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Vaseghi P, Habibi L, Neidich JA, Cao Y, Fattahi N, Rashidi-Nezhad R, Salehnezhad T, Dalili H, Rahimi Sharbaf F, Zarkesh MR, Malekian M, Mokhberdezfuli M, Mehrtash A, Ardeshirdavani A, Kariminejad R, Ghorbansabagh V, Sadeghimoghadam P, Naddaf A, Esmaeilnia Shirvany T, Mosayebi Z, Sahebdel B, Golshahi F, Shirazi M, Shamel S, Moeini R, Heidari A, Daneshmand MA, Ghasemi R, Akrami SM, Rashidi-Nezhad A. Towards solving the genetic diagnosis odyssey in Iranian patients with congenital anomalies. Eur J Hum Genet 2024:10.1038/s41431-024-01533-x. [PMID: 38278869 DOI: 10.1038/s41431-024-01533-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 11/23/2023] [Accepted: 12/12/2023] [Indexed: 01/28/2024] Open
Abstract
Understanding the underlying causes of congenital anomalies (CAs) can be a complex diagnostic journey. We aimed to assess the efficiency of exome sequencing (ES) and chromosomal microarray analysis (CMA) in patients with CAs among a population with a high fraction of consanguineous marriage. Depending on the patient's symptoms and family history, karyotype/Quantitative Fluorescence- Polymerase Chain Reaction (QF-PCR) (n = 84), CMA (n = 81), ES (n = 79) or combined CMA and ES (n = 24) were performed on 168 probands (66 prenatal and 102 postnatal) with CAs. Twelve (14.28%) probands were diagnosed by karyotype/QF-PCR and seven (8.64%) others were diagnosed by CMA. ES findings were conclusive in 39 (49.36%) families, and 61.90% of them were novel variants. Also, 64.28% of these variants were identified in genes that follow recessive inheritance in CAs. The diagnostic rate (DR) of ES was significantly higher than that of CMA in children from consanguineous families (P = 0·0001). The highest DR by CMA was obtained in the non-consanguineous postnatal subgroup and by ES in the consanguineous prenatal subgroup. In a population that is highly consanguineous, our results suggest that ES may have a higher diagnostic yield than CMA and should be considered as the first-tier test in the evaluation of patients with congenital anomalies.
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Affiliation(s)
- Parisa Vaseghi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Department of Photo Healing and Regeneration, Medical Laser Research Center, Yara Institute, ACECR, Tehran, Iran
| | - Laleh Habibi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | - Julie A Neidich
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, USA
| | - Yang Cao
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Neda Fattahi
- Ronash Medical Genetics Laboratory, Tehran, Iran
| | | | | | - Hossein Dalili
- Breastfeeding Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Rahimi Sharbaf
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zarkesh
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | - Mahdieh Mokhberdezfuli
- Ronash Medical Genetics Laboratory, Tehran, Iran
- Multiple Sclerosis Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | | | | | - Vafa Ghorbansabagh
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parvane Sadeghimoghadam
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir Naddaf
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Tahereh Esmaeilnia Shirvany
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ziba Mosayebi
- Department of Pediatrics, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Behrokh Sahebdel
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Golshahi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahboobeh Shirazi
- Department of Obstetrics and Gynecology, School of Medicine, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Shamel
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | - Roksana Moeini
- Department of Neonatology, Yas Hospital Complex, Tehran university of medical sciences, Tehran, Iran
| | | | | | - Reza Ghasemi
- Department of Pathology & Immunology, Division of Laboratory & Genomic Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Ali Rashidi-Nezhad
- Maternal, Fetal and Neonatal Research Center, Family Health Research Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Genetics Ward, Yas Hospital Complex, Tehran University of Medical Sciences, Tehran, Iran.
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Reappraisal of evolving methods in non-invasive prenatal screening: Discovery, biology and clinical utility. Heliyon 2023; 9:e13923. [PMID: 36879971 PMCID: PMC9984859 DOI: 10.1016/j.heliyon.2023.e13923] [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: 07/10/2022] [Revised: 01/16/2023] [Accepted: 02/15/2023] [Indexed: 02/24/2023] Open
Abstract
Non-invasive prenatal screening (NIPS) offers an opportunity to screen or determine features associated with the fetus. Earlier, prenatal testing was done with cytogenetic procedures like karyotyping or fluorescence in-situ hybridization, which necessitated invasive methods such as fetal blood sampling, chorionic villus sampling or amniocentesis. Over the last two decades, there has been a paradigm shift away from invasive prenatal diagnostic methods to non-invasive ones. NIPS tests heavily rely on cell-free fetal DNA (cffDNA). This DNA is released into the maternal circulation by placenta. Like cffDNA, fetal cells such as nucleated red blood cells, placental trophoblasts, leukocytes, and exosomes or fetal RNA circulating in maternal plasma, have enormous potential in non-invasive prenatal testing, but their use is still limited due to a number of limitations. Non-invasive approaches currently use circulating fetal DNA to assess the fetal genetic milieu. Methods with an acceptable detection rate and specificity such as sequencing, methylation, or PCR, have recently gained popularity in NIPS. Now that NIPS has established clinical significance in prenatal screening and diagnosis, it is critical to gain insights into and comprehend the genesis of NIPS de novo. The current review reappraises the development and emergence of non-invasive prenatal screen/test approaches, as well as their clinical application, with a focus, on the scope, benefits, and limitations.
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Gupta N. Deciphering Intellectual Disability. Indian J Pediatr 2023; 90:160-167. [PMID: 36441387 DOI: 10.1007/s12098-022-04345-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 07/05/2022] [Accepted: 07/18/2022] [Indexed: 11/29/2022]
Abstract
Intellectual disability (ID) is a common cause of referral to the pediatricians, geneticists, and pediatric neurologists. A thorough clinical evaluation and a stepwise investigative approach using a combination of traditional genetic techniques and appropriate latest genomic technologies can help in arriving at a diagnosis. In the current "omics" era, adopting a multiomics approach would further assist in solving the undiagnosed cases with intellectual disability.
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Affiliation(s)
- Neerja Gupta
- Division of Genetics, Department of Pediatrics, All India Institute of Medical Sciences, Ansari Nagar, Old OT Block, New Delhi, 110029, India.
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4
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Wójtowicz A, Madetko-Talowska A, Wójtowicz W, Szewczyk K, Huras H, Bik-Multanowski M. Cardiovascular Anomalies among 1005 Fetuses Referred to Invasive Prenatal Testing-A Comprehensive Cohort Study of Associated Chromosomal Aberrations. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10019. [PMID: 36011653 PMCID: PMC9408756 DOI: 10.3390/ijerph191610019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/06/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
This retrospective cohort study comprehensively evaluates cardiovascular anomalies (CVAs) and associated extracardiac structural malformations (ECMs) among 1005 fetuses undergoing invasive prenatal testing at a single tertiary Polish center in the context of chromosomal aberrations detected in them by array comparative genomic hybridization (aCGH) and G-band karyotyping. The results of our study show that CVAs are among the most common malformations detected in fetuses undergoing invasive prenatal testing, as they affected 20% of all cases seen in our department. Septal defects predominated among fetuses with numerical aberrations, while conotruncal defects were the most common findings among fetuses with pathogenic copy number variants (CNVs). In 61% of cases, CVAs were associated with ECMs (the diagnosis was confirmed postnatally or in cases of pregnancy termination by means of autopsy). The most common ECMs were anomalies of the face and neck, followed by skeletal defects. In total, pathogenic chromosomal aberrations were found in 47.5% of CVAs cases, including 38.6% with numerical chromosomal aberrations. Pathogenic CNVs accounted for 14.5% of cases with CVAs and normal karyotype. Thus, our study highlights the importance of assessing the anatomy of the fetus, and of the genetic testing (preferably aCGH) that should be offered in all CVA and ECM cases.
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Affiliation(s)
- Anna Wójtowicz
- Department of Obstetrics & Perinatology, Jagiellonian University Medical College, 31-501 Kraków, Poland
| | - Anna Madetko-Talowska
- Department of Medical Genetics, Jagiellonian University Medical College, 30-663 Kraków, Poland
| | - Wojciech Wójtowicz
- Information Technology Systems Department, Faculty of Management and Social Communication, Jagiellonian University, 30-348 Kraków, Poland
| | - Katarzyna Szewczyk
- Department of Medical Genetics, Jagiellonian University Medical College, 30-663 Kraków, Poland
| | - Hubert Huras
- Department of Obstetrics & Perinatology, Jagiellonian University Medical College, 31-501 Kraków, Poland
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Cokyaman T, Silan F. Diagnostic Utility of Array Comparative Genomic Hybridization in Children with Neurological Diseases. Fetal Pediatr Pathol 2022; 41:68-76. [PMID: 32401632 DOI: 10.1080/15513815.2020.1764683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
INTRODUCTION We evaluated the contribution of array comparative genomic hybridization (aCGH) to the final diagnosis in children with neurocognitive disturbances or dysmorphic findings, but lacked a specific diagnosis. MATERIALS AND METHODS Medical files of pediatric patients with neurocognitive disturbances who underwent aCGH analysis were reviewed retrospectively. RESULTS Of 155 patients, 77 copy number variations were detected and 50% (39/77) were considered causative. The aCGH's final diagnostic rate was 25.1% (39/155). CONCLUSION With aCGH analysis, the diagnosis rate for patients with undiagnosed neurocognitive disturbances or dysmorphic syndrome may increase by 25-30%. If the phenotypic findings of the widely known neurocognitive disturbances cannot be identified during the initial clinical assessment, aCGH analysis may be beneficial.
