1
|
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.
Collapse
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.
| |
Collapse
|
2
|
Pavone P, Pappalardo XG, Parano C, Parano E, Corsello A, Ruggieri M, Cacciaguerra G, Falsaperla R. Severe Unilateral Microtia with Aural Atresia, Hair White Patch, Stereotypes in a Young Boy with De novo 16p13.11 Deletion: Reasons for a New Genotype-Phenotype Correlation. Glob Med Genet 2023; 10:370-375. [PMID: 38053544 PMCID: PMC10695706 DOI: 10.1055/s-0043-1777362] [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] [Indexed: 12/07/2023] Open
Abstract
Background Microtia is an uncommon congenital malformation ranging from mild anatomic structural abnormalities to partial or complete absence of the ear leading to hearing impairment. Congenital microtia may present as a single malformation (isolated microtia) or sometimes associated with other congenital anomalies involving various organs. Microtia has been classified in three degrees according to the complexity of the auricular malformation and to anotia referred to the total absence of the ear. Genetic role in causing auricular malformation has been widely demonstrated, and genotype-phenotype correlation has been reported in cases of syndromic microtia. Case Presentation We report here a young patient with a third degree of scale classification and aural atresia. The patient showed unspecific facial dysmorphism, speech delay, precocious teething, hair white patch, and stereotypic anomalous movements. Genetic analysis displayed a de novo 16p13.11 deletion. Conclusion Microtia with aural atresia is an uncommon and severe birth defect, which affects functional and esthetic aspects, often associated with other malformations. As traumatic this disorder may be for the parents, the microtia and aural atresia are treatable, thanks to the improving and evolving surgical techniques. Based on the genetic analysis and the clinical features observed in the present case, a genotype-phenotype correlation has been proposed.
Collapse
Affiliation(s)
- Piero Pavone
- Section of Paediatrics and Child Neuropsychiatry, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Xena Giada Pappalardo
- Unit of Catania, Institute for Biomedical Research and Innovation, National Council of Research, Catania, Italy
| | - Claudia Parano
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Catania, Italy
| | - Enrico Parano
- Unit of Catania, Institute for Biomedical Research and Innovation, National Council of Research, Catania, Italy
| | - Antonio Corsello
- Neonatal Intensive Care Unit, Department of Sciences for Health Promotion, Maternal Infant Care, Internal Medicine and Medical Specialties “G. D'Alessandro,” University Hospital “P. Giaccone,” Palermo, Italy
| | - Martino Ruggieri
- Section of Paediatrics and Child Neuropsychiatry, Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Giovanni Cacciaguerra
- Section of Paediatrics and Child Neuropsychiatry, Unit of Rare Diseases of the Nervous System in Childhood, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Raffaele Falsaperla
- Neonatal Intensive Care Unit, AUO Policlinico “Rodolico-San Marco,” University of Catania, Catania, Italy
- Acute End Emergency Pediatric Unit, Department of General Pediatrics, AUO Policlinico “Rodolico-San Marco,” University of Catania, Catania, Italy
| |
Collapse
|
3
|
Wang D, Peng H, Wang Y, Hou Y, Guo F, Zhu J, Hu T, Yang J. Performance of noninvasive prenatal testing for twin pregnancies in South China. J Assist Reprod Genet 2023; 40:2219-2231. [PMID: 37480419 PMCID: PMC10440307 DOI: 10.1007/s10815-023-02881-1] [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: 03/01/2023] [Accepted: 07/03/2023] [Indexed: 07/24/2023] Open
Abstract
OBJECTIVE The purpose of this study was to evaluate the performance of noninvasive prenatal testing (NIPT) for the detection of chromosomal aneuploidies and copy number variations (CNVs) in twin pregnancies. METHOD A cohort of 2010 women with twin pregnancies was recruited. 1331 patients opted for NIPT, and 679 patients opted for expanded NIPT (NIPT-plus). All high-risk patients were advised to undergo invasive prenatal diagnosis. All participants were followed up until 6 months after birth. RESULTS Twenty-two cases were predicted to have a high risk of chromosome abnormalities by NIPT, of which 14 pregnant women underwent invasive prenatal diagnosis. The 14 cases included 3 cases of trisomy 21, 1 case of trisomy 18, 1 case of trisomy 7, 2 cases of sex chromosome aneuploidies (SCAs), and 7 cases of CNVs, of which the confirmed cases numbered 2, 1, 0, 1, and 0, respectively. Twenty cases were predicted to have a high risk of chromosome abnormalities by NIPT-plus, of which 16 pregnant women underwent invasive prenatal diagnosis. The 16 cases included 1 case of trisomy 21, 1 case of trisomy 7, 7 cases of SCAs, and 7 cases of CNVs, of which were confirmed in 1, 0, 3, and 2, respectively. No false-negative result was reported during the follow-up period. CONCLUSION The NIPT/NIPT-plus has excellent performance in the detection of chromosome aneuploidies in twin pregnancies. But for CNVs, the effectiveness of NIPT is poor, and the NIPT-plus have a certain detection efficiency. It is worth noting that pre- and post-genetic counseling is especially important, and the chorionicity, mode of conception, clinical indications, and fetal fraction should be considered as influencing factors.
Collapse
Affiliation(s)
- Dongmei Wang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Haishan Peng
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Yixia Wang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Yaping Hou
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Fangfang Guo
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Juan Zhu
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Tingting Hu
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China
| | - Jiexia Yang
- Guangdong Women and Children Hospital, Guangzhou, 511442, Guangdong, China.
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
6
|
Da Silva JD, Gonzaga D, Barreta A, Correia H, Fortuna AM, Soares AR, Tkachenko N. Refining the Clinical Spectrum of the 17p13.3 Microduplication Syndrome: Case-Report of a Familial Small Microduplication. Biomedicines 2022; 10:biomedicines10123078. [PMID: 36551834 PMCID: PMC9775100 DOI: 10.3390/biomedicines10123078] [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: 11/07/2022] [Revised: 11/18/2022] [Accepted: 11/26/2022] [Indexed: 12/02/2022] Open
Abstract
The chromosomal region 17p13.3 contains extensive repetitive sequences and is a well-recognized region of genomic instability. The 17p13.3 microduplication syndrome has been associated with a clinical spectrum of moderately non-specific phenotypes, including global developmental delay/intellectual disability, behavioral disorders, autism spectrum disorder and variable dysmorphic features. Depending on the genes involved in the microduplication, it can be categorized in two subtypes with different phenotypes. Here, we report a case of a 7-year-old boy with global developmental delay, speech impairment, hypotonia, behavioral conditions (ADHD and ODD), non-specific dysmorphic features and overgrowth. Genetic testing revealed a small 17p13.3 chromosomal duplication, which included the BHLHA9, CRK and YWHAE genes. Additionally, we observed that this was maternally inherited, and that the mother presented with a milder phenotype including mild learning disabilities, speech impairment and non-specific dysmorphic features, which did not significantly affect her. In conclusion, we present a clinical case of a 17p13.3 duplication that further delineates the clinical spectrum of this syndrome, including its intrafamilial/intergenerational variability.
Collapse
Affiliation(s)
- Jorge Diogo Da Silva
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057 Braga, Portugal
- ICVS/3B’s—PT Government Associate Laboratory, 4806-909 Braga, Portugal
- Correspondence:
| | - Diana Gonzaga
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Centro Materno-Infantil do Norte, Centro Hospital Universitário do Porto, 4099-001 Porto, Portugal
| | - Ana Barreta
- Medical Genetics Service, Joaquim Chaves Saúde, 2685-145 Oeiras, Portugal
| | - Hildeberto Correia
- Medical Genetics Service, Joaquim Chaves Saúde, 2685-145 Oeiras, Portugal
| | - Ana Maria Fortuna
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Biomedical Sciences Institute, Porto University, 4050-345 Porto, Portugal
| | - Ana Rita Soares
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Biomedical Sciences Institute, Porto University, 4050-345 Porto, Portugal
| | - Nataliya Tkachenko
- Centro de Genética Médica Doutor Jacinto Magalhães (CGM), Centro Hospitalar Universitário do Porto, 4050-106 Porto, Portugal
- Unit for Multidisciplinary Research in Biomedicine, Abel Salazar Biomedical Sciences Institute, Porto University, 4050-345 Porto, Portugal
| |
Collapse
|
7
|
Aishworiya R, Protic D, Hagerman R. Autism spectrum disorder in the fragile X premutation state: possible mechanisms and implications. J Neurol 2022; 269:4676-4683. [PMID: 35723724 DOI: 10.1007/s00415-022-11209-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 12/23/2022]
Abstract
There is increasing recognition of the heterogeneity of origin of cases of autism spectrum disorder (ASD) with multiple forms of ASD having been identified over the decades. Among these, a genetic etiology can be identified in 20-40% of cases when a full genetic work-up is completed. The Fragile X premutation state (characterized by the presence of 55-200 CGG repeats in the FMR1 gene) is a relatively newly identified disease state that has since been associated with several disorders including fragile X-associated tremor ataxia syndrome (FXTAS), fragile X-associated primary ovarian insufficiency (FXPOI) and most recently, fragile X-associated neurodevelopmental disorders (FXAND) which commonly includes anxiety and depression. In addition to these associated disorders, extant literature and clinical observations have suggested an association between the premutation state and ASD. In this paper, we review the literature pertinent to this and discuss possible molecular mechanisms that may explain this association. This includes lowered levels of the FMR1 Protein (FMRP), GABA deficits, mitochondrial dysfunction and secondary genetic abnormalities that is seen in premutation carriers as well as their increased vulnerability to environmental stressors. Understanding these mechanisms can facilitate development of targeted treatment for specific sub-groups of ASD and premutation disorders in future.
Collapse
Affiliation(s)
- Ramkumar Aishworiya
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50th Street, Sacramento, CA, 95817, USA. .,Khoo Teck Puat-National University Children's Medical Institute, National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore. .,Department of Pediatrics, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Drive, Singapore, 117597, Singapore.
| | - Dragana Protic
- Department of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Randi Hagerman
- Medical Investigation of Neurodevelopmental Disorders (MIND) Institute, University of California Davis, 2825 50th Street, Sacramento, CA, 95817, USA.,Department of Pediatrics, University of California Davis School of Medicine, 4610 X St, Sacramento, CA, 95817, USA
| |
Collapse
|
8
|
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.
