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Cai M, Lin J, Que Y, Xu L, Lin N, Huang H. Fetal congenital talipes equinovarus: genomic abnormalities and obstetric follow-up results. J Matern Fetal Neonatal Med 2024; 37:2299113. [PMID: 38151241 DOI: 10.1080/14767058.2023.2299113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 12/20/2023] [Indexed: 12/29/2023]
Abstract
OBJECTIVE The etiology of congenital talipes equinovarus (CTEV) is unknown, and the relationship between chromosome microdeletion/microduplication and fetal CTEV is rarely reported. In this study, we retrospectively analyzed fetal CTEV to explore the relationship among the CTEV phenotype, chromosome microdeletion/microduplication, and obstetric outcomes. METHODS Chromosome karyotype analysis and single nucleotide polymorphism (SNP) array were performed for the 68 fetuses with CTEV. RESULTS An SNP array was performed for 68 fetuses with CTEV; pathogenic copy number variations (CNVs) were detected in eight cases (11.8%, 8/68). In addition to one case consistent with karyotype analysis, the SNP array revealed seven additional pathogenic CNVs, including three with 22q11.21 microdeletions, two with 17p12p11.2 microduplications, one with 15q11.2 microdeletions, and one with 7q11.23 microduplications. Of the seven cases carrying pathogenic CNVs, three were tested for family genetics; of these, one was de novo, and two were inherited from either the father or mother. In total, 68 fetuses with CTEV were initially identified, of which 66 cases successfully followed-up. Of these, 9 were terminated, 2 died in utero, and 55 were live births. In 9 cases, no clinical manifestations of CTEV were found at birth; the false-positive rate of prenatal ultrasound CTEVdiagnosis was thus 13.6% (9/66). CONCLUSION CTEV was associated with chromosome microdeletion/microduplication, the most common of which was 22q11.21 microdeletion, followed by 17p12p11.2 microduplication. Thus, further genomic detection is recommended for fetuses with CTEV showing no abnormalities on conventional karyotype analysis.
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Affiliation(s)
- Meiying Cai
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Jiansong Lin
- Department of Pathology, Fujian Maternal and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Yanting Que
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, 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
| | - Hailong Huang
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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Liu Y, Hu T, Qian Y, Wang J, Hu R, Xiao L, Liao N, Liu Z, Wang H, Liu S, Zhang Z. Prenatal diagnosis of chromosomal aberrations by chromosomal microarray analysis and pregnancy outcomes of fetuses with polyhydramnios. J Matern Fetal Neonatal Med 2024; 37:2344089. [PMID: 38710614 DOI: 10.1080/14767058.2024.2344089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 04/12/2024] [Indexed: 05/08/2024]
Abstract
OBJECTIVES To explore the prenatal clinical utility of chromosome microarray analysis (CMA) for polyhydramnios and evaluate the short and long-term prognosis of fetuses with polyhydramnios. METHODS A total of 600 singleton pregnancies with persistent polyhydramnios from 2014 to 2020 were retrospectively enrolled in this study. All cases received amniocentesis and were subjected to CMA results. All cases were categorized into two groups: isolated polyhydramnios and non-isolated polyhydramnios [with soft marker(s) or with sonographic structural anomalies]. All fetuses were followed up from 6 months to five years after amniocentesis to acquire short and long-term prognosis. RESULTS The detection rates of either aneuploidy or pathogenic copy number variants in fetuses with non-isolated polyhydramnios were significantly higher than those with isolated polyhydramnios (5.0 vs. 1.5%, p = 0.0243; 3.6 vs. 0.8%, p = 0.0288). The detection rate of total chromosomal abnormalities in the structural abnormality group was significantly higher than that in the isolated group (10.0 vs. 2.3%, p = 0.0003). In the CMA-negative cases, the incidence of termination of pregnancy, neonatal and childhood death, and non-neurodevelopmental disorders in fetuses combined with structural anomalies was significantly higher than that in fetuses with isolated polyhydramnios (p < 0.05). We did not observe any difference in the prognosis between the isolated group and the combined group of ultrasound soft markers. In addition, the risk of postnatal neurodevelopmental disorders was also consistent among the three groups (1.6 vs. 1.3 vs. 1.8%). CONCLUSION For low-risk pregnancies, invasive prenatal diagnosis of isolated polyhydramnios might be unnecessary. CMA should be considered for fetuses with structural anomalies. In CMA-negative cases, the prognosis of fetuses with isolated polyhydramnios was good, and polyhydramnios itself did not increase the risk of postnatal neurological development disorders. The worse prognosis mainly depends on the combination of polyhydramnios with structural abnormalities.
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Affiliation(s)
- Yanyan Liu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Ting Hu
- Department of Medical Genetics, West China Second University Hospital, Sichuan University, Chengdu, Sichuan, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, China
| | - Yanping Qian
- 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, Sichuan, 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, Sichuan, 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, Sichuan, 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, Sichuan, 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, Sichuan, 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, Sichuan, 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, Sichuan, 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, Sichuan, China
| | - 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, Sichuan, China
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Zhang Y, Du Q, Gao H, Pan Y, Liu N, Qiu C, Liu X. Prenatal risk assessment of Xp21.1 duplication involving the DMD gene by optical genome mapping. Life Sci Alliance 2024; 7:e202402780. [PMID: 39117454 PMCID: PMC11310561 DOI: 10.26508/lsa.202402780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 08/01/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024] Open
Abstract
Structural variants (SVs) of unknown significance are great challenges for prenatal risk assessment, especially when involving dose-sensitive genes such as DMD The pathogenicities of 5'-terminal DMD duplications in the database remain controversial. Four prenatal cases with Xp21.1 duplications were identified by routine prenatal genomic testing, encompassing the 5'-UTR to exons 1-2 in family 1 and family 2, and to exons 1-9 in family 3. The duplication in family 4 was non-contiguous covering the 5'-UTR to exon 1 and exons 3-7. All were traced to unaffected males in the family pedigrees. A new genome-wide approach of optical genome mapping was performed in families 1, 2, and 3 to delineate the breakpoints and orientation of the duplicated fragments. The extra copies were tandemly inserted into the upstream of DMD, preserving the integrity of ORF from the second copy. The pathogenicities were thus reclassified as likely benign. Our data highlight the importance of structural delineation by optical genome mapping in prenatal risk assessment of incidentally identified SVs involving DMD and other similar large dose-sensitive genes.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Qiang Du
- Center of Reproductive Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Haiming Gao
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yujie Pan
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Ningyang Liu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Chuang Qiu
- Department of Orthopedics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xiaoliang Liu
- Department of Clinical Genetics, Shengjing Hospital of China Medical University, Shenyang, China
- Key Laboratory of Reproductive Health, Liaoning Research Institute of Reproductive Health and Development, Reproductive Hospital of China Medical University, Shenyang, China
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Zhang J, Qin M, Ma M, Li H, Wang N, Zhu X, Yan L, Qiao J, Yan Z. Assessing the necessity of screening ≤5 Mb segmental aneuploidy in routine PGT for aneuploidies. Reprod Biomed Online 2024; 49:103991. [PMID: 38936339 DOI: 10.1016/j.rbmo.2024.103991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 03/09/2024] [Accepted: 04/08/2024] [Indexed: 06/29/2024]
Abstract
RESEARCH QUESTION Does routine clinical practice require an increase in the resolution of preimplantation genetic testing for aneuploidies (PGT-A) to detect segmental aneuploidies ≤5 Mb? DESIGN This retrospective study analysed 963 trophectoderm biopsies from 346 couples undergoing PGT between 2019 and 2023. Segmental aneuploidies ≥1 Mb were reported. The characteristics, clinical interpretation and concordance of segmental aneuploidies ≤5 Mb were analysed. RESULTS The incidence of segmental aneuploidies was 15.1% (145/963) in blastocysts, with segmental aneuploidies of ≤5 Mb accounting for 2.3% (22/963). The size of the segmental aneuploidies showed a skewed distribution. Segmental aneuploidies ≤5 Mb were found to occur more frequently on the q arm of the chromosome, compared with the p arm. Losses of ≤5 Mb segmental aneuploidies were more prevalent than gains, with 17 deletions compared with 5 duplications. Of the segmental aneuploidies, 63.6% (14/22) ≤5 Mb were de novo, and 50.0% (7/14) of de-novo segmental aneuploidies were pathogenic/likely pathogenic (P/LP) copy number variations, accounting for 0.7% of 963 blastocysts. For blastocysts carrying ≤5 Mb segmental aneuploidies, a re-analysis of back-up biopsy samples showed that 35.7% of de-novo segmental aneuploidies (5/14) were not detected in the back-up samples. Cases were reported in which prenatal diagnosis (amniocentesis) revealed the absence of embryonic ≤5 Mb segmental aneuploidies detected at the blastocyst stage. CONCLUSIONS The incidence of P/LP de-novo ≤5 Mb segmental aneuploidies in human blastocysts is extremely low. There is no compelling need to increase the resolution of PGT-A to 5 Mb in routine clinical practice.
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Affiliation(s)
- Jiaqi Zhang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Meng Qin
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Mochen Ma
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Hanna Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Nan Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China..
| | - Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, China.; National Clinical Research Center for Obstetrics and Gynecology, Beijing, China.; Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, China.; Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, China..
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Yan J, Huang Y, Cao L, Dong Y, Xu Z, Wang F, Gao Y, Feng D, Zhang M. Clinical, pathological and genetic characteristics of 17 unrelated children with Alagille Syndrome. BMC Pediatr 2024; 24:532. [PMID: 39164659 PMCID: PMC11334458 DOI: 10.1186/s12887-024-04973-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 07/25/2024] [Indexed: 08/22/2024] Open
Abstract
BACKGROUND Alagille syndrome (ALGS) is a multisystem genetic disorder frequently characterized by hepatic manifestations. This study analyzed the clinical, pathological, and molecular genetic features of ALGS to improve the efficiency of clinical diagnosis. METHODS We retrospectively analyzed the clinical manifestations, pathological examination findings, and genetic testing results of 17 children diagnosed with ALGS based on the revised criteria and hospitalized at our center from January 2012 to January 2022. RESULTS The clinical manifestations are as follows: Cholestasis (16/17, 94%), characteristic facies (15/17, 88%), heart disease (12/16, 75%), butterfly vertebrae (12/17, 71%) and posterior embryotoxon (7/12, 58%). Among the 15 patients who underwent liver pathology examination, 13 (87%) were found to have varying degrees of bile duct paucity. Genetic testing was performed on 15 children, and pathogenic variants of the jagged canonical Notch ligand 1 (JAG1) gene were identified in 13 individuals, including 4 novel variants. No pathogenic variant in the notch homolog 2 (NOTCH2) gene were identified, and 2 children exhibited none of the aforementioned gene pathogenic variants. The median follow-up duration was 7 years. Of the remaining 15 patients (excluding 2 lost to follow-up), 11 remained stable, 4 deteriorated, and no patient died during the follow-up period. CONCLUSIONS Among children diagnosed with ALGS, cholestasis stands as the most common feature. To minimize the risk of misdiagnosis, genetic testing should be performed on children exhibiting cholestasis, followed by the application of the revised diagnostic criteria for ALGS. While pharmacological therapy has shown effectiveness for ALGS patients, liver transplantation may be considered in instances of severe pruritus.
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Affiliation(s)
- Jianguo Yan
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yuanzhi Huang
- Peking University 302 Clinical Medical School, 38 Xueyuan Road, 100191, Beijing, China
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Lili Cao
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yi Dong
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Zhiqiang Xu
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Fuchuan Wang
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yinjie Gao
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Danni Feng
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Min Zhang
- Peking University 302 Clinical Medical School, 38 Xueyuan Road, 100191, Beijing, China.
- Senior Department of Liver Diseases, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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Chen X, Lan L, Wu H, Zeng M, Zheng Z, Zhong Q, Lai F, Hu Y. Chromosomal Microarray Analysis in Fetuses with Ultrasound Abnormalities. Int J Gen Med 2024; 17:3531-3540. [PMID: 39161407 PMCID: PMC11332413 DOI: 10.2147/ijgm.s472906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Accepted: 08/09/2024] [Indexed: 08/21/2024] Open
Abstract
Objective To explore and evaluate the value of chromosomal microarray analysis (CMA) in prenatal diagnosis of fetuses with ultrasound abnormalities. Methods A retrospective analysis was performed on 370 fetuses with ultrasound abnormalities received invasive prenatal diagnosis at Meizhou People's Hospital from October 2022 to December 2023. Fetal specimens were analyzed by CMA, and the detection rates of aneuploidy and pathogenic (P)/likely pathogenic (LP) copy number variations (CNVs) in ultrasound structural abnormalities (malformations of fetal anatomy) and non-structural abnormalities (abnormalities of fetal nonanatomical structure) were analyzed. Results There were 114 (30.8%) cases with isolated ultrasound structural abnormalities, 226 (61.1%) cases with isolated non-structural abnormalities (182 isolated ultrasound soft markers abnormalities, 30 isolated fetal growth restriction (FGR), and 8 isolated abnormalities of amniotic fluid volume), and 30 (8.1%) cases with both structural and non-structural abnormalities. The overall detection rate of aneuploidy and P/LP CNVs in isolated ultrasonic structural abnormalities was 5.3%, among which cardiovascular system abnormalities were the highest. In addition, the largest number of fetuses with non-structural abnormalities was nuchal translucency (NT) thickening (n = 81), followed by ventriculomegaly (n = 29), and nasal bone dysplasia (n = 24). The detection rate of chromosomal abnormalities of fetuses with abnormal ultrasound soft markers was 9.9%, and the detection rate in single abnormal ultrasound soft marker, and multiple ultrasound soft markers abnormalities was 9.7% (16/165) and 11.8% (2/17), respectively. Moreover, the detection rate of chromosomal abnormalities of fetuses with FGR and structural abnormalities combined with non-structural abnormalities was 6.7% (2/30), and 13.3% (4/30), respectively. Conclusion The incidence of chromosomal abnormalities (aneuploidy and P/LP CNVs) varies among different fetal ultrasound abnormalities.
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Affiliation(s)
- Xiaoqin Chen
- Department of Prenatal Diagnostic Center, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
- Department of Obstetrics, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Liubing Lan
- Department of Prenatal Diagnostic Center, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
- Department of Obstetrics, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Heming Wu
- Department of Prenatal Diagnostic Center, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Mei Zeng
- Department of Prenatal Diagnostic Center, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
- Department of Obstetrics, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Zhiyuan Zheng
- Department of Prenatal Diagnostic Center, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Qiuping Zhong
- Department of Obstetrics, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Fengdan Lai
- Department of Obstetrics, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
| | - Yonghe Hu
- Department of Obstetrics, Meizhou People’s Hospital, Meizhou Academy of Medical Sciences, Meizhou, People’s Republic of China
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张 利, 毋 盛, 郭 亚, 杨 建, 孙 红, 杨 俊, 陈 永. [Clinical and genetic features of children with 3-methylcrotonyl-coenzyme A carboxylase deficiency: an analysis of six cases]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2024; 26:845-851. [PMID: 39148390 PMCID: PMC11334540 DOI: 10.7499/j.issn.1008-8830.2404026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 07/01/2024] [Indexed: 08/17/2024]
Abstract
OBJECTIVES To investigate the clinical and genetic features of children with 3-methylcrotonyl-coenzyme A carboxylase deficiency (MCCD). METHODS A retrospective analysis was conducted on the clinical manifestations and genetic testing results of six children with MCCD who attended Children's Hospital Affiliated to Zhengzhou University from January 2018 to October 2023. RESULTS Among the six children with MCCD, there were 4 boys and 2 girls, with a mean age of 7 days at the time of attending the hospital and 45 days at the time of confirmed diagnosis. Of all children, one had abnormal urine odor and five had no clinical symptoms. All six children had increases in blood 3-hydroxyisovaleryl carnitine and urinary 3-hydroxyisovaleric acid and 3-methylcrotonoylglycine, and five of them had a reduction in free carnitine. A total of six mutations were identified in the MCCC1 gene, i.e., c.1630del(p.R544Dfs*2), c.269A>G(p.D90G), c.1609T>A(p.F537I), c.639+2T>A, c.761+1G>T, and c.1331G>A(p.R444H), and three mutations were identified in the MCCC2 gene, i.e., c.838G>T(p.D280Y), c.592C>T(p.Q198*,366), and c.1342G>A(p.G448A). Among these mutations, c.269A>G(p.D90G) and c.1609T>A(p.F537I) had not been previously reported in the literature. There was one case of maternal MCCD, and the child carried a heterozygous mutation from her mother. Five children with a reduction in free carnitine were given supplementation of L-carnitine, and free carnitine was restored to the normal level at the last follow-up visit. CONCLUSIONS This study identifies two new mutations, c.269A>G(p.D90G) and c.1609T>A(p.F537I), thereby expanding the mutation spectrum of the MCCC1 gene. A combination of blood amino acid and acylcarnitine profiles, urine organic acid analysis, and genetic testing can facilitate early diagnosis and treatment of MCCD, and provide essential data for genetic counseling.
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Affiliation(s)
| | - 盛楠 毋
- 郑州大学附属儿童医院内分泌遗传代谢科,河南郑州450018
| | - 亚楠 郭
- 郑州大学附属儿童医院内分泌遗传代谢科,河南郑州450018
| | | | | | | | - 永兴 陈
- 郑州大学附属儿童医院内分泌遗传代谢科,河南郑州450018
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Lempel N, Shelly S, Chorin O, Rock R, Eliyahu A, Finezilber Y, Poran H, Feinstein-Goren N, Segev M, Reznik-Wolf H, Barel O, Orion D, Anis S, Regev M, Yonath H, Dominissini D, Blatt I, Hassin-Baer S, Dori A, Pras E, Greenbaum L. The yield of genetic workup for middle-aged and elderly patients with neurological disorders in a real-world setting. J Neurol Sci 2024; 463:123074. [PMID: 38968664 DOI: 10.1016/j.jns.2024.123074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/25/2024] [Accepted: 05/29/2024] [Indexed: 07/07/2024]
Abstract
Genetic workup is becoming increasingly common in the clinical assessment of neurological disorders. We evaluated its yield among middle-aged and elderly neurological patients, in a real-world context. This retrospective study included 368 consecutive Israeli patients aged 50 years and older (202 [54.9%] males), who were referred to a single neurogenetics clinic between 2017 and mid-2023. All had neurological disorders, without a previous molecular diagnosis. Demographic, clinical and genetic data were collected from medical records. The mean age at first genetic counseling at the clinic was 62.3 ± 7.8 years (range 50-85 years), and the main indications for referral were neuromuscular, movement and cerebrovascular disorders, as well as cognitive impairment and dementia. Out of the 368 patients, 245 (66.6%) underwent genetic testing that included exome sequencing (ES), analysis of nucleotide repeat expansions, detection of specific mutations, targeted gene panel sequencing or chromosomal microarray analysis. Overall, 80 patients (21.7%) received a molecular diagnosis due to 36 conditions, accounting for 32.7% of the patients who performed genetic testing. The diagnostic rates were highest for neuromuscular (58/186 patients [31.2%] in this group, 39.2% of 148 tested individuals) and movement disorders (14/79 [17.7%] patients, 29.2% of 48 tested), but lower for other disorders. Testing of nucleotide repeat expansions and ES provided a diagnosis to 28/73 (38.4%) and 19/132 (14.4%) individuals, respectively. Based on our findings, genetic workup and testing are useful in the diagnostic process of neurological patients aged ≥50 years, in particular for those with neuromuscular and movement disorders.