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Affiliation(s)
- Turgay Cokyaman
- Pediatric Neurology, Faculty of Medicine, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - Fatma Silan
- Medical Genetics, Faculty of Medicine, Çanakkale Onsekiz Mart University, Canakkale, Turkey
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Purwar N, Tiwari P, Mathur N, Sharma H, Sahlot R, Garg U, Sharma B, Saxena A, Mathur SK. Higher CNV Frequencies in Chromosome 14 of Girls With Turner Syndrome Phenotype. J Clin Endocrinol Metab 2021; 106:e4935-e4955. [PMID: 34333639 DOI: 10.1210/clinem/dgab572] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Precise genotype-phenotype correlations in Turner syndrome (TS) have not yet been deciphered. The chromosomal basis of the clinical TS phenotype in the absence of X chromosome aberrations on conventional karyotyping remains more and less unexplored. OBJECTIVE To elucidate the high-resolution chromosomal picture and analyze the genotype-phenotype associations in girls with clinical phenotype of TS by chromosomal microarray. DESIGN AND PATIENTS Cross sectional observational study conducted between October 2018 and January 2020 on 47 girls presenting the clinical TS phenotype and fulfilling the criteria for chromosomal analysis. SETTING Outpatient department at Department of Endocrinology and the Molecular Research Lab at tertiary care teaching institution. RESULTS The copy number variation (CNV) polymorphs were more frequent on autosomes than X chromosomes, and they were detected in 89.3%, 61.7%, and 92.8% of patients, respectively, on chromosome 14 or X or both. A total 445 and 64 CNV polymorphs were discovered on chromosome X and 14, respectively. The latter exhibited either gain at 14q32.33, loss at 14q11.2, or both. Karyotype was available for 27 patients; 55.6% of cases displayed X chromosome abnormalities while 44.4% cases had a normal karyotype. Functional interactomes of the genes that were present in chromosome 14 CNVs and those known to be associated with TS showed an overlap of 67% and enriched various development-related cellular pathways underlying TS phenotype. CONCLUSIONS On high-resolution karyotype analysis, clinical phenotype of TS can be associated with CNV defects in autosomes, specifically chromosome 14 or X chromosome or both. The syndrome of chromosome 14 CNV defects with and without X-chromosomal defects clinically mimics TS and shares a common genomic network that deserves further investigations.
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Affiliation(s)
- Naincy Purwar
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
| | - Pradeep Tiwari
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
- Department of Chemistry, School of Basic Sciences, Manipal University Jaipur, Jaipur, India
| | - Nitish Mathur
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
| | - Himanshu Sharma
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
| | - Rahul Sahlot
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
| | - Umesh Garg
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
| | - Balram Sharma
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
| | - Aditya Saxena
- Department of Computer Engineering & Applications, Institute of Engineering & Technology, GLA University, Mathura, India
| | - Sandeep K Mathur
- Department of Endocrinology, Sawai Man Singh Medical College and Hospital, Jaipur 302004, India
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Dai L, Zhang D, Wu Z, Guan X, Ma M, Li L, Zhang Y, Bai Y, Guo H. A Tiered Genetic Screening Strategy for the Molecular Diagnosis of Intellectual Disability in Chinese Patients. Front Genet 2021; 12:669217. [PMID: 34630504 PMCID: PMC8495063 DOI: 10.3389/fgene.2021.669217] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/10/2021] [Indexed: 01/02/2023] Open
Abstract
Objective: Intellectual disability (ID) is one of the most common developmental disabilities. To identify the genetic etiology of IDs in Chongqing, we conducted a multistage study in Chinese Han patients. Methods: We collected the clinical and etiological data of 1665 ID patients, including 1,604 from the disabled children evaluation center and 61 from the pediatric rehabilitation unit. Routine genetic screening results were obtained, including karyotype and candidate gene analysis. Then 105 idiopathic cases with syndromic and severe ID/developmental delay (DD) were selected and tested by chromosomal microarray (CMA) and whole exome sequencing (WES) sequentially. The pathogenicity of the CNVs and SNVs were evaluated according to ACMG guidelines. Results: Molecular diagnosis was made by routine genetic screening in 216 patients, including 196 chromosomal syndromes. Among the 105 idiopathic patients, 49 patients with pathogenic/likely pathogenic CNVs and 21 patients with VUS were identified by CMA. Twenty-six pathogenic CNVs underlying well-known syndromic cases, such as Williams-Beuren syndrome, were confirmed by multiplex ligation-dependent probe amplification (MLPA). Nine novel mutations were identified by WES in thirty-fix CNV-negative ID cases. Conclusions: The study illustrated the genetic aberrations distribution of a large ID cohort in Chongqing. Compared with conventional or single methods, a tiered high-throughput diagnostic strategy was developed to greatly improve the diagnostic yields and extend the variation spectrum for idiopathic syndromic ID cases.
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Affiliation(s)
- Limeng Dai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Danyan Zhang
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China.,Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Zhifeng Wu
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Xingying Guan
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Mingfu Ma
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Lianbing Li
- Chongqing Population and Family Planning Science and Technology Research Institute/NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing, China
| | - Yuping Zhang
- Department of Pediatrics, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yun Bai
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
| | - Hong Guo
- Department of Medical Genetics, College of Basic Medical Science, Army Medical University, Chongqing, China
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Miclea D, Szucs A, Mirea A, Stefan DM, Nazarie F, Bucerzan S, Lazea C, Grama A, Pop TL, Farcas M, Zaharie G, Matyas M, Mager M, Vintan M, Popp R, Alkhzouz C. Diagnostic Usefulness of MLPA Techniques for Recurrent Copy Number Variants Detection in Global Developmental Delay/Intellectual Disability. Int J Gen Med 2021; 14:4511-4515. [PMID: 34429637 PMCID: PMC8378908 DOI: 10.2147/ijgm.s320033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/15/2021] [Indexed: 02/05/2023] Open
Abstract
Background Genetic testing has become a standardized practice in the diagnosis of patients with global developmental delay/intellectual disability (GDD/ID). The aim of this study is to observe the frequency of recurrent copy number variations (CNVs) in patients diagnosed with GDD/ID, using MLPA technique. Methods A total of 501 paediatric patients with GDD/ID were analysed using SALSA MLPA probemix P245 Microdeletion Syndromes-1A, and the technical steps were performed according to the MRC Holland MLPA general protocol. Results Twenty-five of 501 patients (5%) were diagnosed with a microdeletion/microduplication syndrome. Amongst them, 7 of 25 (30%) with clinical suggestion have a confirmed diagnosis, for the other cases the clinical features were not evocative for a specific syndrome. Conclusion This study showed that in cases with a specific clinical diagnosis the MLPA technique could be a useful alternative, less expensive and more efficient to indicate as first intention of a targeted diagnostic test, as it is the case of Williams syndrome, Prader–Willi syndrome or DiGeorge syndrome.