Collapse
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.
| |
Collapse
|
9
|
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
Collapse
|
10
|
Atli EI, Yalcintepe S, Atli E, Demir S, Mail C, Gurkan H. Clinical Implications of Chromosome 16 Copy Number Variation. Mol Syndromol 2022; 13:184-192. [PMID: 35707588 PMCID: PMC9149555 DOI: 10.1159/000517762] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/09/2021] [Indexed: 08/27/2023] Open
Abstract
Chromosome 16 is one of the gene-rich chromosomes; however, approximately 10% of the chromosome 16 sequence is composed of segmental copies, which renders this chromosome instable and predisposes it to rearrangements via frequent nonallelic homologous recombination. Microarray technologies have enabled the analysis of copy number variations (CNV), which may be associated with the risk of developing complex diseases. Through comparative genomic hybridisation in 1,298 patients, we detected 18 cases with chromosome 16 CNV. We identified 2recurrent CNV regions, including 1 at 16p13.11 in 4 patients and another at 16p11.2 in 7 patients. We also detected atypical chromosome 16 rearrangements in 7 patients. Furthermore, we noted an increased frequency of co-occurring genomic changes, supporting the two-hit hypothesis to explain the phenotypic variability in the clinical presentation of CNV syndromes. Our findings can contribute to the creation of a chromosome 16 disease map based on regions that may be associated with disease development.
Collapse
Affiliation(s)
| | | | - Engin Atli
- Department of Medical Genetics, Faculty of Medicine, Trakya University, Edirne, Turkey
| | | | | | | |
Collapse
|
11
|
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.
Collapse
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
| | | |
Collapse
|
12
|
Garrott SR, Gillies JP, DeSantis ME. Nde1 and Ndel1: Outstanding Mysteries in Dynein-Mediated Transport. Front Cell Dev Biol 2022; 10:871935. [PMID: 35493069 PMCID: PMC9041303 DOI: 10.3389/fcell.2022.871935] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/17/2022] [Indexed: 11/17/2022] Open
Abstract
Cytoplasmic dynein-1 (dynein) is the primary microtubule minus-end directed molecular motor in most eukaryotes. As such, dynein has a broad array of functions that range from driving retrograde-directed cargo trafficking to forming and focusing the mitotic spindle. Dynein does not function in isolation. Instead, a network of regulatory proteins mediate dynein’s interaction with cargo and modulate dynein’s ability to engage with and move on the microtubule track. A flurry of research over the past decade has revealed the function and mechanism of many of dynein’s regulators, including Lis1, dynactin, and a family of proteins called activating adaptors. However, the mechanistic details of two of dynein’s important binding partners, the paralogs Nde1 and Ndel1, have remained elusive. While genetic studies have firmly established Nde1/Ndel1 as players in the dynein transport pathway, the nature of how they regulate dynein activity is unknown. In this review, we will compare Ndel1 and Nde1 with a focus on discerning if the proteins are functionally redundant, outline the data that places Nde1/Ndel1 in the dynein transport pathway, and explore the literature supporting and opposing the predominant hypothesis about Nde1/Ndel1’s molecular effect on dynein activity.
Collapse
Affiliation(s)
- Sharon R. Garrott
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - John P. Gillies
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Morgan E. DeSantis
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, United States
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
- *Correspondence: Morgan E. DeSantis,
| |
Collapse
|
13
|
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.
Collapse
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,
| |
Collapse
|
14
|
Buttermore ED, Anderson NC, Chen PF, Makhortova NR, Kim KH, Wafa SMA, Dwyer S, Micozzi JM, Winden KD, Zhang B, Han MJ, Kleiman RJ, Brownstein CA, Sahin M, Gonzalez-Heydrich J. 16p13.11 deletion variants associated with neuropsychiatric disorders cause morphological and synaptic changes in induced pluripotent stem cell-derived neurons. Front Psychiatry 2022; 13:924956. [PMID: 36405918 PMCID: PMC9669751 DOI: 10.3389/fpsyt.2022.924956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/12/2022] [Indexed: 11/05/2022] Open
Abstract
16p13.11 copy number variants (CNVs) have been associated with autism, schizophrenia, psychosis, intellectual disability, and epilepsy. The majority of 16p13.11 deletions or duplications occur within three well-defined intervals, and despite growing knowledge of the functions of individual genes within these intervals, the molecular mechanisms that underlie commonly observed clinical phenotypes remain largely unknown. Patient-derived, induced pluripotent stem cells (iPSCs) provide a platform for investigating the morphological, electrophysiological, and gene-expression changes that result from 16p13.11 CNVs in human-derived neurons. Patient derived iPSCs with varying sizes of 16p13.11 deletions and familial controls were differentiated into cortical neurons for phenotypic analysis. High-content imaging and morphological analysis of patient-derived neurons demonstrated an increase in neurite branching in patients compared with controls. Whole-transcriptome sequencing revealed expression level changes in neuron development and synaptic-related gene families, suggesting a defect in synapse formation. Subsequent quantification of synapse number demonstrated increased numbers of synapses on neurons derived from early-onset patients compared to controls. The identification of common phenotypes among neurons derived from patients with overlapping 16p13.11 deletions will further assist in ascertaining common pathways and targets that could be utilized for screening drug candidates. These studies can help to improve future treatment options and clinical outcomes for 16p13.11 deletion patients.
Collapse
Affiliation(s)
- Elizabeth D Buttermore
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Nickesha C Anderson
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Pin-Fang Chen
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Nina R Makhortova
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Kristina H Kim
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States
| | - Syed M A Wafa
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Sean Dwyer
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - John M Micozzi
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Kellen D Winden
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Bo Zhang
- Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Min-Joon Han
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States
| | - Robin J Kleiman
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Catherine A Brownstein
- The Manton Center of Orphan Disease Research, Boston Children's Hospital, Boston, MA, United States
| | - Mustafa Sahin
- Human Neuron Core, Rosamund Stone Zander Translational Neuroscience Center, Boston Children's Hospital, Boston, MA, United States.,Department of Neurology, Boston Children's Hospital, Boston, MA, United States.,Harvard Medical School Teaching Hospital, Boston, MA, United States
| | - Joseph Gonzalez-Heydrich
- Department of Psychiatry, Developmental Neuropsychiatry Research Program, Boston Children's Hospital, Boston, MA, United States
| |
Collapse
|
15
|
Duplication of Chromosome 16p13.11-p12.3 with Different Expressions in the Same Family. Balkan J Med Genet 2021; 24:89-94. [PMID: 34447664 PMCID: PMC8366479 DOI: 10.2478/bjmg-2021-0010] [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] [Indexed: 12/01/2022] Open
Abstract
The knowledge about genetic involvement in neurodevelopmental disorders, and especially in autism, is currently rising. To date, more than 100 gene mutations related to autistic syndromes have been described. Some disorders that affect multiple family members are caused by gene mutations, which can be inherited. Recently, array comparative genomic hybridization (aCGH) has identified sub microscopic deletions and duplications as a common cause of mental retardation and autism. In this article we report the occurrence of the same genetic finding (chromosome 16p13.11-p12.3 duplication) in a family with four small children, where two older siblings manifested a global neurodevelopmental delay associated with an autism spectrum disorder (ASD), but younger twin brothers with the same mutation, have typical development. Genetic analysis showed that the chromosomal duplication was inherited from the father, in which phenotype and functioning are quite typical. As is known, the duplication can pass from parents to children. The 16p13.11 micro duplication has been implicated in several neurodevelopmental and behavioral disorders and is characterized by variable expressivity and incomplete penetrance.
Collapse
|
16
|
Reynard P, Monin P, Veuillet E, Thai-Van H. A new genetic variant causing auditory neuropathy: A CARE case report. Eur Ann Otorhinolaryngol Head Neck Dis 2021; 139:91-94. [PMID: 34456167 DOI: 10.1016/j.anorl.2021.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
INTRODUCTION Auditory neuropathy refers to impaired synchronization of the auditory signal along the cochlear nerve. The present study, following CARE case report guidelines, describes a case of auditory neuropathy secondary to a genetic variant not previously described. OBSERVATION An 18-year-old patient was followed for multiple learning disorder. His main complaint was speech comprehension, especially in noise. Auditory neuropathy was diagnosed on electrophysiological criteria, linked to a 2.66Mb deletion on the short arm of chromosome 16, at 16p13.11p12.3 (15,492,317-18,162,167, according to the hg19 version of the human reference genome). Adapted speech therapy sessions with auditory training for intelligibility in noise and a hearing aid with high-frequency microphone were prescribed. At 6months, the patient reported improvement in understanding speech in noise. CONCLUSION The involvement of this 16p13.11 deletion in the patient's symptomatology was not obvious, in a probable context of incomplete penetrance and variable expression. Early diagnosis of auditory neuropathy allowed implementation of better adapted multidisciplinary specialized management.
Collapse
Affiliation(s)
- P Reynard
- Université Claude Bernard Lyon 1, 69000 Lyon, France; Service d'audiologie et d'explorations otoneurologiques, hospices civils de Lyon, 69002 Lyon, France; Institut de l'audition, Centre de l'Institut Pasteur, Inserm 1120 (Génétique et Physiologie de l'Audition), 75012 Paris, France; Université Paris la Sorbonne, 75006 Paris, France.
| | - P Monin
- Service de génétique médicale, unité de génétique clinique, hospices civils de Lyon, 69002 Lyon, France
| | - E Veuillet
- Université Claude Bernard Lyon 1, 69000 Lyon, France; Service d'audiologie et d'explorations otoneurologiques, hospices civils de Lyon, 69002 Lyon, France; Institut de l'audition, Centre de l'Institut Pasteur, Inserm 1120 (Génétique et Physiologie de l'Audition), 75012 Paris, France
| | - H Thai-Van
- Université Claude Bernard Lyon 1, 69000 Lyon, France; Service d'audiologie et d'explorations otoneurologiques, hospices civils de Lyon, 69002 Lyon, France; Institut de l'audition, Centre de l'Institut Pasteur, Inserm 1120 (Génétique et Physiologie de l'Audition), 75012 Paris, France
| |
Collapse
|
17
|
Meerschaut I, Vergult S, Dheedene A, Menten B, De Groote K, De Wilde H, Muiño Mosquera L, Panzer J, Vandekerckhove K, Coucke PJ, De Wolf D, Callewaert B. A Reassessment of Copy Number Variations in Congenital Heart Defects: Picturing the Whole Genome. Genes (Basel) 2021; 12:genes12071048. [PMID: 34356064 PMCID: PMC8304049 DOI: 10.3390/genes12071048] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 11/17/2022] Open
Abstract
Copy number variations (CNVs) can modulate phenotypes by affecting protein-coding sequences directly or through interference of gene expression. Recent studies in cancer and limb defects pinpointed the relevance of non-coding gene regulatory elements such as long non-coding RNAs (lncRNAs) and topologically associated domain (TAD)-related gene-enhancer interactions. The contribution of such non-coding elements is largely unexplored in congenital heart defects (CHD). We performed a retrospective analysis of CNVs reported in a cohort of 270 CHD patients. We reviewed the diagnostic yield of pathogenic CNVs, and performed a comprehensive reassessment of 138 CNVs of unknown significance (CNV-US), evaluating protein-coding genes, lncRNA genes, and potential interferences with TAD-related gene-enhancer interactions. Fifty-two of the 138 CNV-US may relate to CHD, revealing three candidate CHD regions, 19 candidate CHD genes, 80 lncRNA genes of interest, and six potentially CHD-related TAD interferences. Our study thus indicates a potential relevance of non-coding gene regulatory elements in CNV-related CHD pathogenesis. Shortcomings in our current knowledge on genomic variation call for continuous reporting of CNV-US in international databases, careful patient counseling, and additional functional studies to confirm these preliminary findings.