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Affiliation(s)
- Noga Lempel
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Shahar Shelly
- Department of Neurology, Rambam Medical Center, Haifa, Israel; Rappaport Faculty of Medicine, Technion, Haifa, Israel; Department of Neurology, Mayo Clinic, Rochester, MN, United States of America
| | - Odelia Chorin
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Rachel Rock
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Aviva Eliyahu
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Yael Finezilber
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Hana Poran
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Neta Feinstein-Goren
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Meirav Segev
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Haike Reznik-Wolf
- The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Ortal Barel
- The Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - David Orion
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | - Saar Anis
- Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel; Movement Disorders Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Miriam Regev
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Hagith Yonath
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; Department of Internal Medicine A, Sheba Medical Center, Tel Hashomer, Israel
| | - Dan Dominissini
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Genomics Unit, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel; The Wohl Institute for Translational Medicine, Sheba Cancer Research Center, Sheba Medical Center, Tel Hashomer, Israel
| | - Ilan Blatt
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Sharon Hassin-Baer
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel; Movement Disorders Institute, Sheba Medical Center, Tel Hashomer, Israel
| | - Amir Dori
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Department of Neurology, Sheba Medical Center, Tel Hashomer, Israel
| | - Elon Pras
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel
| | - Lior Greenbaum
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; The Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel; The Joseph Sagol Neuroscience Center, Sheba Medical Center, Tel Hashomer, Israel.
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9
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Zouaghi Y, Choudhary AM, Irshad S, Adamo M, Rehman KU, Fatima A, Shahid M, Najmi N, De Azevedo Correa F, Habibi I, Boizot A, Niederländer NJ, Ansar M, Santoni F, Acierno J, Pitteloud N. Genome sequencing reveals novel causative structural and single nucleotide variants in Pakistani families with congenital hypogonadotropic hypogonadism. BMC Genomics 2024; 25:787. [PMID: 39143522 PMCID: PMC11325732 DOI: 10.1186/s12864-024-10598-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 07/05/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND/OBJECTIVES This study aims to elucidate the genetic causes of congenital hypogonadotropic hypogonadism (CHH), a rare genetic disorder resulting in GnRH deficiency, in six families from Pakistan. METHODS Eighteen DNA samples from six families underwent genome sequencing followed by standard evaluation for pathogenic single nucleotide variants (SNVs) and small indels. All families were subsequently analyzed for pathogenic copy number variants (CNVs) using CoverageMaster. RESULTS Novel pathogenic homozygous SNVs in known CHH genes were identified in four families: two families with variants in GNRHR, and two others harboring KISS1R variants. Subsequent investigation of CNVs in the remaining two families identified novel unique large deletions in ANOS1. CONCLUSION A combined, systematic analysis of single nucleotide and CNVs helps to improve the diagnostic yield for variants in patients with CHH.
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Affiliation(s)
- Yassine Zouaghi
- University of Lausanne, Lausanne, Switzerland
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
| | - Anbreen Mazhar Choudhary
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
- FMH College of Medicine & Dentistry, Lahore, Pakistan
| | - Saba Irshad
- School of Biochemistry and Biotechnology, University of the Punjab, Lahore, Pakistan
| | - Michela Adamo
- University of Lausanne, Lausanne, Switzerland
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
| | | | - Ambrin Fatima
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Mariam Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Nida Najmi
- Department of Obstetrics and Gynaecology, The Aga Khan University Hospital, Karachi, Pakistan
| | - Fernanda De Azevedo Correa
- University of Lausanne, Lausanne, Switzerland
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
| | - Imen Habibi
- University of Lausanne, Lausanne, Switzerland
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
| | - Alexia Boizot
- University of Lausanne, Lausanne, Switzerland
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
| | - Nicolas J Niederländer
- University of Lausanne, Lausanne, Switzerland
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
| | - Muhammad Ansar
- Department of Ophthalmology, University of Lausanne, Jules Gonin Eye Hospital, Fondation Asile Des Aveugles, Lausanne, Switzerland
- Advanced Molecular Genetics and Genomics Disease Research and Treatment Centre, Dow University of Health Sciences, Karachi, Pakistan
| | - Federico Santoni
- University of Lausanne, Lausanne, Switzerland
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
- , Medigenome, Geneva, Switzerland
| | - James Acierno
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland
| | - Nelly Pitteloud
- University of Lausanne, Lausanne, Switzerland.
- Service of Endocrinology, Diabetology and Metabolism, Lausanne University Hospital, Avenue de La Sallaz 8, Lausanne, CH-1011, Switzerland.
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10
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D’Gama AM, Shao W, Smith L, Koh HY, Davis M, Koh J, Oby BT, Urzua CI, Sheidley BR, Rockowitz S, Poduri A. Utility of Genome Sequencing After Nondiagnostic Exome Sequencing in Unexplained Pediatric Epilepsy. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.08.08.24307445. [PMID: 39148850 PMCID: PMC11326351 DOI: 10.1101/2024.08.08.24307445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Importance Epilepsy is the most common neurological disorder of childhood. Identifying genetic diagnoses underlying epilepsy is critical to developing effective therapies and improving outcomes. Most children with non-acquired (unexplained) epilepsy remain genetically unsolved, and the utility of genome sequencing after nondiagnostic exome sequencing is unknown. Objective To determine the diagnostic (primary) and clinical (secondary) utility of genome sequencing after nondiagnostic exome sequencing in individuals with unexplained pediatric epilepsy. Design This cohort study performed genome sequencing and comprehensive analyses for 125 participants and available biological parents enrolled from August 2018 to May 2023, with data analysis through April 2024 and clinical return of diagnostic and likely diagnostic genetic findings. Clinical utility was evaluated. Setting Pediatric referral center. Participants Participants with unexplained pediatric epilepsy and previous nondiagnostic exome sequencing; biological parents when available. Exposures Short-read genome sequencing and analysis. Main Outcomes and Measures Primary outcome measures were the diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding, and the unique diagnostic yield of genome sequencing, defined as the percentage of participants receiving a diagnostic or likely diagnostic genetic finding that required genome sequencing. The secondary outcome measure was clinical utility of genome sequencing, defined as impact on evaluation, treatment, or prognosis for the participant or their family. Results 125 participants (58 [46%] female) were enrolled with median age at seizure onset 3 [IQR 1.25, 8] years, including 44 (35%) with developmental and epileptic encephalopathies. The diagnostic yield of genome sequencing was 7.2% (9/125), with diagnostic genetic findings in five cases and likely diagnostic genetic findings in four cases. Among the solved cases, 7/9 (78%) required genome sequencing for variant detection (small copy number variant, three noncoding variants, and three difficult to sequence small coding variants), for a unique diagnostic yield of genome sequencing of 5.6% (7/125). Clinical utility was documented for 4/9 solved cases (44%). Conclusions and Relevance These findings suggest that genome sequencing can have diagnostic and clinical utility after nondiagnostic exome sequencing and should be considered for patients with unexplained pediatric epilepsy.
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Affiliation(s)
- Alissa M. D’Gama
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
- Division of Newborn Medicine, Department of Pediatrics, Boston Children’s Hospital, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
- Children’s Rare Disease Collaborative, Boston Children’s Hospital, Boston, MA
| | - Wanqing Shao
- Children’s Rare Disease Collaborative, Boston Children’s Hospital, Boston, MA
| | - Lacey Smith
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
| | - Hyun Yong Koh
- Department of Pediatrics, Section of Neurology and Developmental Neuroscience, Baylor College of Medicine, Houston, TX
| | - Maya Davis
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
| | - Julia Koh
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
| | - Brandon T. Oby
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
| | - Cesar I. Urzua
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
| | - Beth R. Sheidley
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
| | - Shira Rockowitz
- Children’s Rare Disease Collaborative, Boston Children’s Hospital, Boston, MA
- Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA
- The Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, MA
| | - Annapurna Poduri
- Epilepsy Genetics Program, Department of Neurology, Boston Children’s Hospital, Boston, MA
- Children’s Rare Disease Collaborative, Boston Children’s Hospital, Boston, MA
- Department of Neurology, Harvard Medical School, Boston, MA
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11
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Pereira SSS, Pinto IP, Santos VCDP, Silva RC, Costa EOA, da Cruz AS, da Cruz AD, da Silva CC, Minasi LB. Analysis of parental origin of de novo pathogenic CNVs in patients with intellectual disability. Genet Mol Biol 2024; 47:e20230313. [PMID: 39136576 PMCID: PMC11320663 DOI: 10.1590/1678-4685-gmb-2023-0313] [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: 11/01/2023] [Accepted: 06/25/2024] [Indexed: 08/16/2024] Open
Abstract
Chromosomal Microarray Analysis (CMA) has increased the comprehension of the mechanisms of copy number variation (CNV) formation, classification of these rearrangements, type of recurrence, and its origin, and has also been a powerful approach to identifying CNVs in individuals with intellectual disability. The aim of this study was to establish the parental origin of de novo pathogenic CNV in a cohort of patients with intellectual disability from the public health system of Goiás-Brazil. CMA was done in 76 trios and we identified 15 de novo pathogenic CNVs in 12 patients with intellectual disability. In a total of 15 de novo pathogenic CNV, 60% were derived from the maternal germline and 40% from the paternal germline. CNV flanked by low copy repeats (LCR) were identified in 46.7% and most of them were of maternal origin. No significant association was observed between paternal age and the mutation rate of de novo CNVs. The presence of high-identity LCRs increases the occurrence of CNV formation mediated by non-allelic homologous recombination and the majority of paternal CNVs are non-recurrent. The mechanism of formation of these CNV may have been by microhomology-mediated break-induced replication or non-homologous end joining.
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Affiliation(s)
- Samara Socorro Silva Pereira
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Irene Plaza Pinto
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Victor Cortázio do Prado Santos
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Rafael Carneiro Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Emília Oliveira Alves Costa
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Alex Silva da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
| | - Aparecido Divino da Cruz
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
- Universidade Federal de Goiás, Programa de Pós-Graduação em Genética e Biologia Molecular, Goiânia, GO, Brazil
| | - Cláudio Carlos da Silva
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
- Secretaria Estadual de Saúde de Goiás, Centro Estadual de Reabilitação e Readaptação Dr. Henrique Santillo, Goiânia, GO, Brazil
| | - Lysa Bernardes Minasi
- Pontifícia Universidade Católica de Goiás, Escola de Ciências Médicas e da Vida, Programa de Pós-Graduação em Genética, Núcleo de Pesquisa Replicon, Goiânia, GO, Brazil
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12
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Long X, Xiong W, Wang X, Geng J, Zhong M, Huang Y, Liu M, Bu F, Cheng J, Lu Y, Yuan H. Genotype-phenotype spectrum and correlation of PHARC Syndrome due to pathogenic ABHD12 variants. BMC Med Genomics 2024; 17:203. [PMID: 39123271 PMCID: PMC11312174 DOI: 10.1186/s12920-024-01984-7] [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: 12/18/2023] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
BACKGROUND A comprehensive understanding of the genetic basis of rare diseases and their regulatory mechanisms is essential for human molecular genetics. However, the genetic mutant spectrum of pathogenic genes within the Chinese population remains underrepresented. Here, we reported previously unreported functional ABHD12 variants in two Chinese families and explored the correlation between genetic polymorphisms and phenotypes linked to PHARC syndrome. METHODS Participants with biallelic pathogenic ABHD12 variants were recruited from the Chinese Deafness Genetics Cohort. These participants underwent whole-genome sequencing. Subsequently, a comprehensive literature review was conducted. RESULTS Two Han Chinese families were identified, one with a compound heterozygous variant and the other with a novel homozygous variant in ABHD12. Among 65 PHARC patients, including 62 from the literature and 3 from this study, approximately 90% (57 out of 63) exhibited hearing loss, 82% (50 out of 61) had cataracts, 82% (46 out of 56) presented with retinitis pigmentosa, 79% (42 out of 53) experienced polyneuropathy, and 63% (36 out of 57) displayed ataxia. Seventeen different patterns were observed in the five main phenotypes of PHARC syndrome. A total of 33 pathogenic variants were identified in the ABHD12. Compared with other genotypes, individuals with biallelic truncating variants showed a higher incidence of polyneuropathy (p = 0.006), but no statistically significant differences were observed in the incidence of hearing loss, ataxia, retinitis pigmentosa and cataracts. CONCLUSIONS The diagnosis of PHARC syndrome is challenging because of its genetic heterogeneity. Therefore, exploring novel variants and establishing genotype-phenotype correlations can significantly enhance gene diagnosis and genetic counseling for this complex disease.
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Affiliation(s)
- Xicui Long
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Wenyu Xiong
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Xuegang Wang
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Jia Geng
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Mingjun Zhong
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Yu Huang
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Man Liu
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Fengxiao Bu
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Jing Cheng
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China
| | - Yu Lu
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China.
| | - Huijun Yuan
- Department of Oto-Rhino-Laryngology, West China Hospital of Sichuan University, Chengdu, 610000, China.
- Institute of Rare Diseases, West China Hospital of Sichuan University, Chengdu, 610000, China.
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13
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Jiang C, He Y, Chen X, Xia F, Shi F, Xu X, Sun T, You K. X-linked severe combined immunodeficiency complicated by disseminated bacillus Calmette-Guérin disease caused by a novel pathogenic mutation in exon 3 of the IL2RG gene: a case report and literature review. Front Immunol 2024; 15:1453046. [PMID: 39176082 PMCID: PMC11338812 DOI: 10.3389/fimmu.2024.1453046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/24/2024] Open
Abstract
X-linked severe combined immunodeficiency (X-SCID), caused by mutations in the gamma-chain gene of the interleukin-2 receptor (IL2RG), is a prevalent form of SCID characterized by recurrent and fatal opportunistic infections that occur early in life. The incidence of disseminated bacillus Calmette-Guérin (BCG) disease among children with SCID is much higher than in the general population. Here, we report the case of a 4-month-old male infant who presented with subcutaneous induration, fever, an unhealed BCG vaccination site, and hepatosplenomegaly. Metagenomic next-generation sequencing in blood, and the detection of gastric juice and skin nodule pus all confirmed the infection of Mycobacterium tuberculosis. Lymphocyte subset analysis confirmed the presence of T-B+NK immunodeficiency. Whole-exome and Sanger sequencing revealed a novel microdeletion insertion mutation (c.316_318delinsGTGAT p.Leu106ValfsTer42) in the IL2RG gene, resulting in a rare shift in the amino acid sequence of the coding protein. Consequently, the child was diagnosed with X-SCID caused by a novel mutation in IL2RG, complicated by systemic disseminated BCG disease. Despite receiving systemic anti-infection treatment and four days of hospitalization, the patient died three days after discharge. To the best of our knowledge, this specific IL2RG mutation has not been previously reported. In our systemic review, we outline the efficacy of systemic anti-tuberculosis therapy, hematopoietic stem cell transplantation, and gene therapy in children with SCID and BCG diseases caused by IL2RG gene mutation.
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Affiliation(s)
- Chunxue Jiang
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yunhan He
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xin Chen
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Fei Xia
- Computer Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Feng Shi
- Computer Center, Shengjing Hospital of China Medical University, Shenyang, China
| | - Xuewen Xu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Tingting Sun
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
| | - Kai You
- Department of Pediatrics, Shengjing Hospital of China Medical University, Shenyang, China
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14
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Freitas I, Albuquerque A, de Marco L, Eduardo, Melo JR, Drummond J, Rocha B. From Nonfunctioning Adrenocortical Cancer to Biochemically Silent Paraganglioma Associated with SDHB Mutation: An Uncommon Presentation of a Patient with a Retroperitoneal Mass. Case Rep Endocrinol 2024; 2024:6664694. [PMID: 39129823 PMCID: PMC11315972 DOI: 10.1155/2024/6664694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 04/19/2024] [Accepted: 06/12/2024] [Indexed: 08/13/2024] Open
Abstract
The combination of clinical characteristics and diagnostic exams including imaging, laboratory, and molecular tests help in the differential diagnosis of retroperitoneal lesions. We report a 41-year-old male with a metastatic retroperitoneal lesion with atypical characteristics, displaying pathological findings consistent with both nonsecretory pheochromocytomas/paragangliomas and adrenal cortex carcinoma. The patient was examined for abdominal pain, weight loss, and hypertension. Abdominal computed tomography showed a 21 × 8 × 10-cm right retroperitoneal mass. He was initially diagnosed as pheochromocytoma/paraganglioma (PHEO/PGL). However, the diagnosis was later changed to adrenocortical carcinoma based on histopathological features of the metastatic lesions and the findings of normal urinary levels of catecholamines/metanephrines. Systemic chemotherapy and abdominal radiotherapy were performed, in addition to multiple surgical resections, with no satisfactory response. The indolent course of the disease and minimal impact on the patient's performance status led to a genetic evaluation which resulted in the identification of a germline mutation in the succinate dehydrogenase complex subunit B (SDHB). An immunohistology review of previous slides was consistent with the hypothesis of a neuroendocrine tumor. Forty percent of the patients with PHEO/PGL have an underlying germline mutation. SDHB mutation is frequently associated with metastatic disease and dominant secretion of noradrenaline and/or dopamine. In addition to the metastatic disease, few cases with the mutations can be a biochemically silent PHEO/PGL. We concluded that the patient presented a metastatic abdominal paraganglioma associated with an SDHB mutation and we reinforced the need to perform genetic screening for all adrenal/extra-adrenal lesions characteristic of PHEO/PGL.
