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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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Berendes LS, Westhoff PS, Wittkowski H, Seelhöfer A, Varga G, Marquardt T, Park JH. Clinical and molecular analysis of a novel variant in heme oxygenase-1 deficiency: Unraveling its role in inflammation, heme metabolism, and pulmonary phenotype. Mol Genet Metab Rep 2024; 38:101038. [PMID: 38178812 PMCID: PMC10764348 DOI: 10.1016/j.ymgmr.2023.101038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/06/2024] Open
Abstract
Heme oxygenase 1 (HO-1) is the pivotal catalyst for the primary and rate-determining step in heme catabolism, playing a crucial role in mitigating heme-induced oxidative damage. Pathogenic variants in the HMOX1 gene which encodes HO-1, are responsible for a severe, multisystem disease characterized by recurrent inflammatory episodes, organ failure, and an ultimately fatal course. Chronic hemolysis and abnormally low bilirubin levels are cardinal laboratory features of this disorder. In this study, we describe a patient with severe interstitial lung disease, frequent episodes of hyperinflammation non-responsive to immunosuppression, and fatal pulmonary hemorrhage. Employing exome sequencing, we identified two protein truncating variants in HMOX1, c.262_268delinsCC (p.Ala88Profs*51) and a previously unreported variant, c.55dupG (p.Glu19Glyfs*14). Functional analysis in patient-derived lymphoblastoid cells unveiled the complete absence of HO-1 protein expression and a marked reduction in cell viability upon exposure to hemin. These findings confirm the pathogenicity of the identified HMOX1 variants, further underscoring their association with severe pulmonary manifestations . This study describes the profound clinical consequences stemming from disruptions in redox metabolism.
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Affiliation(s)
| | | | - Helmut Wittkowski
- University of Münster, Department of Pediatric Rheumatology and Immunology, Münster, Germany
| | - Anja Seelhöfer
- University of Münster, Department of General Pediatrics, Münster, Germany
| | - Georg Varga
- University of Münster, Department of Pediatric Rheumatology and Immunology, Münster, Germany
| | - Thorsten Marquardt
- University of Münster, Department of General Pediatrics, Münster, Germany
| | - Julien H. Park
- University of Münster, Department of General Pediatrics, Münster, Germany
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3
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Tolezano GC, Bastos GC, da Costa SS, Freire BL, Homma TK, Honjo RS, Yamamoto GL, Passos-Bueno MR, Koiffmann CP, Kim CA, Vianna-Morgante AM, de Lima Jorge AA, Bertola DR, Rosenberg C, Krepischi ACV. Burden of Rare Copy Number Variants in Microcephaly: A Brazilian Cohort of 185 Microcephalic Patients and Review of the Literature. J Autism Dev Disord 2024; 54:1181-1212. [PMID: 36502452 DOI: 10.1007/s10803-022-05853-z] [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] [Accepted: 11/26/2022] [Indexed: 12/14/2022]
Abstract
Microcephaly presents heterogeneous genetic etiology linked to several neurodevelopmental disorders (NDD). Copy number variants (CNVs) are a causal mechanism of microcephaly whose investigation is a crucial step for unraveling its molecular basis. Our purpose was to investigate the burden of rare CNVs in microcephalic individuals and to review genes and CNV syndromes associated with microcephaly. We performed chromosomal microarray analysis (CMA) in 185 Brazilian patients with microcephaly and evaluated microcephalic patients carrying < 200 kb CNVs documented in the DECIPHER database. Additionally, we reviewed known genes and CNV syndromes causally linked to microcephaly through the PubMed, OMIM, DECIPHER, and ClinGen databases. Rare clinically relevant CNVs were detected in 39 out of the 185 Brazilian patients investigated by CMA (21%). In 31 among the 60 DECIPHER patients carrying < 200 kb CNVs, at least one known microcephaly gene was observed. Overall, four gene sets implicated in microcephaly were disclosed: known microcephaly genes; genes with supporting evidence of association with microcephaly; known macrocephaly genes; and novel candidates, including OTUD7A, BBC3, CNTN6, and NAA15. In the review, we compiled 957 known microcephaly genes and 58 genomic CNV loci, comprising 13 duplications and 50 deletions, which have already been associated with clinical findings including microcephaly. We reviewed genes and CNV syndromes previously associated with microcephaly, reinforced the high CMA diagnostic yield for this condition, pinpointed novel candidate loci linked to microcephaly deserving further evaluation, and provided a useful resource for future research on the field of neurodevelopment.
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Affiliation(s)
- Giovanna Cantini Tolezano
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Giovanna Civitate Bastos
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Silvia Souza da Costa
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Bruna Lucheze Freire
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Thais Kataoka Homma
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Rachel Sayuri Honjo
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Guilherme Lopes Yamamoto
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Maria Rita Passos-Bueno
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Celia Priszkulnik Koiffmann
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Chong Ae Kim
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Angela Maria Vianna-Morgante
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Alexander Augusto de Lima Jorge
- Unidade de Endocrinologia Genética (LIM25), Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 455 Avenida Doutor Arnaldo, São Paulo, SP, 01246-903, Brazil
| | - Débora Romeo Bertola
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
- Unidade de Genética do Instituto da Criança, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo, 647 Avenida Doutor Enéas Carvalho de Aguiar, São Paulo, SP, 05403-900, Brazil
| | - Carla Rosenberg
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil
| | - Ana Cristina Victorino Krepischi
- Department of Genetics and Evolutionary Biology, Human Genome and Stem-Cell Research Center, Institute of Biosciences, University of São Paulo, 106 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
- Institute of Biosciences, University of São Paulo, 277 Rua do Matão, São Paulo, SP, 05508-090, Brazil.
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4
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Kim EB, Song JH, Le LNH, Kim H, Koh JW, Seo Y, Jeong HR, Kim HT, Ryu S. Characterization of exosomal microRNAs in preterm infants fed with breast milk and infant formula. Front Nutr 2024; 11:1339919. [PMID: 38304545 PMCID: PMC10830786 DOI: 10.3389/fnut.2024.1339919] [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: 11/29/2023] [Accepted: 01/04/2024] [Indexed: 02/03/2024] Open
Abstract
Breastfeeding not only reduces infection-related morbidity, but also increases growth of preterm infants. Advantages of breast milk (BM) for preterm infants are significant. They continue to be studied. However, because not all preterm infants can receive breastfeeding, bovine-based infant formula (IF) is used as an alternative, which may increase the risk of several preterm complications. Exosomes isolated from biofluids are emerging as biomarkers in research of various diseases. Here, we characterized miRNA contents of exosomes in urine and serum samples of preterm infants who were BM and IF fed and performed transcriptomic analysis of small RNA libraries. We identified significantly up-regulated 6 miRNAs and 10 miRNAs, respectively. Gene Ontology (GO) analysis revealed that target genes of these miRNAs might participate in neuronal development, immunity modulation, detoxification of reactive oxygen species, and transmembrane exchange. Our data suggest that exosome-based systemic screening for preterm infants with breastfeeding might be a screening tool for identifying target molecules involved in therapy for preterm infants in neonatal intensive care unit (NICU) and for future application as nutraceutical formulations or pharmaceuticals.
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Affiliation(s)
- Eun-Bit Kim
- Soonchunhyang Institute of Med-bio Science (SIMS), Soonchunhyang University, Cheonan, Republic of Korea
| | - Jun Hwan Song
- Soonchunhyang University Cheonan Hospital, College of Medicine, Soon-chunhyang University, Cheonan, Republic of Korea
| | - Linh Nguy-Hoang Le
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, Republic of Korea
| | - Ho Kim
- Soonchunhyang University Cheonan Hospital, College of Medicine, Soon-chunhyang University, Cheonan, Republic of Korea
| | - Ji Won Koh
- Soonchunhyang University Cheonan Hospital, College of Medicine, Soon-chunhyang University, Cheonan, Republic of Korea
| | - Yekyeng Seo
- Soonchunhyang University Cheonan Hospital, College of Medicine, Soon-chunhyang University, Cheonan, Republic of Korea
| | - Hwal Rim Jeong
- Department of Pediatrics, College of Medicine, Soonchunhyang University, Cheonan, Republic of Korea
| | - Hyun-Taek Kim
- Soonchunhyang Institute of Med-bio Science (SIMS), Soonchunhyang University, Cheonan, Republic of Korea
| | - Seongho Ryu
- Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan, Republic of Korea
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Liang B, Yang F, Huang H, Liu Z, Ji Q, Wang Y, Wu X, Lin Y, Xie L, Zhao W, Cao H, Xu L, Lin N. Prenatal diagnosis of fetal digestive system malformations and pregnancy outcomes at a tertiary referral center in Fujian, China: A retrospective study. Heliyon 2023; 9:e21546. [PMID: 38027951 PMCID: PMC10663823 DOI: 10.1016/j.heliyon.2023.e21546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023] Open
Abstract
Fetal digestive system malformations (DSMs) are correlated with chromosomal anomalies. The prenatal diagnosis of DSMs allows for timely treatment and reduces perinatal morbidity and mortality. However, genetic screening for fetal DSMs is rarely reported. This study aimed to investigate genetic etiology and pregnancy outcomes in cases of fetal DSM by analyzing correlations between DSM types and chromosomal anomalies. This retrospective single-center study included 126 fetuses in whom DSMs were detected via prenatal ultrasonography. Genetic etiology was investigated using conventional karyotyping, chromosome microarray analysis (CMA), and whole-exome sequencing (WES). DSMs were categorized as simple DSM (Group A), DSM combined with abnormal ultrasound soft markers (Group B), and DSM combined with comorbidities of other systems (Group C). Abnormal karyotypes were detected in 11/126 (8.7 %) fetuses. Four more pathogenic copy number variants (CNVs) were detected using CMA, increasing the detection rate to 11.9 %. The detection rates significantly differed between the three DSM types (1.78 %, 8.11 %, and 33.33 % in Groups A, B, and C, respectively). The overall adverse pregnancy outcome rate was 33.9 %, and 11.5 %, 23.5 %, and 81.3 %, (P < 0.001), respectively, in Groups A, B, and C. Out of 83 live births, three neonates died, 26 underwent postnatal surgery with 24 favorable outcomes, and 54 did not undergo surgery and were basically normal. Two neonates who underwent WES were diagnosed with CHD7-associated Charge syndrome and JAG1-associated Alagille syndrome, respectively. Our findings demonstrate that fetal DSM is closely related to chromosome aneuploidies, CNVs, and point mutations. The prognoses of most fetuses with simple DSM and those with comorbid abnormal ultrasound soft markers were favorable in the absence of chromosomal anomalies and severe structural malformations, provided they underwent timely surgery as neonates. These findings provide guidance for the prenatal diagnosis and clinical management of fetal DSMs and the genetic counseling of parents.