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Affiliation(s)
- Diana Miclea
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Adriana Szucs
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Andreea Mirea
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Delia-Maria Stefan
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Florina Nazarie
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,Emergency Clinical Hospital for Children, Cluj-Napoca, Romania
| | - Simona Bucerzan
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Cecilia Lazea
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Alina Grama
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Tudor Lucian Pop
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Marius Farcas
- County Emergency Clinical Hospital, Cluj-Napoca, Romania
| | - Gabriela Zaharie
- Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,County Emergency Clinical Hospital, Cluj-Napoca, Romania
| | - Melinda Matyas
- Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania.,County Emergency Clinical Hospital, Cluj-Napoca, Romania
| | - Monica Mager
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Mihaela Vintan
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Radu Popp
- Department of Molecular Sciences, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Camelia Alkhzouz
- Emergency Clinical Hospital for Children, Cluj-Napoca, Romania.,Department of Mother and Child, "Iuliu Hatieganu" University of Medicine and Pharmacy, Cluj-Napoca, Romania
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Kritioti E, Theodosiou A, Parpaite T, Alexandrou A, Nicolaou N, Papaevripidou I, Séjourné N, Coste B, Christophidou-Anastasiadou V, Tanteles GA, Sismani C. Unravelling the genetic causes of multiple malformation syndromes: A whole exome sequencing study of the Cypriot population. PLoS One 2021; 16:e0253562. [PMID: 34324503 PMCID: PMC8320927 DOI: 10.1371/journal.pone.0253562] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/08/2021] [Indexed: 11/19/2022] Open
Abstract
Multiple malformation syndromes (MMS) belong to a group of genetic disorders characterised by neurodevelopmental anomalies and congenital malformations. Here we explore for the first time the genetic aetiology of MMS using whole-exome sequencing (WES) in undiagnosed patients from the Greek-Cypriot population after prior extensive diagnostics workup including karyotype and array-CGH. A total of 100 individuals (37 affected), from 32 families were recruited and family-based WES was applied to detect causative single-nucleotide variants (SNVs) and indels. A genetic diagnosis was reported for 16 MMS patients (43.2%), with 10/17 (58.8%) of the findings being novel. All autosomal dominant findings occurred de novo. Functional studies were also performed to elucidate the molecular mechanism relevant to the abnormal phenotypes, in cases where the clinical significance of the findings was unclear. The 17 variants identified in our cohort were located in 14 genes (PCNT, UBE3A, KAT6A, SPR, POMGNT1, PIEZO2, PXDN, KDM6A, PHIP, HECW2, TFAP2A, CNOT3, AGTPBP1 and GAMT). This study has highlighted the efficacy of WES through the high detection rate (43.2%) achieved for a challenging category of undiagnosed patients with MMS compared to other conventional diagnostic testing methods (10-20% for array-CGH and ~3% for G-banding karyotype analysis). As a result, family-based WES could potentially be considered as a first-tier cost effective diagnostic test for patients with MMS that facilitates better patient management, prognosis and offer accurate recurrence risks to the families.
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Affiliation(s)
- Evie Kritioti
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Athina Theodosiou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | | | - Angelos Alexandrou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nayia Nicolaou
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ioannis Papaevripidou
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Nina Séjourné
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | - Bertrand Coste
- Aix Marseille Université, CNRS, LNC-UMR 7291, Marseille, France
| | | | - George A. Tanteles
- Clinical Genetics Clinic, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carolina Sismani
- Department of Cytogenetics and Genomics, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- The Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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10
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García-Payá E, Gutiérrez-Agulló M, García-Prieto FF, Francés Ferre J. An 88.8-kb Novel Deletion of 19q13.2 Encompassing the ATP1A3 Gene Detected by Array CGH in a Patient with Delayed Psychomotor Development, Generalized Hypotonia and Macrocephaly. Mol Syndromol 2021; 12:234-239. [PMID: 34421501 PMCID: PMC8339483 DOI: 10.1159/000515043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/04/2021] [Indexed: 11/19/2022] Open
Abstract
Many neurodevelopmental disorders are caused by the presence of CNVs. Chromosome microarray technology is widely used to accurately detect CNVs. We report the case of a male, aged 3 years, presenting with delayed psychomotor development, generalized hypotonia, encephalopathy, delayed myelination in the central nervous system, and poor motor coordination. The array CGH revealed an interstitial deletion of chromosome 19q13.2 with a size of 88.8 kb involving 3 OMIM genes: RABAC1, ARHGEF1, and ATP1A3. Heterozygous mutations in the ATP1A3 gene are associated with delayed psychomotor development, alternating hemiplegia of childhood type 2 (AHC2), dystonia type 12, and cerebellarataxia-areflexia-pes cavus-optic atrophy-sensorineural hearing loss syndrome, also called CAPOS syndrome. The phenotypic expression of partial ATP1A3 deletion is, however, poorly described in the literature. The deletion was confirmed by MLPA, and we identified a hitherto undescribed novel deletion of exons 3b-21 of the ATP1A3 gene. Our data suggest that the deletion of the ATP1A3 gene is a causative factor of the AHC2 phenotype in the patient.
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Affiliation(s)
- Elena García-Payá
- Laboratory of Molecular Cytogenetics, Instituto de Investigación Sanitaria y Biomédica de Alicante (ISABIAL), Hospital General Universitario de Alicante, Alicante, Spain
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11
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Eno CC, Graakjaer J, Svaneby D, Nizon M, Kianmahd J, Signer R, Martinez-Agosto JA, Quintero-Rivera F. 14q32.11 microdeletion including CALM1, TTC7B, PSMC1, and RPS6KA5: A new potential cause of developmental and language delay in three unrelated patients. Am J Med Genet A 2021; 185:1519-1524. [PMID: 33634591 DOI: 10.1002/ajmg.a.62117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 12/14/2020] [Accepted: 01/23/2021] [Indexed: 12/18/2022]
Abstract
Three unrelated patients with similar microdeletions of chromosome 14q32.11 with shared phenotypes including language and developmental delay, and four overlapping genes -CALM1, TTC7B, PSMC1, and RPS6KA5 have been presented. All four genes are expressed in the brain and have haploinsufficiency scores, which reflect low tolerance to loss of function variation. An insight on the genes in the overlapping region, which may influence the resulting phenotype has been provided. Given the three patients' similar phenotypes and lack of normal variation in this region, it was suggested that this microdeletion may be associated with developmental and language delay.
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Affiliation(s)
- Celeste C Eno
- Department of Academic Pathology, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jesper Graakjaer
- Department of Clinical Genetics, Lillebaelt Hospital, Vejle, Denmark
| | - Dea Svaneby
- Department of Clinical Genetics, Lillebaelt Hospital, Vejle, Denmark
| | - Mathilde Nizon
- Department of Medical Genetics, CHU Nantes, Nantes, France
| | - Jessica Kianmahd
- Departments of Human Genetics and Pediatrics, Division of Medical Genetics, UCLA, Los Angeles, California, USA
| | - Rebecca Signer
- Departments of Human Genetics and Pediatrics, Division of Medical Genetics, UCLA, Los Angeles, California, USA
| | - Julian A Martinez-Agosto
- Departments of Human Genetics and Pediatrics, Division of Medical Genetics, UCLA, Los Angeles, California, USA
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, University of California Irvine, Irvine, California, USA
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12
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Çebi AH, Altıner Ş. Application of Chromosome Microarray Analysis in the Investigation of Developmental Disabilities and Congenital Anomalies: Single Center Experience and Review of NRXN3 and NEDD4L Deletions. Mol Syndromol 2020; 11:197-206. [PMID: 33224013 PMCID: PMC7675229 DOI: 10.1159/000509645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/27/2020] [Indexed: 01/01/2023] Open
Abstract
Chromosomal microarray analysis (CMA) is a first step test used for the diagnosis of patients with developmental delay, intellectual disability, autistic spectrum disorder, and multiple congenital anomalies. Its widespread usage has allowed genome-wide identification of copy number variations (CNVs). In our study, we performed a retrospective study on clinical and microarray data of 237 patients with developmental disabilities and/or multiple congenital anomalies and investigated the clinical utility of CMA. Phenotype-associated CNVs were detected in 15.18% of patients. Besides, we detected submicroscopic losses on 14q24.3q31.1 in a patient with speech delay and on 18q21.31q21.32 in twin patients with seizures. Deletions of NRXN3 and NEDD4L were responsible for the phenotypes, respectively. This study showed that CMA is a powerful diagnostic tool in this patient group and expands the genotype-phenotype correlations on developmental disabilities.
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Affiliation(s)
- Alper Han Çebi
- Department of Medical Genetics, Karadeniz Technical University School of Medicine, Trabzon, Turkey
| | - Şule Altıner
- Department of Medical Genetics, University of Health Sciences, Trabzon Kanuni Training and Research Hospital, Trabzon, Turkey
- Department of Medical Genetics, Ankara University School of Medicine, Ankara, Turkey
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13
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Sun Y, Ye X, Fan Y, Wang L, Luo X, Liu H, Gao X, Gong Z, Wang Y, Qiu W, Zhang H, Han L, Liang L, Ye H, Xiao B, Gu X, Yu Y. High Detection Rate of Copy Number Variations Using Capture Sequencing Data: A Retrospective Study. Clin Chem 2020; 66:455-462. [PMID: 32031585 DOI: 10.1093/clinchem/hvz033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Accepted: 11/18/2019] [Indexed: 12/30/2022]
Abstract
BACKGROUND Capture sequencing (CS) is widely applied to detect small genetic variations such as single nucleotide variants or indels. Algorithms based on depth comparison are becoming available for detecting copy number variation (CNV) from CS data. However, a systematic evaluation with a large sample size has not been conducted to evaluate the efficacy of CS-based CNV detection in clinical diagnosis. METHODS We retrospectively studied 3010 samples referred to our diagnostic laboratory for CS testing. We used 68 chromosomal microarray analysis-positive samples (true set [TS]) and 1520 reference samples to build a robust CS-CNV pipeline. The pipeline was used to detect candidate clinically relevant CNVs in 1422 undiagnosed samples (undiagnosed set [UDS]). The candidate CNVs were confirmed by an alternative method. RESULTS The CS-CNV pipeline detected 78 of 79 clinically relevant CNVs in TS samples, with analytical sensitivity of 98.7% and positive predictive value of 49.4%. Candidate clinically relevant CNVs were identified in 106 UDS samples. CNVs were confirmed in 96 patients (90.6%). The diagnostic yield was 6.8%. The molecular etiology includes aneuploid (n = 7), microdeletion/microduplication syndrome (n = 40), and Mendelian disorders (n = 49). CONCLUSIONS These findings demonstrate the high yield of CS-based CNV. With further improvement of our CS-CNV pipeline, the method may have clinical utility for simultaneous evaluation of CNVs and small variations in samples referred for pre- or postnatal analysis.