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Affiliation(s)
- Izabella Freitas
- Department of EndocrinologyFederal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Anna Albuquerque
- Department of Molecular MedicineUFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Luiz de Marco
- Department of Molecular MedicineUFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo
- Department of PathologyUFMG, Belo Horizonte, Minas Gerais, Brazil
| | - José Renan Melo
- Department of SurgeryUFMG, Belo Horizonte, Minas Gerais, Brazil
| | - Juliana Drummond
- Department of EndocrinologyFederal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Beatriz Rocha
- Department of EndocrinologyFederal University of Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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Boughalem A, Ciorna-Monferrato V, Sloboda N, Guegan A, Page F, Zimmer S, Benazra M, Kleinfinger P, Lohmann L, Valduga M, Receveur A, Martin F, Trost D. Optical genome mapping identifies a homozygous deletion in the non-coding region of the SCN9A gene in individuals from the same family with congenital insensitivity to pain. Front Genet 2024; 15:1375770. [PMID: 39156962 PMCID: PMC11327051 DOI: 10.3389/fgene.2024.1375770] [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: 02/01/2024] [Accepted: 07/18/2024] [Indexed: 08/20/2024] Open
Abstract
We report an index patient with complete insensitivity to pain and a history of painless fractures, joint hypermobility, and behavioral problems. The index patient descends from a family with notable cases among his maternal relatives, including his aunt and his mother's first cousin, both of whom suffer from congenital insensitivity to pain. The patient had normal results for prior genetic testing: fragile-X syndrome testing, chromosomal microarray analysis, and exome sequencing. Optical genome mapping detected a homozygous deletion affecting the noncoding 5' untranslated region (UTR) and the first non-coding exon of the SCN9A gene in all affected family members, compatible with recessive disease transmission. Pathogenic homozygous loss-of-function variants in the SCN9A gene are associated with impaired pain sensation in humans. Optical genome mapping can thus detect pathogenic structural variants in patients without molecular etiology by standard diagnostic procedures and is a more accessible diagnostic tool than short-read or long-read whole-genome sequencing.
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Affiliation(s)
- Aïcha Boughalem
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Viorica Ciorna-Monferrato
- Génétique Médicale et Oncogénétique, Hôpital Femme Mère Enfant, CHR Metz-Thionville, site de Mercy, 1, Allée du Château, Metz Cedex, France
| | - Natacha Sloboda
- Génétique Médicale et Oncogénétique, Hôpital Femme Mère Enfant, CHR Metz-Thionville, site de Mercy, 1, Allée du Château, Metz Cedex, France
| | - Amélie Guegan
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - François Page
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Sophie Zimmer
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Marion Benazra
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Pascale Kleinfinger
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Laurence Lohmann
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Mylène Valduga
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Aline Receveur
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Fernando Martin
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
| | - Detlef Trost
- Department of Human Genetics, Laboratoire CERBA SA, Saint Ouen L’aumône, France
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16
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Wang Y, Wang H, Yang W, Guo H, Zhang M, Gao Y, Kang B, Liao S. A novel de novo synonymous variant in GREB1L impacts the mRNA splicing associated with aplasia of the urogenital system. Am J Med Genet A 2024:e63823. [PMID: 39091162 DOI: 10.1002/ajmg.a.63823] [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: 04/30/2024] [Revised: 07/02/2024] [Accepted: 07/07/2024] [Indexed: 08/04/2024]
Abstract
GREB1-like retinoic acid receptor coactivator (GREB1L) gene is associated with autosomal dominant renal hypodysplasia/aplasia 3 (RHDA3) and deafness, autosomal dominant 80 (DFNA80). Among the GREB1L variants reported, most of them are missense or frameshift, while no pathogenic synonymous variants have been recorded. Classical theory paid little attention to synonymous variants and classified it as nonpathogenic; however, recent studies suggest that the variants might be equally important. Here, we report a 7-year-old girl with new symptoms of clitoromegaly, uterovaginal, and ovarian agenesis as well as right kidney missing. A novel de novo GREB1L synonymous variant (NM_001142966: c.4731C>T, p.G1577=) was identified via whole exome sequencing. The variant was predicted to be disease-causing through in silico analysis and was classified as likely pathogenic. Minigene splicing assays confirmed a 6 bp deletion in mutant cDNA comparing with the wild type, leading to two amino acids lost in GREB1L protein. Secondary and tertiary structure modeling showed alterations in protein structure. Our finding reveals a novel GREB1L variant with a new phenotype of urogenital system and is the first to report a pathogenic synonymous variant in GREB1L which affects mRNA splicing, suggesting synonymous variants cannot be ignored in prenatal diagnosis and genetic counseling.
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Affiliation(s)
- Yaoping Wang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Hongdan Wang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Key Laboratory of Population Defects Prevention, Zhengzhou, China
| | - Wenke Yang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Han Guo
- Department of Pharmacy, Huadong Hospital, Fudan University, Shanghai, China
| | - Mengting Zhang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Yue Gao
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Bing Kang
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
| | - Shixiu Liao
- Medical Genetic Institute of Henan Province, Zhengzhou University People's Hospital, Henan Provincial People's Hospital, Zhengzhou, China
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17
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Reis LM, Seese SE, Costakos D, Semina EV. Congenital anterior segment ocular disorders: Genotype-phenotype correlations and emerging novel mechanisms. Prog Retin Eye Res 2024; 102:101288. [PMID: 39097141 DOI: 10.1016/j.preteyeres.2024.101288] [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: 03/30/2023] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Development of the anterior segment of the eye requires reciprocal sequential interactions between the arising tissues, facilitated by numerous genetic factors. Disruption of any of these processes results in congenital anomalies in the affected tissue(s) leading to anterior segment disorders (ASD) including aniridia, Axenfeld-Rieger anomaly, congenital corneal opacities (Peters anomaly, cornea plana, congenital primary aphakia), and primary congenital glaucoma. Current understanding of the genetic factors involved in ASD remains incomplete, with approximately 50% overall receiving a genetic diagnosis. While some genes are strongly associated with a specific clinical diagnosis, the majority of known factors are linked with highly variable phenotypic presentations, with pathogenic variants in FOXC1, CYP1B1, and PITX2 associated with the broadest spectrum of ASD conditions. This review discusses typical clinical presentations including associated systemic features of various forms of ASD; the latest functional data and genotype-phenotype correlations related to 25 ASD factors including newly identified genes; promising novel candidates; and current and emerging treatments for these complex conditions. Recent developments of interest in the genetics of ASD include identification of phenotypic expansions for several factors, discovery of multiple modes of inheritance for some genes, and novel mechanisms including a growing number of non-coding variants and alleles affecting specific domains/residues and requiring further studies.
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Affiliation(s)
- Linda M Reis
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Sarah E Seese
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Deborah Costakos
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
| | - Elena V Semina
- Department of Ophthalmology and Visual Sciences, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Pediatrics and Children's Research Institute, Medical College of Wisconsin and Children's Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA; Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI, 53226, USA.
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18
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Balla C, Margutti A, De Carolis B, Canovi L, Di Domenico A, Vivaldi I, Vitali F, De Raffele M, Malagù M, Sassone B, Biffi M, Selvatici R, Ferlini A, Gualandi F, Bertini M. Cardiac conduction disorders in young adults: Clinical characteristics and genetic background of an underestimated population. Heart Rhythm 2024; 21:1363-1369. [PMID: 38467355 DOI: 10.1016/j.hrthm.2024.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/04/2024] [Accepted: 03/05/2024] [Indexed: 03/13/2024]
Abstract
BACKGROUND Cardiac conduction disorder (CCD) in patients <50 years old is a rare and mostly unknown condition. OBJECTIVE We aimed to assess clinical characteristics and genetic background of patients <50 years old with CCD of unknown origin. METHODS We retrospectively reviewed a consecutive series of patients with a diagnosis of CCD before the age of 50 years referred to our center between January 2019 and December 2021. Patients underwent complete clinical examination and genetic evaluation. RESULTS We enrolled 39 patients with a median age of 40 years (28-47 years) at the onset of symptoms. A cardiac implantable electronic device was implanted in 69% of the patients. In 15 of 39 CCD index patients (38%), we found a total of 13 different gene variations (3 pathogenic, 6 likely pathogenic, and 4 variants of uncertain significance), mostly in 3 genes (SCN5A, TRPM4, and LMNA). In our cohort, genetic testing led to the decision to implant an implantable cardioverter-defibrillator in 2 patients for the increased risk of sudden cardiac death. CONCLUSION Patients with the occurrence of CCD before the age of 50 years present with a high rate of pathologic gene variations, mostly in 3 genes (SCN5A, TRPM4, and LMNA). The presence of pathogenic variations may add information about the prognosis and lead to an individualized therapeutic approach.
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Affiliation(s)
- Cristina Balla
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy.
| | - Alice Margutti
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Beatrice De Carolis
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Luca Canovi
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Assunta Di Domenico
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Ilaria Vivaldi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Francesco Vitali
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Martina De Raffele
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Michele Malagù
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
| | - Biagio Sassone
- Division of Cardiology, SS.ma Annunziata Hospital, Department of Emergency, AUSL Ferrara, Cento (Ferrara), Italy
| | - Mauro Biffi
- Cardiology Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Rita Selvatici
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Alessandra Ferlini
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Francesca Gualandi
- Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Matteo Bertini
- Cardiology Unit, Azienda Ospedaliero-Universitaria di Ferrara, Cona (Ferrara), Italy
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19
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Bayat A, Grimes H, de Boer E, Herlin MK, Dahl RS, Lund ICB, Bayat M, Bolund ACS, Gjerulfsen CE, Gregersen PA, Zilmer M, Juhl S, Cebula K, Rahikkala E, Maystadt I, Peron A, Vignoli A, Alfano RM, Stanzial F, Benedicenti F, Currò A, Luk HM, Jouret G, Zurita E, Heuft L, Schnabel F, Busche A, Veenstra-Knol HE, Tkemaladze T, Vrielynck P, Lederer D, Platzer K, Ockeloen CW, Goel H, Low KJ. Natural history of adults with KBG syndrome: A physician-reported experience. Genet Med 2024; 26:101170. [PMID: 38818797 DOI: 10.1016/j.gim.2024.101170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 05/22/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
PURPOSE KBG syndrome (KBGS) is a rare neurodevelopmental syndrome caused by haploinsufficiency of ANKRD11. The childhood phenotype is extensively reported but limited for adults. Thus, we aimed to delineate the clinical features of KBGS. METHODS We collected physician-reported data of adults with molecularly confirmed KBGS through an international collaboration. Moreover, we undertook a systematic literature review to determine the scope of previously reported data. RESULTS The international collaboration identified 36 adults from 31 unrelated families with KBGS. Symptoms included mild/borderline intellectual disability (n = 22); gross and/or fine motor difficulties (n = 15); psychiatric and behavioral comorbidities including aggression, anxiety, reduced attention span, and autistic features (n = 26); nonverbal (n = 3), seizures with various seizure types and treatment responses (n = 10); ophthalmological comorbidities (n = 20). Cognitive regression during adulthood was reported once. Infrequent features included dilatation of the ascending aorta (n = 2) and autoimmune conditions (n = 4). Education, work, and residence varied, and the diversity of professional and personal roles highlighted the range of abilities seen. The literature review identified 154 adults reported across the literature, and we have summarized the features across both data sets. CONCLUSION Our study sheds light on the long-term neurodevelopmental outcomes, seizures, behavioral and psychiatric features, and education, work, and living arrangements for adults with KBGS.
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Affiliation(s)
- Allan Bayat
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark; Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark; Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
| | - Hannah Grimes
- Department of Clinical Genetics, University Hospital Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom
| | - Elke de Boer
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; Donders Institute for Brain, Cognition and Behavior, Radboud University, Nijmegen, The Netherlands; Department of Clinical Genetics, Erasmus Medical Centre - Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Morten Krogh Herlin
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Rebekka Staal Dahl
- Department of Epilepsy Genetics and Personalized Medicine, Danish Epilepsy Center, Dianalund, Denmark
| | - Ida Charlotte Bay Lund
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Michael Bayat
- Department of Neurology, Aarhus University Hospital, Aarhus, Denmark; Center for Rare Diseases, Department of Pediatric and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Pernille Axél Gregersen
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark; Department of Clinical Medicine, Aarhus University, Aarhus, Denmark; Center for Rare Diseases, Department of Pediatric and Adolescent Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Monica Zilmer
- Department of Child Neurology, Danish Epilepsy Center, Dianalund, Denmark
| | - Stefan Juhl
- Department of Neurology, Danish Epilepsy Center, Dianalund, Denmark
| | - Katarzyna Cebula
- Department of Neurology, Danish Epilepsy Center, Dianalund, Denmark
| | - Elisa Rahikkala
- Dept of Clinical Genetics, Research Unit of Clinical Medicine, Medical Research Center Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Isabelle Maystadt
- Center for Human Genetics, Institute for Pathology and Genetics, Gosselies, Belgium; URPhyM, Faculty of Medicine, University of Namur, Namur, Belgium
| | - Angela Peron
- Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy; Division of Medical Genetics, Meyer Children's Hospital IRCCS, Florence, Italy; Department of Experimental and Clinical Biomedical Sciences "Mario Serio," Università degli Studi di Firenze, Florence, Italy
| | - Aglaia Vignoli
- Child Neuropsychiatry Unit, Grande Ospedale Metropolitano Niguarda, University of Milan, Milan, Italy
| | - Rosa Maria Alfano
- Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Aurora Currò
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Ho-Ming Luk
- Clinical Genetics Service Unit, Hong Kong Children's Hospital, HKSAR, Hong Kong
| | - Guillaume Jouret
- National Center of Genetics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Ella Zurita
- Hunter Genetics, New South Wales Health, Waratah, NSW, Australia
| | - Lara Heuft
- Institute for Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Franziska Schnabel
- Institute for Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | - Andreas Busche
- Department of Medical Genetics, University Hospital Münster, Germany
| | | | - Tinatin Tkemaladze
- Department of Molecular and Medical Genetics, Tbilisi State Medical University, Tbilisi, Georgia; Givi Zhvania Pediatric Academic Clinic, Tbilisi State Medical University, Tbilisi, Georgia
| | - Pascal Vrielynck
- Reference Center for Refractory Epilepsy, Catholic University of Louvain, William Lennox Neurological Hospital, Ottignies, Belgium
| | - Damien Lederer
- Institute for Pathology and Genetics, 6040, Gosselies, Belgium
| | - Konrad Platzer
- Institute for Human Genetics, University of Leipzig Medical Center, Leipzig, Germany
| | | | - Himanshu Goel
- Hunter Genetics, New South Wales Health, Waratah, NSW, Australia
| | - Karen Jaqueline Low
- Department of Clinical Genetics, University Hospital Bristol and Weston NHS Foundation Trust, Bristol, United Kingdom; Centre for Academic Child Health, Bristol Medical School, University of Bristol, United Kingdom
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20
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Kanwar K, Bashey S, Bohnsack BL, Drackley A, Ing A, Rahmani S, Ranaivo HR, McMullen P, Skol A, Yap K, Allegretti V, Rossen JL. Ocular manifestations of CHARGE syndrome in a pediatric cohort with genotype/phenotype analysis. Am J Med Genet A 2024; 194:e63618. [PMID: 38597178 DOI: 10.1002/ajmg.a.63618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/11/2024]
Abstract
CHARGE syndrome is a rare multi-system condition associated with CHD7 variants. However, ocular manifestations and particularly ophthalmic genotype-phenotype associations, are not well-studied. This study evaluated ocular manifestations and genotype-phenotype associations in pediatric patients with CHARGE syndrome. A retrospective chart review included pediatric patients under 20 years-old with clinical diagnosis of CHARGE syndrome and documented ophthalmic examination. Demographics, genetic testing, and ocular findings were collected. Comprehensive literature review enhanced the genotype-phenotype analysis. Forty-two patients (20 male) underwent eye examination at an average age of 9.45 ± 6.52 years-old. Thirty-nine (93%) had ophthalmic manifestations in at least one eye. Optic nerve/chorioretinal colobomas were most common (38 patients), followed by microphthalmia (13), cataract (6), and iris colobomas (4). Extraocular findings included strabismus (32 patients), nasolacrimal duct obstructions (11, 5 with punctal agenesis), and cranial nerve VII palsy (10). Genotype-phenotype analyses (27 patients) showed variability in ocular phenotypes without association to location or variant types. Splicing (10 patients) and frameshift (10) variants were most prevalent. Patients with CHARGE syndrome may present with a myriad of ophthalmic manifestations. There is limited data regarding genotype-phenotype correlations and additional studies are needed.
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Affiliation(s)
- Kunal Kanwar
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Saffiya Bashey
- Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Brenda L Bohnsack
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Andy Drackley
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Alexander Ing
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Safa Rahmani
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Hantamalala Ralay Ranaivo
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Patrick McMullen
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Andrew Skol
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Kailee Yap
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Valerie Allegretti
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Jennifer L Rossen
- Department of Ophthalmology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Division of Ophthalmology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
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21
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Rodriguez KM, Vaught J, Salz L, Foley J, Boulil Z, Van Dongen-Trimmer HM, Whalen D, Oluchukwu O, Liu KC, Burton J, Syngal P, Vargas-Shiraishi O, Kingsmore SF, Kobayashi ES, Coufal NG. Rapid Whole-Genome Sequencing and Clinical Management in the PICU: A Multicenter Cohort, 2016-2023. Pediatr Crit Care Med 2024; 25:699-709. [PMID: 38668387 PMCID: PMC11300160 DOI: 10.1097/pcc.0000000000003522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 08/06/2024]
Abstract
OBJECTIVES Analysis of the clinical utility of rapid whole-genome sequencing (rWGS) outside of the neonatal period is lacking. We describe the use of rWGS in PICU and cardiovascular ICU (CICU) patients across four institutions. DESIGN Ambidirectional multisite cohort study. SETTING Four tertiary children's hospitals. PATIENTS Children 0-18 years old in the PICU or CICU who underwent rWGS analysis, from May 2016 to June 2023. INTERVENTIONS None. MEASUREMENTS AND MAIN RESULTS A total of 133 patients underwent clinical, phenotype-driven rWGS analysis, 36 prospectively. A molecular diagnosis was identified in 79 patients (59%). Median (interquartile range [IQR]) age was 6 months (IQR 1.2 mo-4.6 yr). Median time for return of preliminary results was 3 days (IQR 2-4). In 79 patients with a molecular diagnosis, there was a change in ICU management in 19 patients (24%); and some change in clinical management in 63 patients (80%). Nondiagnosis changed management in 5 of 54 patients (9%). The clinical specialty ordering rWGS did not affect diagnostic rate. Factors associated with greater odds ratio (OR [95% CI]; OR [95% CI]) of diagnosis included dysmorphic features (OR 10.9 [95% CI, 1.8-105]) and congenital heart disease (OR 4.2 [95% CI, 1.3-16.8]). Variables associated with greater odds of changes in management included obtaining a genetic diagnosis (OR 16.6 [95% CI, 5.5-62]) and a shorter time to genetic result (OR 0.8 [95% CI, 0.76-0.9]). Surveys of pediatric intensivists indicated that rWGS-enhanced clinical prognostication ( p < 0.0001) and contributed to a decision to consult palliative care ( p < 0.02). CONCLUSIONS In this 2016-2023 multiple-PICU/CICU cohort, we have shown that timely genetic diagnosis is feasible across institutions. Application of rWGS had a 59% (95% CI, 51-67%) rate of diagnostic yield and was associated with changes in critical care management and long-term patient management.