Collapse
Affiliation(s)
- Ilse Meerschaut
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Sarah Vergult
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Annelies Dheedene
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Katya De Groote
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Hans De Wilde
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Laura Muiño Mosquera
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Joseph Panzer
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Kristof Vandekerckhove
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
| | - Paul J. Coucke
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
| | - Daniël De Wolf
- Department of Pediatric Cardiology, Ghent University Hospital, 9000 Ghent, Belgium; (K.D.G.); (H.D.W.); (J.P.); (K.V.); (D.D.W.)
- Department of Pediatric Cardiology, Brussels University Hospital, 1090 Brussels, Belgium
| | - Bert Callewaert
- Center for Medical Genetics, Ghent University Hospital, Belgium and Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium; (I.M.); (S.V.); (A.D.); (B.M.); (L.M.M.); (P.J.C.)
- Correspondence: ; Tel.: +32-9-332-3603
| |
Collapse
|
18
|
Sherer DM, Hsieh V, Kheyman M, Field A, Dalloul M. Mid-trimester absent nasal bone and transient unilateral hydronephrosis associated with 16p13.3 microduplication. JOURNAL OF CLINICAL ULTRASOUND : JCU 2021; 49:622-624. [PMID: 33778969 DOI: 10.1002/jcu.23007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 02/18/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Characteristic phenotypic features of 16p13.3 microduplication include impaired mental development, arthrogryposis-like musculoskeletal anomalies (club-feet, congenital hip dislocation, and camptodactyly of fingers and toes), facial dysmorphology, and at times congenital cardiac disease. Most of the described affected individuals have microduplications involving the CREBBP gene. Findings indicate this gene to be dosage-sensitive and likely involved in the phenotypes of 16p13.3 microduplication syndrome. We describe the incidental finding of 16p13.3 microduplication in a fetus with mid-trimester sonographic examination showing absent nasal bone and transient unilateral hydronephrosis.
Collapse
Affiliation(s)
- David M Sherer
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Vicky Hsieh
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Mila Kheyman
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Alessia Field
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| | - Mudar Dalloul
- The Division of Maternal-Fetal Medicine, The Department of Obstetrics and Gynecology, State University of New York (SUNY), Downstate Health Sciences University, Brooklyn, New York, USA
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Poot M. Chromothripsis and Duplications as Underappreciated Genomic Gremlins. Mol Syndromol 2021; 11:239-242. [PMID: 33510597 DOI: 10.1159/000512565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/19/2022] Open
|
21
|
Zhang J, Xia K, Ahn M, Jha SC, Blanchett R, Crowley JJ, Szatkiewicz JP, Zou F, Zhu H, Styner M, Gilmore JH, Knickmeyer RC. Genome-Wide Association Analysis of Neonatal White Matter Microstructure. Cereb Cortex 2021; 31:933-948. [PMID: 33009551 PMCID: PMC7786356 DOI: 10.1093/cercor/bhaa266] [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: 08/15/2019] [Revised: 07/15/2020] [Accepted: 08/16/2020] [Indexed: 11/14/2022] Open
Abstract
A better understanding of genetic influences on early white matter development could significantly advance our understanding of neurological and psychiatric conditions characterized by altered integrity of axonal pathways. We conducted a genome-wide association study (GWAS) of diffusion tensor imaging (DTI) phenotypes in 471 neonates. We used a hierarchical functional principal regression model (HFPRM) to perform joint analysis of 44 fiber bundles. HFPRM revealed a latent measure of white matter microstructure that explained approximately 50% of variation in our tractography-based measures and accounted for a large proportion of heritable variation in each individual bundle. An intronic SNP in PSMF1 on chromosome 20 exceeded the conventional GWAS threshold of 5 x 10-8 (p = 4.61 x 10-8). Additional loci nearing genome-wide significance were located near genes with known roles in axon growth and guidance, fasciculation, and myelination.
Collapse
Affiliation(s)
- J Zhang
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - K Xia
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - M Ahn
- Department of Mathematics and Statistics, University of Nevada, Reno, NV, USA
| | - S C Jha
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - R Blanchett
- Genetics and Genome Sciences Program, Michigan State University, East Lansing, MI, USA
| | - J J Crowley
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Department of Clinical Neuroscience, Karolinska Institute, Stockholm, Sweden
| | - J P Szatkiewicz
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - F Zou
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - H Zhu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - M Styner
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - J H Gilmore
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - R C Knickmeyer
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Pediatrics and Human Development, Michigan State University, East Lansing, MI, USA
- Institute for Quantitative Health Sciences and Engineering, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
22
|
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.
Collapse
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
| |
Collapse
|
23
|
Cabet S, Guibaud L, Sanlaville D. [Microlissencephaly due to pathogenic variants of NDE1: from pathology to normal brain development]. Med Sci (Paris) 2020; 36:866-871. [PMID: 33026328 DOI: 10.1051/medsci/2020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Pathogenic variants of the gene NDE1 (Nuclear Distribution Element 1) in humans lead to microlissencephaly which associates a reduced head circumference and a simplified gyration. Microlissencephaly is the most severe deficit of neurogenesis described to date but its precise physiopathological mechanism is not yet well known. The NDE1 gene encodes a phosphoprotein that is essential to neurogenesis and that is expressed in various cell compartments of neuroblasts. More than 60 interaction partners with NDE1 have been reported, notably various proteins involved in formation of the mitotic spindle, in ciliation, in genome protection of dividing neuroblasts or even in apoptosis (like LIS1, dynein or cohesin), which are all avenues that we explore in this review.
Collapse
Affiliation(s)
- Sara Cabet
- Service de génétique, Hospices Civils de Lyon, groupement hospitalier Est, France - Service de radiologie, Hospices Civils de Lyon, groupement hospitalier Est, 59 boulevard Pinel, 69677 Bron Cedex, France
| | - Laurent Guibaud
- Service de radiologie, Hospices Civils de Lyon, groupement hospitalier Est, 59 boulevard Pinel, 69677 Bron Cedex, France
| | - Damien Sanlaville
- Service de génétique, Hospices Civils de Lyon, groupement hospitalier Est, France - Inserm U1028, CNRS UMR5292, équipe GENDEV, Centre de recherche en neurosciences de Lyon, 69000 Lyon, France
| |
Collapse
|
24
|
Murakami H, Tsurusaki Y, Enomoto K, Kuroda Y, Yokoi T, Furuya N, Yoshihashi H, Minatogawa M, Abe-Hatano C, Ohashi I, Nishimura N, Kumaki T, Enomoto Y, Naruto T, Iwasaki F, Harada N, Ishikawa A, Kawame H, Sameshima K, Yamaguchi Y, Kobayashi M, Tominaga M, Ishikiriyama S, Tanaka T, Suzumura H, Ninomiya S, Kondo A, Kaname T, Kosaki K, Masuno M, Kuroki Y, Kurosawa K. Update of the genotype and phenotype of KMT2D and KDM6A by genetic screening of 100 patients with clinically suspected Kabuki syndrome. Am J Med Genet A 2020; 182:2333-2344. [PMID: 32803813 DOI: 10.1002/ajmg.a.61793] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/05/2020] [Accepted: 06/23/2020] [Indexed: 12/15/2022]
Abstract
Kabuki syndrome is characterized by a variable degree of intellectual disability, characteristic facial features, and complications in various organs. Many variants have been identified in two causative genes, that is, lysine methyltransferase 2D (KMT2D) and lysine demethylase 6A (KDM6A). In this study, we present the results of genetic screening of 100 patients with a suspected diagnosis of Kabuki syndrome in our center from July 2010 to June 2018. We identified 76 variants (43 novel) in KMT2D and 4 variants (3 novel) in KDM6A as pathogenic or likely pathogenic. Rare variants included a deep splicing variant (c.14000-8C>G) confirmed by RNA sequencing and an 18% mosaicism level for a KMT2D mutation. We also characterized a case with a blended phenotype consisting of Kabuki syndrome, osteogenesis imperfecta, and 16p13.11 microdeletion. We summarized the clinical phenotypes of 44 patients including a patient who developed cervical cancer of unknown origin at 16 years of age. This study presents important details of patients with Kabuki syndrome including rare clinical cases and expands our genetic understanding of this syndrome, which will help clinicians and researchers better manage and understand patients with Kabuki syndrome they may encounter.
Collapse
Affiliation(s)
- Hiroaki Murakami
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yoshinori Tsurusaki
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Keisuke Enomoto
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yukiko Kuroda
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takayuki Yokoi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noritaka Furuya
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Hiroshi Yoshihashi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Mari Minatogawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Chihiro Abe-Hatano
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Ikuko Ohashi
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Naoto Nishimura
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Tatsuro Kumaki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Yumi Enomoto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Takuya Naruto
- Clinical Research Institute, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Fuminori Iwasaki
- Division of Hematology/Oncology, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Noriaki Harada
- Department of Clinical Laboratory, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Aki Ishikawa
- Department of Medical Genetics and Genomics, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kawame
- Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Kiyoko Sameshima
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Yu Yamaguchi
- Division of Medical Genetics, Gunma Children's Medical Center, Gunma, Japan
| | - Masahisa Kobayashi
- Department of Pediatrics, Jikei University School of Medicine, Tokyo, Japan
| | - Makiko Tominaga
- Children's Medical Center, Northern Yokohama Hospital, Showa University, Yokohama, Japan
| | - Satoshi Ishikiriyama
- Division of Clinical Genetics and Cytogenetics, Shizuoka Children's Hospital, Shizuoka, Japan
| | | | - Hiroshi Suzumura
- Department of Pediatrics, Dokkyo Medical University, Tochigi, Japan
| | - Shinsuke Ninomiya
- Department of Clinical Genetics, Kurashiki Central Hospital, Kurashiki, Japan
| | - Akane Kondo
- Department of Gynecology, Shikoku Medical Center for Children and Adults, Kagawa, Japan
| | - Tadashi Kaname
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, Japan
| | - Mitsuo Masuno
- Genetic Counseling Program, Graduate School of Health and Welfare, Kawasaki University of Medical Welfare, Kurashiki, Japan
| | - Yoshikazu Kuroki
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Kenji Kurosawa
- Division of Medical Genetics, Kanagawa Children's Medical Center, Yokohama, Japan
| |
Collapse
|
25
|
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: 4] [Impact Index Per Article: 1.0] [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.
