METHOD Amniocentesis was performed in 1035 pregnant women carrying fetuses with CHD between September 2014 and December 2019. Chromosomal aberrations in fetuses with CHD were evaluated using CMA. The pregnancy outcomes were followed up from 6 months to 5 years. RESULTS The overall CHD detection rate by CMA was 10.1% (105/1035; 50 fetuses: aneuploidy, 55 fetuses: pathogenic or likely pathogenic copy number variations). Among 1003 fetuses who were followed up, 4, 236, 763, and 18 cases were of miscarriages, pregnancy termination, live births, and postnatal deaths, respectively. Self-healed CHD was observed in 401 (52.6%) fetuses. The pregnancy termination rate of fetuses with chromosomal anomalies was significantly higher than that of fetuses without chromosomal anomalies (93.1% vs. 15.5%, p < 0.001). However, other pregnancy outcomes, including mortality, preterm labor, and low-weight birth rate, were similar between the two groups. CONCLUSION The outcome of CMA is an important factor influencing parents' choice of whether to continue the pregnancy. Self-healing rate of prenatal diagnosed CHD is high. The mortality and morbidity of fetuses with CHD following prenatal CMA testing are relatively low.
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Affiliation(s)
- Zhu Zhang
- 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
| | - 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
| | - Jiamin Wang
- 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
| | - Rui 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
| | - Qinqin Li
- 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
| | - Like Xiao
- 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
| | - Na Liao
- 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
| | - Zhushu 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
| | - He Wang
- 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
| | - Shanling 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
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22
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Qiao F, Wang Y, Zhang C, Zhou R, Wu Y, Wang C, Meng L, Mao P, Cheng Q, Luo C, Hu P, Xu Z. Comprehensive evaluation of genetic variants using chromosomal microarray analysis and exome sequencing in fetuses with congenital heart defect. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:377-387. [PMID: 33142350 DOI: 10.1002/uog.23532] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To evaluate comprehensively, using chromosomal microarray analysis (CMA) and exome sequencing (ES), the prevalence of chromosomal abnormalities and sequence variants in unselected fetuses with congenital heart defect (CHD) and to evaluate the potential diagnostic yields of CMA and ES for different CHD subgroups. METHODS This was a study of 360 unselected singleton fetuses with CHD detected by echocardiography, referred to our department for genetic testing between February 2018 and December 2019. We performed CMA, as a routine test for aneuploidy and copy number variations (CNV), and then, in cases without aneuploidy or pathogenic CNV on CMA, we performed ES. RESULTS Overall, positive genetic diagnoses were made in 84 (23.3%) fetuses: chromosomal abnormalities were detected by CMA in 60 (16.7%) and sequence variants were detected by ES in a further 24 (6.7%) cases. The detection rate of pathogenic and likely pathogenic genetic variants in fetuses with non-isolated CHD (32/83, 38.6%) was significantly higher than that in fetuses with isolated CHD (52/277, 18.8%) (P < 0.001), this difference being due mainly to the difference in frequency of aneuploidy between the two groups. The prevalence of a genetic defect was highest in fetuses with an atrioventricular septal defect (36.8%), ventricular septal defect with or without atrial septal defect (28.4%), conotruncal defect (22.2%) or right ventricular outflow tract obstruction (20.0%). We also identified two novel missense mutations (c.2447G>C, p.Arg816Pro; c.1171C>T, p.Arg391Cys) and a new phenotype caused by variants in PLD1. CONCLUSIONS Chromosomal abnormalities were identified in 16.7% and sequence variants in a further 6.7% of fetuses with CHD. ES should be offered to all pregnant women with a CHD fetus without chromosomal abnormality or pathogenic CNV identified by CMA, regardless of whether the CHD is isolated. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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Affiliation(s)
- F Qiao
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Zhang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - R Zhou
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Y Wu
- Department of Ultrasound, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Wang
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - L Meng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Mao
- Personnel Division, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Q Cheng
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - C Luo
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - P Hu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Z Xu
- Department of Prenatal Diagnosis, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
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23
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Findley TO, Northrup H. The current state of prenatal detection of genetic conditions in congenital heart defects. Transl Pediatr 2021; 10:2157-2170. [PMID: 34584888 PMCID: PMC8429866 DOI: 10.21037/tp-20-315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/05/2020] [Indexed: 11/06/2022] Open
Abstract
The incidence of congenital heart defect (CHD) has increased over the past fifty years, partly attributed to routine fetal anatomical examination by sonography during obstetric care and improvements in ultrasound technology and technique. Fetal findings on ultrasound in addition to maternal biomarkers are the backbone of first- and second-trimester screening for common genetic conditions, namely aneuploidy. Since the introduction of non-invasive prenatal testing (NIPT) using next-generation sequencing to sequence cell-free fetal DNA, the detection rate of common trisomies as well as sex chromosomal aneuploidies have markedly increased. As the use of NIPT continues to broaden, the best means of incorporating NIPT into prenatal care is less clear and complicated by misunderstanding of the limitations and non-diagnostic role of NIPT by clinicians and families. In other advancements in prenatal genetic testing, recommendations on the role of chromosomal microarray (CMA) for prenatal diagnosis has led to its increasing use to identify genetic conditions in fetuses diagnosed with CHD. Lastly, as whole exome sequencing (WES) becomes more available and affordable, the next clinical application of next-generation sequencing in prenatal diagnostic testing is on the horizon. While newer genetic tests may provide answers in terms of genetic diagnosis, even more questions will likely ensue for clinicians, researchers, and parents. The objective of this review is to provide the perspective of the evolution of maternal and fetal obstetric care against the backdrop of advancing genetic technology and its impact on families and clinicians.
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Affiliation(s)
- Tina O Findley
- Division of Neonatal-Perinatal Medicine, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Hope Northrup
- Division of Medical Genetics, Department of Pediatrics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
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24
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Cai M, Huang H, Su L, Wu X, Xie X, Xu L, Lin N. Choroid Plexus Cysts: Single Nucleotide Polymorphism Array Analysis of Associated Genetic Anomalies and Resulting Obstetrical Outcomes. Risk Manag Healthc Policy 2021; 14:2491-2497. [PMID: 34163268 PMCID: PMC8214565 DOI: 10.2147/rmhp.s312813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/03/2021] [Indexed: 11/23/2022] Open
Abstract
Objective Choroid plexus cysts (CPC) are pseudocysts in the fetal choroid plexus and can be detected during ultrasound examination. However, the etiology of fetuses with CPC is still unknown. This study aimed to evaluate the genetic anomalies of fetuses with CPC using single nucleotide polymorphism (SNP) array analysis, as well as their obstetrical outcomes. Patients and Methods Among 201 fetuses, 108, 69, and 24 had isolated CPC (iCPC), CPC with sonographic soft markers, and CPC with sonographic structural malformations, respectively. All fetuses underwent conventional karyotyping analysis and SNP array analysis. Results Among 201 fetuses with CPC, 15 had chromosomal abnormalities (7.5%, 15/201), including nine fetuses with trisomy 18. Further, SNP array results were consistent with the conventional karyotype analysis and additionally revealed 6.0% (12/201) abnormal copy number variations (CNVs). The rates of pathogenic CNVs in fetuses with iCPC, CPC combined with sonographic soft markers, and CPC combined with sonographic structural malformations were 6.5%, 6.0%, and 45.8%, respectively, with significant differences among the groups. Conclusion The results of the SNP array affected the obstetrical outcomes. CPC is thus associated with pathogenic CNVs in approximately 10.9% of cases. Therefore, SNP array should be offered for prenatal testing of fetuses with CPC.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, People's Republic of China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, People's Republic of China
| | - Linjuan Su
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, People's Republic of China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, People's Republic of China
| | - Xiaorui Xie
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, People's Republic of China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, People's Republic of China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, People's Republic of China
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25
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Chen L, Wang L, Tang F, Zeng Y, Yin D, Zhou C, Zhu H, Li L, Zhang L, Wang J. Copy number variation sequencing combined with quantitative fluorescence polymerase chain reaction in clinical application of pregnancy loss. J Assist Reprod Genet 2021; 38:2397-2404. [PMID: 34052955 DOI: 10.1007/s10815-021-02243-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/23/2021] [Indexed: 12/24/2022] Open
Abstract
PURPOSE In this study, we evaluated the feasibility of the combining CNV-seq and quantitative fluorescence polymerase chain reaction (QF-PCR) for miscarriage analysis in clinical practice. METHODS Over a 35-month period, a total of 389 fetal specimens including 356 chorionic villi and 33 fetal muscle tissues were analyzed by CNV-seq and QF-PCR. Relationships between the risk factors (e.g., advanced maternal age, abnormal pregnancy history, and gestational age) and incidence of these chromosomal abnormalities were further analyzed by subgroup. RESULTS Clinically significant chromosomal abnormalities were identified in 58.95% cases. Aneuploidy was the most common abnormality (46.84%), followed by polyploidy (8.16%) and structural chromosome anomalies (3.95%). In sub-group analysis, significant differences were found in the total frequency of chromosomal abnormalities between the early abortion and the late abortion group, as well as in the distribution of chromosomal abnormalities between the advanced and the younger maternal age group. Meanwhile, the results of the logistic regression analysis identified a trend suggesting that the percentage of fetal chromosomal abnormalities is significantly higher in advanced maternal age, lesser gestational age, and lesser number of prior miscarriages. CONCLUSION Our study suggests that CNV-seq and QF-PCR are efficient and reliable technologies in the fetal chromosome analysis of miscarriages and could be used as a routine selection method for the genetic analysis of spontaneous abortion.