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Affiliation(s)
- Katherine M. Rodriguez
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
| | - Jordan Vaught
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
| | - Lisa Salz
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
| | | | | | | | | | - Okonkwo Oluchukwu
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Kuang Chuen Liu
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Jennifer Burton
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | - Prachi Syngal
- OSF Children’s Hospital of Illinois, Peoria, IL
- University of Illinois College of Medicine at Peoria, Peoria, IL
| | | | | | - Erica Sanford Kobayashi
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
- Cedars-Sinai Medical Center, Department of Pediatrics, Los Angeles, CA
- Children’s Hospital of Orange County, Orange, CA
| | - Nicole G. Coufal
- Rady Children’s Hospital, San Diego, CA
- Department of Pediatrics, University of California, San Diego
- Rady Children’s Institute for Genomic Medicine, San Diego, CA
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Chowdhury SR, Whitney R, RamachandranNair R, Bijarnia Mahay S, Sharma S. Genetic Testing in Pediatric Epilepsy: Tools, Tips, and Navigating the Traps. Pediatr Neurol 2024; 157:42-49. [PMID: 38865949 DOI: 10.1016/j.pediatrneurol.2024.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 04/17/2024] [Accepted: 05/13/2024] [Indexed: 06/14/2024]
Abstract
With the advent of high-throughput sequencing and computational methods, genetic testing has become an integral part of contemporary clinical practice, particularly in epilepsy. The toolbox for genetic testing has evolved from conventional chromosomal microarray and epilepsy gene panels to state-of-the-art sequencing techniques in the modern genomic era. Beyond its potential for therapeutic benefits through precision medicine, optimizing the choice of antiseizure medications, or exploring nonpharmacological therapeutic modalities, genetic testing carries substantial diagnostic, prognostic, and personal implications. Developmental and epileptic encephalopathies, the coexistence of neurodevelopmental comorbidities, early age of epilepsy onset, unexplained drug-refractory epilepsy, and positive family history have demonstrated the highest likelihood of yielding positive genetic test results. Given the diagnostic efficacy across different testing modalities, reducing costs of next-generation sequencing tests, and genetic diversity of epilepsies, exome sequencing or genome sequencing, where feasible and available, have been recommended as the first-tier test. Comprehensive clinical phenotyping at the outset, corroborative evidence from radiology and electrophysiology-based investigations, reverse phenotyping, and periodic reanalysis are some of the valuable strategies when faced with inconclusive test results. In this narrative review, the authors aim to simplify the approach to genetic testing in epilepsy by guiding on the selection of appropriate testing tools in the indicated clinical scenarios, addressing crucial aspects during pre- and post-test counseling sessions, adeptly navigating the traps posed by uncertain or negative genetic variants, and paving the way forward to the emerging testing modalities beyond DNA sequencing.
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Affiliation(s)
- Sayoni Roy Chowdhury
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India
| | - Robyn Whitney
- Comprehensive Paediatric Epilepsy Program, Division of Neurology, Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Rajesh RamachandranNair
- Comprehensive Paediatric Epilepsy Program, Division of Neurology, Department of Pediatrics, McMaster Children's Hospital, Hamilton, Ontario, Canada
| | - Sunita Bijarnia Mahay
- Sr. Consultant, Clinical & Metabolic Geneticist, Institute of Medical Genetics & Genomics, Sir Ganga Ram Hospital, New Delhi, India
| | - Suvasini Sharma
- Department of Paediatrics, Lady Hardinge Medical College and Associated Kalawati Saran Children's Hospital, New Delhi, India.
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23
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Zhang M, Gao Y, Liang M, Wang Y, Guo L, Wu D, Xiao H, Lin L, Wang H, Liao S. Correlation between maternal serum biomarkers and the risk of fetal chromosome copy number variants: a single-center retrospective study. Arch Gynecol Obstet 2024; 310:933-942. [PMID: 38814455 DOI: 10.1007/s00404-024-07514-1] [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: 02/07/2024] [Accepted: 04/07/2024] [Indexed: 05/31/2024]
Abstract
OBJECTIVE To explore the association between the concentration of maternal serum biomarkers and the risk of fetal carrying chromosome copy number variants (CNVs). METHODS Pregnant women identified as high risk in the second-trimester serological triple screening and underwent traditional amniotic fluid karyotype analysis, along with comparative genomic hybridization array (aCGH)/copy number variation sequencing (CNV-seq), were included in the study. We divided the concentration of serum biomarkers, free beta-human chorionic gonadotropin (fβ-hCG), alpha fetoprotein (AFP) and unconjugated estriol (uE3), into three levels: abnormally low, normal and abnormally high. The prevalence of abnormally low, normal and abnormally high serum fβ-hCG, AFP and uE3 levels in pregnant women with aberrant aCGH/CNV-seq results and normal controls was calculated. RESULTS Among the 2877 cases with high risk in the second-trimester serological triple screening, there were 98 chromosome abnormalities revealed by karyotype analysis, while 209 abnormalities were detected by aCGH/CNVseq (P<0.001) . The carrying rate of aberrant CNVs increased significantly when the maternal serum uE3 level was less than 0.4 multiple of median (MoM) of corresponding gestational weeks compared to normal controls, while the carrying rate of aberrant CNVs decreased significantly when the maternal serum fβ-hCG level was greater than 2.5 MoM compared to normal controls. No significant difference was found in the AFP group. CONCLUSION Low serum uE3 level (<0.4 MoM) was associated with an increased risk of aberrant CNVs.
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Affiliation(s)
- Mengting Zhang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China
| | - Yue Gao
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China
| | - Mingyu Liang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
| | - Yaoping Wang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China
| | - Liangjie Guo
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China
| | - Dong Wu
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China
| | - Hai Xiao
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China
| | - Li Lin
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China
| | - Hongdan Wang
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China.
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China.
| | - Shixiu Liao
- Medical Genetics Institute of Henan Province, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Zhengzhou, 450003, China.
- National Health Commission Key Laboratory of Birth Defects Prevention, Henan Provincial Key Laboratory of Genetic Diseases and Functional Genomics, Zhengzhou, 450003, China.
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24
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Ormond C, Ryan NM, Byerley W, Heron EA, Corvin A. Investigating copy number variants in schizophrenia pedigrees using a new consensus pipeline called PECAN. Sci Rep 2024; 14:17518. [PMID: 39080331 PMCID: PMC11289470 DOI: 10.1038/s41598-024-66021-0] [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: 12/19/2023] [Accepted: 06/26/2024] [Indexed: 08/02/2024] Open
Abstract
Copy number variants (CNVs) have been implicated in many human diseases, including psychiatric disorders. Whole genome sequencing offers advantages in CNV calling compared to previous array-based methods. Here we present a robust and transparent CNV calling pipeline, PECAN (PEdigree Copy number vAriaNt calling), for short-read, whole genome sequencing data, comprised of a novel combination of four calling methods and structural variant genotyping. This method is scalable and can incorporate pedigree information to retain lower-confidence CNVs that would otherwise be discarded. We have robustly benchmarked PECAN using gold-standard CNV calls for two well-established evaluation samples, NA12878 and HG002, showing that PECAN performs with high precision and recall on both datasets, outperforming another pedigree-based CNV calling pipeline. As part of this work, we provide a list of high-confidence gold standard CNVs for the NA12878 reference sample, curated from multiple studies. We applied PECAN to a collection of pedigrees multiply affected with schizophrenia and identified a rare deletion that perfectly co-segregates with schizophrenia in one of the pedigrees. The CNV overlaps the gene PITRM1, which has been implicated in a complex phenotype including ataxia, developmental delay, and schizophrenia-like episodes in affected adults.
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Affiliation(s)
- Cathal Ormond
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland
| | - Niamh M Ryan
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland
| | - William Byerley
- Department of Psychiatry and Behavioral Sciences, University of California, San Francisco, CA, USA
| | - Elizabeth A Heron
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland
| | - Aiden Corvin
- Neuropsychiatric Genetics Research Group, Department of Psychiatry, Trinity Centre for Health Sciences, Trinity College Dublin, James' Street, Dublin 8, Ireland.
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25
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Cai M, Lin N, Fu M, Que Y, Huang H, Xu L. Fetal agenesis of corpus callosum: chromosomal copy number abnormalities and postnatal follow-up. Mol Biol Rep 2024; 51:872. [PMID: 39080034 PMCID: PMC11289215 DOI: 10.1007/s11033-024-09821-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: 04/16/2024] [Accepted: 07/23/2024] [Indexed: 08/02/2024]
Abstract
OBJECTIVE Agenesis of the corpus callosum (ACC) is an anomaly that can occur in fetuses during pregnancy. However, there is currently no treatment for fetal ACC. Therefore, we conducted a retrospective analysis of obstetric outcomes of fetal ACC to explore the relationship between fetal ACC phenotypes and chromosomal copy number abnormalities. METHODS AND RESULTS Amniotic fluid or umbilical cord blood were extracted from pregnant women with fetal ACC for karyotype analysis and chromosomal microarray analysis (CMA). Among the 48 fetuses with ACC, 22 (45.8%, 22/48) had isolated ACC, and 26 (54.2%, 26/48) had non-isolated ACC. Chromosomal abnormalities were detected via karyotype analysis in four cases. In addition to the four cases of pathogenic copy number variations (CNVs) detected using karyotype analysis, CMA revealed two cases of pathogenic CNVs with 17q12 microduplication and 16p12.2 microdeletion. The obstetric outcomes of 26 patients with non-isolated ACC were followed up, and 17 chose to terminate the pregnancy. In addition, seven of the nine cases with non-isolated ACC showed no obvious abnormality during postnatal follow-up, whereas only one case with normal CMA showed an abnormal phenotype at six months. Of the 22 patients with isolated ACC, six chose to terminate the pregnancy. Postnatal follow-up of 16 isolated ACC cases revealed only one with benign CNV, presenting with intellectual disability. CONCLUSION Pregnant women with fetal ACC should be offered prenatal CMA, particularly non-isolated ACC. Patients with ACC should undergo prolonged postnatal follow-up, and appropriate intervention should be provided if necessary.
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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 Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Clinical Research Center for Maternal-Fetal Medicine, Fujian Medical University, National Key Obstetric Clinical Specialty Construction Institution of China, 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 Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Clinical Research Center for Maternal-Fetal Medicine, Fujian Medical University, National Key Obstetric Clinical Specialty Construction Institution of China, 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 Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Clinical Research Center for Maternal-Fetal Medicine, Fujian Medical University, National Key Obstetric Clinical Specialty Construction Institution of China, 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 Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Clinical Research Center for Maternal-Fetal Medicine, Fujian Medical University, National Key Obstetric Clinical Specialty Construction Institution of China, 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 Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Clinical Research Center for Maternal-Fetal Medicine, Fujian Medical University, National Key Obstetric Clinical Specialty Construction Institution of China, 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 Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Clinical Research Center for Maternal-Fetal Medicine, Fujian Medical University, National Key Obstetric Clinical Specialty Construction Institution of China, Fuzhou, China.
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26
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Lian R, Wu G, Xu F, Zhao S, Li M, Wang H, Jia T, Dong Y. Clinical cases series and pathogenesis of Lamb-Shaffer syndrome in China. Orphanet J Rare Dis 2024; 19:281. [PMID: 39075495 PMCID: PMC11285261 DOI: 10.1186/s13023-024-03279-7] [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: 02/07/2024] [Accepted: 07/03/2024] [Indexed: 07/31/2024] Open
Abstract
BACKGROUND Lamb-Shaffer syndrome (LAMSHF, OMIM: 616803) is a rare neurodevelopmental disorder characterized by global developmental delay, intellectual disability, poor expressive speech, which is attributed to haploinsufficiency by heterozygous variants of SOX5 gene (SRY-Box Transcription Factor 5, HGNC: 11201) on chromosome 12p12. A total of 113 cases have been reported in the world, however, only 3 cases have been reported.in China. Here, we aimed to report novel variants of SOX5 gene and provide examples for clinical diagnosis by reporting the clinical phenotype of a series of Chinese patients with LAMSHF. METHODS This study retrospectively collected the information of families of LAMSHF patients in China. Whole Exome Sequencing (WES) were performed to confirm the diagnosis of 4 children with unexplained developmental delay or epilepsy. A minigene splicing assay was used to verify whether the splice variant affected splicing. Meanwhile, a literature review was conducted to analyze the clinical and genetic characteristics of patients with LAMSHF. RESULTS Three of the LAMSHF patients had a de novo heterozygous mutation in the SOX5 gene respectively, c.290delC (p.Pro97fs*30), chr12:23686019_24048958del, c.1772-1C > A, and the remaining one had a mutation inherited from his father, c.1411C > T (p.Arg471*). The main clinical manifestations of these children were presented with global developmental delays, and one of them also had seizures. And the results of the minigene experiment indicated that the splice variant, c.1772-1C > A, transcribed a novel mRNA product which leaded to the formation of a truncated protein. CONCLUSIONS Through a comprehensive review and analysis of existing literature and this study showed intellectual disability, speech delay and facial dysmorphisms were common clinical manifestation, while the seizures and EEG abnormalities were rare (21/95, 22.16%). Notably, we represent the largest sample size of LAMSHF in Asia that encompasses previously unreported SOX5 gene mutation, and a minigene testing have been conducted to validate the pathogenicity of the c.1772-1C > A splice variant. The research further expands the phenotype and genotype of LAMSHF while offers novel insights for potential pathogenicity of genes locus.
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Affiliation(s)
- Ruofei Lian
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China
| | - Gongao Wu
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China
| | - Falin Xu
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China
| | - Shichao Zhao
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China
| | - Mengchun Li
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China
| | - Haiyan Wang
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China
| | - Tianming Jia
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China
| | - Yan Dong
- Department of Pediatrics, The Third Affiliated Hospital of Zhengzhou University, No. 7, Kangfu Front Street, Erqi District, Zhengzhou, Henan Province, 450052, China.
- Henan Key Laboratory of Child Brain Injury and Henan Pediatric Clinical Research Center, the Third Affiliated Hospital and Institute of Neuroscience, Zhengzhou, China.
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27
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Mitrakos A, Kekou K, Tilemis FN, Svingou M, Papadimas G, Sofocleous C, Traeger-Synodinos J, Tzetis M. Nablus mask-like facial syndrome: Report of an atypical case with 8q21.3-q22.1 deletion. Am J Med Genet A 2024:e63826. [PMID: 39037278 DOI: 10.1002/ajmg.a.63826] [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: 04/18/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
Nablus mask-like facial syndrome (NMLFS) is a rare condition characterized by unique facial features, initially described in a 4-year-old boy from Nablus, Palestine. These features include expressionless facial appearance, tight facial skin, blepharophimosis, sparse eyebrows, and a flat nose. Genetic studies have identified a deletion of 8q22.1 as the cause of the syndrome, however while 26 patients have been reported with the deletion, only 13 displayed the characteristic facial features. Here we report on a 35-year-old male with 8q21.3-q22.1 deletion identified by whole exome sequencing and Chromosomal microarray analysis (CMA) that presents with typical and atypical features, including neurodevelopmental disorder, mild facial features, and myopathy, which has not been described in a patient with NMLFS to date. Further research will be required to understand the underlying pathogenetic mechanism of this rare genetic disorder.
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Affiliation(s)
- A Mitrakos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
- University Research Institute for the Study of Genetic and Malignant Disorders in Childhood, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
| | - K Kekou
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
| | - F-N Tilemis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
- University Research Institute for the Study of Genetic and Malignant Disorders in Childhood, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
| | - M Svingou
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
| | - G Papadimas
- 1st Department of Neurology, Medical School, National and Kapodistrian University of Athens, Eginition Hospital, Athens, Greece
| | - C Sofocleous
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
| | - J Traeger-Synodinos
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
| | - M Tzetis
- Laboratory of Medical Genetics, Medical School, National and Kapodistrian University of Athens, "Ag. Sofia" Children's Hospital, Athens, Greece
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Levy B, Liu J, Iqbal MA, DuPont B, Sahajpal N, Ho M, Yu J, Brody SJ, Ganapathi M, Rajkovic A, Smolarek TA, Boyar F, Bui P, Dubuc AM, Kolhe R, Stevenson RE. Multisite Evaluation and Validation of Optical Genome Mapping for Prenatal Genetic Testing. J Mol Diagn 2024:S1525-1578(24)00157-0. [PMID: 39032820 DOI: 10.1016/j.jmoldx.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 05/07/2024] [Accepted: 06/26/2024] [Indexed: 07/23/2024] Open
Abstract
Prenatal diagnostic testing of amniotic fluid, chorionic villi, or more rarely, fetal cord blood is recommended following a positive or unreportable noninvasive cell-free fetal DNA test, abnormal maternal biochemical serum screen, abnormal ultrasound, or increased genetic risk for a cytogenomic abnormality based on family history. Although chromosomal microarray is recommended as the first-tier prenatal diagnostic test, in practice, multiple assays are often assessed in concert to achieve a final diagnostic result. The use of multiple methodologies is costly, time consuming, and labor intensive. Optical genome mapping (OGM) is an emerging technique with application for prenatal diagnosis because of its ability to detect and resolve, in a single assay, all classes of pathogenic cytogenomic aberrations. In an effort to characterize the potential of OGM as a novel alternative to traditional standard of care (SOC) testing of prenatal samples, OGM was performed on a total of 200 samples representing 123 unique cases, which were previously tested with SOC methods (92/123 = 74.7% cases tested with at least two SOCs). OGM demonstrated an overall accuracy of 99.6% when compared with SOC methods, a positive predictive value of 100%, and 100% reproducibility between sites, operators, and instruments. The standardized workflow, cost-effectiveness, and high-resolution cytogenomic analysis demonstrate the potential of OGM to serve as a first-tier test for prenatal diagnosis.