Collapse
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
| |
Collapse
|
26
|
Wang J, Chen L, Wang L, Yin D, Zeng Y, Tang F, Tian Y, Liu H. Segmental aneuploidies in fetuses with isolated echogenic intracardiac focus among women younger than 35 years. Sci Rep 2020; 10:10496. [PMID: 32591622 PMCID: PMC7320167 DOI: 10.1038/s41598-020-67501-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/09/2020] [Indexed: 11/09/2022] Open
Abstract
Studies on the occurrence of segmental aneuploidoidy in fetuses with isolated echogenic intracardiac focus (EIF) are scarce. The aim of this study was to analyze whether there is an association between abnormal segmental aneuploidies and isolated EIF. This was a prospective case-control study. The study participants in the case group were fetuses that were diagnosed with isolated EIF. Samples without fetal ultrasound abnormalities but received prenatal diagnosis for other reasons (serological screening high-risk, voluntary request) were set as controls. All pregnant women were younger than 35 years old at the expected date of childbirth. Copy number variation sequencing (CNV-seq) was performed for all samples. The case group and control group successfully underwent CNV-seq analysis and exhibited 1,099 and 5,616 amniotic fluid samples, respectively. The detection rates of abnormal segmental aneuploidies in the case group and control group were 0.6% (7/1,099) and 1.1% (64/5,616), respectively; no statistically significant difference was found between the two groups (x2 = 2.220, P = 0.136). Isolated EIF did not increase the risk of fetal segmental aneuploidies.
Collapse
Affiliation(s)
- Jing Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Lin Chen
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Li Wang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Daishu Yin
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yang Zeng
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Feng Tang
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
| | - Yu Tian
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China
- Department of Ultrasonography, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Hongqian Liu
- Department of Obstetrics and Gynecology, West China Second University Hospital of Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Ministry of Education, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
27
|
Muys J, Jacquemyn Y, Blaumeiser B, Bourlard L, Brison N, Bulk S, Chiarappa P, De Leener A, De Rademaeker M, Désir J, Destrée A, Devriendt K, Dheedene A, Duquenne A, Fieuw A, Fransen E, Gatot J, Jamar M, Janssens S, Kerstjens J, Keymolen K, Lederer D, Menten B, Pichon B, Rombout S, Sznajer Y, Van Den Bogaert A, Van Den Bogaert K, Vermeesch J, Janssens K. Prenatally detected copy number variants in a national cohort: A postnatal follow‐up study. Prenat Diagn 2020; 40:1272-1283. [DOI: 10.1002/pd.5751] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 01/17/2023]
Affiliation(s)
- Joke Muys
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Yves Jacquemyn
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- ASTARC and Global Health Institute Universiteit Antwerpen Antwerpen Belgium
| | - Bettina Blaumeiser
- Department of Gynaecology University Hospital Antwerp Edegem Belgium
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Laura Bourlard
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Nathalie Brison
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | - Saskia Bulk
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | - Patrizia Chiarappa
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Anne De Leener
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | | | - Julie Désir
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Anne Destrée
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Koenraad Devriendt
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | | | - Armelle Duquenne
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | - Annelies Fieuw
- Center for Medical Genetics Vrije Universiteit Brussel Brussel Belgium
| | - Erik Fransen
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| | - Jean‐Stéphane Gatot
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | - Mauricette Jamar
- Center for Medical Genetics Centre Hospitalier Universitaire de Liège Liege Belgium
| | | | - Jorien Kerstjens
- Faculty for Medical Sciences Rijksuniversteit Groningen Groningen The Netherlands
| | | | - Damien Lederer
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Björn Menten
- Center for Medical Genetics Universiteit Gent Gent Belgium
| | - Bruno Pichon
- Center for Medical Genetics Université Libre de Bruxelles Bruxelles Belgium
| | - Sonia Rombout
- Center for Medical Genetics Institut de Pathologie et de Génétique Gosselies Gosselies Belgium
| | - Yves Sznajer
- Center for Medical Genetics Université Catholique de Louvain Louvain‐la‐Neuve Belgium
| | | | | | - Joris Vermeesch
- Center for Medical Genetics Katholieke Universiteit Leuven Leuven Belgium
| | - Katrien Janssens
- Center for Medical Genetics, Universiteit Antwerpen Antwerpen Belgium
| |
Collapse
|
28
|
Mountford HS, Bishop DVM, Thompson PA, Simpson NH, Newbury DF. Copy number variation burden does not predict severity of neurodevelopmental phenotype in children with a sex chromosome trisomy. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2020; 184:256-266. [PMID: 32452638 DOI: 10.1002/ajmg.c.31791] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 04/22/2020] [Accepted: 04/23/2020] [Indexed: 12/14/2022]
Abstract
Sex chromosome trisomies (SCTs) (XXX, XXY, and XYY karyotypes) are associated with an elevated risk of neurodevelopmental disorders. The range of severity of the phenotype is substantial. We considered whether this variable outcome was related to the presence of copy number variants (CNVs)-stretches of duplicated or deleted DNA. A sample of 125 children with an SCT were compared with 181 children of normal karyotype who had been given the same assessments. First, we compared the groups on measures of overall CNV burden: number of CNVs, total span of CNVs, and likely functional impact (probability of loss-of-function intolerance, pLI, summed over CNVs). Differences between groups were small relative to within-group variance and not statistically significant on overall test. Next, we considered whether a measure of general neurodevelopmental impairment was predicted by pLI summed score, SCT versus comparison group, or the interaction between them. There was a substantial effect of SCT/comparison status but the pLI score was not predictive of outcomes in either group. We conclude that variable presence of CNVs is not a likely explanation for the wide phenotypic variation in children with SCTs. We discuss methodological challenges of testing whether CNVs are implicated in causing neurodevelopmental problems.
Collapse
Affiliation(s)
- Hayley S Mountford
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
| | - Dorothy V M Bishop
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Paul A Thompson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Nuala H Simpson
- Department of Experimental Psychology, University of Oxford, Oxford, Oxfordshire, UK
| | - Dianne F Newbury
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, Oxfordshire, UK
| |
Collapse
|
29
|
Wu X, An G, Xie X, Su L, Cai M, Chen X, Li Y, Lin N, He D, Wang M, Huang H, Xu L. Chromosomal microarray analysis for pregnancies with or without ultrasound abnormalities in women of advanced maternal age. J Clin Lab Anal 2020; 34:e23117. [PMID: 31762079 PMCID: PMC7171339 DOI: 10.1002/jcla.23117] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/15/2019] [Accepted: 10/26/2019] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Chromosomal microarray analysis (CMA) has been suggested to be routinely conducted for fetuses with ultrasound abnormalities (UA), especially with ultrasound structural anomalies (USA). Whether to routinely offer CMA to women of advanced maternal age (AMA) without UA when undergoing invasive prenatal testing is inconclusive. OBJECTIVE This study aimed to evaluate the efficiency of CMA in detecting clinically significant chromosomal abnormalities in fetuses, with or without UA, of women with AMA. METHODS Data from singleton pregnancies referred for prenatal CMA due to AMA, with or without UA were obtained. The enrolled cases were divided into AMA group (group A) and AMA accompanied by UA group (group B). Single nucleotide polymorphism (SNP) array technology and conventional karyotyping were performed simultaneously. RESULTS A total of 703 cases were enrolled and divided into group A (N = 437) and group B (N = 266). Clinically significant abnormalities were detected by CMA in 52 cases (7.4%, 52/703; the value in group A was significantly lower than that in group B (3.9% vs 13.2%, P < .05); no statistic difference was observed with respect to submicroscopic variants of clinical significance between the two groups (0.9% vs 2.6%, P > .05). CONCLUSIONS Chromosomal microarray analysis should be available to all women with AMA undergoing invasive prenatal testing, regardless of ultrasound findings.
Collapse
Affiliation(s)
- Xiaoqing Wu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Gang An
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Xiaorui Xie
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Linjuan Su
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Meiying Cai
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Xuemei Chen
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Ying Li
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Na Lin
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Deqin He
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Meiying Wang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Hailong Huang
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| | - Liangpu Xu
- Fujian Key Laboratory for Prenatal Diagnosis and Birth DefectFujian Provincial Maternity and Children's HospitalAffiliated Hospital of Fujian Medical UniversityFuzhouChina
| |
Collapse
|
30
|
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.
Collapse
|
31
|
Prenatal Diagnostic Value of Chromosomal Microarray in Fetuses with Nuchal Translucency Greater than 2.5 mm. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6504159. [PMID: 32908864 PMCID: PMC7471829 DOI: 10.1155/2019/6504159] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 09/17/2019] [Indexed: 02/03/2023]
Abstract
Objective To assess the clinical value of prenatal diagnosis using quantitative fluorescent polymerase chain reaction (QF-PCR) and chromosomal microarray analysis (CMA) for the examination of genomic imbalances in prenatal amniotic fluid samples from fetuses with a nuchal translucency (NT) greater than or equal to 2.5 mm. Materials and Methods A total of 494 amniotic fluid samples and 5 chorionic villus samples were included in this study, with a fetal NT ≥ 2.5 mm at 11–13+6 weeks of gestation from November 2015 to December 2018. All cases were examined with QF-PCR, and those with normal QF-PCR results were then analyzed by CMA. Results Of the 499 cases, common aneuploidies were detected by QF-PCR in 61 (12.2%) cases. One case of triploidy, one case of trisomy 21 mosaicism, and two cases of X/XX mosaicism were further confirmed by fluorescence in situ hybridization (FISH). Among the 434 cases with normal QF-PCR results, microarray detected additional pathogenic copy number variants (CNVs) in 4.8% (21/434) of cases. Six cases would have been expected to be detectable by conventional karyotyping because of large deletions/duplications (>10 Mb), leaving fifteen (3.5%, 15/428) cases with pathogenic CNVs only detectable by CMA. Pathogenic CNVs, especially those <10 Mb, were centralized in cases with an NT < 4.5 mm, including 5 pathogenic CNVs in cases with an NT of 2.5–3.5 mm and 7 pathogenic CNVs in cases with an NT of 3.5–4.5 mm. Conclusions It is rational to use a diagnostic strategy in which CMA is preceded by a less-expensive, rapid method, namely, QF-PCR, to detect common aneuploidies. CMA allows for the detection of a number of pathogenic chromosomal aberrations in fetuses with an NT ≥ 2.5 mm.