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Affiliation(s)
- Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Feng Tang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yang Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Daishu Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Cong Zhou
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Hongmei Zhu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Linping Li
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Lili Zhang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Block 3 No. 20, Ren Min Nan Road, Wuhou district, Chengdu, China. .,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
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26
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Zhou XY, Zheng HY, Han L, Wang Y, Zhang L, Shu XM, Zhang ML, Liu GN, Ding LS. Copy Number Variations Analysis Identifies QPRT as a Candidate Gene Associated With Susceptibility for Solitary Functioning Kidney. Front Genet 2021; 12:575830. [PMID: 34079576 PMCID: PMC8165445 DOI: 10.3389/fgene.2021.575830] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 04/06/2021] [Indexed: 01/03/2023] Open
Abstract
Background The lack of understanding of molecular pathologies of the solitary functioning kidney makes improving and strengthening the continuity of care between pediatric and adult nephrological patients difficult. Copy number variations (CNVs) account for a molecular cause of solitary functioning kidney, but characterization of the pathogenic genes remains challenging. Methods In our prospective cohort study, 99 fetuses clinically diagnosed with a solitary functioning kidney were enrolled and evaluated using chromosomal microarray analysis (CMA). The genetic drivers for the pathogenic CNVs were analyzed. We characterized QPRT localization in fetal kidneys using immunohistochemistry and its expression in adult kidneys using quantitative RT-PCR. Further, QPRT was knocked down using siRNA in human embryonic kidney (HEK293T) cells, and the cell cycle and proliferation were tested. Results Besides one Triple X syndrome and one Down syndrome, we identified a total of 45 CNVs out of 34 subjects. Among the 14 pathogenic CNVs, CNV 16p11.2 reached the highest number of records with the phenotype of kidney anomalies in the Decipher database. Among the 26 genes within the 16p11.2 region, as a key enzyme for nicotinamide adenine dinucleotide (NAD+) biosynthesis, QPRT was distinctly localized in renal tubules but was barely observed in renal interstitial and glomeruli in fetal kidneys. The loss of QPRT prevented cells’ efficient transition into S phase, affected cell-cycle progression, and abrogated proliferation of human embryonic kidney cells. Conclusion Our data suggest that QPRT is a candidate gene associated with susceptibility for solitary functioning kidney. The CNVs discovered in our study exhibit great potential for future applications in genetic counseling and pregnancy management.
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Affiliation(s)
- Xiao Y Zhou
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Hao Y Zheng
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Han
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yan Wang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Li Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Xiao M Shu
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Mu L Zhang
- Department of Obstetrics, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
| | - Guan N Liu
- College of Biological and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Lian S Ding
- Department of Neurosurgery, The Affiliated Huai'an No. 1 People's Hospital of Nanjing Medical University, Huai'an, China
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27
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Chen S, Zhang L, Gao J, Li S, Chang C, Chen Y, Fei H, Zhang J, Wang Y, Huang H, Xu C, Lu D. Expanding the Scope of Non-invasive Prenatal Testing to Detect Fetal Chromosomal Copy Number Variations. Front Mol Biosci 2021; 8:649169. [PMID: 34055879 PMCID: PMC8149898 DOI: 10.3389/fmolb.2021.649169] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 04/16/2021] [Indexed: 11/30/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) for common fetal trisomies is effective. However, the usefulness of cell-free DNA testing to detect other chromosomal abnormalities is poorly understood. We analyzed the positive rate at different read depths in next-generation sequencing (NGS) and identified a strategy for fetal copy number variant (CNV) detection in NIPT. Pregnant women who underwent NIPT by NGS at read depths of 4–6 M and fetuses with suspected CNVs were analyzed by amniocentesis and chromosomal microarray analysis (CMA). These fetus samples were re-sequenced at a read depth of 25 M and the positive detection rate was determined. With the increase in read depth, the positive CNV detection rate increased. The positive CNV detection rates at 25 M with small fragments were higher by NGS than by karyotype analysis. Increasing read depth in NGS improves the positive CNV detection rate while lowering the false positive detection rate. NIPT by NGS may be an accurate method of fetal chromosome analysis and reduce the rate of birth defects.
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Affiliation(s)
- Songchang Chen
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China.,Genetics Center of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Lanlan Zhang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China.,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jiong Gao
- Shanghai Medical Laboratory, BGI-Shanghai, BGI-Shenzhen, Shanghai, China
| | - Shuyuan Li
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Chunxin Chang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Yiyao Chen
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Hongjun Fei
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Junyu Zhang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Yanlin Wang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Hefeng Huang
- The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Chenming Xu
- Genetics Center of Obstetrics and Gynecology, Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China.,The International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, China.,Shanghai Municipal Key Clinical Specialty, Shanghai, China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, China.,Key Laboratory of Birth Defects and Reproductive Health of National Health Commission, Chongqing Population and Family Planning, Science and Technology Research Institute, Chongqing, China
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28
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Huang J, Deng X, Wang Y, Tang N, Zeng D. Analysis of Copy Number Variations by Low-Depth Whole-Genome Sequencing in Fetuses with Congenital Cardiovascular Malformations. Cytogenet Genome Res 2021; 160:643-649. [PMID: 33647914 DOI: 10.1159/000512605] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
Abstract
Congenital cardiovascular malformations (CVMs) due to genomic mutations bring a greater risk of morbidity and comorbidity and increase the risks related to heart surgery. However, reports on CVMs induced by genomic mutations based on actual clinical data are still limited. In this study, 181 fetuses were screened by fetal echocardiography for prenatal diagnosis of congenital heart disease, including 146 cases without ultrasound extracardiac findings (Group A) and 35 cases with ultrasound extracardiac findings (Group B). All cases were analyzed by clinical data, karyotyping, and low-depth whole-genome sequencing. The rates of chromosomal abnormalities in Groups A and B were 4.8% (7/146) and 37.1% (13/35), respectively. There was a significant difference in the incidence of chromosomal abnormalities between Groups A and B (p < 0.001). In Group A, CNV-seq identified copy number variations (CNVs) in an additional 9.6% (14/146) of cases with normal karyotypes, including 7 pathogenic CNVs and 7 variations of uncertain clinical significance. In Group B, one pathogenic CNV was identified in a case with normal karyotype. Chromosomal abnormality is one of the most common causes of CVM with extracardiac defects. Low-depth whole-genome sequencing could effectively become a first approach for CNV diagnosis in fetuses with CVMs.