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Affiliation(s)
- Brynn Levy
- Columbia University Irving Medical Center, New York, New York
| | - Jie Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, New York
| | | | | | - Monique Ho
- University of Rochester Medical Center, Rochester, New York
| | - Jingwei Yu
- University of California San Francisco, San Francisco, California
| | - Sam J Brody
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | | | | | - Teresa A Smolarek
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
| | - Fatih Boyar
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Peter Bui
- Quest Diagnostics Nichols Institute, San Juan Capistrano, California
| | - Adrian M Dubuc
- Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ravindra Kolhe
- Department of Pathology, Medical College of Georgia, Augusta University, Augusta, Georgia.
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29
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van der Laan L, Lauffer P, Rooney K, Silva A, Haghshenas S, Relator R, Levy MA, Trajkova S, Huisman SA, Bijlsma EK, Kleefstra T, van Bon BW, Baysal Ö, Zweier C, Palomares-Bralo M, Fischer J, Szakszon K, Faivre L, Piton A, Mesman S, Hochstenbach R, Elting MW, van Hagen JM, Plomp AS, Mannens MMAM, Alders M, van Haelst MM, Ferrero GB, Brusco A, Henneman P, Sweetser DA, Sadikovic B, Vitobello A, Menke LA. DNA methylation episignature and comparative epigenomic profiling for Pitt-Hopkins syndrome caused by TCF4 variants. HGG ADVANCES 2024; 5:100289. [PMID: 38571311 PMCID: PMC11087720 DOI: 10.1016/j.xhgg.2024.100289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 03/26/2024] [Accepted: 03/26/2024] [Indexed: 04/05/2024] Open
Abstract
Pitt-Hopkins syndrome (PTHS) is a neurodevelopmental disorder caused by pathogenic variants in TCF4, leading to intellectual disability, specific morphological features, and autonomic nervous system dysfunction. Epigenetic dysregulation has been implicated in PTHS, prompting the investigation of a DNA methylation (DNAm) "episignature" specific to PTHS for diagnostic purposes and variant reclassification and functional insights into the molecular pathophysiology of this disorder. A cohort of 67 individuals with genetically confirmed PTHS and three individuals with intellectual disability and a variant of uncertain significance (VUS) in TCF4 were studied. The DNAm episignature was developed with an Infinium Methylation EPIC BeadChip array analysis using peripheral blood cells. Support vector machine (SVM) modeling and clustering methods were employed to generate a DNAm classifier for PTHS. Validation was extended to an additional cohort of 11 individuals with PTHS. The episignature was assessed in relation to other neurodevelopmental disorders and its specificity was examined. A specific DNAm episignature for PTHS was established. The classifier exhibited high sensitivity for TCF4 haploinsufficiency and missense variants in the basic-helix-loop-helix domain. Notably, seven individuals with TCF4 variants exhibited negative episignatures, suggesting complexities related to mosaicism, genetic factors, and environmental influences. The episignature displayed degrees of overlap with other related disorders and biological pathways. This study defines a DNAm episignature for TCF4-related PTHS, enabling improved diagnostic accuracy and VUS reclassification. The finding that some cases scored negatively underscores the potential for multiple or nested episignatures and emphasizes the need for continued investigation to enhance specificity and coverage across PTHS-related variants.
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Affiliation(s)
- Liselot van der Laan
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Peter Lauffer
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Ananília Silva
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada
| | - Slavica Trajkova
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Sylvia A Huisman
- Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Department of Pediatrics, Amsterdam, the Netherlands; Zodiak, Prinsenstichting, Purmerend, the Netherlands
| | - Emilia K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, the Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Bregje W van Bon
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Özlem Baysal
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Christiane Zweier
- Department of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany; Department of Human Genetics, University of Bern, Inselspital Universitätsspital Bern, Bern, Switzerland
| | - María Palomares-Bralo
- Institute of Medical and Molecular Genetics (INGEMM), La Paz University Hospital, Madrid, Spain
| | - Jan Fischer
- Institute for Clinical Genetics, University Hospital Carl Gustav Carus at the Technische Universität Dresden, Dresden, Germany
| | - Katalin Szakszon
- Institute of Paediatrics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Laurence Faivre
- UFR Des Sciences de Santé, INSERM-Université de Bourgogne UMR1231 GAD «Génétique des Anomalies du Développement», FHUTRANSLAD, Dijon, France; CHU Dijon Bourgogne, Centre de Génétique, Centre de Référence Maladies Rares «Anomalies du Développement et Syndromes Malformatifs», FHU-TRANSLDAD, Dijon, France
| | - Amélie Piton
- Genetic Diagnosis Laboratories, Strasbourg University Hospital, Strasbourg 67000, France
| | - Simone Mesman
- Swammerdam Institute for Life Sciences, FNWI, University of Amsterdam, Amsterdam, the Netherlands
| | - Ron Hochstenbach
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mariet W Elting
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Johanna M van Hagen
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Astrid S Plomp
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Marcel M A M Mannens
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mariëlle Alders
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Mieke M van Haelst
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - Giovanni B Ferrero
- Department of Public Health and Pediatrics, University of Torino, Turin, Italy
| | - Alfredo Brusco
- Department of Medical Sciences, University of Torino, Turin, Italy
| | - Peter Henneman
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands
| | - David A Sweetser
- Division of Medical Genetics and Metabolism and Center for Genomic Medicine, Massachusetts General for Children, Boston, MA, USA
| | - Bekim Sadikovic
- Department of Human Genetics, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, the Netherlands; Amsterdam Reproduction & Development, Amsterdam, the Netherlands; Verspeeten Clinical Genome Centre, London Health Science Centre, London, ON, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Antonio Vitobello
- Unité Fonctionnelle Innovation en Diagnostic Génomique des Maladies Rares, FHU-TRANSLAD, CHU Dijon Bourgogne, Dijon, France
| | - Leonie A Menke
- Amsterdam Reproduction & Development, Amsterdam, the Netherlands; Amsterdam UMC location University of Amsterdam, Emma Children's Hospital, Department of Pediatrics, Amsterdam, the Netherlands; Amsterdam Neuroscience - Cellular & Molecular Mechanisms, Amsterdam, the Netherlands.
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30
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Trajkova S, Kerkhof J, Rossi Sebastiano M, Pavinato L, Ferrero E, Giovenino C, Carli D, Di Gregorio E, Marinoni R, Mandrile G, Palermo F, Carestiato S, Cardaropoli S, Pullano V, Rinninella A, Giorgio E, Pippucci T, Dimartino P, Rzasa J, Rooney K, McConkey H, Petlichkovski A, Pasini B, Sukarova-Angelovska E, Campbell CM, Metcalfe K, Jenkinson S, Banka S, Mussa A, Ferrero GB, Sadikovic B, Brusco A. DNA methylation analysis in patients with neurodevelopmental disorders improves variant interpretation and reveals complexity. HGG ADVANCES 2024; 5:100309. [PMID: 38751117 PMCID: PMC11216013 DOI: 10.1016/j.xhgg.2024.100309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/09/2024] [Accepted: 05/07/2024] [Indexed: 06/07/2024] Open
Abstract
Analysis of genomic DNA methylation by generating epigenetic signature profiles (episignatures) is increasingly being implemented in genetic diagnosis. Here we report our experience using episignature analysis to resolve both uncomplicated and complex cases of neurodevelopmental disorders (NDDs). We analyzed 97 NDDs divided into (1) a validation cohort of 59 patients with likely pathogenic/pathogenic variants characterized by a known episignature and (2) a test cohort of 38 patients harboring variants of unknown significance or unidentified variants. The expected episignature was obtained in most cases with likely pathogenic/pathogenic variants (53/59 [90%]), a revealing exception being the overlapping profile of two SMARCB1 pathogenic variants with ARID1A/B:c.6200, confirmed by the overlapping clinical features. In the test cohort, five cases showed the expected episignature, including (1) novel pathogenic variants in ARID1B and BRWD3; (2) a deletion in ATRX causing MRXFH1 X-linked mental retardation; and (3) confirmed the clinical diagnosis of Cornelia de Lange (CdL) syndrome in mutation-negative CdL patients. Episignatures analysis of the in BAF complex components revealed novel functional protein interactions and common episignatures affecting homologous residues in highly conserved paralogous proteins (SMARCA2 M856V and SMARCA4 M866V). Finally, we also found sex-dependent episignatures in X-linked disorders. Implementation of episignature profiling is still in its early days, but with increasing utilization comes increasing awareness of the capacity of this methodology to help resolve the complex challenges of genetic diagnoses.
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Affiliation(s)
- Slavica Trajkova
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Matteo Rossi Sebastiano
- Molecular Biotechnology Center "Guido Tarone" University of Turin, 10126 Turin, Italy; Department of Molecular Biotechnology and Health Sciences, University of Turin, CASSMedChem, 10126 Turin, Italy
| | - Lisa Pavinato
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Enza Ferrero
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Chiara Giovenino
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Diana Carli
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy
| | - Eleonora Di Gregorio
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Roberta Marinoni
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Giorgia Mandrile
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Flavia Palermo
- Medical Genetics Unit and Thalassemia Center, San Luigi University Hospital, Orbassano, TO 10049, Italy
| | - Silvia Carestiato
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Simona Cardaropoli
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy
| | - Verdiana Pullano
- Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy
| | - Antonina Rinninella
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Biomedical and Biotechnological Sciences, Medical Genetics, University of Catania, 94124 Catania, Italy
| | - Elisa Giorgio
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy; Neurogenetics Research Center, IRCCS Mondino Foundation, 27100 Pavia, Italy
| | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Paola Dimartino
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
| | - Jessica Rzasa
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Kathleen Rooney
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Aleksandar Petlichkovski
- Department of Immunology and Human Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Barbara Pasini
- Department of Medical Sciences, University of Turin, 10126 Turin, Italy; Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy
| | - Elena Sukarova-Angelovska
- Department of Endocrinology and Genetics, Faculty of Medicine, University "Sv. Kiril I Metodij", Skopje 1000, Republic of Macedonia
| | - Christopher M Campbell
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Kay Metcalfe
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Sarah Jenkinson
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St. Mary's Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution, Infection & Genomics, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester M13 9WL, UK
| | - Alessandro Mussa
- Department of Public Health and Pediatric Sciences, University of Turin, 10126 Turin, Italy; Pediatric Clinical Genetics Unit, Regina Margherita Childrens' Hospital, 10126 Turin, Italy
| | | | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A3K7, Canada
| | - Alfredo Brusco
- Medical Genetics Unit, Città della Salute e della Scienza University Hospital, 10126 Turin, Italy; Department of Neurosciences Rita Levi-Montalcini, University of Turin, Turin 10126, Italy.
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31
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Segarra-Casas A, Yépez VA, Demidov G, Laurie S, Esteve-Codina A, Gagneur J, Parkhurst Y, Muni-Lofra R, Harris E, Marini-Bettolo C, Straub V, Töpf A. An Integrated Transcriptomics and Genomics Approach Detects an X/Autosome Translocation in a Female with Duchenne Muscular Dystrophy. Int J Mol Sci 2024; 25:7793. [PMID: 39063034 PMCID: PMC11276803 DOI: 10.3390/ijms25147793] [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: 06/15/2024] [Revised: 07/08/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024] Open
Abstract
Duchenne and Becker muscular dystrophies, caused by pathogenic variants in DMD, are the most common inherited neuromuscular conditions in childhood. These diseases follow an X-linked recessive inheritance pattern, and mainly males are affected. The most prevalent pathogenic variants in the DMD gene are copy number variants (CNVs), and most patients achieve their genetic diagnosis through Multiplex Ligation-dependent Probe Amplification (MLPA) or exome sequencing. Here, we investigated a female patient presenting with muscular dystrophy who remained genetically undiagnosed after MLPA and exome sequencing. RNA sequencing (RNAseq) from the patient's muscle biopsy identified an 85% reduction in DMD expression compared to 116 muscle samples included in the cohort. A de novo balanced translocation between chromosome 17 and the X chromosome (t(X;17)(p21.1;q23.2)) disrupting the DMD and BCAS3 genes was identified through trio whole genome sequencing (WGS). The combined analysis of RNAseq and WGS played a crucial role in the detection and characterisation of the disease-causing variant in this patient, who had been undiagnosed for over two decades. This case illustrates the diagnostic odyssey of female DMD patients with complex structural variants that are not detected by current panel or exome sequencing analysis.
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Affiliation(s)
- Alba Segarra-Casas
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK; (A.S.-C.)
- Genetics Department, Institut de Recerca Sant Pau (IR SANT PAU), Hospital de la Santa Creu i Sant Pau, Genetics and Microbiology Department, Universitat Autonoma de Barcelona, 08041 Barcelona, Spain
| | - Vicente A. Yépez
- School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany
| | - German Demidov
- Universitätsklinikum Tübingen—Institut für Medizinische Genetik und angewandte Genomik, 72076 Tübingen, Germany
| | - Steven Laurie
- Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, Spain
| | - Anna Esteve-Codina
- Centro Nacional de Análisis Genómico (CNAG), 08028 Barcelona, Spain
- Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Julien Gagneur
- School of Computation, Information and Technology, Technical University of Munich, 85748 Garching, Germany
- Institute of Human Genetics, School of Medicine, Technical University of Munich, 81675 Munich, Germany
- Computational Health Center, Helmholtz Center Munich, 85764 Neuherberg, Germany
| | - Yolande Parkhurst
- Muscle Immunoanalysis Unit, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE7 7DN, UK
| | - Robert Muni-Lofra
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK; (A.S.-C.)
| | - Elizabeth Harris
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK; (A.S.-C.)
| | - Chiara Marini-Bettolo
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK; (A.S.-C.)
| | - Volker Straub
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK; (A.S.-C.)
| | - Ana Töpf
- John Walton Muscular Dystrophy Research Centre, Translational and Clinical Research Institute, Newcastle University and Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne NE1 3BZ, UK; (A.S.-C.)
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32
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Rodriguez-Gil JL, Nagy PL, Francke U. Optical genome mapping with genome sequencing identifies subtelomeric Xq28 deletion and inserted 7p22.3 duplication in a male with multisystem developmental disorder. Am J Med Genet A 2024:e63814. [PMID: 39011850 DOI: 10.1002/ajmg.a.63814] [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: 11/01/2023] [Revised: 03/24/2024] [Accepted: 06/27/2024] [Indexed: 07/17/2024]
Abstract
We report a 17-year-old male with supravalvular stenosis, initial failure to thrive and delayed early development, short stature, acromelia, dysmorphic facial features, hypertelorism, macrocephaly, syringomyelia, hypertension, and anxiety disorder. Fluorescent in situ hybridization (FISH), chromosomal microarray analysis (CMA), and exome sequencing (ES) were nondiagnostic. Combined optical genome mapping (OGM) and genome sequencing (GS) showed a complex rearrangement including an X chromosome with a 22.5 kb deletion in band Xq28 replaced by a 61.4 kb insertion of duplicated chromosome 7p22.3 material. The deletion removes the distal 3' untranslated region (UTR) of FUNDC2, the entire CMC4 and MTCP1, and the first five exons of BRCC3. Transcriptome analysis revealed absent expression of CMC4 and MTCP1 and BRCC3 with normal transcript level of FUNDC2. The inserted duplication includes only one known gene: UNCX. Similar overlapping Xq28 deletions have been reported to be associated with Moyamoya disease (MMD), short stature, hypergonadotropic hypogonadism (HH), and facial dysmorphism. Although he has short stature, our patient does not have signs of Moyamoya arteriopathy or hypogonadism. The structurally abnormal X chromosome was present in his mother, but not in his unaffected brother, maternal uncle, or maternal grandparents. We propose that the combination of his absent Xq28 and duplicated 7p22.3 genomic material is responsible for his phenotype. This case highlights the potential of combined OGM and GS for detecting complex structural variants compared with standard of care genetic testing such as CMA and ES.
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Affiliation(s)
- Jorge L Rodriguez-Gil
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Pediatrics, Division of Neonatal and Developmental Medicine, Stanford University, Stanford, California, USA
| | | | - Uta Francke
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Stanford, California, USA
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33
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Fang X, Ma M, Rong W, Lian YY, Wu X, Gao Y, Li HP, Sheng X. Exome sequencing confirms the clinical diagnosis of both joubert syndrome and klinefelter syndrome with keratoconus in a han Chinese family. Front Genet 2024; 15:1417584. [PMID: 39076169 PMCID: PMC11284097 DOI: 10.3389/fgene.2024.1417584] [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: 04/15/2024] [Accepted: 06/26/2024] [Indexed: 07/31/2024] Open
Abstract
Introduction Joubert syndrome a rare genetic disorder, is characterized by abnormalities in the development of the central nervous system with "molar signs" on magnetic resonance imaging of the brain and accompanied by cerebellar vermis hypoplasia, ataxia, hypotonia, and developmental delay. Keratoconus (KC) is a kind of genetically predisposed eye disease that causes blindness characterized by a dilated thinning of the central or paracentral cornea conically projected forward, highly irregular astigmatism, and severe visual impairment. Klinefelter syndrome is caused by an extra X chromosome in the cells of male patients, and the main phenotype is tall stature and dysplasia with secondary sex characteristics. This study was intended to identify the genetic etiology and determine the clinical diagnosis of one Han Chinese family with specific clinical manifestations of keratoconus and multiorgan involvement. Methods A comprehensive ocular and related general examination was performed on one patient and his asymptomatic parents and brother. Pathogenic genes were tested by exome sequencing. CNV-seq was used to verify the copy number variation, and peripheral blood was cultured for karyotype analysis. The pathogenicity of the identified variant was determined subject to ACMG guidelines. The Gene Expression Omnibus (GEO) dataset of keratoconus-related genes in the NCBI database was obtained to analyze the differentially expressed genes in corneal tissues of the keratoconus group and the normal control group, and analysis of protein-protein interaction networks (PPI) was performed. Results Proband, a 25-year-old male, had sudden loss of vision in the left eye for 1 week. Best corrected visual acuity (BCVA): 0.5 (-1.00DS/-5.00DC*29°) in the right eye, counting fingers/40 cm in the left eye. Slit-lamp microscopy of the right eye showed mild anterior protrusion of the cornea and thinning of the cone-topped cornea. The left eye showed marked thinning of the central region of the cornea, rounded edema in the form of a cone-like bulge, epithelial bullae, edema and turbidity of the stroma, and bulging of the Descemet's membrane. Cranial magnetic resonance imaging (MRI) revealed changes in the midbrain and cerebellum, with a "molar sign" and a "bat-winged" ventriculus quartus cerebri. General check-up: 168 cm in height, decreased muscle tone in all four limbs, knee jerk elicited, negative Babinski sign, abdominal reflexes elicited, finger-to-nose test positive, intentional tremor evident in both hands, positive Romberg's sign, instability of gait, level I intellectual disability, poor adaptive behavior, communication disorders, teeth all dentures, a peculiar face with blepharophimosis, wide inner canthus distance, mild ptosis, severe positive epicanthus, high palatal arches, exotropia, hypotrichosis of beard and face, inconspicuous prominentia laryngea, and short upper and lower limbs. Exome sequencing detected compound heterozygous frameshift variants M1:c.9279dup:p.His3094Thrfs*18 and M2:c.6515_6522del:p.Lys2172Thrfs*37 in the patient's CPLANE1 gene and the presence of duplication-type CNV on the X chromosome. Sanger sequencing showed that the mother and father carried the M1 and M2 variants, respectively, and the younger brother carried the M2 variant, which was a novel variant. CNV-seq analysis showed the presence of a duplication-type CNV Xp22.33-Xq28 (2757837-156030895) of approximately 155 Mb on the X chromosome of the proband, which was a de novo variant and carried by neither of the parents. The two heterozygous frameshift variants and duplication-type CNV were pathogenic according to the ACMG guidelines. Differential expression analysis of keratoconus-related genes showed that CPLANE1 was upregulated in the corneal tissues of keratoconus patients compared with normal controls, and such a difference was statistically significant (p = 0.000515, <0.05). PPI analysis showed that the CPLANE1-NPHP3 complex protein acted as a bridge between cilia and extracellular matrix tissue. According to the genetic test results and clinical phenotype analysis, the family was finally diagnosed with Joubert syndrome combined with Keratoconus and Klinefelter syndrome. Discussion In this study, we report a proband in a Han Chinese family with both Joubert syndrome and X-linked Klinefelter syndrome as well as keratoconus, and the phenotype spectrum of CPLANE1-Joubert syndrome may be expanded accordingly. Meanwhile, the significance of exome sequencing was emphasized in aiding the clinical diagnosis of complex cases, which is difficult to make.