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Affiliation(s)
- Yu Sun
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xiantao Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yanjie Fan
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Lili Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xiaomei Luo
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Huili Liu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xueren Gao
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Zhuwen Gong
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yu Wang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Wenjuan Qiu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Huiwen Zhang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Lianshu Han
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Lili Liang
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Hui Ye
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Bing Xiao
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Xuefan Gu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetic Metabolism, Shanghai Institute for Pediatric Research, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200092, China
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14
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Espeche LD, Solari AP, Mori MÁ, Arenas RM, Palomares M, Pérez M, Martínez C, Lotersztein V, Segovia M, Armando R, Dain LB, Nevado J, Lapunzina P, Rozental S. Implementation of chromosomal microarrays in a cohort of patients with intellectual disability at the Argentinean public health system. Mol Biol Rep 2020; 47:6863-6878. [PMID: 32920771 DOI: 10.1007/s11033-020-05743-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 08/28/2020] [Indexed: 01/03/2023]
Abstract
Intellectual disability is a neurodevelopmental disorder in which genetic, epigenetic and environmental factors are involved. In consequence, the determination of its etiology is usually complex. Though many countries have migrated from conventional cytogenetic analysis to chromosomal microarrays as the first-tier genetic test for patients with this condition, this last technique was implemented in our country a few years ago. We report on the results of the implementation of chromosomal microarrays in a cohort of 133 patients with intellectual disability and dysmorphic features, normal karyotype and normal subtelomeric MLPA results in an Argentinean public health institution. Clinically relevant copy number variants were found in 12% of the patients and one or more copy number variants classified as variants of uncertain significance were found in 5.3% of them. Although the diagnostic yield of chromosomal microarrays is greater than conventional cytogenetics for these patients, there are financial limitations to adopt this technique as a first-tier test in our country, especially in the public health system.
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Affiliation(s)
- Lucía Daniela Espeche
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Andrea Paula Solari
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - María Ángeles Mori
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Rubén Martín Arenas
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - María Palomares
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Myriam Pérez
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Cinthia Martínez
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Vanesa Lotersztein
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Mabel Segovia
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Romina Armando
- Servicio de Genética, Hospital de Niños "Dr. Ricardo Gutiérrez", Buenos Aires, Argentina
| | - Liliana Beatriz Dain
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina
| | - Julián Nevado
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Pablo Lapunzina
- Instituto de Genética Médica y Molecular (INGEMM), IdiPAZ, Hospital Universitario La Paz, Universidad Autónoma de Madrid, Madrid, Spain.,CIBERER (Centro de Investigación Biomédica en Red de Enfermedades Raras), ISCIII, Madrid, Spain.,ITHACA European Reference Network, Madrid, Spain
| | - Sandra Rozental
- Centro Nacional de Genética Médica "Dr. Eduardo Castilla"- ANLIS "Dr. Carlos G. Malbrán", Ministerio de Salud, Buenos Aires, Argentina.
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15
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Pang H, Yu X, Kim YM, Wang X, Jinkins JK, Yin J, Li S, Gu H. Disorders Associated With Diverse, Recurrent Deletions and Duplications at 1q21.1. Front Genet 2020; 11:577. [PMID: 32655619 PMCID: PMC7325322 DOI: 10.3389/fgene.2020.00577] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/11/2020] [Indexed: 01/22/2023] Open
Abstract
The subchromosomal region 1q21.1 is one of the hotspots in the human genome for deletions and reciprocal duplications, owing to the existence of hundreds of segmental duplications. Recurrent deletions and duplications in this region are thought to be causative in patients with variable clinical manifestations. Based on the genomic locations, deletions and duplications at the 1q21.1 locus have been associated with distinguishable syndromes: chromosome 1q21.1 deletion syndrome, chromosome 1q21.1 duplication syndrome, and thrombocytopenia-absent radius (TAR) syndrome, which is partially due to deletions at the proximal 1q21.1 region. We report here diverse, recurrent deletions and duplications at the 1q21.1 locus in 36 patients from a cohort of 5,200 individuals. Among the 36 patients, 18 patients carry 1q21.1 deletions, nine individuals have reciprocal duplications at 1q21.1, two patients share an identical short deletion, and the remaining seven possess variable sizes of duplications at the proximal 1q21.1 region. Furthermore, we provide cytogenetic characterization and detailed clinical features for each patient. Notably, duplications at the proximal 1q21.1 region have not been associated with a defined disorder in publications. However, recurrent duplications at the proximal 1q21.1 region among the seven patients strongly suggested that the variants are likely pathogenic. The common phenotypical features of those disorders are also summarized to facilitate clinical diagnoses and genetic counseling.
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Affiliation(s)
- Hui Pang
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Xiaowei Yu
- The First Affiliated Hospital of Jilin University, Changchun, China
| | - Young Mi Kim
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Xianfu Wang
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Jeremy K Jinkins
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Jianing Yin
- The First Affiliated Hospital of Jilin University, Changchun, China
| | - Shibo Li
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States
| | - Hongcang Gu
- Department of Pediatrics, The University of Oklahoma Health Sciences Center, Oklahoma, OK, United States.,Broad Institute of MIT and Harvard, Cambridge, MA, United States
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16
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Sciacca FL, Ciaccio C, Fontana F, Strano C, Gilardoni F, Pantaleoni C, D'Arrigo S. Severe Phenotype in a Patient With Homozygous 15q21.2 Microdeletion Involving BCL2L10, GNB5, and MYO5C Genes, Resembling Infantile Developmental Disorder With Cardiac Arrhythmias (IDDCA). Front Genet 2020; 11:399. [PMID: 32477400 PMCID: PMC7237723 DOI: 10.3389/fgene.2020.00399] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 03/30/2020] [Indexed: 11/29/2022] Open
Abstract
Homozygous and compound heterozygous mutations in GNB5 gene have been associated with a wide spectrum of clinical presentations, ranging from neurodevelopmental issues with or without cardiac arrhythmia (LADCI) to severe developmental delay with epileptic encephalopathy, retinal dystrophy, and heart rhythm abnormalities (IDDCA). While missense or missense/non-sense mutations usually lead to milder form, the biallelic loss of function of GNB5 gene causes the severe multisystemic IDDCA phenotype. So far, only 27 patients have been described with GNB5-associated disease. We report the first case of a patient carrying a homozygous 15q21.2 microdeletion, encompassing GNB5 and the two contiguous genes BCL2L10 and MYO5C. The clinical features of the child are consistent with the severe IDDCA phenotype, thus confirming the GNB5 loss-of-function mechanism in determining such presentation of the disease.
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Affiliation(s)
- Francesca L Sciacca
- Neurological Biochemistry and Neuropharmacology Unit, Laboratory of Cytogenetic, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Claudia Ciaccio
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Federica Fontana
- Neurological Biochemistry and Neuropharmacology Unit, Laboratory of Cytogenetic, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Camilla Strano
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesca Gilardoni
- Neurological Biochemistry and Neuropharmacology Unit, Laboratory of Cytogenetic, Department of Diagnostic and Technology, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Chiara Pantaleoni
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Stefano D'Arrigo
- Developmental Neurology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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17
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Elliott AM. Genetic Counseling and Genome Sequencing in Pediatric Rare Disease. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036632. [PMID: 31501267 DOI: 10.1101/cshperspect.a036632] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Both genome sequencing (GS) and exome sequencing (ES) have proven to be revolutionary in the diagnosis of pediatric rare disease. The diagnostic potential and increasing affordability make GS and ES more accessible as a routine clinical test in some centers. Herein, I review aspects of rare disease in pediatrics associated with the use of genomic technologies with an emphasis on the benefits and limitations of both ES and GS, complexities of variant classification, and the importance of genetic counseling. Indications for testing, the role of genetic counselors in genomic test selection, and the diagnostic potential of ES and GS in various pediatric multisystem disorders are discussed. The neonatal population represents an important cohort in pediatric rare disease. Rapid ES and GS in critically ill neonates can have an immediate impact on medical management and present unique genetic counseling challenges. This work includes reviews of recommendations for genetic counseling for families considering genome-wide sequencing, and issues of access to genetic counseling that affect clinical use and will necessitate implementation of innovative methods such as online decision aids. Finally, this work will also review the challenges of having a child with a rare disease, the impact of results from ES and GS on these families, and the role of various support agencies.