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Affiliation(s)
- Jiwei Huang
- Central Laboratory/Biobank, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Xine Deng
- Department of Perinatal Healthcare, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Yuanliu Wang
- Department of Perinatal Healthcare, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Ning Tang
- Central Laboratory/Biobank, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China
| | - Dingyuan Zeng
- Department of Obstetrics and Gynecology, Liuzhou Maternal and Child Healthcare Hospital, Liuzhou, China,
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29
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Ma N, Xi H, Chen J, Peng Y, Jia Z, Yang S, Hu J, Pang J, Zhang Y, Hu R, Wang H, Liu J. Integrated CNV-seq, karyotyping and SNP-array analyses for effective prenatal diagnosis of chromosomal mosaicism. BMC Med Genomics 2021; 14:56. [PMID: 33632221 PMCID: PMC7905897 DOI: 10.1186/s12920-021-00899-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/09/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Emerging studies suggest that low-coverage massively parallel copy number variation sequencing (CNV-seq) more sensitive than chromosomal microarray analysis (CMA) for detecting low-level mosaicism. However, a retrospective back-to-back comparison evaluating accuracy, efficacy, and incremental yield of CNV-seq compared with CMA is warranted. METHODS A total of 72 mosaicism cases identified by karyotyping or CMA were recruited to the study. There were 67 mosaic samples co-analysed by CMA and CNV-seq, comprising 40 with sex chromosome aneuploidy, 22 with autosomal aneuploidy and 5 with large cryptic genomic rearrangements. RESULTS Of the 67 positive mosaic cases, the levels of mosaicism defined by CNV-seq ranged from 6 to 92% compared to the ratio from 3 to 90% by karyotyping and 20% to 72% by CMA. CNV-seq not only identified all 43 chromosomal aneuploidies or large cryptic genomic rearrangements detected by CMA, but also provided a 34.88% (15/43) increased yield compared with CMA. The improved yield of mosaicism detection by CNV-seq was largely due to the ability to detect low level mosaicism below 20%. CONCLUSION In the context of prenatal diagnosis, CNV-seq identified additional and clinically significant mosaicism with enhanced resolution and increased sensitivity. This study provides strong evidence for applying CNV-seq as an alternative to CMA for detection of aneuploidy and mosaic variants.
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Affiliation(s)
- Na Ma
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Hui Xi
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Jing Chen
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Ying Peng
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Zhengjun Jia
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Shuting Yang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Jiancheng Hu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Jialun Pang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Yanan Zhang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Rong Hu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China.
- National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, 410008, Hunan, China.
| | - Jing Liu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, 410008, Hunan, China.
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30
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Huang H, Cai M, Wang Y, Liang B, Lin N, Xu L. SNP Array as a Tool for Prenatal Diagnosis of Congenital Heart Disease Screened by Echocardiography: Implications for Precision Assessment of Fetal Prognosis. Risk Manag Healthc Policy 2021; 14:345-355. [PMID: 33542665 PMCID: PMC7851374 DOI: 10.2147/rmhp.s286001] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/30/2020] [Indexed: 12/21/2022] Open
Abstract
Objective This study aimed to examine the effectiveness of the SNP array for the prenatal diagnosis of congenital heart disease (CHD) screened by echocardiography. Patients and Methods A total of 356 pregnant women with fetal congenital heart malformations revealed by echocardiography at the Center for Prenatal Diagnosis of Fujian Maternal and Children Hospital during the period from November 2016 through July 2019 were recruited. The fetuses were assigned into three cohorts, including 142 with a single cardiac malformation, 106 with multiple cardiac malformations and 108 with cardiac and extracardiac malformations. All fetuses underwent chromosomal karyotyping and SNP array simultaneously, and the effectiveness of the SNP array for the prenatal diagnosis of CHD was evaluated. Results The overall prevalence of abnormal karyotypes was 9.3% among the 356 fetuses with CHD, and a higher proportion was found in fetuses with cardiac and extracardiac malformations (18.5%) than in those with single (5.6%) or multiple cardiac malformations (4.7%) (P<0.05). Consistent with karyotype analysis, SNP array detected an additional 25 fetuses with pathogenic copy number variations (CNVs), seven with variant of unknown significance (VOUS) and seven with benign CNVs, and a lower proportion of abnormal CNV was found in fetuses with a single cardiac malformation (4.2%) than in those with multiple cardiac malformations (9.4%) or cardiac and extracardiac malformations (14.8%) (P<0.05). Among the 33 fetuses with chromosomal abnormality, postnatal follow-up showed termination of pregnancy in 25 with pathogenic CNVs, one with VOUS, and six with normal karyotypes and SNP array findings but severe multiple malformations by ultrasonography. Conclusion SNP array increases the overall detection of abnormal CNVs by 9%, which improves the detection of CNVs associated with CHD. SNP array may serve as a tool for prenatal diagnosis of CHD that facilitates the discovery of pathogenic genes associated with CHD and provide valuable insights into the precision assessment of fetal prognosis during the prenatal counseling.
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Affiliation(s)
- Hailong Huang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Meiying Cai
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Yan Wang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Bin Liang
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Na Lin
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
| | - Liangpu Xu
- Center for Prenatal Diagnosis, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fuzhou 350001, Fujian Province, People's Republic of China.,Fujian Key Laboratory for Prenatal Diagnosis and Birth Defects, Fuzhou 350001, Fujian Province, People's Republic of China
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Tzadikevitch Geffen K, Singer A, Maya I, Ben-Shachar S, Sagi-Dain L, Daum H, Michaelson-Cohen R, Greenbaum L, Feingold-Zadok M, Sukenik Halevy R. The Yield of Chromosomal Microarray in Pregnancies Complicated with Fetal Growth Restriction Can Be Predicted According to Clinical Parameters. Fetal Diagn Ther 2020; 48:140-148. [PMID: 33352557 DOI: 10.1159/000511475] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/09/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION We evaluated the yield of chromosomal microarray analysis in pregnancies complicated with fetal growth restriction (FGR) according to specific clinical parameters. METHODS The study was based on national records from the Israeli Ministry of Health. Chromosomal microarray analyses of amniocenteses performed nationwide for the indication of FGR, from January 2016 to March 2018, were included. The CMA yield was compared to 2 cohorts that reported the background risk. RESULTS Of 174 tests performed for the indication of FGR, there were 11 cases with a pathogenic/likely pathogenic result (6.3%). The yield of CMA was significantly higher in cases with major structural findings (29.4 vs. 3.4%, p = 0.001), compared to isolated FGR but not for minor structural findings (6.1 vs. 3.4%, p = 0.5). The rate of chromosomal aberrations was significantly higher for all cases with FGR, when compared to the background risk of a cohort of normal pregnancies (odds ratio [OR] 4.7, 95% CI 2.5-9 and OR 6.09, 95% CI 3.2-11.4) but not for isolated cases or cases diagnosed after 24 weeks of pregnancy. CONCLUSIONS Chromosomal microarray analysis should be performed for all pregnancies complicated with FGR diagnosed before 24 weeks and for cases with major structural anomalies.