Collapse
|
32
|
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.
Collapse
|
33
|
Extrusion pump ABCC1 was first linked with nonsyndromic hearing loss in humans by stepwise genetic analysis. Genet Med 2019; 21:2744-2754. [PMID: 31273342 DOI: 10.1038/s41436-019-0594-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/17/2019] [Indexed: 11/08/2022] Open
Abstract
PURPOSE To determine the genetic etiology of deafness in a family (HN-SD01) with autosomal dominant nonsyndromic hearing loss (NSHL). METHODS Stepwise genetic analysis was performed on family HN-SD01, including hotspot variant screening, exome sequencing, virtual hearing loss gene panel, and genome-wide linkage analysis. Targeted region sequencing was used to screen ABCC1 in additional cases. Cochlear expression of Abcc1 was evaluated by messenger RNA (mRNA) and protein levels. Computational prediction, immunofluorescence, real-time quantitative polymerase chain reaction, and flow cytometry were conducted to uncover functional consequences of candidate variants. RESULTS Stepwise genetic analysis identified a heterozygous missense variant, ABCC1:c.1769A>G (p.Asn590Ser), cosegregating with phenotype in HN-SD01. Screening of ABCC1 in an additional 217 cases identified candidate pathogenic variants c.692G>A (p.Gly231Asp) in a sporadic case and c.887A>T (p.Glu296Val) in a familial proband. Abcc1 expressed in stria vascularis and auditory nerve of mouse cochlea. Immunofluorescence showed p.Asn590Ser distributed in cytomembrane and cytoplasm, while wild type was shown only in cytomembrane. Besides, it generated unstable mRNA and decreased efflux capacity of ABCC1. CONCLUSION Stepwise genetic analysis is efficient to analyze the genetic etiology of NSHL. Variants in ABCC1 are linked with NSHL and suggest an important role of extruding pumps in maintaining cochlea function.
Collapse
|
34
|
Sriretnakumar V, Zai CC, Wasim S, Barsanti-Innes B, Kennedy JL, So J. Copy number variant syndromes are frequent in schizophrenia: Progressing towards a CNV-schizophrenia model. Schizophr Res 2019; 209:171-178. [PMID: 31080157 DOI: 10.1016/j.schres.2019.04.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 02/26/2019] [Accepted: 04/30/2019] [Indexed: 12/23/2022]
Abstract
The genetic underpinnings of schizophrenia (SCZ) remain unclear. SCZ genetic studies thus far have only identified numerous single nucleotide polymorphisms with small effect sizes and a handful of copy number variants (CNVs). This study investigates the prevalence of well-characterized CNV syndromes and candidate CNVs within a cohort of 348 SCZ patients, and explores correlations to their phenotypic findings. There was an enrichment of syndromic CNVs in the cohort, as well as brain-related and immune pathway genes within the detected CNVs. SCZ patients with brain-related CNVs had increased CNV burden, neurodevelopmental features, and types of hallucinations. Based on these results, we propose a CNV-SCZ model wherein specific phenotypic profiles should be prioritized for CNV screening within the SCZ patient population.
Collapse
Affiliation(s)
- Venuja Sriretnakumar
- Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, 250 College Street, Toronto M5T 1R8, Canada
| | - Clement C Zai
- Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, 250 College Street, Toronto M5T 1R8, Canada
| | - Syed Wasim
- The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network & Mount Sinai Hospital, 60 Murray Street, Toronto M5T 3L9, Canada
| | - Brianna Barsanti-Innes
- Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, 250 College Street, Toronto M5T 1R8, Canada
| | - James L Kennedy
- Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, 250 College Street, Toronto M5T 1R8, Canada
| | - Joyce So
- Centre for Addiction and Mental Health, Campbell Family Mental Health Research Institute, 250 College Street, Toronto M5T 1R8, Canada; The Fred A. Litwin Family Centre in Genetic Medicine, University Health Network & Mount Sinai Hospital, 60 Murray Street, Toronto M5T 3L9, Canada.
| |
Collapse
|
35
|
Su L, Huang H, An G, Cai M, Wu X, Li Y, Xie X, Lin Y, Wang M, Xu L. Clinical application of chromosomal microarray analysis in fetuses with increased nuchal translucency and normal karyotype. Mol Genet Genomic Med 2019; 7:e811. [PMID: 31209990 PMCID: PMC6687862 DOI: 10.1002/mgg3.811] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 05/22/2019] [Accepted: 05/29/2019] [Indexed: 11/24/2022] Open
Abstract
Background Submicroscopic chromosomal imbalance is associated with an increased nuchal translucency (NT). Most previous research has recommended the use of chromosomal microarray analysis (CMA) for prenatal diagnosis if the NT ≥ 3.5 mm. However, there is no current global consensus on the cutoff value for CMA. In this study, we aimed to discuss the fetuses with smaller increased NT which was between cutoff value of NT for karyotype analysis (NT of 2.5 mm in China) and the recommended cutoff value for CMA (NT of 3.5 mm) whether should be excluded from CMA test. Methods Singleton pregnant women (N = 192) who had undergone invasive procedures owing to an increased NT (NT ≥ 2.5 mm) were enrolled. Fetal cells were collected and subjected to single nucleotide polymorphism array and karyotype analyses simultaneously. Cases were excluded if the karyotype analysis indicated aneuploidy and apparent structural aberrations. Results Fourteen cases of aneuploidy and four cases of structural abnormalities were excluded. Of the remaining 174 cases, 119 fetuses had NTs of 2.5–3.4 mm, and 55 fetuses with NT ≥ 3.5 mm. Eleven copy number variants (CNVs) were identified. In fetuses with smaller NTs, six (6/119, 5.9%) variations were detected, including two (2/119, 1.6%) clinically significant CNVs (pathogenic or likely pathogenic CNV), one likely benign CNV, two variants unknown significance, and one incidental CNV. Five (5/55, 9.1%) variations were found in fetuses with NT ≥ 3.5 mm. Among these CNVs, three (3/55, 5.5%) cases had clinically significant CNVs, and two had likely benign CNV. There were no statistically significant differences in the incidence of all CNVs and clinically significant CNVs in the two groups (p > 0.05). Conclusion CMA improved the diagnostic yield of chromosomal aberrations for fetuses with NTs of 2.5–3.4 mm and apparently normal karyotype, regardless of whether other ultrasonic abnormalities were observed.
Collapse
Affiliation(s)
- Linjuan Su
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Hailong Huang
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Gang An
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meiying Cai
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaoqing Wu
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Ying Li
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Xiaorui Xie
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Yuan Lin
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Meiying Wang
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| | - Liangpu Xu
- Fujian Provincial Maternity and Children's Hospital, Affiliated Hospital of Fujian Medical University, Fujian Provincial Key Laboratory for Prenatal Diagnosis and Birth Defect, Fuzhou, China
| |
Collapse
|
36
|
Kloth K, Renner S, Burmester G, Steinemann D, Pabst B, Lorenz B, Simon R, Kolbe V, Hempel M, Rosenberger G. 16p13.11 microdeletion uncovers loss‐of‐function of a
MYH11
missense variant in a patient with megacystis‐microcolon‐intestinal‐hypoperistalsis syndrome. Clin Genet 2019; 96:85-90. [DOI: 10.1111/cge.13557] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/18/2019] [Accepted: 04/28/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Katja Kloth
- Institute of Human GeneticsUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Sina Renner
- Institute of Human GeneticsUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Gunter Burmester
- Department of PediatricsAltonaer Kinderkrankenhaus Hamburg Germany
| | - Doris Steinemann
- Department of Human GeneticsMedical Center Hannover Hannover Germany
| | - Brigitte Pabst
- Department of Human GeneticsMedical Center Hannover Hannover Germany
| | | | - Ronald Simon
- Institute of PathologyUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Verena Kolbe
- Institute of Human GeneticsUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Maja Hempel
- Institute of Human GeneticsUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| | - Georg Rosenberger
- Institute of Human GeneticsUniversity Medical Center Hamburg‐Eppendorf Hamburg Germany
| |
Collapse
|
37
|
Smith AE, Jnah A, Newberry D. Chromosome 16p13.11 Microdeletion Syndrome in a Newborn: A Case Study. Neonatal Netw 2019; 37:303-309. [PMID: 30567812 DOI: 10.1891/0730-0832.37.5.303] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Chromosome 16p13.11 microdeletion syndrome is a rare copy number variant that carries increased risks for complications in the neonatal period and throughout the life span. Clinical manifestations and associated defects known to present in the neonatal period include motor delay, facial dysmorphisms, microcephaly, gastroesophageal reflux disease (GERD), and congenital heart defects. Management in the neonatal period focuses on associated comorbidities, including motor delay with or without GERD, which commonly manifests as feeding difficulties. Life span implications of chromosome 16p13.11 microdeletion syndrome include developmental, speech, and language delay; psychiatric and behavioral problems; seizure disorders; and, less commonly, obesity. Nursing assessment is critical to the early identification of nonspecific abnormalities associated with de novo genetic disorders. Early identification and diagnosis of chromosome 16p13.11 microdeletion syndrome are critical to optimizing outcomes throughout infancy and across the life span. We present a case report of an infant diagnosed with chromosome 16p13.11 microdeletion. A discussion of genetic influences, associated clinical manifestations, diagnostics, management, and health promotion strategies are presented to establish core knowledge of chromosome 16p13.11 microdeletion.