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Affiliation(s)
- Alison M Elliott
- Department of Medical Genetics, University of British Columbia Investigator, BC Children's Hospital Research Institute and BC Women's Health Research Institute, and Provincial Medical Genetics Program, Vancouver, British Columbia V6H 3N1, Canada
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18
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Coysh T, Hogg SL, Parker AP. Fifteen-minute consultation: Efficient investigation of the child with early developmental impairment in the era of genomic sequencing. Arch Dis Child Educ Pract Ed 2020; 105:13-18. [PMID: 31092397 DOI: 10.1136/archdischild-2018-315123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Revised: 03/26/2019] [Accepted: 04/03/2019] [Indexed: 01/04/2023]
Abstract
The investigation of children with early developmental impairment (EDI) is challenging in terms of selecting investigations and supporting families through the diagnostic pathway. Modern genomic sequencing has the potential to greatly improve yield of investigation, but produces challenges in terms of timing and explaining its strengths/weaknesses to families. We present an evidence-based and practical guideline to help the paediatrician through all stages of investigation. We emphasise the importance of a really good history and examination, allowing targeted investigation for specific disorders and outline an approach for isolated EDI when this is not possible. This prioritises genetic investigation- after appropriate counselling to families, and balances the very low yield of biochemical/radiological investigations in isolated EDI, with the need to detect extremely rare, but potentially treatable disorders. Collaboration with both families and regional specialists to ensure appropriate testing is likely to reduce parental and clinician anxiety.
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Affiliation(s)
- Thomas Coysh
- Neurology Department, Imperial College Healthcare NHS Trust, London, UK
| | - Sarah Louise Hogg
- Biochemical Genetics Unit, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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19
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Chromosomal Aberrations in Pediatric Patients with Developmental Delay/Intellectual Disability: A Single-Center Clinical Investigation. BIOMED RESEARCH INTERNATIONAL 2019; 2019:9352581. [PMID: 31781653 PMCID: PMC6875000 DOI: 10.1155/2019/9352581] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/03/2019] [Accepted: 09/18/2019] [Indexed: 12/12/2022]
Abstract
Introduction Chromosomal microarray analysis (CMA) has currently been considered as the first-tier genetic test for patients with developmental delay/intellectual disability (DD/ID) in many countries. In this study, we performed an extensive assessment of the value of CMA for the diagnosis of children with ID/DD in China. Methods A total of 633 patients diagnosed with DD/ID in West China Second University Hospital, Sichuan University, were recruited from January 2014 to March 2019. The patients were classified into 4 subgroups: isolated DD/ID, DD/ID with multiple congenital anomalies (MCA), isolated autism spectrum disorders (ASDs), and DD/ID with epilepsy. CMA was performed on Affymetrix 750K platform. Results Among the 633 patients, 127 cases were identified as having pathogenic copy number variations (pCNVs) with an overall positive rate of 20.06%. Of the 127 cases with abnormal results, 76 cases had 35 types of microdeletion/microduplication syndromes (59.84%) including 5 cases caused by uniparental disomy (UPD), and 18 cases had unbalanced rearrangements (14.17%) including 10 cases inherited from parental balanced translocations or pericentric inversions. The diagnostic yields of pCNVs for the subgroups of isolated DD/ID, DD/ID with MCA, isolated ASD, and DD/ID with epilepsy were 18.07% (60/332), 34.90% (52/149), 3.70% (3/81), and 16.90% (12/71), respectively. The diagnostic yield of pCNVs in DD/ID patients with MCA was significantly higher than that of the other three subgroups, and the diagnostic yield of pCNVs in isolated ASD patients was significantly lower than that of the other three subgroups (p < 0.05). Conclusion Microdeletion/microduplication syndromes and unbalanced rearrangements are probably the main genetic etiological factors for DD/ID. DD/ID patients with MCA have a higher rate of chromosomal aberrations. Parents of DD/ID children with submicroscopic unbalance rearrangements are more likely to have chromosome balanced translocations or pericentric inversions, which might have been missed by karyotyping. CMA can significantly improve the diagnostic rate for patients with DD/ID, which is of great value for medical management and clinical guidance for genetic counseling.
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20
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Lopes F, Torres F, Soares G, Barbosa M, Silva J, Duque F, Rocha M, Sá J, Oliveira G, Sá MJ, Temudo T, Sousa S, Marques C, Lopes S, Gomes C, Barros G, Jorge A, Rocha F, Martins C, Mesquita S, Loureiro S, Cardoso EM, Cálix MJ, Dias A, Martins C, Mota CR, Antunes D, Dupont J, Figueiredo S, Figueiroa S, Gama-de-Sousa S, Cruz S, Sampaio A, Eijk P, Weiss MM, Ylstra B, Rendeiro P, Tavares P, Reis-Lima M, Pinto-Basto J, Fortuna AM, Maciel P. Genomic imbalances defining novel intellectual disability associated loci. Orphanet J Rare Dis 2019; 14:164. [PMID: 31277718 PMCID: PMC6612161 DOI: 10.1186/s13023-019-1135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/12/2019] [Indexed: 11/29/2022] Open
Abstract
Background High resolution genome-wide copy number analysis, routinely used in clinical diagnosis for several years, retrieves new and extremely rare copy number variations (CNVs) that provide novel candidate genes contributing to disease etiology. The aim of this work was to identify novel genetic causes of neurodevelopmental disease, inferred from CNVs detected by array comparative hybridization (aCGH), in a cohort of 325 Portuguese patients with intellectual disability (ID). Results We have detected CNVs in 30.1% of the patients, of which 5.2% corresponded to novel likely pathogenic CNVs. For these 11 rare CNVs (which encompass novel ID candidate genes), we identified those most likely to be relevant, and established genotype-phenotype correlations based on detailed clinical assessment. In the case of duplications, we performed expression analysis to assess the impact of the rearrangement. Interestingly, these novel candidate genes belong to known ID-related pathways. Within the 8% of patients with CNVs in known pathogenic loci, the majority had a clinical presentation fitting the phenotype(s) described in the literature, with a few interesting exceptions that are discussed. Conclusions Identification of such rare CNVs (some of which reported for the first time in ID patients/families) contributes to our understanding of the etiology of ID and for the ever-improving diagnosis of this group of patients. Electronic supplementary material The online version of this article (10.1186/s13023-019-1135-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fátima Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Fátima Torres
- CGC Genetics, Porto, Portugal.,Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Gabriela Soares
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Mafalda Barbosa
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal.,The Mindich Child Health & Development Institute and the Department of Genetics & Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,The Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, NY, USA.,Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - João Silva
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Frederico Duque
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Miguel Rocha
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Medical Genetics Unit, Hospital de Braga, Braga, Portugal
| | - Joaquim Sá
- CGC Genetics, Porto, Portugal.,Department of Medical Genetics, Hospital de Faro, Faro, Portugal
| | - Guiomar Oliveira
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal.,University Clinic of Pediatrics and Institute for Biomedical Imaging and Life Science, Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - Maria João Sá
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,Unit for Multidisciplinary Research in Biomedicine, Institute of Biomedical Sciences Abel Salazar (ICBAS), University of Porto, Porto, Portugal
| | - Teresa Temudo
- Pediatric Neurology Department, Centro Materno-Infantil Centro Hospitalar do Porto, Porto, Portugal
| | - Susana Sousa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.,Centro de Genética Preditiva e Preventiva - CGPP, Instituto de Biologia Molecular e Celular - IBMC, Universidade do Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde - i3S, Universidade do Porto, Porto, Portugal
| | - Carla Marques
- Unidade de Neurodesenvolvimento e Autismo do Serviço do Centro de Desenvolvimento da Criança and Centro de Investigação e Formação Clínica, Pediatric Hospital, Centro Hospitalar e Universitário de Coimbra, 3041-80, Coimbra, Portugal
| | - Sofia Lopes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Catarina Gomes