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Affiliation(s)
- Keren Tzadikevitch Geffen
- Department of Obstetrics and Gynecology, Meir Medical Center, Kfar Saba, Israel, .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,
| | - Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Idit Maya
- Recanati Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | - Shay Ben-Shachar
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Genetic Institute, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,Clalit Research Insatitute, Ramat Gan, Israel
| | - Lena Sagi-Dain
- Genetics Institute and Department of Obstetrics and Gynecology, Carmel Medical Center, Haifa, Israel.,Ruth and Bruce Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa, Israel
| | - Hagit Daum
- Department of Genetics, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Rachel Michaelson-Cohen
- Genetics Institute and Department of OB-GYN, Shaare Zedek Medical Center, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lior Greenbaum
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Danek Gertner Institute of Human Genetics and The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Michal Feingold-Zadok
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Genetic Institute, Shamir Medical Center (Assaf Harofeh), Zerifin, Israel
| | - Rivka Sukenik Halevy
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Recanati Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
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Nees SN, Chung WK. Genetic Basis of Human Congenital Heart Disease. Cold Spring Harb Perspect Biol 2020; 12:cshperspect.a036749. [PMID: 31818857 DOI: 10.1101/cshperspect.a036749] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Congenital heart disease (CHD) is the most common major congenital anomaly with an incidence of ∼1% of live births and is a significant cause of birth defect-related mortality. The genetic mechanisms underlying the development of CHD are complex and remain incompletely understood. Known genetic causes include all classes of genetic variation including chromosomal aneuploidies, copy number variants, and rare and common single-nucleotide variants, which can be either de novo or inherited. Among patients with CHD, ∼8%-12% have a chromosomal abnormality or aneuploidy, between 3% and 25% have a copy number variation, and 3%-5% have a single-gene defect in an established CHD gene with higher likelihood of identifying a genetic cause in patients with nonisolated CHD. These genetic variants disrupt or alter genes that play an important role in normal cardiac development and in some cases have pleiotropic effects on other organs. This work reviews some of the most common genetic causes of CHD as well as what is currently known about the underlying mechanisms.
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Affiliation(s)
| | - Wendy K Chung
- Department of Pediatrics.,Department of Medicine, Columbia University Irving Medical Center, New York, New York 10032, USA
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Liu T, Xie H, Zhang J, Wang X, Sha J, Zhai J. Fetus of 8q22.2q24.3 duplication and 13q33.2q34 deletion derived from a maternal balanced translocation. J Obstet Gynaecol Res 2020; 46:1900-1906. [PMID: 32643293 PMCID: PMC7496467 DOI: 10.1111/jog.14386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 05/29/2020] [Accepted: 06/13/2020] [Indexed: 01/01/2023]
Abstract
The concomitant occurrence of 8q duplication and 13q deletion is the first to be detected by noninvasive prenatal testing (NIPT) to date. Through case analysis, we could provide a clinical approach to pregnant women with chromosomal abnormalities revealed by NIPT. The combination of traditional karyotype and copy number variation sequencing (CNV-seq) could better locate the abnormal chromosomal region and further identify the source of fetal chromosomal abnormalities. Simultaneously, we evaluated the fetal morphology by ultrasound examination. The karyotype of the fetus was 46,XY,der(13)t(8;13)(q22;q32)mat and CNV-seq results showed that there was an approximately 45.26-Mb duplication in 8q22.2-q24.3 (101040001-146 300 000) and an approximately 9.54-Mb deletion in 13q33.2-q34 (105560001-115 100 000). Prenatal ultrasound revealed the fetal structural abnormalities presented with hypoplasia of the cerebellar vermis, a flat nose, echogenic bowel and absent gallbladder. Herein, we consider that combination detection of traditional karyotyping, CNV-seq and ultrasonography provides a valuable method for pregnant women with abnormal NIPT.
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Affiliation(s)
- Tong Liu
- Department of Prenatal Diagnosis Medical Center, XuZhou Central HospitalXuZhou Clinical School of Xuzhou Medical UniversityJiangsuChina
| | - Huihui Xie
- Department of Prenatal Diagnosis Medical Center, XuZhou Central HospitalXuZhou Clinical School of Xuzhou Medical UniversityJiangsuChina
| | - Jingbo Zhang
- Department of Prenatal Diagnosis Medical Center, XuZhou Central HospitalXuZhou Clinical School of Xuzhou Medical UniversityJiangsuChina
| | - Xia Wang
- Department of Prenatal Diagnosis Medical Center, XuZhou Central HospitalXuZhou Clinical School of Xuzhou Medical UniversityJiangsuChina
| | - Jing Sha
- Department of Prenatal Diagnosis Medical Center, XuZhou Central HospitalXuZhou Clinical School of Xuzhou Medical UniversityJiangsuChina
| | - Jingfang Zhai
- Department of Prenatal Diagnosis Medical Center, XuZhou Central HospitalXuZhou Clinical School of Xuzhou Medical UniversityJiangsuChina
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Wang J, Chen L, Wang L, Yin D, Zeng Y, Tang F, Tian Y, Liu H. Segmental aneuploidies in fetuses with isolated echogenic intracardiac focus among women younger than 35 years. Sci Rep 2020; 10:10496. [PMID: 32591622 PMCID: PMC7320167 DOI: 10.1038/s41598-020-67501-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/09/2020] [Indexed: 11/09/2022] Open
Abstract
Studies on the occurrence of segmental aneuploidoidy in fetuses with isolated echogenic intracardiac focus (EIF) are scarce. The aim of this study was to analyze whether there is an association between abnormal segmental aneuploidies and isolated EIF. This was a prospective case-control study. The study participants in the case group were fetuses that were diagnosed with isolated EIF. Samples without fetal ultrasound abnormalities but received prenatal diagnosis for other reasons (serological screening high-risk, voluntary request) were set as controls. All pregnant women were younger than 35 years old at the expected date of childbirth. Copy number variation sequencing (CNV-seq) was performed for all samples. The case group and control group successfully underwent CNV-seq analysis and exhibited 1,099 and 5,616 amniotic fluid samples, respectively. The detection rates of abnormal segmental aneuploidies in the case group and control group were 0.6% (7/1,099) and 1.1% (64/5,616), respectively; no statistically significant difference was found between the two groups (x2 = 2.220, P = 0.136). Isolated EIF did not increase the risk of fetal segmental aneuploidies.
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Affiliation(s)
- Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Daishu Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yang Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Feng Tang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yu Tian
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
- Department of Ultrasonography, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongqian Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
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Peng Y, Pang J, Hu J, Jia Z, Xi H, Ma N, Yang S, Liu J, Huang X, Tang C, Wang H. Clinical and molecular characterization of 12 prenatal cases of Cri-du-chat syndrome. Mol Genet Genomic Med 2020; 8:e1312. [PMID: 32500674 PMCID: PMC7434726 DOI: 10.1002/mgg3.1312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/20/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Background This study aimed to define the molecular basis for 12 prenatal cases of Cri‐du‐chat syndrome (CdCS) and the potential genotyping‐phenotyping association. Methods Karyotyping and single nucleotide polymorphism array analyses for copy number variants were performed. Results Nine cases had 5p terminal deletions and three had 5p interstitial deletions, and these cases had variable deletion sizes with partial overlapping. Phenotypically, besides intrauterine growth restriction (IUGR) and brain as well as heart abnormalities, hypospadias, and lung dysplasia were observed. Potential genetic causes for specific phenotypes in these cases were identified. Conclusion This study defined the molecular bases for the patients of CdCS, which is important for genetic counseling for these families. The findings of present study expand the clinical features of CdCS in the fetal period, and provided important information for further refining the genotypic–phenotypic correlations for this syndrome.