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Affiliation(s)
- Bin Liang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Fang Yang
- Department of Obstetrics, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Zhaozhen Liu
- Department of Obstetrics, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Qingqiang Ji
- Department of Obstetrics, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Yan Wang
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Xiaoqing Wu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Yuan Lin
- Department of Gynecology, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Lanting Xie
- Department of Obstetrics, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Wantong Zhao
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Hua Cao
- Medical Research Center, Fujian Maternity and Child Health Hospital, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
- NHC Key Laboratory of Technical Evaluation of Fertility Regulation for Non-human Primates, Fujian Maternity and Child Health Hospital, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, 350001, China
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Yang M, Gao X, Hu C, Wang S, Sheng H, Ma Y. Bta-miR-484 Targets SFRP1 and Affects Preadipocytes Proliferation, Differentiation, and Apoptosis. Int J Mol Sci 2023; 24:12710. [PMID: 37628891 PMCID: PMC10454478 DOI: 10.3390/ijms241612710] [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: 06/07/2023] [Revised: 08/02/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
MicroRNAs (miRNAs) are essential regulators of numerous biological processes in animals, including adipogenesis. Despite the abundance of miRNAs associated with adipogenesis, their exact mechanisms of action remain largely unknown. Our study highlights the role of bta-miR-484 as a major regulator of adipocyte proliferation, apoptosis, and differentiation. Here, we demonstrated that the expression of bta-miR-484 initially increased during adipogenesis before decreasing. Overexpression of bta-miR-484 in adipocytes ultimately inhibited cell proliferation and differentiation, reduced the number of EdU fluorescence-stained cells, increased the number of G1 phase cells, reduced the number of G2 and S phase cells, and downregulated the expression of proliferation markers (CDK2 and PCNA) and differentiation markers (CEBPA, FABP4, and LPL). Additionally, overexpression of bta-miR-484 promoted the expression of apoptosis-related genes (Caspase 3, Caspase 9, and BAX), and increased the number of apoptotic cells observed via flow cytometry. In contrast, bta-miR-484 inhibition in adipocytes yielded opposite effects to those observed during bta-miR-484 overexpression. Moreover, luciferase reporter assays confirmed SFRP1 as a target gene of bta-miR-484, and revealed that bta-miR-484 downregulates SFRP1 mRNA expression. These findings offer compelling evidence that bta-miR-484 targets SFRP1, inhibits proliferation and differentiation, and promotes apoptosis. Therefore, these results offer novel insights into the bta-miR-484 regulation of adipocyte growth and development.
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Affiliation(s)
| | | | | | | | | | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, College of Animal Science and Technology, Ningxia University, Yinchuan 750021, China
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7
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Pennings M, Meijer RPP, Gerrits M, Janssen J, Pfundt R, de Leeuw N, Gilissen C, Gardeitchik T, Schouten M, Voermans N, van de Warrenburg B, Kamsteeg EJ. Copy number variants from 4800 exomes contribute to ~7% of genetic diagnoses in movement disorders, muscle disorders and neuropathies. Eur J Hum Genet 2023; 31:654-662. [PMID: 36781956 PMCID: PMC10250492 DOI: 10.1038/s41431-023-01312-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 01/11/2023] [Accepted: 02/01/2023] [Indexed: 02/15/2023] Open
Abstract
Various groups of neurological disorders, including movement disorders and neuromuscular diseases, are clinically and genetically heterogeneous. Diagnostic panel-based exome sequencing is a routine test for these disorders. Despite the success rates of exome sequencing, it results in the detection of causative sequence variants in 'only' 25-30% of cases. Copy number variants (CNVs), i.e. deletion or duplications, explain 10-20% of individuals with multisystemic phenotypes, such as co-existing intellectual disability, but may also have a role in disorders affecting a single system (organ), like neurological disorders with normal intelligence. In this study, CNVs were extracted from clinical exome sequencing reports of 4800 probands primarily with a movement disorder, myopathy or neuropathy. In 88 (~2%) probands, phenotype-matching CNVs were detected, representing ~7% of genetically confirmed cases. CNVs varied from involvement of over 100 genes to single exons and explained X-linked, autosomal dominant, or - recessive disorders, the latter due to either a homozygous CNV or a compound heterozygous CNV with a sequence variant on the other allele. CNVs were detected affecting genes where deletions or duplications are established as a common mechanism, like PRKN (in Parkinson's disease), DMD (in Duchenne muscular dystrophy) and PMP22 (in neuropathies), but also genes in which no intragenic CNVs have been reported to date. Analysis of CNVs as part of panel-based exome sequencing for genetically heterogeneous neurological diseases provides an additional diagnostic yield of ~2% without extra laboratory costs. Therefore it is recommended to perform CNV analysis for movement disorders, muscle disease, neuropathies, or any other single-system disorder.
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Affiliation(s)
- Maartje Pennings
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Rowdy P P Meijer
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Monique Gerrits
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Jannie Janssen
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicole de Leeuw
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Thatjana Gardeitchik
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Meyke Schouten
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands
| | - Nicol Voermans
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Bart van de Warrenburg
- Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud university medical Center, Nijmegen, the Netherlands
| | - Erik-Jan Kamsteeg
- Department of Human Genetics, Radboud university medical center, Nijmegen, the Netherlands.
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8
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Dalton SE, Workalemahu T, Allshouse AA, Page JM, Reddy UM, Saade GR, Pinar H, Goldenberg RL, Dudley DJ, Silver RM. Copy number variants and fetal growth in stillbirths. Am J Obstet Gynecol 2023; 228:579.e1-579.e11. [PMID: 36356697 PMCID: PMC10149588 DOI: 10.1016/j.ajog.2022.11.1274] [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: 04/27/2022] [Revised: 10/30/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
BACKGROUND Fetal growth abnormalities are associated with a higher incidence of stillbirth, with small and large for gestational age infants incurring a 3 to 4- and 2 to 3-fold increased risk, respectively. Although clinical risk factors such as diabetes, hypertension, and placental insufficiency have been associated with fetal growth aberrations and stillbirth, the role of underlying genetic etiologies remains uncertain. OBJECTIVE This study aimed to assess the relationship between abnormal copy number variants and fetal growth abnormalities in stillbirths using chromosomal microarray. STUDY DESIGN A secondary analysis utilizing a cohort study design of stillbirths from the Stillbirth Collaborative Research Network was performed. Exposure was defined as abnormal copy number variants including aneuploidies, pathogenic copy number variants, and variants of unknown clinical significance. The outcomes were small for gestational age and large for gestational age stillbirths, defined as a birthweight <10th percentile and greater than the 90th percentile for gestational age, respectively. RESULTS Among 393 stillbirths with chromosomal microarray and birthweight data, 16% had abnormal copy number variants. The small for gestational age outcome was more common among those with abnormal copy number variants than those with a normal microarray (29.5% vs 16.5%; P=.038). This finding was consistent after adjusting for clinically important variables. In the final model, only abnormal copy number variants and maternal age remained significantly associated with small for gestational age stillbirths, with an adjusted odds ratio of 2.22 (95% confidence interval, 1.12-4.18). Although large for gestational age stillbirths were more likely to have an abnormal microarray: 6.2% vs 3.3% (P=.275), with an odds ratio of 2.35 (95% confidence interval, 0.70-7.90), this finding did not reach statistical significance. CONCLUSION Genetic abnormalities are more common in the setting of small for gestational age stillborn fetuses. Abnormal copy number variants not detectable by traditional karyotype make up approximately 50% of the genetic abnormalities in this population.
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Affiliation(s)
- Susan E Dalton
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT
| | | | | | | | | | - George R Saade
- University of Texas Medical Branch at Galveston, Galveston, TX
| | - Halit Pinar
- Brown University School of Medicine, Providence, RI
| | | | | | - Robert M Silver
- University of Utah Health, Salt Lake City, UT; Intermountain Healthcare, Salt Lake City, UT.
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9
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Hamad A, Sherlaw-Sturrock CA, Glover K, Salmon R, Low K, Nair R, Sansbury FH, Rawlins L, Carmichael J, Horton R, Wedderburn S, Edgerley K, Irving R, Callaghan M, Mercer C, McGowan R, Robert L, Titheradge H, Naik S. Expanding the phenotypic spectrum of Chromosome 16p13.11 microduplication: A multicentric analysis of 206 patients. Eur J Med Genet 2023; 66:104714. [PMID: 36724812 DOI: 10.1016/j.ejmg.2023.104714] [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: 01/11/2022] [Revised: 11/23/2022] [Accepted: 01/24/2023] [Indexed: 01/30/2023]
Abstract
INTRODUCTION Recurrent chromosome 16p13.11 microduplication has been characterised in the literature as a cause of developmental delay, learning difficulties and behavioural abnormalities. It is a neurosusceptibility locus and has incomplete penetrance and variable expression. Other clinical features, such as cardiac abnormalities have also been reported. The duplicated region contains the MYH11 gene, which encodes the protein myosin-11 and is a component of the myosin heavy chain in smooth muscle. Recent literature has suggested 16p13.11 microduplication as one of the possible risk factors for thoracic aortic aneurysms and dissection (TAAD). Therefore, we studied the detailed phenotype of cases of chromosome 16p13.11 microduplication from seven centres in the United Kingdom (UK) to expand the phenotype, focusing on the cardiac abnormalities. METHODS All individuals with a chromosome 16p13.11 microduplication seen in Clinical Genetics prior to June 2017 in 6 centres (prior to 2018 in the seventh centre) were identified through the regional genetics laboratory databases. A Microsoft Excel® proforma was created and clinical data was collected retrospectively from clinical genetics databases from the seven genetics services in the UK. The data was collated and analysed collectively. RESULTS The majority of the individuals presented with (72%) developmental delay and (62%) behavioural abnormalities, in keeping with the published literature. 27% had some dysmorphic features, 14% had visual impairment and 8% had congenital cardiac abnormalities. Echocardiograms were performed in 50% of patients, and only 3.8% patients had aortic dilatation and no one had aortic dissection. 9.7% of patients were found to have a second genetic/chromosomal diagnosis, especially where there were additional phenotypic features. CONCLUSION 16p13.11 microduplication is a neurosusceptibility locus and is associated with variable expression. It may be helpful to refer children with 16p13.11 microduplication for a cardiac review for congenital cardiac abnormalities and also for ophthalmological assessment. Further prospective studies with cardiac assessments are recommended in this cohort of patients to determine whether ongoing aortic surveillance is indicated. Guidelines about the frequency of surveillance are indicated, especially in individuals with normal cardiac findings. We also highlight the importance of considering a second diagnosis if the phenotype is inconsistent with that reported.