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Gisela Barros
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Arminda Jorge
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal.,CICS - Health Sciences Research Centre, University of Beira Interior, Covilhã, Portugal
| | - Felisbela Rocha
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Cecília Martins
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sandra Mesquita
- Development Unit, Pediatrics Service, Hospital Centre of Cova da Beira, Covilhã, Portugal
| | - Susana Loureiro
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Elisa Maria Cardoso
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Maria José Cálix
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Andreia Dias
- Department of Pediatrics, Hospital S. Teotónio, Tondela/Viseu Hospital Center, Viseu, Portugal
| | - Cristina Martins
- Neuropaediatric Unit - Garcia de Orta Hospital, Almada, Portugal
| | - Céu R Mota
- Pediatric and Neonatal Intensive Care, Department of Pediatrics, Porto Hospital Center, Porto, Portugal
| | - Diana Antunes
- Department of Genetics, Hospital D. Estefânia, Lisboa-Norte Hospital Center, Lisbon, Portugal
| | - Juliette Dupont
- Genetics Service, Paediatric Department, University Hospital Santa Maria, Lisbon, Portugal
| | - Sara Figueiredo
- Department of Pediatrics, Médio Ave Hospital Center, Santo Tirso, Portugal
| | - Sónia Figueiroa
- Division of Pediatric Neurology, Department of Child and Adolescent, Centro Hospitalar do Porto e Hospital de Santo António, Porto, Portugal
| | - Susana Gama-de-Sousa
- Department of Pediatrics, Médio Ave Hospital Center, Vila Nova de Famalicão, Portugal
| | - Sara Cruz
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Adriana Sampaio
- Neuropsychophysiology Lab, CIPsi, School of Psychology, University of Minho, Braga, Portugal
| | - Paul Eijk
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Marjan M Weiss
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, 1007, MB, The Netherlands
| | | | | | - Margarida Reis-Lima
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal.,GDPN- SYNLAB, Porto, Portugal
| | | | - Ana Maria Fortuna
- Center for Medical Genetics Dr. Jacinto Magalhães, Porto Hospital Center, Praça Pedro Nunes, Porto, Portugal
| | - Patrícia Maciel
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, 4710-057, Braga, Portugal. .,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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Additive Diagnostic Yield of Homozygosity Regions Identified During Chromosomal microarray Testing in Children with Developmental Delay, Dysmorphic Features or Congenital Anomalies. Biochem Genet 2019; 58:74-101. [PMID: 31273557 DOI: 10.1007/s10528-019-09931-3] [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: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 11/26/2022]
Abstract
Chromosomal microarray (CMA) has emerged as a robust tool for identifying microdeletions and microduplications, termed copy number variants (CNVs). Nevertheless, data regarding its utility in different patient populations with developmental delay (DD), dysmorphic features (DF) and congenital anomalies (CA), is a matter of dense debate. Although regions of homozygosity (ROH) are not diagnostic of a specific condition, they may have pathogenic implications. Certain CNVs and ROH have ethnically specific occurrences and frequencies. We aimed to determine whether CMA testing offers additional diagnostic information over classical cytogenetics for identifying genomic imbalances in a pediatric cohort with idiopathic DD, DF, or CA. One hundred sixty-nine patients were offered cytogenetics and CMA simultaneously for etiological diagnosis of DD (n = 67), DF (n = 52) and CA (n = 50). CMA could identify additional, clinically significant anomalies as compared with cytogenetics. CMA detected 61 CNVs [21 (34.4%) pathogenic CNVs, 37 (60.7%) variants of uncertain clinical significance and 3 (4.9%) benign CNVs] in 44 patients. CMA identified one or more ROH in 116/169 (68.6%) patients. When considering pathogenic CNVs and aneuploidies as positive findings, 9/169 (5.3%) received a genetic diagnosis from cytogenetics, while 25/169 (14.8%) could have a genetic diagnosis from CMA. The identification of ROH was clinically significant in two cases (2/169), thereby, adding 1.2% to the diagnostic yield of CMA (16% vs. 5.3%, p < 0.001). CMA uncovers additional genetic diagnoses over cytogenetics, thereby, offering a much higher diagnostic yield. Our findings convincingly demonstrate the additive diagnostic value of clinically significant ROH identified during CMA testing, highlighting the need for careful clinical interpretation of these ROH.
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22
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Park KB, Nam KE, Cho AR, Jang W, Kim M, Park JH. Effects of Copy Number Variations on Developmental Aspects of Children With Delayed Development. Ann Rehabil Med 2019; 43:215-223. [PMID: 31072088 PMCID: PMC6509583 DOI: 10.5535/arm.2019.43.2.215] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/19/2018] [Indexed: 11/06/2022] Open
Abstract
Objective To determine effects of copy number variations (CNV) on developmental aspects of children suspected of having delayed development. Methods A retrospective chart review was done for 65 children who underwent array-comparative genomic hybridization after visiting physical medicine & rehabilitation department of outpatient clinic with delayed development as chief complaints. Children were evaluated with Denver Developmental Screening Test II (DDST-II), Sequenced Language Scale for Infants (SELSI), or Preschool Receptive-Expressive Language Scale (PRES). A Mann-Whitney U test was conducted to determine statistical differences of developmental quotient (DQ), receptive language quotient (RLQ), and expressive language quotient (ELQ) between children with CNV (CNV(+) group, n=16) and children without CNV (CNV(–) group, n=37). Results Of these subjects, the average age was 35.1 months (mean age, 35.1±24.2 months). Sixteen (30.2%) patients had copy number variations. In the CNV(+) group, 14 children underwent DDST-II. In the CNV(–) group, 29 children underwent DDST-II. Among variables, gross motor scale was significantly (p=0.038) lower in the CNV(+) group compared with the CNV(–) group. In the CNV(+) group, 5 children underwent either SELSI or PRES. In the CNV(–) group, 27 children underwent above language assessment examination. Both RLQ and ELQ were similar between the two groups. Conclusion The gross motor domain in DQ was significantly lower in children with CNV compared to that in children without CNV. This result suggests that additional genetic factors contribute to this variability. Active detection of genomic imbalance could play a vital role when prominent gross motor delay is presented in children with delayed development.
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Affiliation(s)
- Kee-Boem Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Kyung Eun Nam
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Ah-Ra Cho
- Department of Rehabilitation Medicine, St. Paul's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Woori Jang
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Myungshin Kim
- Department of Laboratory Medicine College of Medicine, The Catholic University of Korea, Seoul, Korea.,Department of Catholic Genetic Laboratory Center, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Joo Hyun Park
- Department of Rehabilitation Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Korea
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23
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Jiao Q, Sun H, Zhang H, Wang R, Li S, Sun D, Yang XA, Jin Y. The combination of whole-exome sequencing and copy number variation sequencing enables the diagnosis of rare neurological disorders. Clin Genet 2019; 96:140-150. [PMID: 30945278 DOI: 10.1111/cge.13548] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/01/2019] [Accepted: 04/02/2019] [Indexed: 12/31/2022]
Abstract
This retrospective study aims to investigate the diagnostic yields of multiple strategies of next-generation sequencing (NGS) for children with rare neurological disorders (NDs). A total of 220 pediatric patients with NDs who visited our hospital between Jan 2017 and Dec 2018 and had undergone NGS were included. Most patients were 5 years old or younger, and the number of patients visiting the hospital decreased with age. Seizures were the most common symptom in this cohort. The positive rates for targeted NGS panels (Panel), whole-exome sequencing (WES), and copy number variation sequencing (CNVseq) were 26.5% (9/34), 36.6% (63/172), and 16.7% (22/132), respectively. The positive rate for patients undergoing a combination of WES and CNVseq (WES + CNVseq) was 47.8% (54/113), which was significantly better than the positive rate for patients who underwent WES alone (32.7%, 37/113). A total of 83 variants were found in 42 genes, and SCN1A was the most frequently mutanted gene. Twenty-four CNVs were identified in 22 patients: two CNVs were inherited from the mother; 12 CNVs were de novo; and the CNV origins could not be determined in 10 patients. WES + CNVseq may potentially be the mostly effective NGS approach for diagnosis of rare NDs in pediatric patients.