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Affiliation(s)
- Ying Peng
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Jialun Pang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Jiancheng Hu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Zhengjun Jia
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Hui Xi
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Na Ma
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Shuting Yang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Jing Liu
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Xiaoliang Huang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
| | - Chengyuan Tang
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hua Wang
- Department of Medical Genetics, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, Hunan, China.,National Health Commission Key Laboratory of Birth Defects Research, Prevention and Treatment, Changsha, Hunan, China
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Chen L, Wang L, Yin D, Zeng Y, Tang F, Wang J. Influence of the detection of parent-of-origin on the pregnancy outcomes of fetuses with copy number variation of unknown significance. Sci Rep 2020; 10:8864. [PMID: 32483189 PMCID: PMC7264138 DOI: 10.1038/s41598-020-65904-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/11/2020] [Indexed: 11/08/2022] Open
Abstract
The widespread application of high-resolution chromosome detection technology in clinical practice has identified many variants of unknown significance (VOUS) in prenatal diagnosis. The purpose of this study was to prospectively analyze the chromosomal results of parents and the follow-up information of pregnancy outcomes of prenatal samples with VOUS, so as to determine the influence of the detection of parent-of-origin on the pregnancy outcomes of fetuses with VOUS. The present study analyzed amniotic fluid samples obtained from women with different risk indications between February 2017 and December 2018. The samples were subjected to copy number variation sequencing, and detection of parent-of-origin was suggested in cases of samples with VOUS. The pregnancy outcome was followed up. In a total of 14073 amniotic fluid samples, 729 cases of VOUS were detected (5.2%, 729/14073) and 721 cases were followed up successfully. Among the 721 cases, 525 patients agreed to detect the parent-of-origin (72.8%, 525/721). It was revealed that the VOUS in 460 of the fetuses were hereditary (87.6%, 460/525). The percentages of abnormal pregnancy outcomes (included pregnancy loss, fetal pathological abnormality, preterm delivery, neonatal death, birth defects) in the inherited, de novo, and refusal to detect the parent-of-origin (i.e. unknown origin) groups were 4.3% (20/460), 6.2% (4/65), and 6.6% (13/196), respectively. There was no significant difference among the three groups (P > 0.05). The rate of voluntary termination of pregnancy (TOP) in the unknown origin group was significantly higher than that in the group that had determined the parent-of-origin (14.3% vs 7.4%, P = 0.005). There is currently no evidence that suggests that the proportion of abnormal pregnancy outcomes is higher in fetuses with VOUS than in other fetuses. However, the present study revealed that determining the parent-of-origin affects the decision to undergo voluntary TOP, as the rate of voluntary TOP in the group that refused detection was higher than that in the group that consented.
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Affiliation(s)
- Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Daishu Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yang Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Feng Tang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
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Chen CP, Huang JP, Chen YY, Chern SR, Wu PS, Chen SW, Wang W, Lee CC. Detection of a familial 1q21.1 microdeletion and concomitant CHD1L mutation in a fetus with oligohydramnios and bilateral renal dysplasia on prenatal ultrasound. Taiwan J Obstet Gynecol 2020; 58:859-863. [PMID: 31759543 DOI: 10.1016/j.tjog.2019.07.031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2019] [Indexed: 01/21/2023] Open
Abstract
OBJECTIVE We present detection of a familial 1q21.1 microdeletion and concomitant CHD1L mutation in a fetus with oligohydramnios and bilateral renal dysplasia on prenatal ultrasound. CASE REPORT A 37-year-old, primigravid woman was referred for level II ultrasound examination at 16 weeks of gestation because of oligohydramnios. The parents were phenotypically normal, and there were no congenital malformations in the family. Prenatal ultrasound at 17 weeks of gestation revealed a fetus with fetal growth biometry equivalent to 16 weeks, oligohydramnios with an amniotic fluid index (AFI) of 1.4 cm and bilateral renal dysplasia without sonographic demonstration of bilateral renal arteries. The pregnancy was subsequently terminated, and a 137-g fetus was delivered without characteristic facial dysmorphism. Postnatal cytogenetic analysis of the umbilical cord and parental bloods revealed normal karyotypes. However, array comparative genomic hybridization (aCGH) analysis on the DNA extracted from the umbilical cord revealed a 2.038-Mb microdeletion of 1q21.1-q21.2 encompassing 11 [Online Mendelian Inheritance in Man (OMIM)] genes of PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8, GPR89B, NBPF14, TRN-GTT2-1 and NBPF20. The mother was found to carry the same microdeletion. A missense mutation of c.2353T > G, p.Ser785Ala in CHD1L was detected in the umbilical cord. The father was found to carry a heterozygous mutation of c.2353T > G, p.Ser785Ala in CHD1L. CONCLUSION Fetuses with a 1q21.1 microdeletion and concomitant CHD1L mutation may present oligohydramnios and bilateral renal dysplasia on prenatal ultrasound.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Jian-Pei Huang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; MacKay Junior College of Medicine, Nursing and Management, Taipei, Taiwan
| | - Yi-Yung Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
| | - Chen-Chi Lee
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
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Lan L, Wu H, She L, Zhang B, He Y, Luo D, Wang H, Zheng Z. Analysis of copy number variation by sequencing in fetuses with nuchal translucency thickening. J Clin Lab Anal 2020; 34:e23347. [PMID: 32342531 PMCID: PMC7439336 DOI: 10.1002/jcla.23347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/30/2020] [Accepted: 04/03/2020] [Indexed: 12/20/2022] Open
Abstract
Objective Copy number variation sequencing (CNV‐seq) technique was used to analyze the genetic etiology of fetuses with increased nuchal translucency (NT). Methods A total of 139 women with gestational 11‐14 weeks whose fetuses were detected with increased NT (NT ≥ 2.5 mm) in our hospital from July 2016 to December 2018 were selected. Fetal specimens were performed for karyotyping analysis and CNV sequencing. Results According to the nuchal translucency thickness, 2.5‐3.4, 3.5‐4.4, 4.5‐5.4, and more than 5.5 mm, the rates of chromosomal abnormalities were 22.8% (13/57), 30.8% (12/39), 42.1% (8/19), and 62.5% (15/24), respectively. There was significant difference among the incidences of chromosomal abnormalities in four groups (χ2 = 37.69, P < .01) and the incidences increased with fetal NT thickness. Among 139 cases, there were 36 cases (25.9%) with abnormal chromosome karyotypes. Meanwhile, there were 45 cases (32.3%) with abnormal CNV. In the 12 cases with abnormal CNV and normal chromosome karyotypes, there were 2 cases of pathogenic CNV, 7 cases of CNV with unknown clinical significance, and 3 cases of possibly benign CNV. There was no significant difference in CNV between pregnant women in advanced maternal age and those in normal maternal age (χ2 = 1.389, P = .239). In the fetus who showed abnormalities in NT and ultrasonography (χ2 = 5.13, P < .05) and the fetus aborted (χ2 = 113.19, P < .05), the abnormal rate of CNV was higher with statistically significant difference. Conclusion CNV‐seq combined karyotype analysis should be performed simultaneously in fetuses with increased NT, providing a basis for genetic counseling, which is of great significance for prenatal diagnosis.
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Affiliation(s)
- Liubing Lan
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Heming Wu
- Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Lingna She
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Bosen Zhang
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Yanhong He
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Dandan Luo
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Department of Obstetrics, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Huaxian Wang
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
| | - Zhiyuan Zheng
- Prenatal Diagnosis Center, Meizhou People's Hospital (Huangtang Hospital), Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Guangdong Provincial Key Laboratory of Precision Medicine and Clinical Translational Research of Hakka Population, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Meizhou Municipal Engineering and Technology Research Center for Molecular Diagnostics of Major Genetic Disorders, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China.,Center for Precision Medicine, Meizhou People's Hospital (Huangtang Hospital), Meizhou Academy of Medical Sciences, Meizhou Hospital Affiliated to Sun Yat-sen University, Meizhou, China
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Application of next-generation sequencing for the diagnosis of fetuses with congenital heart defects. Curr Opin Obstet Gynecol 2020; 31:132-138. [PMID: 30608255 DOI: 10.1097/gco.0000000000000520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Congenital heart defects (CHDs) are the most common type of birth defects, and are thought to result from genetic-environmental interactions. Currently, karyotype and chromosomal microarray analyses are the primary methods used to detect chromosomal abnormalities and copy number variations in fetuses with CHD. Recently, with the introduction of next-generation sequencing (NGS) in prenatal diagnosis, gene mutations have been identified in cases of CHD. The purpose of this review is to summarize current studies about the genetic cause of fetal CHD, paying particular attention to the application of NGS for fetuses with CHD. RECENT FINDINGS In addition to chromosomal abnormalities, gene mutations are an important genetic cause of fetal CHD. Furthermore, incidences of pathogenic mutations in fetuses with CHD are associated with the presence of other structural anomalies, but are irrelevant to the categories of CHD. SUMMARY Gene mutations are important causes of fetal CHD and NGS should be applied to all fetuses with normal karyotype and copy number variations, regardless of whether the CHD is isolated or syndromic.