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Affiliation(s)
- Asma Hamad
- West Midlands Genetics Services, Birmingham Women and Childrens NHS Foundation Trust, Birmingham. UK
| | | | - Kate Glover
- West Midlands Genetics Services, Birmingham Women and Childrens NHS Foundation Trust, Birmingham. UK
| | - Rachel Salmon
- West Midlands Genetics Services, Birmingham Women and Childrens NHS Foundation Trust, Birmingham. UK
| | - Karen Low
- Clinical Genetics Department, University Hospitals Bristol and Weston NHS Foundation Trust St Michael's Hospital, Bristol, UK
| | - Ramya Nair
- West Midlands Genetics Services, Birmingham Women and Childrens NHS Foundation Trust, Birmingham. UK
| | - Francis H Sansbury
- Clinical Genetics Department, University Hospitals Bristol and Weston NHS Foundation Trust St Michael's Hospital, Bristol, UK; All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, University Hospital of Wales, Cardiff, UK
| | - LettieE Rawlins
- Peninsula Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Jenny Carmichael
- Clinical Genetics Department, Oxford Centre for Genomic Medicine, Oxford, UK; Department of Clinical Genetics, Addenbrooke's Hospital, Cambridge, UK
| | - Rachael Horton
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | - Katherine Edgerley
- Clinical Genetics Department, University Hospitals Bristol and Weston NHS Foundation Trust St Michael's Hospital, Bristol, UK
| | - Rachel Irving
- Peninsula Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Mary Callaghan
- Peninsula Clinical Genetics, Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - Catherine Mercer
- Wessex Clinical Genetics Service, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Ruth McGowan
- West of Scotland Centre for Genomic Medicine, Glasgow, UK
| | - Leema Robert
- Clinical Genetics Department, Guy's and St Thomas' Hospital, London, UK
| | - Hannah Titheradge
- West Midlands Genetics Services, Birmingham Women and Childrens NHS Foundation Trust, Birmingham. UK.
| | - Swati Naik
- West Midlands Genetics Services, Birmingham Women and Childrens NHS Foundation Trust, Birmingham. UK
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10
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Zhang Y, Li Y, Guo R, Xu W, Liu X, Zhao C, Guo Q, Xu W, Ni X, Hao C, Cui Y, Li W. Genetic diagnostic yields of 354 Chinese ASD children with rare mutations by a pipeline of genomic tests. Front Genet 2023; 14:1108440. [PMID: 37035742 PMCID: PMC10076746 DOI: 10.3389/fgene.2023.1108440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 03/15/2023] [Indexed: 04/11/2023] Open
Abstract
Purpose: To establish an effective genomic diagnosis pipeline for children with autism spectrum disorder (ASD) for its genetic etiology and intervention. Methods: A cohort of 354 autism spectrum disorder patients were obtained from Beijing Children's Hospital, Capital Medical University. Peripheral blood samples of the patients were collected for whole genome sequencing (WGS) and RNA sequencing (RNAseq). Sequencing data analyses were performed for mining the single nucleotide variation (SNV), copy number variation (CNV) and structural variation (SV). Sanger sequencing and quantitative PCR were used to verify the positive results. Results: Among 354 patients, 9 cases with pathogenic/likely pathogenic copy number variation and 10 cases with pathogenic/likely pathogenic single nucleotide variations were detected, with a total positive rate of 5.3%. Among these 9 copy number variation cases, 5 were de novo and 4 were inherited. Among the 10 de novo single nucleotide variations, 7 were previously unreported. The pathological de novo mutations account for 4.2% in our cohort. Conclusion: Rare mutations of copy number variations and single nucleotide variations account for a relatively small proportion of autism spectrum disorder children, which can be easily detected by a genomic testing pipeline of combined whole genome sequencing and RNA sequencing. This is important for early etiological diagnosis and precise management of autism spectrum disorder with rare mutations.
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Affiliation(s)
- Yue Zhang
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Ying Li
- Department of Psychiatry, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Ruolan Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Wenjian Xu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xuanshi Liu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Chunlin Zhao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Qi Guo
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Wenshan Xu
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xin Ni
- National Center for Children’s Health, Beijing, China
- *Correspondence: Wei Li, ; Yonghua Cui, ; Chanjuan Hao, ; Xin Ni,
| | - Chanjuan Hao
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- *Correspondence: Wei Li, ; Yonghua Cui, ; Chanjuan Hao, ; Xin Ni,
| | - Yonghua Cui
- Department of Psychiatry, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- *Correspondence: Wei Li, ; Yonghua Cui, ; Chanjuan Hao, ; Xin Ni,
| | - Wei Li
- Beijing Key Laboratory for Genetics of Birth Defects, Beijing Pediatric Research Institute, MOE Key Laboratory of Major Diseases in Children, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
- *Correspondence: Wei Li, ; Yonghua Cui, ; Chanjuan Hao, ; Xin Ni,
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11
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Cai M, Que Y, Chen X, Chen Y, Liang B, Huang H, Xu L, Lin N. 16p13.11 microdeletion/microduplication in fetuses: investigation of associated ultrasound phenotypes, genetic anomalies, and pregnancy outcome follow-up. BMC Pregnancy Childbirth 2022; 22:913. [PMID: 36476185 PMCID: PMC9727942 DOI: 10.1186/s12884-022-05267-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES 16p13.11 microdeletion/microduplication are rare genetic diseases with incomplete penetrance, most of which have been reported in adults and children, with ultrasound phenotyping in fetuses rarely described. Here, we have analyzed prenatal ultrasound phenotypic characteristics associated with 16p13.11 microdeletion/microduplication, in order to improve the understanding, diagnosis and monitoring of this disease in the fetus. METHODS A total of 9000 pregnant women who underwent invasive prenatal diagnosis for karyotyping and SNP-array were retrospectively analyzed in tertiary referral institutions from October 2016 to January 2022. RESULTS SNP-array revealed that 20 fetuses had copy number variation (CNV) in the 16p13.11 region, out of which 5 had 16p13.11 microdeletion and the rest showed microduplication, along with different ultrasound phenotypes. Furthermore, 4/20 cases demonstrated structural abnormalities, while the remaining 16 cases were atypical in ultrasound. Taken together, 16p13.1 microdeletion was closely related to thickened nuchal translucency, while 16p13.11 microduplication was more closely associated with echogenic bowel. Only 5/15 fetuses were verified by pedigree, with one case of 16p13.11 microdeletion being de novo, and the other cases of 16p13.11 microduplication were inherited from one parent. In 4/20 cases, the pregnancy was terminated. Except for one case with short stature and another one who underwent lung cystadenoma surgery, no abnormalities were reported in the other cases during follow-up. CONCLUSION Fetuses with 16p13.11 microdeletion/microduplication had no characteristic phenotype of intrauterine ultrasound and was in good health after birth, thus providing a reference for the perinatal management of such cases.
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Affiliation(s)
- Meiying Cai
- grid.256112.30000 0004 1797 9307 Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yanting Que
- grid.256112.30000 0004 1797 9307College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fuzhou, China
| | - Xuemei Chen
- grid.256112.30000 0004 1797 9307 Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuqing Chen
- grid.256112.30000 0004 1797 9307 Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Bin Liang
- grid.256112.30000 0004 1797 9307 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
- grid.256112.30000 0004 1797 9307 Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- grid.256112.30000 0004 1797 9307 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
- grid.256112.30000 0004 1797 9307 Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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12
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Ehrlich L, Prakash SK. Copy-number variation in congenital heart disease. Curr Opin Genet Dev 2022; 77:101986. [PMID: 36202051 DOI: 10.1016/j.gde.2022.101986] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 01/27/2023]
Abstract
Genomic copy-number variants (CNVs) contribute to as many congenital heart disease (CHD) cases (10-15%) as chromosomal aberrations or single-gene mutations and influence clinical outcomes. CNVs in a few genomic hotspots (1q21.1, 2q13, 8p23.1, 11q24, 15q11.2, 16p11.2, and 22q11.2) are recurrently enriched in CHD cohorts and affect dosage-sensitive transcriptional regulators that are required for cardiac development. Reduced penetrance and pleiotropic effects on brain and heart development are common features of these CNVs. Therefore, additional genetic 'hits,' such as a second CNV or gene mutation, are probably required to cause CHD in most cases. Integrative analysis of CNVs, genome sequence, epigenetic alterations, and gene function will be required to delineate the complete genetic landscape of CHD.
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Affiliation(s)
- Laurent Ehrlich
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA
| | - Siddharth K Prakash
- Department of Internal Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, 6431 Fannin Street, Houston, TX 77030, USA.
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13
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Mahjani B, Birnbaum R, Buxbaum Grice A, Cappi C, Jung S, Avila MN, Reichenberg A, Sandin S, Hultman CM, Buxbaum JD, Grice DE. Phenotypic Impact of Rare Potentially Damaging Copy Number Variation in Obsessive-Compulsive Disorder and Chronic Tic Disorders. Genes (Basel) 2022; 13:1796. [PMID: 36292681 PMCID: PMC9601402 DOI: 10.3390/genes13101796] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/21/2022] [Accepted: 09/22/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Recent studies report an important-and previously underestimated-role of rare variation in risk of obsessive-compulsive disorder (OCD) and chronic tic disorders (CTD). Using data from a large epidemiological study, we evaluate the distribution of potentially damaging copy number variation (pdCNV) in OCD and CTD, examining associations between pdCNV and the phenotypes of probands, including a consideration of early- vs. late-diagnoses. METHOD The Obsessive-Compulsive Inventory-Revised (OCI-R) questionnaire was used to ascertain psychometric profiles of OCD probands. CNV were identified genome-wide using chromosomal microarray data. RESULTS For 993 OCD cases, 86 (9%) were identified as pdCNV carriers. The most frequent pdCNV found was at the 16p13.11 region. There was no significant association between pdCNV and the OCI-R total score. However, pdCNV was associated with Obsessing and Checking subscores. There was no significant difference in pdCNV frequency between early- vs. late-diagnosed OCD probands. Of the 217 CTD cases, 18 (8%) were identified as pdCNV carriers. CTD probands with pdCNV were significantly more likely to have co-occurring autism spectrum disorder (ASD). CONCLUSIONS pdCNV represents part of the risk architecture for OCD and CTD. If replicated, our findings suggest pdCNV impact some OCD symptoms. Genes within the 16p13.11 region are potential OCD risk genes.