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Affiliation(s)
- Xinhe Fang
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Meijiao Ma
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Weining Rong
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Yuan-Yuan Lian
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Xueli Wu
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
| | - Yongying Gao
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Hui-Ping Li
- Ningxia Eye Hospital, People’s Hospital of Ningxia Hui Autonomous Region, Third Clinical Medical College of Ningxia Medical University, Yinchuan, China
| | - Xunlun Sheng
- Gansu Aier Ophthalmology and Optometry Hospital, Lanzhou, China
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Baer S, Schalk A, Miguet M, Schaefer É, El Chehadeh S, Ginglinger E, de Saint Martin A, Abi Wardé MT, Laugel V, de Feraudy Y, Gauer L, Hirsch E, Boulay C, Bansept C, Bolocan A, Kitadinis I, Gouronc A, Gérard B, Piton A, Scheidecker S. Copy Number Variation and Epilepsy: State of the Art in the Era of High-Throughput Sequencing-A Multicenter Cohort Study. Pediatr Neurol 2024; 159:16-25. [PMID: 39094250 DOI: 10.1016/j.pediatrneurol.2024.07.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 06/12/2024] [Accepted: 07/09/2024] [Indexed: 08/04/2024]
Abstract
BACKGROUND Genetic epilepsy diagnosis is increasing due to technological advancements. Although the use of molecular diagnosis is increasing, chromosomal microarray analysis (CMA) remains an important diagnostic tool for many patients. We aim to explore the role and indications of CMA in epilepsy, given the current genomic advances. METHODS We obtained data from 378 epileptic described patients, who underwent CMA between 2015 and 2021. Different types of syndromic or nonsyndromic epilepsy were represented. RESULTS After excluding patients who were undertreated or had missing data, we included 250 patients with treated epilepsy and relevant clinical information. These patients mostly had focal epilepsy or developmental and epileptic encephalopathy, with a median start age of 2 years. Ninety percent of the patients had intellectual disability, more than two thirds had normal head size, and 60% had an abnormal magnetic resonance imaging. We also included 10 patients with epilepsy without comorbidities. In our cohort, we identified 35 pathogenic copy number variations (CNVs) explaining epilepsy with nine recurrent CNVs enriched in patients with epilepsy, 12 CNVs related to neurodevelopmental disorder phenotype with possible epilepsy, five CNVs including a gene already known in epilepsy, and nine CNVs based on size combined with de novo occurrence. The diagnosis rate in our study reached 14% (35 of 250) with first-line CMA, as previously reported. Although targeted gene panel sequencing could potentially diagnose some of the reported epilepsy CNVs (34% [12 of 35]). CONCLUSIONS CMA remains a viable option as the first-line genetic test in cases where other genetic tests are not available and as a second-line diagnostic technique if gene panel or exome sequencing yields negative results.
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Affiliation(s)
- Sarah Baer
- Department of Neuropediatrics, ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, France.
| | - Audrey Schalk
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals Strasbourg France, Strasbourg, France
| | | | - Élise Schaefer
- Clinical Genetics Unit, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg, France
| | - Salima El Chehadeh
- Clinical Genetics Unit, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg, France
| | | | - Anne de Saint Martin
- Department of Neuropediatrics, ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Marie-Thérèse Abi Wardé
- Department of Neuropediatrics, ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Vincent Laugel
- Department of Neuropediatrics, ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Yvan de Feraudy
- Department of Neuropediatrics, ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Lucas Gauer
- Epilepsy Unit "Francis Rohmer," ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Neurology Department, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Edouard Hirsch
- Epilepsy Unit "Francis Rohmer," ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Neurology Department, Hôpitaux Universitaires de Strasbourg, Strasbourg, France
| | - Clotilde Boulay
- Epilepsy Unit "Francis Rohmer," ERN EpiCare, French Centre de référence des Épilepsies Rares (CréER), Neurology Department, Hôpitaux Universitaires de Strasbourg, Strasbourg, France; Department of Pediatrics, Émile Muller Hospital, Mulhouse, France
| | - Claire Bansept
- Department of Pediatrics, Émile Muller Hospital, Mulhouse, France
| | - Anamaria Bolocan
- Department of Pediatrics, Émile Muller Hospital, Mulhouse, France
| | - Ismini Kitadinis
- Department of Pediatrics, Émile Muller Hospital, Mulhouse, France
| | - Aurélie Gouronc
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals Strasbourg France, Strasbourg, France
| | - Bénédicte Gérard
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals Strasbourg France, Strasbourg, France
| | - Amélie Piton
- Institute for Genetics and Molecular and Cellular Biology (IGBMC), University of Strasbourg, CNRS UMR7104, INSERM U1258, Illkirch, France; Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals Strasbourg France, Strasbourg, France
| | - Sophie Scheidecker
- Laboratories of Genetic Diagnosis, Institut de Génétique Médicale d'Alsace (IGMA), Strasbourg University Hospitals Strasbourg France, Strasbourg, France
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Iturriaga A, Mounts E, Picchetta L, Vega C, Mulas F, Ottolini CS, Whitehead C, Tao X, Zhan Y, Loia N, Jobanputra V, Capalbo A, Jalas C. Confirmation and pathogenicity of small copy number variations incidentally detected via a targeted next-generation sequencing-based preimplantation genetic testing for aneuploidy platform. Fertil Steril 2024:S0015-0282(24)00601-0. [PMID: 38996904 DOI: 10.1016/j.fertnstert.2024.07.008] [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: 01/16/2024] [Revised: 07/04/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024]
Abstract
OBJECTIVE To evaluate the technical accuracy, inheritance, and pathogenicity of small copy number variants (CNVs) detected by a targeted next-generation sequencing-based preimplantation genetic testing for aneuploidy (PGT-A) platform. DESIGN Retrospective observational study performed between 2020 and 2022. SETTING Clinic. PATIENT(S) A total of 12,157 patients who underwent clinical PGT-A performed by targeted next-generation sequencing for whole chromosome and large segmental aneuploidies. INTERVENTION(S) An incidental finding was reported when a CNV gain/loss of at least 3 consecutive amplicons appeared in at least 2 embryos from the same in vitro fertilization cycle. MAIN OUTCOME MEASURE(S) The primary outcome measures were the specificity, incidence, inheritance, and pathogenicity of small CNVs detected by the PGT-A platform. Accuracy of the PGT-A platform CNV calls was assessed via concordance with the CNV calls (size and genomic location) on chromosomal microarray of the gamete provider(s). Parental origin of the CNV and pathogenicity classifications were also reported. RESULT(S) An incidental finding that met reporting criteria was identified in 75 (0.62%; 95% confidence interval, 0.5%-0.8%) of 12,157 unique PGT-A patients. Chromosomal microarray follow-up was requested for all cases, and results were received for 1 or both members of 65 reproductive couples. In all cases, 1 of the gamete providers was confirmed to have the CNV identified in the embryos (100.0%, N = 65/65; 95% confidence interval, 94.5-100). The identified CNV was of maternal origin in 34 cases (52.3%) and of paternal origin in 31 cases (47.7%). A significant correlation was identified between PGT-A-predicted CNV sizes and chromosomal microarray detected sizes (r = 0.81) and genomic coordinates on parental deoxyribonucleic acid. Twenty-six (40%) of the CNVs were classified as benign/likely benign, 30 (46.2%) as a variant of uncertain significance, and 9 (13.8%) as pathogenic/likely pathogenic. CONCLUSION(S) Certain PGT-A platforms may enable the detection of inherited, small CNVs with extremely high specificity without prior knowledge of parental status. Most CNVs in this data set were confirmed to be benign/likely benign or a variant of uncertain significance. Pathogenic/likely pathogenic CNVs associated with a broad range of phenotypic features may also be detected, although a reliable negative predictive value for small CNVs with current PGT-A technologies is unknown because of the many technical challenges.
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Affiliation(s)
| | - Emily Mounts
- Juno Genetics-US, Genetic Lab, Basking Ridge, New Jersey
| | | | - Cara Vega
- Juno Genetics-US, Genetic Lab, Basking Ridge, New Jersey
| | | | - Christian Simon Ottolini
- Juno Genetics-Italy, Reproductive Genetics, Rome, Italy; Department of Maternal and Fetal Medicine, University College of London Institute for Women's Health, University College London, London, United Kingdom
| | | | - Xin Tao
- Juno Genetics-US, Genetic Lab, Basking Ridge, New Jersey
| | - Yiping Zhan
- Juno Genetics-US, Genetic Lab, Basking Ridge, New Jersey
| | - Nicole Loia
- Juno Genetics-US, Genetic Lab, Basking Ridge, New Jersey
| | - Vaidehi Jobanputra
- Juno Genetics-US, Genetic Lab, Basking Ridge, New Jersey; Columbia University Irving Medical Center, New York, New York
| | - Antonio Capalbo
- Juno Genetics-Italy, Reproductive Genetics, Rome, Italy; Unit of Molecular Genetics, Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy; Department of Psychological Health and Territorial Sciences, School of Medicine and Health Sciences, "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy.
| | - Chaim Jalas
- Juno Genetics-US, Genetic Lab, Basking Ridge, New Jersey
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Antolin M, Tarrasó G, Sánchez MÁ, Plaja A, Martínez-Cruz D, Xunclà M, Castells N, Carreras E, Tizzano EF, García-Arumí E. Performance of Massive Parallel Sequencing-Based Cell-Free DNA Testing in Compromised Pregnancies. J Clin Med 2024; 13:4007. [PMID: 39064047 PMCID: PMC11277969 DOI: 10.3390/jcm13144007] [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: 05/09/2024] [Revised: 06/26/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024] Open
Abstract
Background/Objectives: Non-Invasive prenatal test (NIPT) is used as a universal or contingent test after prior risk assessment. Screening is mainly performed for common trisomies (T21, T13, T18), although other chromosomal anomalies may be detected. Our objective was to study the performance of GWNIPT in the detection of chromosomal abnormalities in pregnancies in which an invasive prenatal study was performed and in early pregnancy losses, in comparison with the reference test. Method: VeriSeqTM NIPT Solution v2, a genome-wide NIPT (GWNIPT), was performed prior to invasive testing in fetal diagnostic study cases (FDS, n = 155) and in early pregnancy losses (EPL, n = 68). Results: In the FDS group, the diagnostic test (QFPCR, array and karyotype) detected anomalies in 32 pregnancies (21%), in twenty of them (61%) also detected by GWNIPT. Eleven of the twelve cases undetected by GWNIPT were balanced translocations (n = 4) or deletions/duplications <7 Mb (n = 7). In the EPL group, GWNIPT detected anomalies in 46% of cases (31/68) but comparison with reference test (QFPCR and karyotype) in products of conception (POC) was only possible in 18 cases. Concordant results between POC and GWNIPT test were obtained in 16 of the 18 cases. In EPL, with GWNIPT testing, common trisomies accounted for 25.8% of cases (8/31), rare trisomies 54.8% (17/31) and microdeletions/duplications 16.1% (5/31). Conclusions: The GWNIPT test may be useful in clinical practice in prenatal and in EPL's genetic diagnosis when the appropriate sample is not available.
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Affiliation(s)
- Maria Antolin
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Guillermo Tarrasó
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - María Ángeles Sánchez
- Maternal-Fetal Medicine Unit, Department of Obstetrics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Alberto Plaja
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Desiree Martínez-Cruz
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Mar Xunclà
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Neus Castells
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Elena Carreras
- Maternal-Fetal Medicine Unit, Department of Obstetrics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Eduardo F. Tizzano
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
| | - Elena García-Arumí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain (E.G.-A.)
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d’Hebron Research Institut (VHIR), Universitat Autònoma de Barcelona (UAB), 08035 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, 08041 Barcelona, Spain
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37
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Zeng Y, Ding H, Wang X, Huang Y, Liu L, Du L, Lu J, Wu J, Zeng Y, Mai M, Zhu J, Yu L, He W, Guo F, Peng H, Yao C, Qi Y, Liu Y, Li F, Yang J, Hu R, Liang J, Wang J, Wang W, Zhang Y, Yin A. High positive predictive value of CNVs detected by clinical exome sequencing in suspected genetic diseases. J Transl Med 2024; 22:644. [PMID: 38982507 PMCID: PMC11234535 DOI: 10.1186/s12967-024-05468-1] [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: 04/07/2024] [Accepted: 07/03/2024] [Indexed: 07/11/2024] Open
Abstract
BACKGROUND Genetic disorders often manifest as abnormal fetal or childhood development. Copy number variations (CNVs) represent a significant genetic mechanism underlying such disorders. Despite their importance, the effectiveness of clinical exome sequencing (CES) in detecting CNVs, particularly small ones, remains incompletely understood. We aimed to evaluate the detection of both large and small CNVs using CES in a substantial clinical cohort, including parent-offspring trios and proband only analysis. METHODS We conducted a retrospective analysis of CES data from 2428 families, collected from 2018 to 2021. Detected CNV were categorized as large or small, and various validation techniques including chromosome microarray (CMA), Multiplex ligation-dependent probe amplification assay (MLPA), and/or PCR-based methods, were employed for cross-validation. RESULTS Our CNV discovery pipeline identified 171 CNV events in 154 cases, resulting in an overall detection rate of 6.3%. Validation was performed on 113 CNVs from 103 cases to assess CES reliability. The overall concordance rate between CES and other validation methods was 88.49% (100/113). Specifically, CES demonstrated complete consistency in detecting large CNV. However, for small CNVs, consistency rates were 81.08% (30/37) for deletions and 73.91% (17/23) for duplications. CONCLUSION CES demonstrated high sensitivity and reliability in CNV detection. It emerges as an economical and dependable option for the clinical CNV detection in cases of developmental abnormalities, especially fetal structural abnormalities.
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Affiliation(s)
- Yimo Zeng
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Hongke Ding
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Xingwang Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yanlin Huang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Ling Liu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Li Du
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jian Lu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jing Wu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yukun Zeng
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Mingqin Mai
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Juan Zhu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Lihua Yu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Wei He
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Fangfang Guo
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Haishan Peng
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Cuize Yao
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yiming Qi
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yuan Liu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Fake Li
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jiexia Yang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Rong Hu
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jie Liang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Jicheng Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Wei Wang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China
| | - Yan Zhang
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China.
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China.
| | - Aihua Yin
- Medical Genetics Center, Guangdong Women and Children Hospital, Xingnan Road 521, Guangzhou, 510010, Guangdong, China.
- Maternal and Children Metabolic-Genetic Key Laboratory, Guangdong Women and Children Hospital, Guangzhou, China.
- Guangzhou Key Laboratory of Prenatal Screening and Prenatal Diagnosis, Guangzhou, China.
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Wiener E, Cottino L, Botha G, Nyangiri O, Noyes H, McLeod A, Jakubosky D, Adebamowo C, Awadalla P, Landouré G, Matshaba M, Matovu E, Ramsay M, Simo G, Simuunza M, Tiemessen C, Wonkam A, Sahibdeen V, Krause A, Lombard Z, Hazelhurst S. An assessment of the genomic structural variation landscape in Sub-Saharan African populations. RESEARCH SQUARE 2024:rs.3.rs-4485126. [PMID: 39041024 PMCID: PMC11261963 DOI: 10.21203/rs.3.rs-4485126/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Structural variants are responsible for a large part of genomic variation between individuals and play a role in both common and rare diseases. Databases cataloguing structural variants notably do not represent the full spectrum of global diversity, particularly missing information from most African populations. To address this representation gap, we analysed 1,091 high-coverage African genomes, 545 of which are public data sets, and 546 which have been analysed for structural variants for the first time. Variants were called using five different tools and datasets merged and jointly called using SURVIVOR. We identified 67,795 structural variants throughout the genome, with 10,421 genes having at least one variant. Using a conservative overlap in merged data, 6,414 of the structural variants (9.5%) are novel compared to the Database of Genomic Variants. This study contributes to knowledge of the landscape of structural variant diversity in Africa and presents a reliable dataset for potential applications in population genetics and health-related research.