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Congenital heart diseases: genetics, non-inherited risk factors, and signaling pathways. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-0050-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Abstract
Background
Congenital heart diseases (CHDs) are the most common congenital anomalies with an estimated prevalence of 8 in 1000 live births. CHDs occur as a result of abnormal embryogenesis of the heart. Congenital heart diseases are associated with significant mortality and morbidity. The damage of the heart is irreversible due to a lack of regeneration potential, and usually, the patients may require surgical intervention. Studying the developmental biology of the heart is essential not only in understanding the mechanisms and pathogenesis of congenital heart diseases but also in providing us with insight towards developing new preventive and treatment methods.
Main body
The etiology of congenital heart diseases is still elusive. Both genetic and environmental factors have been implicated to play a role in the pathogenesis of the diseases. Recently, cardiac transcription factors, cardiac-specific genes, and signaling pathways, which are responsible for early cardiac morphogenesis have been extensively studied in both human and animal experiments but leave much to be desired. The discovery of novel genetic methods such as next generation sequencing and chromosomal microarrays have led to further study the genes, non-coding RNAs and subtle chromosomal changes, elucidating their implications to the etiology of congenital heart diseases. Studies have also implicated non-hereditary risk factors such as rubella infection, teratogens, maternal age, diabetes mellitus, and abnormal hemodynamics in causing CHDs.
These etiological factors raise questions on multifactorial etiology of CHDs. It is therefore important to endeavor in research based on finding the causes of CHDs. Finding causative factors will enable us to plan intervention strategies and mitigate the consequences associated with CHDs. This review, therefore, puts forward the genetic and non-genetic causes of congenital heart diseases. Besides, it discusses crucial signaling pathways which are involved in early cardiac morphogenesis. Consequently, we aim to consolidate our knowledge on multifactorial causes of CHDs so as to pave a way for further research regarding CHDs.
Conclusion
The multifactorial etiology of congenital heart diseases gives us a challenge to explicitly establishing specific causative factors and therefore plan intervention strategies. More well-designed studies and the use of novel genetic technologies could be the way through the discovery of etiological factors implicated in the pathogenesis of congenital heart diseases.
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Mustafa HJ, Jacobs KM, Tessier KM, Narasimhan SL, Tofte AN, McCarter AR, Cross SN. Chromosomal microarray analysis in the investigation of prenatally diagnosed congenital heart disease. Am J Obstet Gynecol MFM 2020; 2:100078. [PMID: 33345990 DOI: 10.1016/j.ajogmf.2019.100078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/04/2019] [Accepted: 12/16/2019] [Indexed: 01/25/2023]
Abstract
BACKGROUND Chromosomal microarray analysis has emerged as a primary diagnostic tool in prenatally diagnosed congenital heart disease and other structural anomalies in clinical practice. OBJECTIVE Our study aimed to investigate the diagnostic yield of microarray analysis as a first-tier test for chromosomal abnormalities in fetuses with both isolated and nonisolated congenital heart disease and to identify the association of different pathogenic chromosomal abnormalities with different subgroups of congenital heart disease. STUDY DESIGN Retrospective data from 217 pregnancies that were diagnosed with congenital heart disease between 2011 and 2016 were reviewed. All pregnancies were investigated with the use of microarray analysis during the study period. Classification of chromosomal abnormalities was done based on American College of Medical Genetics and Genomics guidelines into (1) pathogenic chromosomal abnormalities that included numeric chromosomal abnormalities (aneuploidy and partial aneuploidy) and pathogenic copy number variants (22q11.2 deletion and other microdeletions/microduplications), (2) variants of uncertain significance, and (3) normal findings. RESULTS Our study found a detection rate for pathogenic chromosomal abnormalities (numeric and pathogenic copy number variants) of 36.9% in pregnancies (n=80) that were diagnosed prenatally with congenital heart disease who underwent invasive testing with chromosomal microarray. The detection rate for numeric abnormalities was 29.5% (n=64) and for pathogenic copy number variants was 7.4% (n=16) of which 4.2% were 22q11.2 deletion and 3.2% were other pathogenic copy number variants, most of which theoretically could have been missed by the use of conventional karyotype alone. Pathogenic copy number variants were most common in conotruncal defects (19.6%; 11/56) that included 42.9% in cases of interrupted aortic arch, 23.8% in cases of tetralogy of Fallot, 13.3% in cases of transposition of the great arteries, and 8.3% in cases of double outlet right ventricle. Of these changes, 81.8% were 22q11.2 deletion, and 18.2% were other microdeletions/microduplications. After conotruncal defects, pathogenic copy number variants were most common in right ventricular outflow tract and left ventricular outflow tract groups (8% and 2.2%, respectively) in which none were 22q11.2 deletion. Pathogenic chromosomal abnormalities (numeric and pathogenic copy number variants) detected by chromosomal microarray analysis were significantly more common in the nonisolated congenital heart disease group (64.5%; n=49) compared with the isolated group (22%; n=31; P<.001). CONCLUSION In pregnancies that were diagnosed with congenital heart disease and had undergone diagnostic genetic testing, our study showed that chromosomal microarray analysis has an added value in the detection of pathogenic chromosomal abnormalities compared with conventional karyotype, particularly in cases of pathogenic copy number variants. This yield is influenced not only by the type of congenital heart disease but also by the presence of extracardiac anomalies.
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Affiliation(s)
- Hiba J Mustafa
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Eden Prairie, MN
| | - Katherine M Jacobs
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Eden Prairie, MN
| | - Katelyn M Tessier
- Biostatistics Core, Masonic Cancer Center, University of Minnesota, Eden Prairie, MN
| | - Shanti L Narasimhan
- Department of Pediatric Cardiology, University of Minnesota, Eden Prairie, MN
| | - Alena N Tofte
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Eden Prairie, MN
| | - Allison R McCarter
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Eden Prairie, MN
| | - Sarah N Cross
- Department of Obstetrics, Gynecology & Women's Health, University of Minnesota, Eden Prairie, MN
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Nees SN, Chung WK. The genetics of isolated congenital heart disease. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 184:97-106. [PMID: 31876989 DOI: 10.1002/ajmg.c.31763] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/06/2019] [Accepted: 12/12/2019] [Indexed: 12/12/2022]
Abstract
The genetic mechanisms underlying congenital heart disease (CHD) are complex and remain incompletely understood. The majority of patients with CHD have an isolated heart defect without other organ system involvement, but the genetic basis of isolated CHD has been even more difficult to elucidate compared to syndromic CHD. Our understanding of the genetics of isolated CHD is advancing in large part due to advances in next generation sequencing, and the list of genes associated with CHD is rapidly expanding. Variants in hundreds of genes have been identified that may cause or contribute to CHD, but a genetic cause can still only be identified in about 20-30% of patients. Identifying a genetic cause for CHD can have an impact on clinical outcomes and prognosis and thus it is important for clinicians to understand when and what to test in patients with isolated CHD. This chapter reviews some of the known genetic mechanisms that contribute to isolated inherited and sporadic CHD as well as recommendations for evaluation and genetic testing in patients with isolated CHD.
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Affiliation(s)
- Shannon N Nees
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York
| | - Wendy K Chung
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York.,Department of Medicine, Columbia University Irving Medical Center, New York, New York
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Petracchi F, Sisterna S, Igarzabal L, Wilkins-Haug L. Fetal cardiac abnormalities: Genetic etiologies to be considered. Prenat Diagn 2019; 39:758-780. [PMID: 31087396 DOI: 10.1002/pd.5480] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 04/16/2019] [Accepted: 04/27/2019] [Indexed: 12/21/2022]
Abstract
Congenital heart diseases are a common prenatal finding. The prenatal identification of an associated genetic syndrome or a major extracardiac anomaly helps to understand the etiopathogenic diagnosis. Besides, it also assesses the prognosis, management, and familial recurrence risk while strongly influences parental decision to choose termination of pregnancy or postnatal care. This review article describes the most common genetic diagnoses associated with a prenatal finding of a congenital heart disease and a suggested diagnostic process.