Collapse
|
38
|
Refining the Phenotype of Recurrent Rearrangements of Chromosome 16. Int J Mol Sci 2019; 20:ijms20051095. [PMID: 30836598 PMCID: PMC6429492 DOI: 10.3390/ijms20051095] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 01/08/2023] Open
Abstract
Chromosome 16 is one of the most gene-rich chromosomes of our genome, and 10% of its sequence consists of segmental duplications, which give instability and predisposition to rearrangement by the recurrent mechanism of non-allelic homologous recombination. Microarray technologies have allowed for the analysis of copy number variations (CNVs) that can contribute to the risk of developing complex diseases. By array comparative genomic hybridization (CGH) screening of 1476 patients, we detected 27 cases with CNVs on chromosome 16. We identified four smallest regions of overlapping (SROs): one at 16p13.11 was found in seven patients; one at 16p12.2 was found in four patients; two close SROs at 16p11.2 were found in twelve patients; finally, six patients were found with atypical rearrangements. Although phenotypic variability was observed, we identified a male bias for Childhood Apraxia of Speech associated to 16p11.2 microdeletions. We also reported an elevated frequency of second-site genomic alterations, supporting the model of the second hit to explain the clinical variability associated with CNV syndromes. Our goal was to contribute to the building of a chromosome 16 disease-map based on disease susceptibility regions. The role of the CNVs of chromosome 16 was increasingly made clear in the determination of developmental delay. We also found that in some cases a second-site CNV could explain the phenotypic heterogeneity by a simple additive effect or a pejorative synergistic effect.
Collapse
|
39
|
Johnstone M, Vasistha NA, Barbu MC, Dando O, Burr K, Christopher E, Glen S, Robert C, Fetit R, Macleod KG, Livesey MR, Clair DS, Blackwood DHR, Millar K, Carragher NO, Hardingham GE, Wyllie DJA, Johnstone EC, Whalley HC, McIntosh AM, Lawrie SM, Chandran S. Reversal of proliferation deficits caused by chromosome 16p13.11 microduplication through targeting NFκB signaling: an integrated study of patient-derived neuronal precursor cells, cerebral organoids and in vivo brain imaging. Mol Psychiatry 2019; 24:294-311. [PMID: 30401811 PMCID: PMC6344377 DOI: 10.1038/s41380-018-0292-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 09/13/2018] [Accepted: 10/08/2018] [Indexed: 01/22/2023]
Abstract
The molecular basis of how chromosome 16p13.11 microduplication leads to major psychiatric disorders is unknown. Here we have undertaken brain imaging of patients carrying microduplications in chromosome 16p13.11 and unaffected family controls, in parallel with iPS cell-derived cerebral organoid studies of the same patients. Patient MRI revealed reduced cortical volume, and corresponding iPSC studies showed neural precursor cell (NPC) proliferation abnormalities and reduced organoid size, with the NPCs therein displaying altered planes of cell division. Transcriptomic analyses of NPCs uncovered a deficit in the NFκB p65 pathway, confirmed by proteomics. Moreover, both pharmacological and genetic correction of this deficit rescued the proliferation abnormality. Thus, chromosome 16p13.11 microduplication disturbs the normal programme of NPC proliferation to reduce cortical thickness due to a correctable deficit in the NFκB signalling pathway. This is the first study demonstrating a biologically relevant, potentially ameliorable, signalling pathway underlying chromosome 16p13.11 microduplication syndrome in patient-derived neuronal precursor cells.
Collapse
Affiliation(s)
- Mandy Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK.
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
| | - Navneet A Vasistha
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Miruna C Barbu
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Owen Dando
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, UK
| | - Karen Burr
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
| | - Edward Christopher
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Sophie Glen
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Christelle Robert
- Royal (Dick) School of Veterinary Studies, The Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Rana Fetit
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kenneth G Macleod
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Matthew R Livesey
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
| | - David St Clair
- Institute of Medical Sciences, University of Aberdeen, Foresterhill, Aberdeen, UK
| | - Douglas H R Blackwood
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Kirsty Millar
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Neil O Carragher
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
| | - Giles E Hardingham
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, UK
| | - David J A Wyllie
- Centre for Discovery Brain Sciences, University of Edinburgh, Hugh Robson Building, 15 George Square, Edinburgh, UK
| | - Eve C Johnstone
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Heather C Whalley
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Stephen M Lawrie
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Siddharthan Chandran
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK.
- UK Dementia Research Institute at University of Edinburgh, Edinburgh Medical School, Edinburgh, UK.
- Centre for Brain Development and Repair, Bangalore, India.
| |
Collapse
|
40
|
LaCroix AJ, Stabley D, Sahraoui R, Adam MP, Mehaffey M, Kernan K, Myers CT, Fagerstrom C, Anadiotis G, Akkari YM, Robbins KM, Gripp KW, Baratela WAR, Bober MB, Duker AL, Doherty D, Dempsey JC, Miller DG, Kircher M, Bamshad MJ, Nickerson DA, Mefford HC, Sol-Church K. GGC Repeat Expansion and Exon 1 Methylation of XYLT1 Is a Common Pathogenic Variant in Baratela-Scott Syndrome. Am J Hum Genet 2019; 104:35-44. [PMID: 30554721 PMCID: PMC6323552 DOI: 10.1016/j.ajhg.2018.11.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 11/05/2018] [Indexed: 01/25/2023] Open
Abstract
Baratela-Scott syndrome (BSS) is a rare, autosomal-recessive disorder characterized by short stature, facial dysmorphisms, developmental delay, and skeletal dysplasia caused by pathogenic variants in XYLT1. We report clinical and molecular investigation of 10 families (12 individuals) with BSS. Standard sequencing methods identified biallelic pathogenic variants in XYLT1 in only two families. Of the remaining cohort, two probands had no variants and six probands had only a single variant, including four with a heterozygous 3.1 Mb 16p13 deletion encompassing XYLT1 and two with a heterozygous truncating variant. Bisulfite sequencing revealed aberrant hypermethylation in exon 1 of XYLT1, always in trans with the sequence variant or deletion when present; both alleles were methylated in those with no identified variant. Expression of the methylated XYLT1 allele was severely reduced in fibroblasts from two probands. Southern blot studies combined with repeat expansion analysis of genome sequence data showed that the hypermethylation is associated with expansion of a GGC repeat in the XYLT1 promoter region that is not present in the reference genome, confirming that BSS is a trinucleotide repeat expansion disorder. The hypermethylated allele accounts for 50% of disease alleles in our cohort and is not present in 130 control subjects. Our study highlights the importance of investigating non-sequence-based alterations, including epigenetic changes, to identify the missing heritability in genetic disorders.
Collapse
Affiliation(s)
- Amy J LaCroix
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Deborah Stabley
- Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Rebecca Sahraoui
- Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA; Biological Sciences, University of Delaware, Newark, DE 19716, USA
| | - Margaret P Adam
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Michele Mehaffey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Kelly Kernan
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | | | | | | | | | - Katherine M Robbins
- Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Karen W Gripp
- Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Wagner A R Baratela
- Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA; Instituto da Criança, Departamento de Pediatria, Universidade de São Paulo, São Paulo, SP Brazil
| | - Michael B Bober
- Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Angela L Duker
- Division of Orthogenetics, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA
| | - Dan Doherty
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Jennifer C Dempsey
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Daniel G Miller
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA; Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Heather C Mefford
- Department of Pediatrics, Division of Genetic Medicine, University of Washington, Seattle, WA 98195, USA; Brotman Baty Institute for Precision Medicine, Seattle, WA 98195, USA.
| | - Katia Sol-Church
- Nemours Biomedical Research Department, Alfred I. duPont Hospital for Children, Wilmington, DE 19803, USA; Department of Pathology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.
| |
Collapse
|
41
|
Vevera J, Zarrei M, Hartmannová H, Jedličková I, Mušálková D, Přistoupilová A, Oliveriusová P, Trešlová H, Nosková L, Hodaňová K, Stránecký V, Jiřička V, Preiss M, Příhodová K, Šaligová J, Wei J, Woodbury-Smith M, Bleyer AJ, Scherer SW, Kmoch S. Rare copy number variation in extremely impulsively violent males. GENES BRAIN AND BEHAVIOR 2018; 18:e12536. [DOI: 10.1111/gbb.12536] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/29/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022]
Affiliation(s)
- Jan Vevera
- Department of Psychiatry; Faculty of Medicine and University Hospital in Pilsen, Charles University; Prague Czech Republic
- Department of Psychiatry, First Faculty of Medicine; Charles University and General University Hospital in Prague; Prague Czech Republic
- Institute for Postgraduate Medical Education; Prague Czech Republic
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Mehdi Zarrei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Hana Hartmannová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Ivana Jedličková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Dita Mušálková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Anna Přistoupilová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Petra Oliveriusová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Helena Trešlová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Lenka Nosková
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Kateřina Hodaňová
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Viktor Stránecký
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| | - Václav Jiřička
- Prison Service of the Czech Republic, Directorate General; Department of Psychology; Prague Czech Republic
| | - Marek Preiss
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
- Psychology Department; University of New York in Prague; Prague Czech Republic
| | - Kateřina Příhodová
- Psychology Department; National Institute of Mental Health; Klecany Czech Republic
| | - Jana Šaligová
- Children's Faculty Hospital; Department of Pediatrics and Adolescent Medicine; Kosice Slovakia
- Department of Pediatrics and Adolescent Medicine, Faculty of Medicine of Pavel Jozef Šafárik University Kosice; Kosice Slovakia
| | - John Wei
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
| | - Marc Woodbury-Smith
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Institute of Neuroscience, Newcastle University, Sir James Spence Institute, Royal Victoria Infirmary; Newcastle upon Tyne UK
| | - Anthony J. Bleyer
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
- Section on Nephrology, Wake Forest School of Medicine; Medical Center Blvd.; Winston-Salem North Carolina USA
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology; The Hospital for Sick Children; Toronto Ontario Canada
- Department of Molecular Genetics and McLaughlin Centre; University of Toronto; Toronto Ontario Canada
| | - Stanislav Kmoch
- Research Unit for Rare Diseases, Department of Pediatrics and Adolescent Medicine; First Faculty of Medicine, Charles University; Prague Czech Republic
| |
Collapse
|
42
|
Allach El Khattabi L, Heide S, Caberg JH, Andrieux J, Doco Fenzy M, Vincent-Delorme C, Callier P, Chantot-Bastaraud S, Afenjar A, Boute-Benejean O, Cordier MP, Faivre L, Francannet C, Gerard M, Goldenberg A, Masurel-Paulet A, Mosca-Boidron AL, Marle N, Moncla A, Le Meur N, Mathieu-Dramard M, Plessis G, Lesca G, Rossi M, Edery P, Delahaye-Duriez A, De Pontual L, Tabet AC, Lebbar A, Suiro L, Ioos C, Natiq A, Chafai Elalaoui S, Missirian C, Receveur A, François-Fiquet C, Garnier P, Yardin C, Laroche C, Vago P, Sanlaville D, Dupont JM, Benzacken B, Pipiras E. 16p13.11 microduplication in 45 new patients: refined clinical significance and genotype-phenotype correlations. J Med Genet 2018; 57:301-307. [PMID: 30287593 DOI: 10.1136/jmedgenet-2018-105389] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 08/30/2018] [Accepted: 09/10/2018] [Indexed: 11/04/2022]
Abstract
BACKGROUND The clinical significance of 16p13.11 duplications remains controversial while frequently detected in patients with developmental delay (DD), intellectual deficiency (ID) or autism spectrum disorder (ASD). Previously reported patients were not or poorly characterised. The absence of consensual recommendations leads to interpretation discrepancy and makes genetic counselling challenging. This study aims to decipher the genotype-phenotype correlations to improve genetic counselling and patients' medical care. METHODS We retrospectively analysed data from 16 013 patients referred to 12 genetic centers for DD, ID or ASD, and who had a chromosomal microarray analysis. The referring geneticists of patients for whom a 16p13.11 duplication was detected were asked to complete a questionnaire for detailed clinical and genetic data for the patients and their parents. RESULTS Clinical features are mainly speech delay and learning disabilities followed by ASD. A significant risk of cardiovascular disease was noted. About 90% of the patients inherited the duplication from a parent. At least one out of four parents carrying the duplication displayed a similar phenotype to the propositus. Genotype-phenotype correlations show no impact of the size of the duplicated segment on the severity of the phenotype. However, NDE1 and miR-484 seem to have an essential role in the neurocognitive phenotype. CONCLUSION Our study shows that 16p13.11 microduplications are likely pathogenic when detected in the context of DD/ID/ASD and supports an essential role of NDE1 and miR-484 in the neurocognitive phenotype. Moreover, it suggests the need for cardiac evaluation and follow-up and a large study to evaluate the aortic disease risk.