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Affiliation(s)
- Behrang Mahjani
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Tics, OCD and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Rebecca Birnbaum
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ariela Buxbaum Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Carolina Cappi
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Seulgi Jung
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marina Natividad Avila
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Abraham Reichenberg
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sven Sandin
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Christina M. Hultman
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Joseph D. Buxbaum
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dorothy E. Grice
- Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Division of Tics, OCD and Related Disorders, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
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14
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Kagan M, Pleniceanu O, Vivante A. The genetic basis of congenital anomalies of the kidney and urinary tract. Pediatr Nephrol 2022; 37:2231-2243. [PMID: 35122119 DOI: 10.1007/s00467-021-05420-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 10/19/2022]
Abstract
During the past decades, remarkable progress has been made in our understanding of the molecular basis of kidney diseases, as well as in the ability to pinpoint disease-causing genetic changes. Congenital anomalies of the kidney and urinary tract (CAKUT) are remarkably diverse, and may be either isolated to the kidney or involve other systems, and are notorious in their variable genotype-phenotype correlations. Genetic conditions underlying CAKUT are individually rare, but collectively contribute to disease etiology in ~ 16% of children with CAKUT. In this review, we will discuss basic concepts of kidney development and genetics, common causes of monogenic CAKUT, and the approach to diagnosing and managing a patient with suspected monogenic CAKUT. Altogether, the concepts presented herein represent an introduction to the emergence of nephrogenetics, a fast-growing multi-disciplinary field that is focused on deciphering the causes and manifestations of genetic kidney diseases as well as providing the framework for managing patients with genetic forms of CAKUT.
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Affiliation(s)
- Maayan Kagan
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Oren Pleniceanu
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Kidney Research Lab, The Institute of Nephrology and Hypertension, Sheba Medical Center, Tel Hashomer, Ramat Gan, Israel
| | - Asaf Vivante
- Pediatric Department B and Pediatric Nephrology Unit, Edmond and Lily Safra Children's Hospital, Sackler Faculty of Medicine, Sheba Medical Center, Tel Hashomer, 5265601, Ramat Gan, Israel. .,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel. .,Talpiot Medical Leadership Program, Tel HaShomer, Ramat Gan, Israel.
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15
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Cheng K, Zhou H, Fu F, Lei T, Li F, Huang R, Wang Y, Yang X, Li R, Li D, Liao C. Should prenatal chromosomal microarray analysis be offered for isolated ventricular septal defect? A single-center retrospective study from China. Front Cardiovasc Med 2022; 9:988438. [PMID: 36158810 PMCID: PMC9489942 DOI: 10.3389/fcvm.2022.988438] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
ObjectiveTo evaluate the utility of chromosomal microarray analysis (CMA) in fetuses with isolated ventricular septal defect (VSD) and to explore the favorable factors for predicting spontaneous closure of defects.MethodsThe study included 436 singleton pregnancies seen at a referral prenatal diagnosis center, between January 2016 and May 2020, of which 168 fetuses with isolated VSD were diagnosed in the prenatal setting. VSD was classified as an isolated VSD whether it had ultrasound soft markers or not. All patients underwent testing employing quantitative fluorescent polymerase chain reaction (QF-PCR) and CMA as the first-line genetic detection strategies, mainly in amniotic fluid and umbilical blood samples. Rates of chromosomal abnormalities were compared by subgroups of isolated VSD (muscular or perimembranous). Binary logistic regression analysis was performed to predict the independent determinants of spontaneous closure by 2 years.ResultsOverall, the CMA identified clinically significant copy number variations (CNVs) in 7/168 (4.2%) fetuses and variants of unknown significance (VOUS) in 15/168 (8.9%). Muscular and perimembranous VSDs were found in 53.6 and 46.4%, respectively. Clinically significant relevant subchromosomal aberrations were revealed in seven (9.0%) perimembranous VSDs compared with none in 90 muscular defects (P < 0.01). The median initial size of the defect in the muscular VSDs was 2.2(1.8–2.7) mm, as compared to that of 2.8 (2.2–3.2) mm in the perimembranous VSDs group (p = 0.000). In muscular vs. perimembranous VSDs, spontaneous closure occurred more frequently and earlier [40.0 vs. 15.4% in utero (p = 0.000), 61.1 vs. 30.8% at 1-year (p = 0.000), and 75.6 vs. 42.3% at 2-year (P = 0.000)]. Postnatal surgical closure was warranted in 4/90 (4.4%) of the infants with muscular VSDs, as compared to 29/71 (40.8%) with perimembranous defects (p = 0.000). Furthermore, isolated muscular type VSD, smaller defect size, and maternal age of less than 35 years are all positive predictors of spontaneous closure of the defects.ConclusionThis study highlighted the value of microarray for unbalanced subchromosomal abnormalities in fetuses with isolated VSD, particularly in the perimembranous defects. The detection of an isolated muscular VSD prenatally may be considered a benign or likely benign finding; in contrast, for perimembranous VSD, a prenatal CMA should be offered.
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Affiliation(s)
- Ken Cheng
- School of Medicine, South China University of Technology, Guangzhou, China
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Hang Zhou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Tingying Lei
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Fucheng Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ruibin Huang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - You Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Dongzhi Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Can Liao
- School of Medicine, South China University of Technology, Guangzhou, China
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou, China
- *Correspondence: Can Liao
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16
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Nicolle R, Siquier-Pernet K, Rio M, Guimier A, Ollivier E, Nitschke P, Bole-Feysot C, Romana S, Hastie A, Cantagrel V, Malan V. 16p13.11p11.2 triplication syndrome: a new recognizable genomic disorder characterized by optical genome mapping and whole genome sequencing. Eur J Hum Genet 2022; 30:712-720. [PMID: 35388186 PMCID: PMC9177583 DOI: 10.1038/s41431-022-01094-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 03/06/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022] Open
Abstract
Highly identical segmental duplications (SDs) account for over 5% of the human genome and are enriched in the short arm of the chromosome 16. These SDs are susceptibility factors for recurrent chromosomal rearrangements mediated by non-allelic homologous recombination (NAHR). Chromosomal microarray analysis (CMA) has been widely used as the first-tier test for individuals with developmental disabilities and/or congenital anomalies and several genomic disorders involving the 16p-arm have been identified with this technique. However, the resolution of CMA and the limitations of short-reads whole genome sequencing (WGS) technology do not allow the full characterization of the most complex chromosomal rearrangements. Herein, we report on two unrelated patients with a de novo 16p13.11p11.2 triplication associated with a 16p11.2 duplication, detected by CMA. These patients share a similar phenotype including hypotonia, severe neurodevelopmental delay with profound speech impairment, hyperkinetic behavior, conductive hearing loss, and distinctive facial features. Short-reads WGS could not map precisely any of the rearrangement's breakpoints that lie within SDs. We used optical genome mapping (OGM) to determine the relative orientation of the triplicated and duplicated segments as well as the genomic positions of the breakpoints, allowing us to propose a mechanism involving recombination between allelic SDs and a NAHR event. In conclusion, we report a new clinically recognizable genomic disorder. In addition, the mechanism of these complex chromosomal rearrangements involving SDs could be unraveled by OGM.
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Affiliation(s)
- Romain Nicolle
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Karine Siquier-Pernet
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Marlène Rio
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Anne Guimier
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
| | - Emmanuelle Ollivier
- Université de Paris, Bioinformatics Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Patrick Nitschke
- Université de Paris, Bioinformatics Core Facility, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Christine Bole-Feysot
- Université de Paris, Genomics Platform, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Serge Romana
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | | | - Vincent Cantagrel
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France
| | - Valérie Malan
- Fédération de Génétique et Médecine Génomique, Service de Médecine Génomique des Maladies Rares, Hôpital Necker-Enfants Malades, Paris, France.
- Université de Paris, Developmental Brain Disorders Laboratory, Imagine Institute, INSERM UMR 1163, F-75015, Paris, France.
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17
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Nde1 is Required for Heterochromatin Compaction and Stability in Neocortical Neurons. iScience 2022; 25:104354. [PMID: 35601919 PMCID: PMC9121328 DOI: 10.1016/j.isci.2022.104354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 03/28/2022] [Accepted: 04/29/2022] [Indexed: 11/20/2022] Open
Abstract
The NDE1 gene encodes a scaffold protein essential for brain development. Although biallelic NDE1 loss of function (LOF) causes microcephaly with profound mental retardation, NDE1 missense mutations and copy number variations are associated with multiple neuropsychiatric disorders. However, the etiology of the diverse phenotypes resulting from NDE1 aberrations remains elusive. Here we demonstrate Nde1 controls neurogenesis through facilitating H4K20 trimethylation-mediated heterochromatin compaction. This mechanism patterns diverse chromatin landscapes and stabilizes constitutive heterochromatin of neocortical neurons. We demonstrate that NDE1 can undergo dynamic liquid-liquid phase separation, partitioning to the nucleus and interacting with pericentromeric and centromeric satellite repeats. Nde1 LOF results in nuclear architecture aberrations and DNA double-strand breaks, as well as instability and derepression of pericentromeric satellite repeats in neocortical neurons. These findings uncover a pivotal role of NDE1/Nde1 in establishing and protecting neuronal heterochromatin. They suggest that heterochromatin instability predisposes a wide range of brain dysfunction. Cortical neurogenesis is coupled with heterochromatin compaction marked by H4K20me3 Nde1 undergoes liquid-liquid phase separation and interacts with heterochromatin Nde1 mutations impair H4K20me3 during neural progenitor differentiation Neurons lacking Nde1 derepress heterochromatin and lose nuclear and genomic integrity
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18
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Arslan AB, Zamani AG, Yıldırım MS. Novel Findings, Mini-Review and Dysmorphological Characterization of 16p13.11 Microduplication syndrome. Int J Dev Neurosci 2022; 82:289-294. [PMID: 35470466 DOI: 10.1002/jdn.10188] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/25/2022] [Accepted: 04/12/2022] [Indexed: 11/07/2022] Open
Abstract
The short arm of chromosome 16 and especially the region 16p13.11 is a chromosome region where many structural variants, especially deletions and duplications, can be observed. While deletions of this region are clinically well defined, duplications are rare, and so far, there is no established clinical consensus in regard with its clinical picture, and especially the dysmorphic perspective of the disease is far from being clear. A 5-year-and-2-month-old patient who presented with epilepsy, autism and late speech onset complaints, was evaluated in our genetics department. On physical examination unilateral preauricular skin tag and upslanting palpebral fissures were noted. Microarray analysis was performed and reported as ([hg19]: 16p13.11 (14.897.804-16.730.375) x3). The literature review revealed only a few reports about the syndrome, but some dysmorphological findings appear to recur in different reports, which enables a possible characterization. Dysmorphic findings were discussed.