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Affiliation(s)
- Florencia Petracchi
- Sección Genética Departamento de Ginecología y Obstetricia, CEMIC Instituto Universitario, Buenos Aires, Argentina
| | - Silvina Sisterna
- Sección Genética Departamento de Ginecología y Obstetricia, CEMIC Instituto Universitario, Buenos Aires, Argentina
| | - Laura Igarzabal
- Sección Genética Departamento de Ginecología y Obstetricia, CEMIC Instituto Universitario, Buenos Aires, Argentina
| | - Louise Wilkins-Haug
- Harvard Medical School Department of Obstetrics, Gynecology and Reproductive Medicine Division Chief Maternal Fetal Medicine and Reproductive Genetics, Brigham and Women's Hospital, Boston, MA
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Chahal G, Tyagi S, Ramialison M. Navigating the non-coding genome in heart development and Congenital Heart Disease. Differentiation 2019; 107:11-23. [PMID: 31102825 DOI: 10.1016/j.diff.2019.05.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 01/14/2019] [Accepted: 05/06/2019] [Indexed: 12/12/2022]
Abstract
Congenital Heart Disease (CHD) is characterised by a wide range of cardiac defects, from mild to life-threatening, which occur in babies worldwide. To date, there is no cure to CHD, however, progress in surgery has reduced its mortality allowing children affected by CHD to reach adulthood. In an effort to understand its genetic basis, several studies involving whole-genome sequencing (WGS) of patients with CHD have been undertaken and generated a great wealth of information. The majority of putative causative mutations identified in WGS studies fall into the non-coding part of the genome. Unfortunately, due to the lack of understanding of the function of these non-coding mutations, it is challenging to establish a causal link between the non-coding mutation and the disease. Thus, here we review the state-of-the-art approaches to interpret non-coding mutations in the context of CHD and address the following questions: What are the non-coding sequences important for cardiac function? Which technologies are used to identify them? Which resources are available to analyse them? What mutations are expected in these non-coding sequences? Learning from developmental process, what is their expected role in CHD?
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Affiliation(s)
- Gulrez Chahal
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia
| | - Sonika Tyagi
- School of Biological Sciences, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Australian Genome Research Facility, 305 Grattan Street, Melbourne, VIC, 3000, Australia.
| | - Mirana Ramialison
- Australian Regenerative Medicine Institute (ARMI), 15 Innovation Walk, Monash University, Wellington Road, Clayton, 3800, VIC, Australia; Systems Biology Institute (SBI), Wellington Road, Clayton, 3800, VIC, Australia.
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Tonni G, Palmisano M, Perez Zamarian AC, Rabachini Caetano AC, Santana EFM, Peixoto AB, Armbruster-Moraes E, Ruano R, Araujo Júnior E. Phenotype to genotype characterization by array-comparative genomic hydridization (a-CGH) in case of fetal malformations: A systematic review. Taiwan J Obstet Gynecol 2019; 58:15-28. [PMID: 30638470 DOI: 10.1016/j.tjog.2018.11.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 11/16/2022] Open
Abstract
The aim of the current review is to report a-CGH abnormalities identified in fetuses with prenatally diagnosed fetal malformations in whom a normal karyotype was diagnosed with conventional cytogenetic analysis. A systematic electronic search of databases (PubMed/Medline, EMBASE/SCOPUS) has been conducted from inception to May, 2017. Bibliographic analysis has been performed according to PRISMA statement for review. The following keywords were used: 'array-CGH' and 'fetal malformations" and "prenatal diagnosis"; alternatively, "microarray", "oligonucleotide array", "molecular biology", "antenatal diagnostics", "fetal diagnostics", "congenital malformations" and "ultrasound" were used to capture both "a-CGH" and "prenatal". One-hundred and twelve fetuses with prenatally diagnosed fetal malformations with normal karyotyping and a-CGH abnormalities detected are described. Single or multiple microarray abnormalities diagnosed have been classified in relation to different organ/system affected. The most frequent a-CGH abnormalities were detected in cases of congenital heart diseases (CDHs), multiple malformations and central nervous system (CNS) malformations. Maternal or paternal carrier-state was seen in 19.64% (22/112), of cases while the number of reported de novo mutations accounted for 46.42% (52/112) of all CNVs microarray abnormalities. Array-comparative genomic hydridization (a-CGH) may become an integral and complemantary genetic testing when fetal malformations are detected prenatally in fetuses with normal cytogenetic karyotype. In addition, a-CGH enables the identification of CNVs and VOUS and improves the calculation of recurrent risk and the genetic counseling.
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Affiliation(s)
- Gabriele Tonni
- Prenatal Diagnostic Service, Department of Obstetrics and Gynecology, Istituto di Ricerca a Carattere Clinico Scientifico (IRCCS) AUSL Reggio Emilia, Italy.
| | - Marcella Palmisano
- Prenatal Diagnostic Service, Department of Obstetrics and Gynecology, Istituto di Ricerca a Carattere Clinico Scientifico (IRCCS) AUSL Reggio Emilia, Italy
| | - Ana Cristina Perez Zamarian
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Ana Carolina Rabachini Caetano
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Eduardo Félix Martins Santana
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Alberto Borges Peixoto
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
| | - Edecio Armbruster-Moraes
- Discipline of Genetics, Faculty of Medicine of ABC (FMABC), Santo André-SP, Brazil; Department of Gynecology and Obstetrics, Faculty of Medicine of the University of São Paulo (FMUSP), São Paulo-SP, Brazil
| | - Rodrigo Ruano
- Department of Obstetrics and Gynecology, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Edward Araujo Júnior
- Department of Obstetrics, Paulista School of Medicine - Federal University of São Paulo (EPM-UNIFESP), São Paulo-SP, Brazil
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Abstract
PURPOSE OF REVIEW Ventriculomegaly is one of the most common abnormal sonographic findings, which is associated with congenital infection, chromosomal and additional structural abnormalities. Currently, karyotype analysis is the primary method to detect chromosomal abnormalities in fetuses with ventriculomegaly. Recently, with the introduction of chromosomal microarray analysis (CMA) in prenatal diagnosis, copy number variations (CNVs) have been identified in cases of ventriculomegaly. The purpose of this review is to summarize the current knowledge about the genetic cause of fetal ventriculomegaly, with particular attention to primary articles regarding the association between CNVs and fetal ventriculomegaly. RECENT FINDINGS Recent studies have disclosed that in addition to numerical chromosomal abnormalities and large chromosomal imbalances, pathogenic CNVs are another important genetic cause of fetal ventriculomegaly, which may be involved in the pathological process of fetal ventriculomegaly as well as postnatal neurodevelopmental disorders. Furthermore, it is reported that the incidences of pathogenic CNVs in fetuses with ventriculomegaly were associated with the presence of other structural anomalies, but were irrelevant to the severity of ventriculomegaly. SUMMARY CNVs are an important cause of fetal ventriculomegaly and CMA should be offered to all fetuses with ventriculomegaly, regardless of the degree of ventriculomegaly or whether combined with other structural anomalies.