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Affiliation(s)
- Qingguo Jiao
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, P. R. China.,Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, P. R. China
| | - Haiming Sun
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, P. R. China.,Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, P. R. China
| | - Haoya Zhang
- School of Medicine, Jianghan University, Wuhan, P. R. China
| | - Ran Wang
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macau, P. R. China.,Department of Pharmacology, Chengde Medical University, Chengde, P. R. China
| | - Suting Li
- School of Basic Medical Science, Chengde Medical University, Chengde, P. R. China
| | - Dan Sun
- Department of Neurology, Wuhan Children's Hospital (Wuhan Maternal and Child Health Care Hospital), Tongji Medical College, Huazhong University of Science and Technology, Wuhan, P. R. China
| | - Xiu-An Yang
- School of Basic Medical Science, Chengde Medical University, Chengde, P. R. China
| | - Yan Jin
- Laboratory of Medical Genetics, Harbin Medical University, Harbin, P. R. China.,Key Laboratory of Medical Genetics (Harbin Medical University), Heilongjiang Higher Education Institutions, Harbin, P. R. China
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24
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Marchuk DS, Crooks K, Strande N, Kaiser-Rogers K, Milko LV, Brandt A, Arreola A, Tilley CR, Bizon C, Vora NL, Wilhelmsen KC, Evans JP, Berg JS. Increasing the diagnostic yield of exome sequencing by copy number variant analysis. PLoS One 2018; 13:e0209185. [PMID: 30557390 PMCID: PMC6296659 DOI: 10.1371/journal.pone.0209185] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/01/2018] [Indexed: 01/17/2023] Open
Abstract
As whole exome sequencing (WES) becomes more widely used in the clinical realm, a wealth of unanalyzed information will be routinely generated. Using WES read depth data to predict copy number variation (CNV) could extend the diagnostic utility of this previously underutilized data by providing clinically important information such as previously unsuspected deletions or duplications. We evaluated ExomeDepth, a free R package, in addition to an aneuploidy prediction method, to detect CNVs in WES data. First, in a blinded pilot study, five out of five genomic alterations were correctly identified from clinical samples with previously defined chromosomal gains or losses, including submicroscopic deletions, duplications, and chromosomal trisomy. We then examined CNV calls among 53 patients participating in the NCGENES research study and undergoing WES, who had existing clinical chromosomal microarray (CMA) data that could be used for validation. For unique CNVs that overlap well with WES coverage regions, sensitivity was 89% for deletions and 65% for duplications. While specificity of the algorithm calls remains a concern, this is less of an issue at high threshold filtering levels. When applied to all 672 patients from the exome sequencing study, ExomeDepth identified eleven diagnostically relevant CNVs ranging in size from a two exon deletion to whole chromosome duplications, as well as numerous other CNVs with varying clinical significance. This opportunistic analysis of WES data yields an additional 1.6% of patients in this study with pathogenic or likely pathogenic CNVs that are clinically relevant to their phenotype as well as clinically relevant secondary findings. Finally, we demonstrate the potential value of copy number analysis in cases where a single heterozygous likely or known pathogenic single nucleotide alteration is identified in a gene associated with an autosomal recessive condition.
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Affiliation(s)
- Daniel S. Marchuk
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kristy Crooks
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Natasha Strande
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kathleen Kaiser-Rogers
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
- Department of Pediatrics, School of Medicine, University of North Carolina, Chapel Hill, NC, United Sates of America
| | - Laura V. Milko
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Alicia Brandt
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Alexandra Arreola
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, United States of America
| | - Christian R. Tilley
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Chris Bizon
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, United States of America
| | - Neeta L. Vora
- Department of Obstetrics and Gynecology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Kirk C. Wilhelmsen
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC, United States of America
| | - James P. Evans
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina, Chapel Hill, NC, United States of America
- * E-mail:
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Keser N, Kuskucu A, Is M, Celikoglu E. Familial Chiari Type 1: A Molecular Karyotyping Study in a Turkish Family and Review of the Literature. World Neurosurg 2018; 121:e852-e857. [PMID: 30315983 DOI: 10.1016/j.wneu.2018.09.235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 09/28/2018] [Accepted: 09/29/2018] [Indexed: 10/28/2022]
Abstract
BACKGROUND The etiology of Chiari I malformation (CMI) has not been fully elucidated. Therefore, we performed a genetic study of a Turkish family in which 3 sisters had a diagnosis of CMI with or without syringomyelia. METHODS In a family with 7 children, 4 daughters complained of occipital headaches. In 2 of these daughters, CMI had been diagnosed during their 30s, and CMI plus syrinx had been diagnosed in the other daughter in her 40s. Cranial magnetic resonance imaging of the fourth daughter who had developed headaches during her 30s showed normal findings. Because the other siblings in the family were asymptomatic, radiological examinations were not performed. The family had a history of distant consanguineous marriage between parents. Additionally, the father had died, and the mother was asymptomatic, with radiologically normal findings. Array comparative genome hybridization studies were performed for 12 persons from 3 generations of this family. RESULTS None of the 12 cases examined harbored copy number variations. CONCLUSIONS This family with 3 sisters having CMI suggested a possible autosomal recessive single-gene etiology. Cases of familial CMI are unusual but important to study because they could reveal the specific genes involved in posterior fossa/foramen magnum structure and function and provide insights into the cause of sporadic cases.
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Affiliation(s)
- Nese Keser
- Department of Neurological Surgery, TR University of Health Sciences, Istanbul Fatih Sultan Mehmet Education and Research Hospital, Istanbul, Turkey.
| | - Aysegul Kuskucu
- Department of Genetics, Yeditepe University Faculty of Medicine, Istanbul, Turkey
| | - Merih Is
- Department of Neurological Surgery, TR University of Health Sciences, Istanbul Fatih Sultan Mehmet Education and Research Hospital, Istanbul, Turkey
| | - Erhan Celikoglu
- Department of Neurological Surgery, TR University of Health Sciences, Istanbul Fatih Sultan Mehmet Education and Research Hospital, Istanbul, Turkey
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26
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Ceylan AC, Citli S, Erdem HB, Sahin I, Acar Arslan E, Erdogan M. Importance and usage of chromosomal microarray analysis in diagnosing intellectual disability, global developmental delay, and autism; and discovering new loci for these disorders. Mol Cytogenet 2018; 11:54. [PMID: 30258496 PMCID: PMC6154794 DOI: 10.1186/s13039-018-0402-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 09/17/2018] [Indexed: 02/06/2023] Open
Abstract
Background Chromosomal microarray analysis is a first-stage test that is used for the diagnosis of intellectual disability and global developmental delay. Chromosomal microarray analysis can detect well-known microdeletion syndromes. It also contributes to the identification of genes that are responsible for the phenotypes in the new copy number variations. Results Chromosomal microarray analysis was conducted on 124 patients with intellectual disability and global developmental delay. Multiplex ligation-dependent probe amplification was used for the confirmation of chromosome 22q11.2 deletion/duplication. 26 pathogenic and likely pathogenic copy number variations were detected in 23 patients (18.55%) in a group of 124 Turkish patients with intellectual disability and global developmental delay. Chromosomal microarray analysis revealed pathogenic de novo Copy number variations, such as a novel 2.9-Mb de novo deletion at 18q22 region with intellectual disability and autism spectrum disorder, and a 22q11.2 region homozygote duplication with new clinical features. Conclusion Our data expand the spectrum of 22q11.2 region mutations, reveal new loci responsible from autism spectrum disorder and provide new insights into the genotype–phenotype correlations of intellectual disability and global developmental delay.
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Affiliation(s)
- Ahmet Cevdet Ceylan
- Trabzon Kanuni Training and Research Hospital, Medical Genetics Unit, Trabzon, Turkey.,2Ankara Yıldırım Beyazıt University, Ankara Atatürk Training and Research Hospital, Department of Medical Genetics, Ankara, Turkey
| | - Senol Citli
- Trabzon Kanuni Training and Research Hospital, Medical Genetics Unit, Trabzon, Turkey
| | - Haktan Bagis Erdem
- Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Medical Genetics Unit, Ankara, Turkey
| | - Ibrahim Sahin
- Ankara Diskapi Yildirim Beyazit Training and Research Hospital, Medical Genetics Unit, Ankara, Turkey
| | - Elif Acar Arslan
- 4Karadeniz Technical University, School of Medicine, Department of Child Neurology, Trabzon, Turkey
| | - Murat Erdogan
- 5Kayseri Training and Research Hospital, Department of Medical Genetics, Kayseri, Turkey
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27
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Hehir-Kwa JY, Tops BBJ, Kemmeren P. The clinical implementation of copy number detection in the age of next-generation sequencing. Expert Rev Mol Diagn 2018; 18:907-915. [PMID: 30221560 DOI: 10.1080/14737159.2018.1523723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The role of copy number variants (CNVs) in disease is now well established. In parallel NGS technologies, such as long-read technologies, there is continual development and data analysis methods continue to be refined. Clinical exome sequencing data is now a reality for many diagnostic laboratories in both congenital genetics and oncology. This provides the ability to detect and report both SNVs and structural variants, including CNVs, using a single assay for a wide range of patient cohorts. Areas covered: Currently, whole-genome sequencing is mainly restricted to research applications and clinical utility studies. Furthermore, detecting the full-size spectrum of CNVs as well as somatic events remains difficult for both exome and whole-genome sequencing. As a result, the full extent of genomic variants in an individual's genome is still largely unknown. Recently, new sequencing technologies have been introduced which maintain the long-range genomic context, aiding the detection of CNVs and structural variants. Expert commentary: The development of long-read sequencing promises to resolve many CNV and SV detection issues but is yet to become established. The current challenge for clinical CNV detection is how to fully exploit all the data which is generated by high throughput sequencing technologies.