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Affiliation(s)
- Ahmet Burak Arslan
- Medical Genetics Department, Necmettin Erbakan University Hospital, Konya, Turkey
| | - Ayşe Gül Zamani
- Medical Genetics Department, Necmettin Erbakan University Hospital, Konya, Turkey
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19
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Jia YZ, Liu J, Wang GQ, Song ZF. miR-484: A Potential Biomarker in Health and Disease. Front Oncol 2022; 12:830420. [PMID: 35356223 PMCID: PMC8959652 DOI: 10.3389/fonc.2022.830420] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 02/11/2022] [Indexed: 01/30/2023] Open
Abstract
Disorders of miR-484 expression are observed in cancer, different diseases or pathological states. There is accumulating evidence that miR-484 plays an essential role in the development as well as the regression of different diseases, and miR-484 has been reported as a key regulator of common cancer and non-cancer diseases. The miR-484 targets that have effects on inflammation, apoptosis and mitochondrial function include SMAD7, Fis1, YAP1 and BCL2L13. For cancer, identified targets include VEGFB, VEGFR2, MAP2, MMP14, HNF1A, TUSC5 and KLF12. The effects of miR-484 on these targets have been documented separately. Moreover, miR-484 is typically described as an oncosuppressor, but this claim is simplistic and one-sided. This review will combine relevant basic and clinical studies to find that miR-484 promotes tumorigenesis and metastasis in liver, prostate and lung tissues. It will provide a basis for the possible mechanisms of miR-484 in early tumor diagnosis, prognosis determination, disease assessment, and as a potential therapeutic target for tumors.
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Affiliation(s)
- Yin-Zhao Jia
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Liu
- Key Laboratory of Coal Science and Technology of Ministry of Education, College of Chemistry and Chemical Engineering, Taiyuan University of Technology, Taiyuan, China
| | - Geng-Qiao Wang
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-Fang Song
- Department of Hepatobiliary Surgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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20
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Shirley Cheng SW, Luk HM, Lo FMI. A further case of Skraban-Deardorff syndrome and review of the literature. Clin Dysmorphol 2022; 31:79-83. [PMID: 34775451 DOI: 10.1097/mcd.0000000000000403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Wang Z, Lu T, Li X, Jiang M, Jia M, Liu J, Zhang D, Li J, Wang L. Altered Expression of Brain-specific Autism-Associated miRNAs in the Han Chinese Population. Front Genet 2022; 13:865881. [PMID: 35342389 PMCID: PMC8942769 DOI: 10.3389/fgene.2022.865881] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 02/14/2022] [Indexed: 11/16/2022] Open
Abstract
Autism is a complex neurodevelopmental disorder. However, its etiology is still unknown. MicroRNAs (miRNAs) are key post-transcriptional regulators. They play an important role in neurodevelopment and brain functions and may be involved in the pathogenesis of autism. Previous studies indicated altered expression of miRNAs in patients with autism. However, the findings were not consistent, and further explorations were needed. This study aimed to investigate whether miRNAs were dysregulated in autism. We examined the expression of 30 brain-specific autism-associated miRNAs in 110 patients with autism and 113 controls in the Han Chinese population using quantitative reverse transcription–polymerase chain reaction. The results demonstrated that 10 miRNAs (hsa-miR-191-5p, hsa-miR-151a-3p, hsa-miR-139-5p, hsa-miR-181a-5p, hsa-miR-432-5p, hsa-miR-181b-5p, hsa-miR-195-5p, hsa-miR-328-3p, hsa-miR-106a-5p, and hsa-miR-484) were significantly differentially expressed (false discovery rate <0.05). All of them were up-regulated in patients with autism compared with controls. The targets of these miRNAs were enriched for genes and pathways related to neurodevelopment, brain functions and autism. These findings suggested the participation of these 10 miRNAs in the pathogenesis of autism in the Han Chinese population.
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Affiliation(s)
- Ziqi Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Tianlan Lu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Xianjing Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Miaomiao Jiang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Meixiang Jia
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Jing Liu
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Dai Zhang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China.,Chinese Institute for Brain Research, Beijing, China.,Guangdong Key Laboratory of Mental Health and Cognitive Science, Institute for Brain Research and Rehabilitation (IBRR), South China Normal University, Guangzhou, China
| | - Jun Li
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
| | - Lifang Wang
- National Clinical Research Center for Mental Disorders (Peking University Sixth Hospital), NHC Key Laboratory of Mental Health (Peking University), Peking University Sixth Hospital, Peking University Institute of Mental Health, Beijing, China
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22
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Granata P, Cocciadiferro D, Zito A, Pessina C, Bassani A, Zambonin F, Novelli A, Fasano M, Casalone R. Whole Exome Sequencing in 16p13.11 Microdeletion Patients Reveals New Variants Through Deductive and Systems Medicine Approaches. Front Genet 2022; 13:798607. [PMID: 35368691 PMCID: PMC8965081 DOI: 10.3389/fgene.2022.798607] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/23/2022] [Indexed: 12/20/2022] Open
Abstract
The 16p13.11 microdeletion, whose prevalence in the general population is about 0.04%, is known in literature as a predisposition factor to neurodevelopmental disorders, being found in about 0.13% of patients with schizophrenia, in 0.5–0.6% of patient with epilepsy, cognitive impairment, autism spectrum disorder (ASD) and aggressiveness. The goal of this study was to identify a specific gene set pattern unique for the affected patients in comparison with other familial components. Due to the incomplete penetrance of this copy number variant (CNV), we studied by whole exome sequencing (WES), with particular regard of 850 SFARI genes, three families with an affected member carrier of inherited 16p13.11 and 16p13.11p12.3 microdeletion and one family with an affected member with a de novo 16p13.11 microdeletion. By combining a deductive approach together with personalized network models, we identified gene signatures potentially capable of explaining the clinical phenotype. Candidate variants in genes of interest were identified as possibly involved in determining the neurological phenotype of the four patients, such as compound heterozygosity in CECR2, variants in MTOR and RICTOR genes, compound heterozygous single nucleotide variants in the LRRK2 gene. Moreover, genes present in the microdeletion region were partially present as central nodes, with a focus on NDE1. No additional pathogenetic or uncertain CNVs were found in all four patients. No significant variants were detected in genes included in the microdeletion in patients 1, 2 and 3, excluding the finding of unmasked recessive variants. In conclusion, WES is a fundamental tool in the genetic investigation of patients having a predisposing variant, which is not sufficient to define the clinical phenotype. Moreover, the analysis of WES data using Systems medicine tools, such as personalized network models, led to the prioritization of genes on a high throughput scale and to discover variants in genes that were not prioritized at first.
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Affiliation(s)
- Paola Granata
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Dario Cocciadiferro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Alessandra Zito
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Chiara Pessina
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- Department of Medicine and Surgery, University of Insubria, Varese, Italy
| | - Alessandro Bassani
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
| | - Fabio Zambonin
- Child Neuropsychiatry Unit, Department of Maternal and Child Health, ASST dei Sette Laghi, Varese, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Ospedale Pediatrico Bambino Gesù, Roma, Italy
| | - Mauro Fasano
- Department of Science and High Technology and Center of Bioinformatics, University of Insubria, Busto Arsizio, Italy
- *Correspondence: Mauro Fasano, ; Rosario Casalone,
| | - Rosario Casalone
- Cytogenetics and Medical Genetics Unit, Department of Services, ASST dei Sette Laghi, Varese, Italy
- *Correspondence: Mauro Fasano, ; Rosario Casalone,
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23
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Chesneau B, Plancke A, Rolland G, Marcheix B, Dulac Y, Edouard T, Plaisancié J, Aubert-Mucca M, Julia S, Langeois M, Lavabre-Bertrand T, Khau Van Kien P. A +3 variant at a donor splice site leads to a skipping of the MYH11 exon 32, a recurrent RNA defect causing Heritable Thoracic Aortic Aneurysm and Dissection and/or Patent Ductus Arteriosus. Mol Genet Genomic Med 2021; 9:e1814. [PMID: 34672437 PMCID: PMC8606209 DOI: 10.1002/mgg3.1814] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/11/2021] [Accepted: 09/03/2021] [Indexed: 12/29/2022] Open
Abstract
Background Pathogenic variants in MYH11 are associated with either heritable thoracic aortic aneurysm and dissection (HTAAD), patent ductus arteriosus (PDA) syndrome, or megacystis‐microcolon‐intestinal hypoperistalsis syndrome (MMIHS). Methods and Results We report a family referred for molecular diagnosis with HTAAD/PDA phenotype in which we found a variant at a non‐conserved position of the 5’ donor splice site of intron 32 of MYH11 potentially altering splicing (NM_002474.3:c.4578+3A>C). Although its cosegregation with disease was observed, it remained of unknown significance. Later, aortic surgery in the proband gave us the opportunity to perform a transcript analysis. This showed a skipping of the exon 32, an RNA defect previously reported to be translated to an in‐frame loss of 71 amino acids and a dominant‐negative effect in the smooth muscle myosin rod. This RNA defect is also reported in 3 other HTAAD/PDA pedigrees. Conclusion This report confirms that among rare variants in MYH11, skipping of exon 32 is recurrent. This finding is of particular interest to establish complex genotype–phenotype correlations where some alleles are associated with autosomal dominant HTAAD/PDA, while others result in recessive or dominant visceral myopathies.