Collapse
Affiliation(s)
- Laïla Allach El Khattabi
- Cytogenetics department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris; Sorbonne Paris Cité, Paris Descartes University, Medical school, Paris, France.,Department of Development, Reproduction and Cancer, Cochin Research Institute, INSERM U1016, CNRS UMR8104, Paris, France.,Nuclear Lymphocyte Biology, NIAMS, National Institutes of Health, Bethesda, Maryland, United States
| | - Solveig Heide
- Cytogenetics department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris; Sorbonne Paris Cité, Paris Descartes University, Medical school, Paris, France
| | | | - Joris Andrieux
- Genetics department, Jeanne de Flandre Hospital, CHRU de Lille, Lille, France
| | - Martine Doco Fenzy
- Genetics department, CHU Reims, Medical school IFR53, EA3801, Reims, France
| | - Caroline Vincent-Delorme
- Genetics department, Guy Fontaine Medical center, CLAD Nord de France, Jeanne de Flandre Hospital, CHRU Lille, CH Arras, Arras, France
| | | | - Sandra Chantot-Bastaraud
- Genetics and Embryology department, Armand-Trousseau Hospital, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Alexandra Afenjar
- Neuropediatrics department, Armand-Trousseau Hospital, Assistance Publique des Hôpitaux de Paris; Reference Center for cerebellar malformations, Paris, France
| | - Odile Boute-Benejean
- Genetics department, Guy Fontaine Medical Center, CLAD Nord de France, Jeanne de Flandre Hospital, CHRU Lille, Lille, France
| | | | | | | | - Marion Gerard
- Genetics department, CHU Côte de Nacre, Caen, France
| | | | | | | | | | - Anne Moncla
- Medical Genetics department, CHU Timone enfants, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Nathalie Le Meur
- Department of Genetics, Reproductive biology and Histology, CHU de Rouen, Rouen, France
| | | | | | - Gaetan Lesca
- Genetics department, GH Est, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, CNRS UMR 5292, INSERM U1028; Claude Bernard Lyon I University, Lyon, France
| | - Massimiliano Rossi
- Genetics department, GH Est, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, CNRS UMR 5292, INSERM U1028; Claude Bernard Lyon I University, Lyon, France
| | - Patrick Edery
- Genetics department, GH Est, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, CNRS UMR 5292, INSERM U1028; Claude Bernard Lyon I University, Lyon, France
| | - Andrée Delahaye-Duriez
- Department of Histology Embryology and Cytogenetics, Jean Verdier Hospital; Paris 13 University, Sorbonne Paris Cité, UFR SMBH Bobigny; PROTECT, INSERM, Paris Diderot University, Bondy, France.,Division of Brain Sciences, Faculty of Medicine, Imperial College, London, UK
| | - Loïc De Pontual
- Pediatrics department, Jean Verdier Hospital, Assistance Publique des Hôpitaux de Paris, Paris 13 University, Bondy, France
| | - Anne Claude Tabet
- Genetics department, CHU Robert Debré, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Aziza Lebbar
- Cytogenetics department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris; Sorbonne Paris Cité, Paris Descartes University, Medical school, Paris, France
| | - Lesley Suiro
- Neuropediatrics department, Hôpital Raymond Poincaré, Assistance Publique des Hôpitaux de Paris, Garches, France
| | - Christine Ioos
- Neuropediatrics department, Hôpital Raymond Poincaré, Assistance Publique des Hôpitaux de Paris, Garches, France
| | - Abdelhafid Natiq
- Medical Genetics department, Institut National d'Hygiène, Rabat, Morocco
| | | | - Chantal Missirian
- Medical Genetics department, CHU Timone enfants, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Aline Receveur
- Cytogenetics and Reproductive Biology department, CHU d'Amiens, Amiens, France
| | - Caroline François-Fiquet
- Plastic reconstructive and aesthetic surgery, Maison Blanche Hospital, Robert Debré Hospital, Reims, France
| | | | - Catherine Yardin
- Department of Histology, Cytology, Cytogenetics, Cell Biology and Reproduction, Limoges University Hospital, Limoges, France
| | - Cécile Laroche
- Pediatrics department, Limoges University Hospital, Limoges, France
| | - Philippe Vago
- Cytogenetics department, CHU Clermont-Ferrand, ERTICA, Auvergne University, Clermont-Ferrand, France
| | - Damien Sanlaville
- Genetics department, GH Est, Hospices Civils de Lyon, Lyon, France.,GENDEV Team, CRNL, CNRS UMR 5292, INSERM U1028; Claude Bernard Lyon I University, Lyon, France
| | - Jean Michel Dupont
- Cytogenetics department, Cochin Hospital, Assistance Publique des Hôpitaux de Paris; Sorbonne Paris Cité, Paris Descartes University, Medical school, Paris, France.,Department of Development, Reproduction and Cancer, Cochin Research Institute, INSERM U1016, CNRS UMR8104, Paris, France
| | - Brigitte Benzacken
- Department of Histology Embryology and Cytogenetics, Jean Verdier Hospital; Paris 13 University, Sorbonne Paris Cité, UFR SMBH Bobigny; PROTECT, INSERM, Paris Diderot University, Bondy, France
| | - Eva Pipiras
- Department of Histology Embryology and Cytogenetics, Jean Verdier Hospital; Paris 13 University, Sorbonne Paris Cité, UFR SMBH Bobigny; PROTECT, INSERM, Paris Diderot University, Bondy, France
| |
Collapse
|
43
|
Catatonia in Children and Adolescents: A High Rate of Genetic Conditions. J Am Acad Child Adolesc Psychiatry 2018; 57:518-525.e1. [PMID: 29960699 DOI: 10.1016/j.jaac.2018.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/17/2018] [Accepted: 05/09/2018] [Indexed: 12/11/2022]
Abstract
Pediatric catatonia is a rare and severe neuropsychiatric syndrome. We previously reported, in 58 children and adolescents with catatonia, a high prevalence (up to 20%) of medical conditions, some of which have specific treatments.1 Here we extend the cohort inclusion and report the first systematic molecular genetic data for this syndrome. Among the 89 patients consecutively admitted for catatonia (according to the pediatric catatonia rating scale)2 between 1993 and 2014, we identify 51 patients (57.3%) who had genetic laboratory testing, of whom 37 had single nucleotide polymorphism (SNP) microarray tests for CNVs and 14 had routine genetic explorations (karyotyping and searches for specific chromosomal abnormalities by fluorescence in situ hybridization [FISH]) or a specific diagnosis test based on clinical history. To assess the causality of observed genetic findings in each patient, we used a causality assessment score (CAUS)3 including 5 causality-support criteria on a 3-point scale (0 = absent; 1 = moderate; 2 = high): the existence of similar cases in the literature; the presence of a clinical contributing factor; the presence of a biological contributing factor; the presence of other paraclinical symptoms; and response to a specific treatment related to the suspected genetic or medical condition.
Collapse
|
44
|
de Sousa P, Kennedy A, Lalani HHS. A novel unbalanced translocation between the short arms of chromosomes 6 and 16 in a newborn girl: Clinical features and management. Clin Case Rep 2018; 6:1282-1286. [PMID: 29988690 PMCID: PMC6028415 DOI: 10.1002/ccr3.1574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 04/08/2018] [Accepted: 04/15/2018] [Indexed: 11/11/2022] Open
Abstract
The reporting of previously undescribed genetic mutations and resulting clinical phenotypes guides management and enables a more accurate prognosis for clinicians treating newborns with similar features. Previous cases of 6p deletions and 16p duplications have been described as separate entities. This patient presents with both and has a unique phenotype.
Collapse
|
45
|
Behnert A, Auber B, Steinemann D, Frühwald MC, Huisinga C, Hussein K, Kratz C, Ripperger T. KBG syndrome patient due to 16q24.3 microdeletion presenting with a paratesticular rhabdoid tumor: Coincidence or cancer predisposition? Am J Med Genet A 2018; 176:1449-1454. [PMID: 29696793 DOI: 10.1002/ajmg.a.38724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Revised: 03/05/2018] [Accepted: 04/04/2018] [Indexed: 11/11/2022]
Abstract
KBG syndrome is a rare autosomal dominant disorder caused by constitutive haploinsufficiency of the ankyrin repeat domain-containing protein 11 (ANKRD11) being the result of either loss-of-function gene variants or 16q24.3 microdeletions. The syndrome is characterized by a variable clinical phenotype comprising a distinct facial gestalt and variable neurological involvement. ANKRD11 is frequently affected by loss of heterozygosity in cancer. It influences the ligand-dependent transcriptional activation of nuclear receptors and tumor suppressive function of tumor protein TP53. ANKRD11 thus serves as a candidate tumor suppressor gene and it has been speculated that its haploinsufficiency may lead to an increased cancer risk in KBG syndrome patients. While no systematic data are available, we report here on the second KBG syndrome patient who developed a malignancy. At 17 years of age, the patient was diagnosed with a left-sided paratesticular extrarenal malignant rhabdoid tumor. Genetic investigations identified a somatic truncating gene variant in SMARCB1, which was not present in the germline, and a constitutional de novo 16q24.3 microdeletion leading to a loss of the entire ANKRD11 locus. Thus, KBG syndrome was diagnosed, which was in line with the clinical phenotype of the patient. At present, no specific measures for cancer surveillance can be recommended for KBG syndrome patients. However, a systematic follow-up and inclusion of KBG syndrome patients in registries (e.g., those currently established for cancer prone syndromes) will provide empiric data to support or deny an increased cancer risk in KBG syndrome in the future.