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Affiliation(s)
- Emma Wiener
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laura Cottino
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Unit, University of Cape Town, Cape Town, South Africa
| | - Oscar Nyangiri
- College of Veterinary Medicine, Animal Resources and Biosecurity Makerere University, Kampala, Uganda
| | - Harry Noyes
- Centre for Genomic Research, University of Liverpool, Liverpool, United Kingdom
| | - Annette McLeod
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - David Jakubosky
- Department of Biomedical Informatics, University of California, San Diego, United States of America
- Institute of Genomic Medicine, University of California, San Diego, United States of America
| | - Clement Adebamowo
- Department of Epidemiology and Public Health and Greenebaum Comprehensive Cancer Center University of Maryland School of Medicine, Baltimore, United States of America
| | - Phillip Awadalla
- Ontario Institute for Cancer Research, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
- Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Guida Landouré
- Faculty of Medicine and Odontostomatology University of Sciences, Techniques and Technology of Bamako, Bamako Mali
- Neurology Department Point ”G” University Hospital, Bamako, Mali
| | - Mogomotsi Matshaba
- Botswana-Baylor Children’s Clinical Center of Excellence, Gaborone, Botswana
- Baylor College of Medicine, Houston, United States
| | - Enock Matovu
- College of Veterinary Medicine, Animal Resources and Biosecurity Makerere University, Kampala, Uganda
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Gustave Simo
- Molecular Parasitology and Entomology Unit, Department of Biochemistry University of Dschang, Dschang, Cameroon
| | - Martin Simuunza
- Department of Disease Control, School of Veterinary Medicine University of Zambia, Lusaka, Zambia
| | - Caroline Tiemessen
- Centre for HIV and STIs, National Institute for Communicable Diseases, National Health Laboratory Services and Faculty of Health Sciences University of the Witwatersrand, Johannesburg, South Africa
| | - Ambroise Wonkam
- McKusick-Nathans Institute and Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, United States of America
- Division of Human Genetics, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Venesa Sahibdeen
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Amanda Krause
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
- School of Electrical & Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
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39
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Hramyka D, Sczakiel HL, Zhao MX, Stolpe O, Nieminen M, Adam R, Danyel M, Einicke L, Hägerling R, Knaus A, Mundlos S, Schwartzmann S, Seelow D, Ehmke N, Mensah M, Boschann F, Beule D, Holtgrewe M. REEV: review, evaluate and explain variants. Nucleic Acids Res 2024; 52:W148-W158. [PMID: 38769069 PMCID: PMC11223839 DOI: 10.1093/nar/gkae366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/07/2024] [Accepted: 05/03/2024] [Indexed: 05/22/2024] Open
Abstract
In the era of high throughput sequencing, special software is required for the clinical evaluation of genetic variants. We developed REEV (Review, Evaluate and Explain Variants), a user-friendly platform for clinicians and researchers in the field of rare disease genetics. Supporting data was aggregated from public data sources. We compared REEV with seven other tools for clinical variant evaluation. REEV (semi-)automatically fills individual ACMG criteria facilitating variant interpretation. REEV can store disease and phenotype data related to a case to use these for phenotype similarity measures. Users can create public permanent links for individual variants that can be saved as browser bookmarks and shared. REEV may help in the fast diagnostic assessment of genetic variants in a clinical as well as in a research context. REEV (https://reev.bihealth.org/) is free and open to all users and there is no login requirement.
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Affiliation(s)
- Dzmitry Hramyka
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Henrike Lisa Sczakiel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Max Xiaohang Zhao
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Oliver Stolpe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Mikko Nieminen
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
| | - Ronja Adam
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Magdalena Danyel
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Lara Einicke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - René Hägerling
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
- Berlin Institute of Health, BIH Center for Regenerative Therapies, Berlin, Germany
| | - Alexej Knaus
- Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, Germany
| | - Stefan Mundlos
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- RG Development & Disease, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Sarina Schwartzmann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Seelow
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Nadja Ehmke
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Martin Atta Mensah
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Digital Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Felix Boschann
- Institute of Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin, Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- BIH Biomedical Innovation Academy, Clinician Scientist Program, Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Dieter Beule
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | - Manuel Holtgrewe
- Berlin Institute of Health, Core Unit Bioinformatics, Berlin, Germany
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Celik NB, Sezer A, Genel N, Savas-Erdeve S, Karaman İ, Cetinkaya S. Case report: An adolescent female with anosmic hypogonadotropic hypogonadism, intellectual disability, and papillary thyroid carcinoma: heterozygous deletion of TCF12. Front Endocrinol (Lausanne) 2024; 15:1426916. [PMID: 39036055 PMCID: PMC11257912 DOI: 10.3389/fendo.2024.1426916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024] Open
Abstract
Background Isolated hypogonadotropic hypogonadism is a heterogeneous clinical entity. There is a growing list of molecular defects that are associated with hypogonadotropic hypogonadism (HH). TCF12, a recently identified molecular defect, causes craniosynostosis and is suggested to be used as a biomarker for prognosis in various cancer types. Recently, TCF12 variants were shown in a cohort with HH. Case presentation A 15.3 years old female patient was referred to the endocrinology clinic for obesity. She had been gaining weight from mid-childhood. She had her first epileptic seizure at the age of 15.1 years and mildly elevated thyroid autoantibodies were detected during evaluation for etiology of seizures. She had not experienced menarche yet. She was operated for left strabismus at the age of 7 years. School performance was poor and she was receiving special education. Tanner stage of breast was 1 and pubic hair was 3. The endocrine workup revealed hypogonadotropic hypogonadism. Also, the Sniffin' Sticks test detected anosmia. Thyroid ultrasonography was performed due to the mildly elevated thyroid autoantibodies, and thyroid nodules with punctate calcifications were detected. Total thyroidectomy and central lymph node dissection were performed regarding the cytological findings of the nodules and multicentric papillary thyroid carcinoma with no lymph node metastasis was detected on pathology specimens. Regarding the phenotypic features of the patients, whole exome sequencing was performed and heterozygous deletion of exon 1 and exon 6-8 in TCF12 was detected. Conclusion Haploinsufficiency of TCF12 causes anosmic HH. Probably due to the incomplete penetrance and variable expressivity of the disease, patients could display variable phenotypic features such as intellectual disability, developmental delay, and craniosynostosis. Further description of new cases with TCF12 variations could enhance our understanding of craniosynostosis and its potential link to Kallmann syndrome associated with this gene.
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Affiliation(s)
- Nur Berna Celik
- Department of Pediatrics, Division of Pediatric Endocrinology, Health Sciences University, Dr Sami Ulus Children’s Health and Disease, Health Implementation and Research Center, Ankara, Türkiye
| | - Abdullah Sezer
- Department of Genetics, Health Sciences University, Dr Sami Ulus Children’s Health and Disease, Health Implementation and Research Center, Ankara, Türkiye
| | - Nebiyye Genel
- Department of Pathology, Health Sciences University, Dr Sami Ulus Children’s Health and Disease, Health Implementation and Research Center, Ankara, Türkiye
| | - Senay Savas-Erdeve
- Department of Pediatrics, Division of Pediatric Endocrinology, Health Sciences University, Dr Sami Ulus Children’s Health and Disease, Health Implementation and Research Center, Ankara, Türkiye
| | - İbrahim Karaman
- Department of Pediatric Surgery, Health Sciences University, Dr Sami Ulus Children’s Health and Disease, Health Implementation and Research Center, Ankara, Türkiye
| | - Semra Cetinkaya
- Department of Pediatrics, Division of Pediatric Endocrinology, Health Sciences University, Dr Sami Ulus Children’s Health and Disease, Health Implementation and Research Center, Ankara, Türkiye
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Xu K, Li G, Niu Y, Wu Z, Zhang TJ, Zhang S, Wu N. First copy number variant in trans with single nucleotide variant in CCN6 causing progressive pseudorheumatoid dysplasia revealed by genome sequencing and deep phenotyping in monozygotic twins. Am J Med Genet A 2024:e63801. [PMID: 38958524 DOI: 10.1002/ajmg.a.63801] [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: 02/12/2024] [Revised: 05/21/2024] [Accepted: 06/14/2024] [Indexed: 07/04/2024]
Abstract
Biallelic pathogenic variants in CCN6 cause progressive pseudorheumatoid dysplasia (PPD), a rare skeletal dysplasia. The predominant features include noninflammatory progressive joint stiffness and enlargement, which are not unique to this condition. Nearly 100% of the reported variants are single nucleotide variants or small indels, and missing of a second variant has been reported. Genome sequencing (GS) covers various types of variants and deep phenotyping (DP) provides detailed and precise information facilitating genetic data interpretation. The combination of GS and DP improves diagnostic yield, especially in rare and undiagnosed diseases. We identified a novel compound heterozygote involving a disease-causing copy number variant (g.112057664_112064205del) in trans with a single nucleotide variant (c.624dup(p.Cys209MetfsTer21)) in CCN6 in a pair of monozygotic twins, through the methods of GS and DP. The twins had received three nondiagnostic results before. The g.112057664_112064205del variant was missed by all the tests, and the recorded phenotypes were inaccurate or even misleading. The twins were diagnosed with PPD, ending a 13-year diagnostic odyssey. There may be other patients with PPD experiencing underdiagnosis and misdiagnosis due to inadequate genetic testing or phenotyping methods. This case highlights the critical role of GS and DP in facilitating an accurate and timely diagnosis.
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Affiliation(s)
- Kexin Xu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
| | - Yuchen Niu
- Clinical Biobank, Medical Research Center, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- Medical Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Shuyang Zhang
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Science, Beijing, China
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing, China
- Key Laboratory of Big Data for spinal Deformities, Chinese Academy of Medical Sciences, Beijing, China
- State Key Laboratory of Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
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Urzua A, Catena S, Morales P, Lay-Son G. Silver-Russell syndrome-like features in a child with recombinant chromosome 11 derived from maternal pericentric inversion. Clin Dysmorphol 2024; 33:105-109. [PMID: 38818816 DOI: 10.1097/mcd.0000000000000483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Silver-Russell syndrome (SRS) is a well-known syndrome but with heterogeneous etiologies. We present the case of a child with severe SRS-like features resulting from a complex rearrangement of chromosome 11 inherited from his mother. We studied the index case with karyotyping, MS-MLPA and molecular karyotyping. The mother was studied with karyotyping and subtelomeric FISH. We found a child with marked developmental delay and fatal outcome due to failure to thrive, carrying an 11p15 duplication and an 11q25 deletion of maternal origin. We discovered that the mother was a carrier of a pericentric inversion of chromosome 11, with a history of recurrence in other family members who had severe growth retardation and early death. To our knowledge, no similar SRS-like cases have been described in the literature. This report supports the importance of identification the causative genetic mechanism in SRS-like individuals with duplication in 11p15 region due to high risk of recurrence and to provide an appropriate genetic counseling to the family.
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Affiliation(s)
- Abraham Urzua
- Centro de Genética y Genómica, Facultad de Medicina, Clínica Alemana Universidad del Desarrollo
- Current affiliation: Laboratorio de Biología Molecular y Citogenética, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Sofía Catena
- Jackson Memorial Hospital, University of Miami, USA
| | - Paulina Morales
- Laboratorio de Citogenética y Genética Molecular, Instituto de Nutrición y Tecnología de los Alimentos, Universidad de Chile
| | - Guillermo Lay-Son
- Hospital Padre Hurtado
- Unidad de Genética y Enfermedades Metabólicas, División de Pediatría, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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Li G, Chen Y, Han X, Li N, Li S. Concurrent of compound heterozygous variant of a novel in-frame deletion and the common hypomorphic haplotype in TBX6 and inherited 17q12 microdeletion in a fetus. BMC Pregnancy Childbirth 2024; 24:456. [PMID: 38951757 PMCID: PMC11218386 DOI: 10.1186/s12884-024-06653-2] [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: 02/19/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024] Open
Abstract
BACKGROUND TBX6, a member of the T-box gene family, encodes the transcription factor box 6 that is critical for somite segmentation in vertebrates. It is known that the compound heterozygosity of disruptive variants in trans with a common hypomorphic risk haplotype (T-C-A) in the TBX6 gene contribute to 10% of congenital scoliosis (CS) cases. The deletion of chromosome 17q12 is a rare cytogenetic abnormality, which often leads to renal cysts and diabetes mellitus. However, the affected individuals often exhibit clinical heterogeneity and incomplete penetrance. METHODS We here present a Chinese fetus who was shown to have CS by ultrasound examination at 17 weeks of gestation. Trio whole-exome sequencing (WES) was performed to investigate the underlying genetic defects of the fetus. In vitro functional experiments, including western-blotting and luciferase transactivation assay, were performed to determine the pathogenicity of the novel variant of TBX6. RESULTS WES revealed the fetus harbored a compound heterozygous variant of c.338_340del (p.Ile113del) and the common hypomorphic risk haplotype of the TBX6 gene. In vitro functional study showed the p.Ile113del variant had no impact on TBX6 expression, but almost led to complete loss of its transcriptional activity. In addition, we identified a 1.85 Mb deletion on 17q12 region in the fetus and the mother. Though there is currently no clinical phenotype associated with this copy number variation in the fetus, it can explain multiple renal cysts in the pregnant woman. CONCLUSIONS This study is the first to report a Chinese fetus with a single amino acid deletion variant and a T-C-A haplotype of TBX6. The clinical heterogeneity of 17q12 microdeletion poses significant challenges for prenatal genetic counseling. Our results once again suggest the complexity of prenatal genetic diagnosis.
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Affiliation(s)
- Guoqiang Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Yiyao Chen
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Xu Han
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China
| | - Niu Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China.
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Shuyuan Li
- Department of Reproductive Genetics, International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, No.910, Hengshan Road, Shanghai, 200030, China.
- Shanghai Key Laboratory of Embryo Original Diseases, Shanghai, 200030, China.
- Faculty of Medical Laboratory Science, College of Health Science and Technology, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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Gippert S, Wagner M, Brunet T, Berruti R, Brugger M, Schwaibold EMC, Haack TB, Hoffmann GF, Bettendorf M, Choukair D. Exome sequencing (ES) of a pediatric cohort with chronic endocrine diseases: a single-center study (within the framework of the TRANSLATE-NAMSE project). Endocrine 2024; 85:444-453. [PMID: 37940764 PMCID: PMC11246252 DOI: 10.1007/s12020-023-03581-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/18/2023] [Indexed: 11/10/2023]
Abstract
BACKGROUND Endocrine disorders are heterogeneous and include a significant number of rare monogenic diseases. METHODS We performed exome sequencing (ES) in 106 children recruited from a single center within the TRANSLATE‑NAMSE project. They were categorized into subgroups: proportionate short stature (PSS), disproportionate short stature (DSS), hypopituitarism (H), differences in sexual development (DSD), syndromic diseases (SD) and others. RESULTS The overall diagnostic yield was 34.9% (n = 37/106), including 5 patients with variants in candidate genes, which have contributed to collaborations to identify gene-disease associations. The diagnostic yield varied significantly between subgroups: PSS: 16.6% (1/6); DSS: 18.8% (3/16); H: 17.1% (6/35); DSD: 37.5% (3/8); SD: 66.6% (22/33); others: 25% (2/8). Confirmed diagnoses included 75% ultrarare diseases. Three patients harbored more than one disease-causing variant, resulting in dual diagnoses. CONCLUSIONS ES is an effective tool for genetic diagnosis in pediatric patients with complex endocrine diseases. An accurate phenotypic description, including comprehensive endocrine diagnostics, as well as the evaluation of variants in multidisciplinary case conferences involving geneticists, are necessary for personalized diagnostic care. Here, we illustrate the broad spectrum of genetic endocrinopathies that have led to the initiation of specific treatment, surveillance, and family counseling.
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Affiliation(s)
- Sebastian Gippert
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Matias Wagner
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Institute for Neurogenomics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Theresa Brunet
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
- Department of Pediatric Neurology and Developmental Medicine, Hauner Children's Hospital, Ludwig Maximilian University of Munich, Munich, Germany
| | - Riccardo Berruti
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | - Melanie Brugger
- Institute of Human Genetics, Klinikum rechts der Isar, School of Medicine, Technical University of Munich, Munich, Germany
| | | | - Tobias B Haack
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tübingen, Germany and Centre for Rare Diseases, University of Tuebingen, Tübingen, Germany
| | - Georg F Hoffmann
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Markus Bettendorf
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniela Choukair
- Division of Pediatric Endocrinology and Diabetes, Center for Pediatrics and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany and Center for Rare Diseases, University Hospital Heidelberg, Heidelberg, Germany.
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Yao L, Cao Y, Zhang C, Huang X, Tian W, Cao L. Clinical and genetic characteristics in a Chinese cohort of complex spastic paraplegia type 4. Clin Genet 2024; 106:56-65. [PMID: 38403837 DOI: 10.1111/cge.14510] [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: 12/09/2023] [Revised: 01/27/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024]
Abstract
Spastic paraplegia type 4 (SPG4), caused by SPAST mutations, is the most predominant subtype of hereditary spastic paraplegia. Most documented SPG4 patients present as pure form, with the complex form rarely reported. We described the clinical and genetic features of 20 patients with complex phenotypes of SPG4 and further explored the genotype-phenotype correlations. We collected detailed clinical data of all SPG4 patients and assessed their phenotypes. SPAST gene mutations were identified by Multiplex ligation-dependent probe amplification in combination with whole exome sequencing. We further performed statistical analysis in genotype and phenotype among patients with various manifestations and different variants. Out of 90 SPG4 patients, 20 patients (male:female = 16:4) with additional neurologic deficits, namely complex form, were included in our study. The bimodal distribution of age of onset at 0-10 and 21-40 years old is concluded. On cranial MRI, obvious white matter lesions can be observed in five patients. We identified 9 novel and 8 reported SPAST mutations, of which 11 mutations were located in AAA (ATPase associated with various cellular activities) domain. The AAA cassette of spastin is the hottest mutated region among complex SPG4. All patients with cognitive impairment (CI) are males (n = 9/9). Additionally, 80% patients with ataxia are due to frameshift mutations (n = 4/5). Overall, our study summarized and analyzed the genetic and phenotypic characteristics of complex SPG4, making up over 1/5 of in-house SPG4 cohort, among which CI and ataxia are the most common features. Further studies are expected to explore the underlying mechanisms.