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Affiliation(s)
- Bertrand Chesneau
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Régional Universitaire de Nîmes, Nîmes, France.,Centre de Référence du syndrome de Marfan et des syndromes apparentés, Hôpital des Enfants, CHU de Toulouse, Toulouse, France
| | - Aurélie Plancke
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Régional Universitaire de Nîmes, Nîmes, France
| | - Guillaume Rolland
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Régional Universitaire de Nîmes, Nîmes, France
| | - Bertrand Marcheix
- Département de Chirurgie Cardiaque, Hôpital Universitaire de Rangueil, Toulouse, France
| | - Yves Dulac
- Centre de Référence du syndrome de Marfan et des syndromes apparentés, Hôpital des Enfants, CHU de Toulouse, Toulouse, France
| | - Thomas Edouard
- Centre de Référence du syndrome de Marfan et des syndromes apparentés, Hôpital des Enfants, CHU de Toulouse, Toulouse, France
| | - Julie Plaisancié
- Service de Génétique Médicale, Hôpital Universitaire de Purpan, Toulouse, France
| | - Marion Aubert-Mucca
- Centre de Référence du syndrome de Marfan et des syndromes apparentés, Hôpital des Enfants, CHU de Toulouse, Toulouse, France.,Service de Génétique Médicale, Hôpital Universitaire de Purpan, Toulouse, France
| | - Sophie Julia
- Service de Génétique Médicale, Hôpital Universitaire de Purpan, Toulouse, France
| | - Maud Langeois
- Centre de Référence du syndrome de Marfan et des syndromes apparentés, Hôpital des Enfants, CHU de Toulouse, Toulouse, France.,Service de Génétique Médicale, Hôpital Universitaire de Purpan, Toulouse, France
| | - Thierry Lavabre-Bertrand
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Régional Universitaire de Nîmes, Nîmes, France.,Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, Montpellier, France.,Faculté de Médecine Montpellier-Nîmes, Laboratoire d'Histologie-Embryologie-Cytogénétique, Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Nîmes, France
| | - Philippe Khau Van Kien
- UF de Génétique Médicale et Cytogénétique, Centre Hospitalier Régional Universitaire de Nîmes, Nîmes, France.,Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Université de Montpellier, Montpellier, France.,Faculté de Médecine Montpellier-Nîmes, Laboratoire d'Histologie-Embryologie-Cytogénétique, Institut des Biomolécules Max Mousseron (IBMM), CNRS UMR5247, Nîmes, France
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24
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Dai L, Zhang D, Wu Z, Guan X, Ma M, Li L, Zhang Y, Bai Y, Guo H. A Tiered Genetic Screening Strategy for the Molecular Diagnosis of Intellectual Disability in Chinese Patients. Front Genet 2021; 12:669217. [PMID: 34630504 PMCID: PMC8495063 DOI: 10.3389/fgene.2021.669217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023] Open
Abstract
Objective: Intellectual disability (ID) is one of the most common developmental disabilities. To identify the genetic etiology of IDs in Chongqing, we conducted a multistage study in Chinese Han patients. Methods: We collected the clinical and etiological data of 1665 ID patients, including 1,604 from the disabled children evaluation center and 61 from the pediatric rehabilitation unit. Routine genetic screening results were obtained, including karyotype and candidate gene analysis. Then 105 idiopathic cases with syndromic and severe ID/developmental delay (DD) were selected and tested by chromosomal microarray (CMA) and whole exome sequencing (WES) sequentially. The pathogenicity of the CNVs and SNVs were evaluated according to ACMG guidelines. Results: Molecular diagnosis was made by routine genetic screening in 216 patients, including 196 chromosomal syndromes. Among the 105 idiopathic patients, 49 patients with pathogenic/likely pathogenic CNVs and 21 patients with VUS were identified by CMA. Twenty-six pathogenic CNVs underlying well-known syndromic cases, such as Williams-Beuren syndrome, were confirmed by multiplex ligation-dependent probe amplification (MLPA). Nine novel mutations were identified by WES in thirty-fix CNV-negative ID cases. Conclusions: The study illustrated the genetic aberrations distribution of a large ID cohort in Chongqing. Compared with conventional or single methods, a tiered high-throughput diagnostic strategy was developed to greatly improve the diagnostic yields and extend the variation spectrum for idiopathic syndromic ID cases.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Danyan Zhang
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China.,Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Zhifeng Wu
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xingying Guan
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Mingfu Ma
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Lianbing Li
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Yuping Zhang
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
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25
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Güleray N, Koşukcu C, Oğuz S, Ürel Demir G, Taşkıran EZ, Kiper PÖŞ, Utine GE, Alanay Y, Boduroğlu K, Alikaşifoğlu M. Investigation of Genetic Causes in a Developmental Disorder: Oculoauriculovertebral Spectrum. Cleft Palate Craniofac J 2021; 59:1114-1124. [PMID: 34410171 DOI: 10.1177/10556656211038115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE Oculoauriculovertebral spectrum (OAVS) is a genetically and clinically heterogeneous disorder that occurs due to a developmental field defect of the first and second pharyngeal arches. Even though recent whole exome sequencing studies (WES) have led to identification of several genes associated with this spectrum in a subset of individuals, complete pathogenesis of OAVS remains unsolved. In this study, molecular genetic etiology of OAVS was systematically investigated. DESIGN/SETTING/PATIENTS A cohort of 23 Turkish patients with OAVS, referred to Hacettepe University Hospital, Department of Pediatric Genetics from 2008 to 2018, was included in this study. Minimal diagnostic criteria for OAVS were considered as unilateral microtia or hemifacial microsomia with preauricular skin tag. The cohort was clinically reevaluated for craniofacial and extracranial findings. Molecular etiology was investigated using candidate gene sequencing following copy number variant (CNV) analysis. WES was also performed for 2 of the selected patients. RESULTS Patients in the study cohort presented similar demographic and phenotypic characteristics to previously described patients in the literature except for a higher frequency of bilaterality, cardiac findings, and intellectual disability/developmental delay. CNV analysis revealed a possible genetic etiology for 3 patients (13%). Additional WES in 1 of the 2 patients uncovered a novel heterozygous nonsense variant in Elongation factor Tu GTP-binding domain-containing 2 (EFTUD2) causing mandibulofacial dysostosis with microcephaly (MFDM), which clinically overlaps with OAVS. CONCLUSION Detailed clinical evaluation for any patient with OAVS is recommended due to a high rate of accompanying systemic findings. We further expand the existing genetic heterogeneity of OAVS by identifying several CNVs and a phenotypically overlapping disorder, MFDM.
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Affiliation(s)
- Naz Güleray
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Can Koşukcu
- Department of Bioinformatics, Hacettepe University Institute of Health Sciences, Ankara, Turkey
| | - Sümeyra Oğuz
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Gizem Ürel Demir
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ekim Z Taşkıran
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | | | - Gülen Eda Utine
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yasemin Alanay
- Department of Pediatric Genetics, Acıbadem University Faculty of Medicine, Istanbul, Turkey
| | - Koray Boduroğlu
- Department of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Mehmet Alikaşifoğlu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
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26
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Cai M, Huang H, Xu L, Lin N. Classifying and Evaluating Fetuses With Ventriculomegaly in Genetic Etiologic Studies. Front Genet 2021; 12:682707. [PMID: 34285689 PMCID: PMC8286336 DOI: 10.3389/fgene.2021.682707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 05/11/2021] [Indexed: 11/26/2022] Open
Abstract
The association between genetics and fetuses with ventriculomegaly (VM) is unknown. This study aimed to classify and evaluate abnormal copy number variations (CNVs) in fetuses with VM. From December 2016 to September 2020, amniotic fluid or umbilical cord blood from 293 pregnant women carrying fetuses with VM was extracted for single-nucleotide polymorphism microarray (SNP array). Among 293 fetuses with VM, 31 were detected with abnormal CNVs, including 22 with pathogenic CNVs (7.51%) and nine with variation of uncertain clinical significance (VUS) CNVs (3.07%). Of the 22 fetuses with pathogenic CNVs, 13 had known disease syndromes. Among the 293 fetuses, 133 had mild isolated VM [pathogenic CNVs, 7/133 (5.26%)]; 142 had mild non-isolated VM [pathogenic CNVs, 13/142 (9.15%)]; 12 had severe isolated VM [pathogenic CNVs, 2/12 (16.67%)]; and six had severe non-isolated VM (no abnormal CNVs was detected). There was no statistical significance in the rate of pathogenic CNVs among the four groups (P = 0.326, P > 0.05). Among the 267 fetuses with successful follow-up, 38 were terminated (of these, 21 had pathogenic CNVs). Of the 229 fetuses, two had developmental delay and the remaining 227 had a good prognosis after birth. Overall, the results are useful for the detection of fetal microdeletion/microduplication syndrome and for the accurate assessment of fetal prognosis in prenatal consultation.
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Affiliation(s)
- Meiying Cai
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Na Lin
- Medical Genetic Diagnosis and Therapy Center, Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
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27
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Liu L, Liu F, Wang Q, Xie H, Li Z, Lu Q, Wang Y, Zhang M, Zhang Y, Picker J, Cui X, Zou L, Chen X. Confirming the contribution and genetic spectrum of de novo mutation in infantile spasms: Evidence from a Chinese cohort. Mol Genet Genomic Med 2021; 9:e1689. [PMID: 33951346 PMCID: PMC8222834 DOI: 10.1002/mgg3.1689] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/24/2021] [Accepted: 03/30/2021] [Indexed: 01/21/2023] Open
Abstract
Objective We determined the yield, genetic spectrum, and actual origin of de novo mutations (DNMs) for infantile spasms (ISs) in a Chinese cohort. The efficacy of levetiracetam (LEV) for STXBP1‐related ISs was explored also. Methods Targeted sequencing of 153 epilepsy‐related candidate genes was applied to 289 Chinese patients with undiagnosed ISs. Trio‐based amplicon deep sequencing was used for all DNMs to distinguish somatic/mosaic mutations from germline ones. Results Total of 26 DNMs were identified from 289 recruited Chinese patients with undiagnosed ISs. Among them, 24 DNMs were interpreted as pathogenic mutations based on American College of Medical Genetics and Genomics guidelines, contributing to 8.3% (24/289) of diagnosis yield in the Chinese IS cohort. CDKL5 and STXBP1 are the top genes with recurrent DNMs, accounting for 3.1% (9/289) of yield. Further deep resequencing for the trio members showed that 22.7% (5/22) of DNMs are actually somatic in the proband or a parent. These somatic carriers presented milder seizure attacks than those with true germline DNMs. After treatment with LEV for half a year, three patients with DNM in STXBP1 showed improved clinical symptoms, including seizure‐free and normal electroencephalogram, except for a patient with a second DNM in DIAPH3. Significance Our study confirmed the contribution and genetic spectrum of DNMs in Chinese IS patients. Somatic mutation account for a quarter of DNMs in IS cases. Treatment with LEV improved the prognosis of STXBP1‐related ISs.