Collapse
Affiliation(s)
- Astrid Behnert
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Bernd Auber
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Doris Steinemann
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Michael C Frühwald
- Swabian Children's Cancer Center, Children's Hospital Augsburg, Augsburg, Germany
| | - Carolin Huisinga
- Department of Diagnostic and Interventional Radiology, Hannover Medical School, Hannover, Germany
| | - Kais Hussein
- Institute of Pathology, Hannover Medical School, Hannover, Germany
| | - Christian Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| |
Collapse
|
46
|
Singer A, Maya I, Koifman A, Nasser Samra N, Baris HN, Falik-Zaccai T, Ben Shachar S, Sagi-Dain L. Microarray analysis in pregnancies with isolated echogenic bowel. Early Hum Dev 2018. [PMID: 29522884 DOI: 10.1016/j.earlhumdev.2018.02.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
INTRODUCTION Fetal echogenic bowel is a frequent sonographic finding, demonstrated in about 1% of pregnancies. The advised evaluation of fetal echogenic bowel includes maternal serology, genetic testing for cystic fibrosis, detailed sonographic anatomic survey, and invasive prenatal testing for fetal chromosomal aberrations. The objective of our study was to evaluate the risk for clinically significant chromosomal microarray analysis (CMA) findings in pregnancies with isolated echogenic bowel. METHODS Data from all CMA analyses performed due to isolated echogenic bowel reported to the Israeli Ministry of Health between January 2013 and September 2016 were retrospectively obtained. Risk estimation was performed comparing the rate of abnormal microarray findings to the control population, based on a systematic review of 9272 pregnancies and a large local cohort of 5541 fetuses with normal ultrasound, undergoing CMA testing due to maternal request. RESULTS Of 103 CMA analyses performed due to isolated echogenic bowel, two (1.94%) pathogenic findings were detected (47,XYY and 16p11.2 duplication). This risk was not significantly elevated compared to the control groups. In addition, three variants of unknown significance were demonstrated. CONCLUSIONS To our best knowledge, our study is the first report describing the rate of clinically significant copy number variants in pregnancies with isolated echogenic bowel. According to our results, it seems that pregnancies with isolated echogenic bowel do not have an increased risk for abnormal CMA compared to fetuses with no evidence of sonographic anomalies. Our findings suggest that the consideration to perform CMA analysis in such pregnancies should not differ from any pregnancy with normal ultrasound.
Collapse
Affiliation(s)
- Amihood Singer
- Community Genetics, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Idit Maya
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Arie Koifman
- Genetics Institute, Soroka Medical Center, Beer Sheva, Israel
| | | | - Hagit N Baris
- The Genetics Institute, Rambam Health Care Campus, and the Technion, - Israel Institute of Technology, Haifa, Israel
| | - Tzipora Falik-Zaccai
- Institute of Human Genetics, Galilee Medical Center, Nahariya, The Galilee Faculty of Medicine, Bar Ilan, Israel
| | - Shay Ben Shachar
- Genetic Institute, Tel Aviv Sourasky Medical Center, affiliated to the Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Lena Sagi-Dain
- Genetics Institute, Carmel Medical Center, Haifa, Israel.
| |
Collapse
|
47
|
|
48
|
Zhang GM, Zheng L, He H, Song CC, Zhang ZJ, Cao XK, Lei CZ, Lan XY, Qi XL, Chen H, Huang YZ. Associations of GBP2 gene copy number variations with growth traits and transcriptional expression in Chinese cattle. Gene 2018; 647:101-106. [PMID: 29325733 DOI: 10.1016/j.gene.2018.01.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/16/2017] [Accepted: 01/02/2018] [Indexed: 12/19/2022]
Abstract
Copy number variations (CNVs) recently have been recognized as another important genetic variability followed single nucleotide polymorphisms (SNPs). The guanylate binding protein 2 (GBP2) gene plays an important role in cell proliferation. This study was performed to determine the presence of GBP2 CNV (relative to Angus cattle) in 466 individuals representing six main cattle breeds from China, identify its relationship with growth, and explore the biological effects of gene expression. There were two CNV regions in the GBP2 gene, for three types, CNV1 loss type (relative to Angus cattle) was more frequent in XN than other breeds, and CNV2 loss type (relative to Angus cattle) was more frequent in XN and CDM than other breeds. Though the GBP2 gene copy number presented no correlation with the transcriptional expression of JX (P > .05), but the transcriptional expression in heart is higher than other tissues, and the copy number in muscles and fat of JX is higher than others breeds. Statistical analysis revealed that the GBP2 gene CNV1 and CNV2 were significantly associated with growth traits (P < .05). In conclusion, this research established the correlations between CNVs of GBP2 gene and growth traits in different cattle breeds, and our results suggested that the CNVs in GBP2 gene may be considered markers for the molecular breeding of Chinese beef cattle.
Collapse
Affiliation(s)
- Gui-Min Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Li Zheng
- Henan University of Animal Husbandry and Economy, Zhengzhou, Henan 450046, PR China
| | - Hua He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China; College of Veterinary Medicine, Northwest A&F University, Yangling, Shaanxi, 712100, PR China
| | - Cheng-Chuang Song
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Zi-Jing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, PR China
| | - Xiu-Kai Cao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Chu-Zhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xian-Yong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Xing-Lei Qi
- Bureau of Animal Husbandry of Biyang County, Biyang, Henan 463700, PR China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China
| | - Yong-Zhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, PR China.
| |
Collapse
|
49
|
Hnoonual A, Thammachote W, Tim-Aroon T, Rojnueangnit K, Hansakunachai T, Sombuntham T, Roongpraiwan R, Worachotekamjorn J, Chuthapisith J, Fucharoen S, Wattanasirichaigoon D, Ruangdaraganon N, Limprasert P, Jinawath N. Chromosomal microarray analysis in a cohort of underrepresented population identifies SERINC2 as a novel candidate gene for autism spectrum disorder. Sci Rep 2017; 7:12096. [PMID: 28935972 PMCID: PMC5608768 DOI: 10.1038/s41598-017-12317-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 09/07/2017] [Indexed: 01/11/2023] Open
Abstract
Chromosomal microarray (CMA) is now recognized as the first-tier genetic test for detection of copy number variations (CNVs) in patients with autism spectrum disorder (ASD). The aims of this study were to identify known and novel ASD associated-CNVs and to evaluate the diagnostic yield of CMA in Thai patients with ASD. The Infinium CytoSNP-850K BeadChip was used to detect CNVs in 114 Thai patients comprised of 68 retrospective ASD patients (group 1) with the use of CMA as a second line test and 46 prospective ASD and developmental delay patients (group 2) with the use of CMA as the first-tier test. We identified 7 (6.1%) pathogenic CNVs and 22 (19.3%) variants of uncertain clinical significance (VOUS). A total of 29 patients with pathogenic CNVs and VOUS were found in 22% (15/68) and 30.4% (14/46) of the patients in groups 1 and 2, respectively. The difference in detected CNV frequencies between the 2 groups was not statistically significant (Chi square = 1.02, df = 1, P = 0.31). In addition, we propose one novel ASD candidate gene, SERINC2, which warrants further investigation. Our findings provide supportive evidence that CMA studies using population-specific reference databases in underrepresented populations are useful for identification of novel candidate genes.
Collapse
Affiliation(s)
- Areerat Hnoonual
- Graduate Program in Biomedical Sciences, Prince of Songkla University, Songkhla, Thailand
| | - Weerin Thammachote
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Thipwimol Tim-Aroon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Kitiwan Rojnueangnit
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tippawan Hansakunachai
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Thammasart University, Pathumthani, Thailand
| | - Tasanawat Sombuntham
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Rawiwan Roongpraiwan
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Juthamas Worachotekamjorn
- Division of Child Development, Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand
| | - Jariya Chuthapisith
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suthat Fucharoen
- Thalassemia Research Center, Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Duangrurdee Wattanasirichaigoon
- Division of Medical Genetics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Nichara Ruangdaraganon
- Division of Developmental-Behavioral Pediatrics, Department of Pediatrics, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Pornprot Limprasert
- Division of Human Genetics, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Natini Jinawath
- Program in Translational Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand. .,Integrative Computational Bioscience Center, Mahidol University, Salaya, Nakhon Pathom, Thailand.
| |
Collapse
|
50
|
Use of clinical chromosomal microarray in Chinese patients with autism spectrum disorder-implications of a copy number variation involving DPP10. Mol Autism 2017; 8:31. [PMID: 28670437 PMCID: PMC5485587 DOI: 10.1186/s13229-017-0136-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/08/2017] [Indexed: 11/23/2022] Open
Abstract
Background Array comparative genomic hybridization (aCGH) is recommended as a first-tier genetic test for children with autism spectrum disorder (ASD). However, interpretation of results can often be challenging partly due to the fact that copy number variants (CNVs) in non-European ASD patients are not well studied. To address this literature gap, we report the CNV findings in a cohort of Chinese children with ASD. Methods DNA samples were obtained from 258 Chinese ASD patients recruited from a child assessment center between January 2011 and August 2014. aCGH was performed using NimbleGen-CGX-135k or Agilent-CGX 60k oligonucleotide array. Results were classified based on existing guidelines and literature. Results Ten pathogenic CNVs and one likely pathogenic CNV were found in nine patients, with an overall diagnostic yield of 3.5%. A 138 kb duplication involving 3′ exons of DPP10 (arr[GRCh37] 2q14.1(116534689_116672358)x3), reported to be associated with ASD, was identified in one patient (0.39%). The same CNV was reported as variant of uncertain significance (VUS) in DECIPHER database. Multiple individuals of typical development carrying a similar duplication were identified among our ancestry-matched control with a frequency of 6/653 (0.92%) as well as from literature and genomic databases. Conclusions The DPP10 duplication is likely a benign CNV polymorphism enriched in Southern Chinese with a population frequency of ~1%. This highlights the importance of using ancestry-matched controls in interpretation of aCGH findings. Electronic supplementary material The online version of this article (doi:10.1186/s13229-017-0136-x) contains supplementary material, which is available to authorized users.
Collapse
|