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Affiliation(s)
- Li Yao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Neurology, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Yuwen Cao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Neurological Rare Disease Biobank and Precision Diagnostic Technical Service Platform, Shanghai, China
| | - Chao Zhang
- Department of Neurology, Suzhou Hospital of Anhui Medical University, Suzhou, China
| | - Xiaojun Huang
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Neurological Rare Disease Biobank and Precision Diagnostic Technical Service Platform, Shanghai, China
| | - Wotu Tian
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Neurological Rare Disease Biobank and Precision Diagnostic Technical Service Platform, Shanghai, China
| | - Li Cao
- Department of Neurology, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Neurological Rare Disease Biobank and Precision Diagnostic Technical Service Platform, Shanghai, China
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Granhøj J, Pedersen KV, Aagaard MM, Graakjaer JA, Lildballe DL, Birn H, Rasmussen M. The role of genomic disorders in chronic kidney failure of undetermined aetiology ≤50 years. Clin Kidney J 2024; 17:sfae166. [PMID: 39021813 PMCID: PMC11252669 DOI: 10.1093/ckj/sfae166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Indexed: 07/20/2024] Open
Abstract
Background Genomic disorders caused by copy number variations (CNVs) are prevalent in patients with kidney disease; however, their contribution to chronic kidney failure (KF) of undetermined aetiology (uKF) is unclear. We screened patients with uKF aged 50 years or younger to establish the prevalence of causative CNVs. Methods We enrolled patients with an onset of KF ≤50 years from suspected undetermined aetiology for initial review of medical records to exclude patients with clear-cut clinical or histopathological kidney diagnoses or patients with already established genetic kidney diseases. Next, we performed single nucleotide polymorphism (SNP) array-based CNV screening. All the detected CNVs were systematically classified and evaluated as possible causes of the patient's kidney disease. Patients with CNVs not explaining the kidney phenotype were additionally screened for causal variants in 540 genes using whole-genome sequencing. Results We enrolled 172 patients, of whom 123 underwent SNP-array. Pathogenic CNVs corresponding to known genomic disorders were identified in 12 patients (9.8%). The identified genomic disorders provided a causative kidney diagnosis in three patients, all of whom had reached KF by age 18 years. The remaining nine patients had CNVs with unclear kidney disease causality. Subsequently, whole-genome sequencing provided a causative genetic diagnosis in an additional four patients, including two diagnostic sequence variants unrelated to the detected CNVs. Conclusions Genomic disorders were prevalent in this cohort with uKF, and causative CNVs were identified in 5 of 123 patients. Further studies combining the analysis of CNVs and sequence variants are needed to clarify the causal role of genomic disorders in kidney disease.
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Affiliation(s)
- Jeff Granhøj
- Department of Clinical Genetics, Lillebaelt Hospital–University Hospital of Southern Denmark, Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
| | - Katja Venborg Pedersen
- Department of Clinical Genetics, Lillebaelt Hospital–University Hospital of Southern Denmark, Vejle, Denmark
| | - Mads Malik Aagaard
- Department of Clinical Genetics, Lillebaelt Hospital–University Hospital of Southern Denmark, Vejle, Denmark
| | - Jesper Aagaard Graakjaer
- Department of Clinical Genetics, Lillebaelt Hospital–University Hospital of Southern Denmark, Vejle, Denmark
| | - Dorte Launholt Lildballe
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Henrik Birn
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Renal Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Maria Rasmussen
- Department of Clinical Genetics, Lillebaelt Hospital–University Hospital of Southern Denmark, Vejle, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense, Denmark
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Stanley KJ, Kalbfleisch KJ, Moran OM, Chaturvedi RR, Roifman M, Chen X, Manshaei R, Martin N, McDermott S, McNiven V, Myles-Reid D, Nield LE, Reuter MS, Schwartz MLB, Shannon P, Silver R, Somerville C, Teitelbaum R, Zahavich L, Bassett AS, Kim RH, Mital S, Chitayat D, Jobling RK. Expanding the phenotypic spectrum of NOTCH1 variants: clinical manifestations in families with congenital heart disease. Eur J Hum Genet 2024; 32:795-803. [PMID: 38778082 PMCID: PMC11219983 DOI: 10.1038/s41431-024-01629-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Revised: 04/28/2024] [Accepted: 05/01/2024] [Indexed: 05/25/2024] Open
Abstract
Pathogenic variants in NOTCH1 are associated with non-syndromic congenital heart disease (CHD) and Adams-Oliver syndrome (AOS). The clinical presentation of individuals with damaging NOTCH1 variants is characterized by variable expressivity and incomplete penetrance; however, data on systematic phenotypic characterization are limited. We report the genotype and phenotype of a cohort of 33 individuals (20 females, 13 males; median age 23.4 years, range 2.5-68.3 years) from 11 families with causative NOTCH1 variants (9 inherited, 2 de novo; 9 novel), ascertained from a proband with CHD. We describe the cardiac and extracardiac anomalies identified in these 33 individuals, only four of whom met criteria for AOS. The most common CHD identified was tetralogy of Fallot, though various left- and right-sided lesions and septal defects were also present. Extracardiac anomalies identified include cutis aplasia (5/33), cutaneous vascular anomalies (7/33), vascular anomalies of the central nervous system (2/10), Poland anomaly (1/33), pulmonary hypertension (2/33), and structural brain anomalies (3/14). Identification of these findings in a cardiac proband cohort supports NOTCH1-associated CHD and NOTCH1-associated AOS lying on a phenotypic continuum. Our findings also support (1) Broad indications for NOTCH1 molecular testing (any familial CHD, simplex tetralogy of Fallot or hypoplastic left heart); (2) Cascade testing in all at-risk relatives; and (3) A thorough physical exam, in addition to cardiac, brain (structural and vascular), abdominal, and ophthalmologic imaging, in all gene-positive individuals. This information is important for guiding the medical management of these individuals, particularly given the high prevalence of NOTCH1 variants in the CHD population.
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Affiliation(s)
- Kaitlin J Stanley
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Kelsey J Kalbfleisch
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Olivia M Moran
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Rajiv R Chaturvedi
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Maian Roifman
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Xin Chen
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Roozbeh Manshaei
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Nicole Martin
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Simina McDermott
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Vanda McNiven
- Division of Genetics, Department of Pediatrics, McMaster Children's Hospital, Hamilton, ON, Canada
| | - Diane Myles-Reid
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Lynne E Nield
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Miriam S Reuter
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, ON, Canada
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marci L B Schwartz
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Patrick Shannon
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rachel Silver
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Cherith Somerville
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
| | - Ronni Teitelbaum
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Laura Zahavich
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
| | - Anne S Bassett
- Genetics and Genome Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Dalglish Family 22q Clinic, University Health Network, Toronto, ON, Canada
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
- Clinical Genetics Research Program and Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Raymond H Kim
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- Fred A. Litwin Family Centre in Genetic Medicine, Department of Medicine, University Health Network, Toronto, ON, Canada
| | - Seema Mital
- Division of Cardiology, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- Ted Rogers Centre for Heart Research, Toronto, ON, Canada
| | - David Chitayat
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada
- The Prenatal Diagnosis and Medical Genetics Program, Department of Obstetrics and Gynecology, Mount Sinai Hospital, Toronto, ON, Canada
| | - Rebekah K Jobling
- Ted Rogers Centre for Heart Research Cardiac Genome Clinic, The Hospital for Sick Children, Toronto, ON, Canada.
- Division of Clinical and Metabolic Genetics, Department of Pediatrics, The Hospital for Sick Children, Toronto, ON, Canada.
- Genome Diagnostics, Department of Pediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada.
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48
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Cakmak HM, Kocabay K, Temizkan RC, Turay S, Ozde S, Kurt F, Sav NM, Erguven M, Coşkun E. Refugee and asylum-seeker children and health problems in the city of Duzce, Türkiye. Child Care Health Dev 2024; 50:e13295. [PMID: 38927007 DOI: 10.1111/cch.13295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 05/24/2024] [Accepted: 05/30/2024] [Indexed: 06/28/2024]
Abstract
INTRODUCTION This study examines the health problems and healthcare needs of refugee and asylum-seeker children and aims to develop strategies for improvement. METHODS Based on quantitative data from 448 refugee and asylum-seeker children and 222 non-refugee local children, this study was conducted at Düzce University, Department of Paediatrics, between 2010 and 2021. The refugee children originated from three countries: Iraq (n = 304), Syria (n = 101) and Afghanistan (n = 43). The data were analysed using the SPSS data analysis program. Ethical clearance was obtained from the Ethics Committee of Düzce Üniversity. RESULTS The results suggest that refugee and asylum-seeker children have significantly higher rates of acute illness or infection, malnutrition (p < 0.001) and anaemia (p < 0.001) than local children as a result of living in overcrowded families (p = 0.017) and unhealthy conditions. Adolescent pregnancy (p = 0.049) emerges as an important social problem as a result of child marriage among refugee children, mostly in the form of consanguineous marriages (p < 0.001). The rate of having at least two adolescent pregnancies (under 18) was highest among Syrian refugee girls (p = 0.01). Although refugee and asylum-seeker children have higher rates of health insurance (between 74% and 95%), they have lower rates of insurance compared to local children. This research also compares the data from three nationalities, including Syria, Afghanistan and Iraq children; Iraqi and Afghan children under the international protection (IP) system with limited social support and rights had worse health conditions compared to other groups. Although Iraqi children had the highest rates of health insurance on admission (p < 0.001), they also had higher rates of chronic diseases (p = 0.001), infections (p = 0.004), allergic rhinitis (p = 0.001) and malnutrition (p < 0.001). The youngest age of admission (p = 0.006) and the shortest length of stay (p = 0.004) were for Afghan children who also had higher rates of upper respiratory infections (p = 0.021). CONCLUSIONS This study highlights the urgent need for improved screening programmes and the importance of collaborative efforts to address the specific health needs of these populations. Addressing the health status of child refugees is a complex and multifaceted task that requires the active participation of healthcare professionals, policymakers and researchers, each of whom has a crucial role to play.
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Affiliation(s)
- Hatice Mine Cakmak
- Department of Pediatrics, Duzce University Faculty of Medicine, Duzce, Turkey
| | - Kenan Kocabay
- Department of Pediatrics, Duzce University Faculty of Medicine, Duzce, Turkey
| | | | - Sevim Turay
- Department of Pediatrics, Duzce University Faculty of Medicine, Duzce, Turkey
| | - Sukriye Ozde
- Department of Pediatrics, Duzce University Faculty of Medicine, Duzce, Turkey
| | - Fatih Kurt
- Department of Pediatrics, Duzce University Faculty of Medicine, Duzce, Turkey
| | - Nadide Melike Sav
- Department of Pediatrics, Duzce University Faculty of Medicine, Duzce, Turkey
| | - Muferet Erguven
- Department of Pediatrics, Duzce University Faculty of Medicine, Duzce, Turkey
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49
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Houge G, Bratland E, Aukrust I, Tveten K, Žukauskaitė G, Sansovic I, Brea-Fernández AJ, Mayer K, Paakkola T, McKenna C, Wright W, Markovic MK, Lildballe DL, Konecny M, Smol T, Alhopuro P, Gouttenoire EA, Obeid K, Todorova A, Jankovic M, Lubieniecka JM, Stojiljkovic M, Buisine MP, Haukanes BI, Lorans M, Roomere H, Petit FM, Haanpää MK, Beneteau C, Pérez B, Plaseska-Karanfilska D, Rath M, Fuhrmann N, Ferreira BI, Stephanou C, Sjursen W, Maver A, Rouzier C, Chirita-Emandi A, Gonçalves J, Kuek WCD, Broly M, Haer-Wigman L, Thong MK, Tae SK, Hyblova M, den Dunnen JT, Laner A. Comparison of the ABC and ACMG systems for variant classification. Eur J Hum Genet 2024; 32:858-863. [PMID: 38778080 PMCID: PMC11219933 DOI: 10.1038/s41431-024-01617-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/11/2024] [Accepted: 04/18/2024] [Indexed: 05/25/2024] Open
Abstract
The ABC and ACMG variant classification systems were compared by asking mainly European clinical laboratories to classify variants in 10 challenging cases using both systems, and to state if the variant in question would be reported as a relevant result or not as a measure of clinical utility. In contrast to the ABC system, the ACMG system was not made to guide variant reporting but to determine the likelihood of pathogenicity. Nevertheless, this comparison is justified since the ACMG class determines variant reporting in many laboratories. Forty-three laboratories participated in the survey. In seven cases, the classification system used did not influence the reporting likelihood when variants labeled as "maybe report" after ACMG-based classification were included. In three cases of population frequent but disease-associated variants, there was a difference in favor of reporting after ABC classification. A possible reason is that ABC step C (standard variant comments) allows a variant to be reported in one clinical setting but not another, e.g., based on Bayesian-based likelihood calculation of clinical relevance. Finally, the selection of ACMG criteria was compared between 36 laboratories. When excluding criteria used by less than four laboratories (<10%), the average concordance rate was 46%. Taken together, ABC-based classification is more clear-cut than ACMG-based classification since molecular and clinical information is handled separately, and variant reporting can be adapted to the clinical question and phenotype. Furthermore, variants do not get a clinically inappropriate label, like pathogenic when not pathogenic in a clinical context, or variant of unknown significance when the significance is known.
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Affiliation(s)
- Gunnar Houge
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway.
| | - Eirik Bratland
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Ingvild Aukrust
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, Skien, Norway
| | - Gabrielė Žukauskaitė
- Department of Human and Medical Genetics, Institute of Biomedical Sciences, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Ivona Sansovic
- Department of Medical and Laboratory Genetics, Endocrinology and Diabetology, Childrens' Hospital Zagreb, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Alejandro J Brea-Fernández
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBERER), Santiago de Compostela, Spain
| | - Karin Mayer
- Center for Human Genetics and Laboratory Diagnostics, MVZ Martinsried GmbH, Martinsried, Germany
| | - Teija Paakkola
- Nordlab Wellbeing Service Group, Genetics Laboratory, Oulu, Finland
| | - Caoimhe McKenna
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - William Wright
- Northern Ireland Regional Molecular Diagnostic Service, Belfast, Northern Ireland
| | - Milica Keckarevic Markovic
- Center for Applied and Forensic Molecular Genetics, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Dorte L Lildballe
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michal Konecny
- Laboratory of Genomic Medicine, GHC GENETICS SK, Bratislava, Slovakia
- Department of Biology, Institute of Biology and Biotechnology, Faculty of Natural Sciences, University of ss. Cyril and Methodius in Trnava, Trnava, Slovakia
| | - Thomas Smol
- Institut de Genetique Medicale-CHU Lille, Lille, France
| | - Pia Alhopuro
- HUS Diagnostic Center, Laboratory of Genetics, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | | | - Katharina Obeid
- Molecular Diagnostics, Institute of Human Genetics, University Hospital Heidelberg, Heidelberg, Germany
| | - Albena Todorova
- Genetic Medico-Diagnostic Laboratory "Genica" and Genome Center Bulgaria, Sofia, Bulgaria
| | - Milena Jankovic
- Neurology Clinic UCCS, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Maja Stojiljkovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Marie-Pierre Buisine
- Molecular Oncogenetics, Department of Biochemistry and Molecular Biology, Lille University Hospital, Lille, France
- Univ. Lille, CNRS, Inserm, CHU Lille, UMR9020-U1277, CANTHER, Lille, France
| | - Bjørn Ivar Haukanes
- Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - Marie Lorans
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Hanno Roomere
- Department of laboratory genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
| | - François M Petit
- Department of Oncopharmacology, Centre Antoine Lacassagne, Nice, France
| | - Maria K Haanpää
- Department of Genomics, Turku University Hospital, Turku, Finland
| | - Claire Beneteau
- CHU Bordeaux, Service de Génétique Médicale, F-33000, Bordeaux, France
| | - Belén Pérez
- Genetics Department of CEDEM, Universidad Autónoma de Madrid, Madrid, Spain
| | - Dijana Plaseska-Karanfilska
- Research Centre for Genetic Engineering and Biotechnology "Georgi D. Efremov", Macedonian Academy of Sciences and Arts, Skopje, North Macedonia
| | - Matthias Rath
- Institute for Molecular Medicine, MSH Medical School Hamburg, Hamburg, Germany
- Department of Human Genetics, University Medicine Greifswald and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Greifswald, Germany
| | - Nico Fuhrmann
- Institute of Human Genetics, University of Cologne, Cologne, Germany
| | - Bibiana I Ferreira
- GENELAB by ABC, Faro, Portugal
- Faculty of Medicine and Biomedical Sciences, University of Algarve, Campus de Gambelas, Faro, Portugal
| | - Coralea Stephanou
- Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Wenche Sjursen
- Department of Medical Genetics, St Olavs Hospital, Trondheim, Norway
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, Ljubljana, Slovenia
| | - Cécile Rouzier
- Department of Medical Genetics, National Centre for Mitocondrial Diseases, CHU de NICE, Université Côte d'Azur, Nice, France
- CNRS, INSERM, IRCAN, Université Côte d'Azur, Nice, France
| | - Adela Chirita-Emandi
- Department of Microscopic Morphology Genetics Discipline, Center of Genomic Medicine, "Victor Babes" University of Medicine and Pharmacy Timisoara, Timisoara, Romania
| | - João Gonçalves
- Human Genetics Department, National Institute of Health Dr Ricardo Jorge, Lisbon, Portugal
| | - Wei Cheng David Kuek
- Molecular Diagnosis Centre, Department of Laboratory Medicine, National University Hospital, Kent Ridge, Singapore
| | - Martin Broly
- Laboratory of Rare and Autoinflammatory Genetic Diseases, Department of Genetics-LBM, Montpellier University Hospital, Montpellier, France
| | - Lonneke Haer-Wigman
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Meow-Keong Thong
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Sok-Kun Tae
- Genetics and Metabolism Unit, Department of Pediatrics, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | | | - Johan T den Dunnen
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Andreas Laner
- Medizinisch Genetisches Zentrum (MGZ) München, Munich, Germany
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50
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Duan H, Wang W, Zhang Y, Chen X, Jiang Z, Li J. Accuracy of expanded noninvasive prenatal testing for maternal copy number variations: A comparative study with CNV-seq of maternal lymphocyte DNA. Taiwan J Obstet Gynecol 2024; 63:536-539. [PMID: 39004482 DOI: 10.1016/j.tjog.2024.02.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/20/2024] [Indexed: 07/16/2024] Open
Abstract
OBJECTIVE To evaluate the accuracy of expanded noninvasive prenatal testing (NIPT) for maternal copy number variations. MATERIALS AND METHODS Expanded NIPT was used to detect CNVs ≥2 Mb at a whole-genome scale. The threshold of maternal deletion was copy numbers (CN) ≤ 1.6, and the threshold of maternal duplication was CN ≥ 2.4. RESULTS Of the 5440 pregnant women with successful expanded NIPT results, 28 maternal CNVs ≥2 Mb were detected in 27 pregnant women. Except for five cases reported as test failure, 23 CNVs ≥2 Mb were confirmed among the remaining 22 pregnant women by CNV-seq of maternal lymphocyte DNA. The genomic location, copy numbers and fragment size of maternal CNVs reported by expanded NIPT were consistent with the results of CNV-seq of maternal lymphocyte DNA. CONCLUSIONS Maternal CNVs ≥2 Mb can be accurately evaluated according to the CN indicated by expanded NIPT results.
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Affiliation(s)
- Honglei Duan
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Wanjun Wang
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Ying Zhang
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Xuemei Chen
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, China
| | - Zihan Jiang
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
| | - Jie Li
- Center for Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Affiliated Hospital of Medical School, Nanjing University, Nanjing, China.
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