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Affiliation(s)
- Liying Liu
- Department of Pediatrics, The First Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Fang Liu
- Graduate School of Peking, Union Medical College, Beijing, China.,Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Qiuhong Wang
- Department of Pediatrics, The First Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Hua Xie
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Zhengchang Li
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China
| | - Qian Lu
- Department of Pediatrics, The First Medical Center of Chinese, PLA General Hospital, Beijing, China.,Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China
| | - Yangyang Wang
- Department of Pediatrics, The First Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Mengna Zhang
- Department of Pediatrics, The First Medical Center of Chinese, PLA General Hospital, Beijing, China
| | - Yu Zhang
- Department of Lab Center, Capital Institute of Pediatrics, Beijing, China
| | - Jonathan Picker
- Division of Genetics & Genomics (Department of Medicine) and Department of Child & Adolescent Psychiatry, Boston Children's Hospital, Boston, MA, USA
| | - Xiaodai Cui
- Department of Lab Center, Capital Institute of Pediatrics, Beijing, China
| | - Liping Zou
- Department of Pediatrics, The First Medical Center of Chinese, PLA General Hospital, Beijing, China.,Center of Epilepsy, Beijing Institute for Brain Disorders, Beijing, China
| | - Xiaoli Chen
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, China.,Beijing Municipal Key Laboratory of Child Development and Nutriomics, Capital Institute of Pediatrics, Beijing, China
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28
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Fan X, Huang H, Lin X, Xue H, Cai M, Lin N, Xu L. Performance of Chromosomal Microarray Analysis for Detection of Copy Number Variations in Fetal Echogenic Bowel. Risk Manag Healthc Policy 2021; 14:1431-1438. [PMID: 33859509 PMCID: PMC8044071 DOI: 10.2147/rmhp.s299806] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/22/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Fetal echogenic bowel (FEB) is associated with an increased risk of poor pregnant outcomes; however, karyotyping fails to detect copy number variations (CNVs) in FEB. This study aimed to evaluate the performance of chromosomal microarray analysis (CMA) for detection of FEB. METHODS The medical records of 147 pregnant women with FEB recruited during December 2015 to December 2018 were retrospectively reviewed, and prenatal samples were collected for karyotyping and CMA. The detection of chromosomal abnormality was compared between karyotyping and CMA. RESULTS Karyotyping identified eight cases with abnormal karyotypes (5.44% prevalence), including four fetuses with pathogenic aneuploidy, three with chromosome polymorphism and one with balanced chromosome translocation. CMA identified 13 abnormal CNVs (8.84% prevalence), including 4 fetuses with pathogenic aneuploidy as detected by karyotyping and 9 additional CNVs with normal karyotypes; however, CMA failed to detect chromosome polymorphism and balanced chromosome translocation. In fetuses with isolated FEB, no cases presented pathogenic findings and CMA detected two cases with variants of uncertain significance (VOUS). In cases presenting FEB along with other ultrasound abnormalities, CMA detected three cases with pathogenic CNVs and four cases with VOUS in addition to four cases with aneuploidy. There was no significant difference in the detection of abnormal CNVs between the fetuses with echogenic bowel alone and along with other ultrasound abnormalities (10% vs 8.67%, P > 0.05). Except 9 fetuses lost to the follow-up, the other 138 fetuses with echogenic bowel were successfully followed up. Pregnancy was terminated in 5 fetuses with chromosomal abnormality, 2 with pathogenic CNVs and 1 with VOUS, and other 16 with normal karyotypes and CMA findings but showing ultrasound abnormalities or multiple malformations. CONCLUSION Isolated FEB is associated with a good prognosis, and a satisfactory pregnant outcome is expected for fetuses with echogenic bowel that are negative for chromosomal anomalies and other severe structure abnormalities. CMA shows an important value in the genetic diagnosis of FEB. As a supplement to karyotyping, CMA may improve the accuracy of prenatal diagnosis of fetal intestinal malformations in pregnant women with FEB.
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Affiliation(s)
- Xiangqun Fan
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Hailong Huang
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Xiyao Lin
- School of Clinical Medicine, Fujian Medical University, Fuzhou City, Fujian Province, 350122, People’s Republic of China
| | - Huili Xue
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Meiying Cai
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Na Lin
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
| | - Liangpu Xu
- Fujian Maternity and Child Health Hospital, Affiliated Hospital of Fujian Medical University, Fujian Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, 350001, Fujian Province, People’s Republic of China
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29
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Li J, Hojlo MA, Chennuri S, Gujral N, Paterson HL, Shefchek KA, Genetti CA, Cohn EL, Sewalk KC, Garvey EA, Buttermore ED, Anderson NC, Beggs AH, Agrawal PB, Brownstein JS, Haendel MA, Holm IA, Gonzalez-Heydrich J, Brownstein CA. Underrepresentation of Phenotypic Variability of 16p13.11 Microduplication Syndrome Assessed With an Online Self-Phenotyping Tool (Phenotypr): Cohort Study. J Med Internet Res 2021; 23:e21023. [PMID: 33724192 PMCID: PMC8074853 DOI: 10.2196/21023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 12/26/2020] [Accepted: 01/16/2021] [Indexed: 12/24/2022] Open
Abstract
Background 16p13.11 microduplication syndrome has a variable presentation and is characterized primarily by neurodevelopmental and physical phenotypes resulting from copy number variation at chromosome 16p13.11. Given its variability, there may be features that have not yet been reported. The goal of this study was to use a patient “self-phenotyping” survey to collect data directly from patients to further characterize the phenotypes of 16p13.11 microduplication syndrome. Objective This study aimed to (1) discover self-identified phenotypes in 16p13.11 microduplication syndrome that have been underrepresented in the scientific literature and (2) demonstrate that self-phenotyping tools are valuable sources of data for the medical and scientific communities. Methods As part of a large study to compare and evaluate patient self-phenotyping surveys, an online survey tool, Phenotypr, was developed for patients with rare disorders to self-report phenotypes. Participants with 16p13.11 microduplication syndrome were recruited through the Boston Children's Hospital 16p13.11 Registry. Either the caregiver, parent, or legal guardian of an affected child or the affected person (if aged 18 years or above) completed the survey. Results were securely transferred to a Research Electronic Data Capture database and aggregated for analysis. Results A total of 19 participants enrolled in the study. Notably, among the 19 participants, aggression and anxiety were mentioned by 3 (16%) and 4 (21%) participants, respectively, which is an increase over the numbers in previously published literature. Additionally, among the 19 participants, 3 (16%) had asthma and 2 (11%) had other immunological disorders, both of which have not been previously described in the syndrome. Conclusions Several phenotypes might be underrepresented in the previous 16p13.11 microduplication literature, and new possible phenotypes have been identified. Whenever possible, patients should continue to be referenced as a source of complete phenotyping data on their condition. Self-phenotyping may lead to a better understanding of the prevalence of phenotypes in genetic disorders and may identify previously unreported phenotypes.
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Affiliation(s)
- Jianqiao Li
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Margaret A Hojlo
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, United States.,Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Sampath Chennuri
- Innovation and Digital Health Accelerator, Boston Children's Hospital, Boston, MA, United States
| | - Nitin Gujral
- Innovation and Digital Health Accelerator, Boston Children's Hospital, Boston, MA, United States
| | - Heather L Paterson
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Kent A Shefchek
- Department of Environmental and Molecular Toxicology, Oregon State University, Corvallis, OR, United States
| | - Casie A Genetti
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Emily L Cohn
- Innovation and Digital Health Accelerator, Boston Children's Hospital, Boston, MA, United States
| | - Kara C Sewalk
- Computational Epidemiology Group, Boston Children's Hospital, Boston, MA, United States
| | - Emily A Garvey
- Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, United States.,Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Elizabeth D Buttermore
- Human Neuron Core, Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Nickesha C Anderson
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Alan H Beggs
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States.,Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, United States
| | - John S Brownstein
- Innovation and Digital Health Accelerator, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Melissa A Haendel
- Center for Health Artificial Intelligence, University of Colorado Anschutz, Aurora, CO, United States
| | - Ingrid A Holm
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
| | - Joseph Gonzalez-Heydrich
- The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States.,Department of Psychiatry and Behavioral Sciences, Boston Children's Hospital, Boston, MA, United States.,Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, United States.,Department of Psychiatry, Harvard Medical School, Boston, MA, United States
| | - Catherine A Brownstein
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, United States.,The Manton Center for Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States.,Tommy Fuss Center for Neuropsychiatric Disease Research, Boston Children's Hospital, Boston, MA, United States.,Department of Pediatrics, Harvard Medical School, Boston, MA, United States
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30
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Brugger M, Brunet T, Wagner M, Orec LE, Schwaibold EMC, Boy N. Locus heterogeneity in two siblings presenting with developmental delay, intellectual disability and autism spectrum disorder. Gene 2020; 768:145260. [PMID: 33164824 DOI: 10.1016/j.gene.2020.145260] [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: 07/17/2020] [Revised: 09/22/2020] [Accepted: 10/20/2020] [Indexed: 11/24/2022]
Abstract
Correct diagnosis of children presenting with developmental delay and intellectual disability remains challenging due to the complex and heterogeneous etiology. High throughput sequencing technologies like exome sequencing have become more commonly available and are significantly improving genetic testing. We present two siblings - a 14-year old male and an 8-year old female patient - with a similar clinical phenotype that was characterized by combined developmental delay primarily affecting speech, mild to moderate intellectual disability, behavioral abnormalities, and autism spectrum disorder, but with no congenital anomalies. The sister showed additional muscular hypotonia and more pronounced dysmorphic features compared to her brother. Both parents had psychiatric disorders and mild to moderate intellectual disability. A common genetic etiology in the siblings was suspected. Metabolic, psychological and neuroradiological examinations were complemented by basic genetic testing including chromosome analysis and array comparative genomics hybridization analysis (CGH), followed by exome sequencing and combined data analysis of the family. Exome sequencing identified two different underlying genetic conditions: in the sister, a maternally inherited pathogenic variant c.1661C > T, p.Pro554Leu in SLC6A8 (NM_005629.4) was identified causing cerebral creatine deficiency syndrome 1 (MIM #300352) which was confirmed by MR spectroscopy and treated accordingly. In the brother, a paternally inherited 16p13.11 duplication was identified by exome sequencing and considered to be likely associated with his and possibly his father's phenotype. The 16p13.11 duplication had been previously identified in an array CGH but had not been prioritized due to the lack of segregation in the siblings. In conclusion, we report a case of intra-familial locus heterogeneity of developmental delay in two siblings. We advocate for the need of unbiased and comprehensive genetic testing to provide accurate diagnosis despite locus heterogeneity.