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Xie H, Hong N, Zhang E, Li F, Sun K, Yu Y. Identification of Rare Copy Number Variants Associated With Pulmonary Atresia With Ventricular Septal Defect. Front Genet 2019; 10:15. [PMID: 30745907 PMCID: PMC6360179 DOI: 10.3389/fgene.2019.00015] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 01/14/2019] [Indexed: 11/13/2022] Open
Abstract
Copy number variants (CNVs) are major variations contributing to the gene heterogeneity of congenital heart diseases (CHD). pulmonary atresia with ventricular septal defect (PA-VSD) is a rare form of cyanotic CHD characterized by complex manifestations and the genetic determinants underlying PA-VSD are still largely unknown. We investigated rare CNVs in a recruited cohort of 100 unrelated patients with PA-VSD, PA-IVS, or TOF and a population-matched control cohort of 100 healthy children using whole-exome sequencing. Comparing rare CNVs in PA-VSD cases and that in PA-IVS or TOF positive controls, we observed twenty-two rare CNVs only in PA-VSD, five rare CNVs only in PA-VSD and TOF as well as thirteen rare CNVs only in PA-VSD and PA-IVS. Six of these CNVs were considered pathogenic or potentially pathogenic to PA-VSD: 16p11.2 del (PPP4C and TBX6), 5q35.3 del (FLT4), 5p13.1 del (RICTOR), 6p21.33 dup (TNXB), 7p15.2 del (HNRNPA2B1), and 19p13.3 dup (FGF22). The gene networks showed that four putative candidate genes for PA-VSD, PPP4C, FLT4, RICTOR, and FGF22 had strong interaction with well-known cardiac genes relevant to heart or blood vessel development. Meanwhile, the analysis of transcriptome array revealed that PPP4C and RICTOR were also significantly expressed in human embryonic heart. In conclusion, three rare novel CNVs were identified only in PA-VSD: 16p11.2 del (PPP4C), 5q35.3 del (FLT4) and 5p13.1 del (RICTOR), implicating novel candidate genes of interest for PA-VSD. Our study provided new insights into understanding for the pathogenesis of PA-VSD and helped elucidate critical genes for PA-VSD.
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Affiliation(s)
- Huilin Xie
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Nanchao Hong
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Erge Zhang
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fen Li
- Department of Pediatric Cardiology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Kun Sun
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yu
- Department of Pediatric Cardiology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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Chen CP, Chang SY, Chen YN, Chern SR, Wu PS, Chen SW, Lai ST, Chuang TY, Yang CW, Chen LF, Wang W. Prenatal diagnosis of a familial 1q21.1-q21.2 microdeletion in a fetus with polydactyly of left foot on prenatal ultrasound. Taiwan J Obstet Gynecol 2019; 57:739-744. [PMID: 30342663 DOI: 10.1016/j.tjog.2018.08.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2018] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE We present prenatal diagnosis of a familial 1q21.1-q21.2 microdeletion in a fetus with polydactyly of left foot on prenatal ultrasound. CASE REPORT A 30-year-old, gravida 2, para 1, woman underwent amniocentesis at 22 weeks of gestation because of fetal polydactyly of left foot and echogenic heart foci on prenatal ultrasound. She and her husband and the 2-year-old son were healthy, and there was no family history of mental disorders, skeletal abnormalities and congenital malformations. Amniocentesis revealed a karyotype of 46,XX. Simultaneous array comparative genomic hybridization (aCGH) analysis on the DNA extracted from uncultured amniocytes revealed a 1.317-Mb 1q21.1-q21.2 microdeletion encompassing PRKAB2, FMO5, CHD1L, BCL9, ACP6, GJA5, GJA8 and GPR89B. aCGH analysis of the family members revealed that the phenotypically normal father and elder son carried the same 1q21.1-q21.2 microdeletion. The mother did not have such a deletion. The parents elected to continue the pregnancy, and a 3416-g female baby was delivered at 40 weeks of gestation with neither facial dysmorphism nor gross abnormalities except postaxial polydactyly of the left foot. CONCLUSION Fetuses with a 1q21.1-q21.2 microdeletion may present polydactyly on prenatal ultrasound, and aCGH is helpful for prenatal diagnosis under such a circumstance.
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Affiliation(s)
- Chih-Ping Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan; Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Biotechnology, Asia University, Taichung, Taiwan; School of Chinese Medicine, College of Chinese Medicine, China Medical University, Taichung, Taiwan; Institute of Clinical and Community Health Nursing, National Yang-Ming University, Taipei, Taiwan; Department of Obstetrics and Gynecology, School of Medicine, National Yang-Ming University, Taipei, Taiwan.
| | - Shu-Yuan Chang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Yen-Ni Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Schu-Rern Chern
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | | | - Shin-Wen Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Shih-Ting Lai
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Tzu-Yun Chuang
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Chien-Wen Yang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan
| | - Li-Feng Chen
- Department of Obstetrics and Gynecology, MacKay Memorial Hospital, Taipei, Taiwan
| | - Wayseen Wang
- Department of Medical Research, MacKay Memorial Hospital, Taipei, Taiwan; Department of Bioengineering, Tatung University, Taipei, Taiwan
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Vijay A, Garg I, Ashraf MZ. Perspective: DNA Copy Number Variations in Cardiovascular Diseases. Epigenet Insights 2018; 11:2516865718818839. [PMID: 30560231 PMCID: PMC6291864 DOI: 10.1177/2516865718818839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 11/08/2018] [Indexed: 12/27/2022] Open
Abstract
Human genome contains many variations, often called mutations, which are difficult to detect and have remained a challenge for years. A substantial part of the genome encompasses repeats and when such repeats are in the coding region they may lead to change in the gene expression profile followed by pathological conditions. Structural variants are alterations which change one or more sequence feature in the chromosome such as change in the copy number, rearrangements, and translocations of a sequence and can be balanced or unbalanced. Copy number variants (CNVs) may increase or decrease the copies of a given region and have a pivotal role in the onset of many diseases including cardiovascular disorders. Cardiovascular disorders have a magnitude of well-established risk factors and etiology, but their correlation with CNVs is still being studied. In this article, we have discussed history of CNVs and a summary on the diseases associated with CNVs. To detect such variations, we shed light on the number of techniques introduced so far and their limitations. The lack of studies on cardiovascular diseases to determine the frequency of such variants needs clinical studies with larger cohorts. This review is a compilation of articles suggesting the importance of CNVs in multitude of cardiovascular anomalies. Finally, future perspectives for better understanding of CNVs and cardiovascular disorders have also been discussed.
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Affiliation(s)
- Aatira Vijay
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Iti Garg
- Genomics Division, Defence Institute of Physiology & Allied Sciences, Delhi, India
| | - Mohammad Zahid Ashraf
- Genomics Division, Defence Institute of Physiology and Allied Sciences, DRDO, Delhi, India
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Cai M, Huang H, Su L, Lin N, Wu X, Xie X, An G, Li Y, Lin Y, Xu L. Fetal congenital heart disease: Associated anomalies, identification of genetic anomalies by single-nucleotide polymorphism array analysis, and postnatal outcome. Medicine (Baltimore) 2018; 97:e13617. [PMID: 30558042 PMCID: PMC6320040 DOI: 10.1097/md.0000000000013617] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Congenital heart disease (CHD) is one of the most common birth defects; however, the mechanisms underlying its development are poorly understood. Recently, heritable genetic factors, including copy number variations (CNVs) and single nucleotide polymorphisms (SNPs), have been implicated in its etiology. The aim of this study was to investigate the utility of a SNP array for the prenatal diagnosis of CHD and the improvement of prenatal genetic counseling and to compare this approach to traditional chromosome analysis. METHODS One hundred and fortysix cases of CHD detected by prenatal echocardiography were analyzed. Of these, 110 were isolated CHD and 36 were of CHD with extracardiac defects. SNP analysis was performed using the Affymetrix CytoScan HD platform, which was followed by karyotype analysis. All annotated CNVs were validated by fluorescence in situ hybridization. RESULTS Karyotype analysis identified chromosomal abnormalities in 19 of 146 cases. In addition to the 15 chromosomal abnormalities that were consistent with the results of karyotype analysis, the SNP array identified abnormal CNVs in an additional 15.2% (22/145) cases; of these, 15 were pathogenic CNVs, three were variations of uncertain clinical significance, and four were benign CNVs. The rates at which the SNP array detected pathogenic CNVs differed significantly between cases of isolated CHD and CHD with extracardiac defects (13.6% vs. 72.2%, P = .001). The results of the SNP array also affected the rate of pregnancy termination. CONCLUSION Combining SNP array with cytogenetic analyses is particularly effective for identifying chromosomal abnormalities in CNVs in fetuses with CHD, which also affects obstetrical outcomes.
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