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Affiliation(s)
- Melanie Brugger
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Theresa Brunet
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany
| | - Matias Wagner
- Institute of Human Genetics, School of Medicine, Technical University of Munich, Munich, Germany; Institute of Neurogenomics, Helmholtz Zentrum München GmbH, German Research Center for Environmental Health, Neuherberg, Germany
| | - Laura Elena Orec
- Division of Pediatric Neurology and Metabolic Medicine, Centre for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
| | | | - Nikolas Boy
- Division of Pediatric Neurology and Metabolic Medicine, Centre for Child and Adolescent Medicine, University Hospital Heidelberg, Heidelberg, Germany
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31
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Yatsenko SA, Aarabi M, Hu J, Surti U, Ortiz D, Madan-Khetarpal S, Saller DN, Bellissimo D, Rajkovic A. Copy number alterations involving 59 ACMG-recommended secondary findings genes. Clin Genet 2020; 98:577-588. [PMID: 33009833 DOI: 10.1111/cge.13852] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/14/2020] [Accepted: 09/13/2020] [Indexed: 12/17/2022]
Abstract
In clinical exome/genome sequencing, the American College of Medical Genetics and Genomics (ACMG) recommends reporting of secondary findings unrelated to a patient's phenotype when pathogenic single-nucleotide variants (SNVs) are observed in one of 59 genes associated with a life-threatening, medically actionable condition. Little is known about the incidence and sensitivity of chromosomal microarray analysis (CMA) for detection of pathogenic copy number variants (CNVs) comprising medically-actionable genes. Clinical CMA has been performed on 8865 individuals referred for molecular cytogenetic testing. We retrospectively reviewed the CMA results to identify patients with CNVs comprising genes included in the 59-ACMG list of secondary findings. We evaluated the clinical significance of these CNVs in respect to pathogenicity, phenotypic manifestations, and heritability. We identified 23 patients (0.26%) with relevant CNV either deletions comprising the entire gene or intragenic alterations involving one or more secondary findings genes. A number of patients and/or their family members with pathogenic CNVs manifest or expected to develop an anticipated clinical phenotype and would benefit from preventive management similar to the patients with pathogenic SNVs. To improve patients' care standardization should apply to reporting of both sequencing and CNVs obtained via clinical genome-wide analysis, including chromosomal microarray and exome/genome sequencing.
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Affiliation(s)
- Svetlana A Yatsenko
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.,Magee-Womens Research Institute, Pittsburgh, Pennsylvania, USA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mahmoud Aarabi
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Jie Hu
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Urvashi Surti
- Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Damara Ortiz
- Department of Medical Genetics, Childrens Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Suneeta Madan-Khetarpal
- Department of Medical Genetics, Childrens Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania, USA
| | - Devereux N Saller
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Daniel Bellissimo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Aleksandar Rajkovic
- Department of Pathology, University of California San Francisco, San Francisco, California, USA.,Department of Obstetrics, Gynecology and Reproductive Sciences, University of California San Francisco, San Francisco, California, USA
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Lou J, Sun M, Zhao Y, Fu Y, Yuan H, Dai Y, Liang F, He Y, Liu Y. Analysis of tissue from pregnancy loss and aborted fetus with ultrasound anomaly using subtelomeric MLPA and chromosomal array analysis. J Matern Fetal Neonatal Med 2020; 35:3064-3069. [PMID: 32811234 DOI: 10.1080/14767058.2020.1808612] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
OBJECTIVE To evaluate the incidence and types of chromosomal abnormalities in pregnancy loss and aborted fetuses with anomaly and compare the performance of subtelomeric MLPA and chromosomal microarray analysis (CMA) in these specimens. METHODS Samples were collected from spontaneous miscarriages, stillbirths and aborted fetuses with anomaly between January 2015 and April 2019. Chromosomal abnormalities were detected using subtelomeric MLPA and CMA. RESULTS Among the 172 miscarriage samples, CMA detected pathogenic chromosomal abnormalities in 88 cases. MLPA could identified all aneuploidies and most pathogenic CNVs, missing all polyploidies; Of the 30 stillbirths, one pathogenic CNV and two VOUS were identified by CMA, all of which were missed from MLPA; Of the 135 aborted fetuses with anomaly, CMA identified pathogenic chromosomal abnormalities in 32 fetuses (23.7%); 18.95% in fetuses with isolated, and 35% in fetuses with multiple anomalies. MLPA can identify all aneuploidies but missing most pathogenic CNVs. CONCLUSION Our systematical comparison of subtelomeric MLPA and CMA for chromosomal analysis of tissue from pregnancy loss and aborted fetuses with anomaly is useful for assessing clinical utility of these techniques. MLPA screening, coupled with CMA analysis, is a cost-effective approach to detect chromosomal abnormalities in miscarriage and anomalous fetuses. However, MLPA might not be appropriate for chromosome analysis in stillbirth without structural anomaly; further research with more samples is needed.
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Affiliation(s)
- Jiwu Lou
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Manna Sun
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Ying Zhao
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Youqing Fu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Haiming Yuan
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Yunshi Dai
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Fuxiao Liang
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Yi He
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
| | - Yanhui Liu
- Department of Prenatal Diagnosis Center, Dongguan Maternal and Child Health Hospital, Dongguan, China
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Niclass T, Le Guyader G, Beneteau C, Joubert M, Pizzuti A, Giuffrida MG, Bernardini L, Gilbert-Dussardier B, Bilan F, Egloff M. 12q21 deletion syndrome: Narrowing the critical region down to 1.6 Mb including SYT1 and PPP1R12A. Am J Med Genet A 2020; 182:2133-2138. [PMID: 32633079 DOI: 10.1002/ajmg.a.61734] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 05/04/2020] [Accepted: 05/21/2020] [Indexed: 11/12/2022]
Abstract
Deletions in the 12q21 region are rare and non-recurrent CNVs. To date, only 11 patients with deletions in this region have been reported in the literature. These patients most often presented with syndromic intellectual deficiency, ventriculomegaly or hydrocephalus, ectodermal abnormalities, growth retardation and renal and cardiac malformations, suggesting a recognizable microdeletion syndrome. We report three new patients with overlapping deletions of the 12q21 region, including the smallest deletion reported to date and the first case characterized by array CGH during pregnancy. We describe specific clinical findings and shared facial features as developmental delay, ectodermal abnormalities, ventriculomegaly or hydrocephalus, axial hypotonia or spastic diplegia, growth retardation, heart defect, hydronephrosis, ureteral reflux or horseshoe kidney, large thorax or pectus excavatum, syndactyly of 2-3 toes, pterygium coli or excess nuchal skin, large anterior fontanel, low set ears, prominent forehead, short-upturned nose with nostril hypoplasia, microretrognathia and hypertelorism. These new patients and a comprehensive review of the literature allow us to define a minimum critical region spanning 1.6 Mb in 12q21. By screening the critical region using prediction tools, we identified two candidate genes: SYT1and PPP1R12A.
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Affiliation(s)
- Tanguy Niclass
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France
| | - Gwenael Le Guyader
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,EA 3808 NEUVACOD, Université de Poitiers, Poitiers, France
| | - Claire Beneteau
- Department of Medical Genetics, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Madeleine Joubert
- Department of Anatomic and Fetal Pathology, Centre Hospitalier Universitaire de Nantes, Nantes, France
| | - Antonio Pizzuti
- Department of Medical Genetics, Policlinico di Roma, Rome, Italy
| | - Maria Grazia Giuffrida
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cytogenetics Unit, San Giovanni Rotondo, FG, Italy
| | - Laura Bernardini
- Fondazione IRCCS Casa Sollievo della Sofferenza, Cytogenetics Unit, San Giovanni Rotondo, FG, Italy
| | - Brigitte Gilbert-Dussardier
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,EA 3808 NEUVACOD, Université de Poitiers, Poitiers, France
| | - Frederic Bilan
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,EA 3808 NEUVACOD, Université de Poitiers, Poitiers, France
| | - Matthieu Egloff
- Department of Medical Genetics, Centre Hospitalier Universitaire de Poitiers, Poitiers, France.,Laboratoire de Neurosciences Experimentales et Cliniques, INSERM, Poitiers, France
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High-resolution chromosomal microarray analysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability. J Neural Transm (Vienna) 2019; 127:81-94. [PMID: 31838600 DOI: 10.1007/s00702-019-02114-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
Copy-number variants (CNVs), in particular rare, small and large ones (< 1% frequency) and those encompassing brain-related genes, have been shown to be associated with neurodevelopmental disorders like autism spectrum disorders (ASDs), attention deficit hyperactivity disorder (ADHD), and intellectual disability (ID). However, the vast majority of CNV findings lack specificity with respect to autistic or developmental-delay phenotypes. Therefore, the aim of the study was to investigate the size and frequency of CNVs in high-functioning ASD (HFA) without ID compared with a random population sample and with published findings in ASD and ID. To investigate the role of CNVs for the "core symptoms" of high-functioning autism, we included in the present exploratory study only patients with HFA without ID. The aim was to test whether HFA have similar large rare (> 1 Mb) CNVs as reported in ASD and ID. We performed high-resolution chromosomal microarray analysis in 108 children and adolescents with HFA without ID. There was no significant difference in the overall number of rare CNVs compared to 124 random population samples. However, patients with HFA carried significantly more frequently CNVs containing brain-related genes. Surprisingly, six HFA patients carried very large CNVs known to be typically present in ID. Our findings provide new evidence that not only small, but also large CNVs affecting several key genes contribute to the genetic etiology/risk of HFA without affecting their intellectual ability.
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Submicroscopic aberrations of chromosome 16 in prenatal diagnosis. Mol Cytogenet 2019; 12:36. [PMID: 31391865 PMCID: PMC6681493 DOI: 10.1186/s13039-019-0448-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 07/10/2019] [Indexed: 12/27/2022] Open
Abstract
Background Nearly 9.89% of chromosome 16 consists of segmental duplications, which makes it prone to non-homologous recombination. The present study aimed to investigate the incidence and perinatal characteristics of submicroscopic chromosome 16 aberrations in prenatal diagnosis. Results A total of 2,414 consecutive fetuses that underwent prenatal chromosomal microarray analysis (CMA) between January 2016 and December 2018 were reviewed. Submicroscopic anomalies of chromosome 16 accounted for 11.1% (15/134) of all submicroscopic anomalies detected in fetuses with normal karyotype, which was larger than the percentage of anomalies in any other chromosome. The 15 submicroscopic anomalies of chromosome 16 were identified in 14 cases; 12 of them had ultrasound abnormalities. They were classified as pathogenic (N = 7), and variants of uncertain significance (N = 8). Seven fetuses with variants of uncertain significance were ended in live-born, and the remaining were end in pregnancy termination. Conclusion Submicroscopic aberrations of chromosome 16 are frequent findings in prenatal diagnosis, which emphasize the challenge of genetic counseling and the value of CMA. Prenatal diagnosis should lead to long-term monitoring of children with such chromosomal abnormalities for better understanding of the phenotype of chromosome 16 microdeletion and microduplication syndromes.
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