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Affiliation(s)
- Jayne Y Hehir-Kwa
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Bastiaan B J Tops
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
| | - Patrick Kemmeren
- a Princess Máxima Center for Pediatric Oncology , Utrecht , Netherlands
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Peycheva V, Kamenarova K, Ivanova N, Stamatov D, Avdjieva-Tzavella D, Alexandrova I, Zhelyazkova S, Pacheva I, Dimova P, Ivanov I, Litvinenko I, Bozhinova V, Tournev I, Simeonov E, Mitev V, Jordanova A, Kaneva R. Chromosomal microarray analysis of Bulgarian patients with epilepsy and intellectual disability. Gene 2018; 667:45-55. [DOI: 10.1016/j.gene.2018.05.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 04/13/2018] [Accepted: 05/03/2018] [Indexed: 12/08/2022]
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Comparative genomic hybridisation as a first option in genetic diagnosis: 1000 cases and a cost–benefit analysis. ANALES DE PEDIATRÍA (ENGLISH EDITION) 2018. [DOI: 10.1016/j.anpede.2017.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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30
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Stoler J. Genetics and Metabolism. Pediatr Ann 2018; 47:e185-e186. [PMID: 29750284 DOI: 10.3928/19382359-20180507-01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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Fu F, Li R, Li Y, Nie ZQ, Lei T, Wang D, Yang X, Han J, Pan M, Zhen L, Ou Y, Li J, Li FT, Jing X, Li D, Liao C. Whole exome sequencing as a diagnostic adjunct to clinical testing in fetuses with structural abnormalities. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2018; 51:493-502. [PMID: 28976722 DOI: 10.1002/uog.18915] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 06/07/2023]
Abstract
OBJECTIVES To evaluate the diagnostic yield of prenatal whole exome sequencing (WES) for monogenic disorders in fetuses with structural malformations and normal results on cytogenetic testing, and to describe information on pathogenic variants that is provided by WES. METHODS Karyotyping, chromosomal microarray analysis (CMA) and WES were performed sequentially on stored samples from a cohort of 3949 pregnancies with fetal structural abnormalities detected on ultrasound and/or magnetic resonance imaging, referred between January 2011 and December 2015. Diagnostic rates of the three techniques were investigated overall, for phenotypic subgroups and for proband-only vs fetus-mother-father samples. Information on pathogenic variants was identified by WES. RESULTS Overall, 18.2% (720/3949) of fetuses had an abnormal karyotype. Pathogenic copy number variants were detected on CMA in 8.2% (138/1680) of fetuses that had a normal karyotype result. WES performed on a subgroup of 196 fetuses with normal CMA and karyotype results revealed the putative genetic variants responsible for the abnormal phenotypes in 47 cases (24%). The molecular diagnosis rates for fetus-mother-father and proband-only samples were 26.5% (13/49) and 23.1% (34/147), respectively. Variants of uncertain significance were detected in 12.8% (25/196) of fetuses, of which 22 were identified in the fetal proband-only group (15%; 22/147) and three in the fetus-mother-father group (6.1%; 3/49). The incidental finding rate was 6.1% (12/196). CONCLUSIONS WES is a promising method for the identification of genetic variants that cause structural abnormalities in fetuses with normal results on karyotyping and CMA. This enhanced diagnostic yield has the potential to improve the clinical management of pregnancies and to inform better the reproductive decisions of affected families. Copyright © 2017 ISUOG. Published by John Wiley & Sons Ltd.
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Affiliation(s)
- F Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - R Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Y Li
- Guanzghou Umbilical Cord Blood Bank, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Z-Q Nie
- Epidemiology Division, Guangdong Cardiovascular Institute, Guangdong General Hospital, Guangzhou, Guangdong, China
| | - T Lei
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - D Wang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - X Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - J Han
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - M Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - L Zhen
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Y Ou
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - J Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - F-T Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - X Jing
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - D Li
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - C Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders. Genet Med 2018; 20:1216-1223. [PMID: 29323667 PMCID: PMC5912505 DOI: 10.1038/gim.2017.246] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/20/2017] [Indexed: 12/15/2022] Open
Abstract
Purpose Given the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalysing previously generated genomic sequence data in light of new knowledge. Methods We tested this hypothesis in the UK-wide Deciphering Developmental Disorders Study, where in 2014 we reported a diagnostic yield of 27% through whole exome sequencing of 1133 children with severe developmental disorders and their parents. We reanalysed existing data using improved variant calling methodologies, novel variant detection algorithms, updated variant annotation, evidence-based filtering strategies, and newly discovered disease-associated genes. Results We are now able to diagnose an additional 182 individuals, taking our overall diagnostic yield to 454/1133 (40%), and another 43 (4%) have a finding of uncertain clinical significance. The majority of these new diagnoses are due to novel developmental disorder-associated genes discovered since our original publication. Conclusion This study highlights the importance of coupling large-scale research with clinical practice, and of discussing the possibility of iterative reanalysis and recontact with patients and health professionals at an early stage. We estimate that implementing parent-offspring whole exome sequencing as a first line diagnostic test for developmental disorders would diagnose >50% of patients.
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Pinchefsky E, Laneuville L, Srour M. Distal 22q11.2 Microduplication: Case Report and Review of the Literature. Child Neurol Open 2017; 4:2329048X17737651. [PMID: 29147671 PMCID: PMC5673001 DOI: 10.1177/2329048x17737651] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/24/2017] [Accepted: 08/19/2017] [Indexed: 12/20/2022] Open
Abstract
Distal chromosome 22q11.2 microduplications are associated with a wide range of phenotypes and unclear pathogenicity. The authors report on a 3-year-old girl with global developmental delay harboring a de novo 1.24 Mb distal chromosome 22q11.2 microduplication and a paternally inherited 0.25 Mb chromosome 4p14 microduplication. The authors review clinical features of 30 reported cases of distal 22q11.2 duplications. Common features include developmental delay (93%), neuropsychiatric features (26%), and nonspecific facial dysmorphisms (74%). In 70% of cases, the distal 22q11.2 duplications were inherited, and the majority of the carrier parents were phenotypically normal. Furthermore, 30% of probands carried an additional copy number variant. Review of the phenotype in individuals carrying microduplications involving similar low copy repeats (LCR) failed to establish any clear genotype–phenotype correlations. Distal 22q11.2 duplications represent a major challenge for genetic counseling and prediction of clinical consequences. Our report suggests a pathogenic role of distal 22q11.2 duplications and supports a “multiple hit” hypothesis underlying its variable expressivity and phenotypic severity.
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Affiliation(s)
- Elana Pinchefsky
- Division of Pediatric Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Québec, Canada
| | | | - Myriam Srour
- Division of Pediatric Neurology, Department of Pediatrics, Montreal Children's Hospital, McGill University Health Centre (MUHC), Montreal, Québec, Canada
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Li X, Liu Y, Yue S, Wang L, Zhang T, Guo C, Hu W, Kagan KO, Wu Q. Uniparental disomy and prenatal phenotype: Two case reports and review. Medicine (Baltimore) 2017; 96:e8474. [PMID: 29137034 PMCID: PMC5690727 DOI: 10.1097/md.0000000000008474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
RATIONALE Uniparental disomy (UPD) gives a description of the inheritance of both homologues of a chromosome pair from the same parent. The consequences of UPD depend on the specific chromosome/segment involved and its parental origin. PATIENT CONCERNS We report prenatal phenotypes of 2 rare cases of UPD. DIAGNOSES The prenatal phenotype of case 1 included sonographic markers such as enlarged nuchal translucency (NT), absent nasal bone, short femur and humerus length, and several structural malformations involving Dandy-Walker malformation and congenital heart defects. The prenatal phenotype of Case 2 are sonographic markers, including enlarged NT, thickened nuchal fold, ascites, and polyhydramnios without apparent structural malformations. INTERVENTIONS Conventional G-band karyotype appears normal in case 1, while it shows normal chromosomes with a small supernumerary marker chromosome (sSMC) in case 2. Genetic etiology was left unknown until single-nucleotide polymorphism-based array (SNP-array) was performed, and segmental paternal UPD 22 was identified in case 1 and segmental paternal UPD 14 was found in case 2. OUTCOMES The parents of case 1 chose termination of pregnancy. The neonate of case 2 was born prematurely with a bellshaped small thorax and died within a day. LESSONS UPD cases are rare and the phenotypes are different, which depend on the origin and affected chromosomal part. If a fetus shows multiple anomalies that cannot be attributed to a common aneuploidy or a genetic syndrome, or manifests some features possibly related to an UPD syndrome, such as detection of sSMC, SNP-array should be considered.
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Affiliation(s)
| | - Yan Liu
- Department of Obstetrics, Beijing Obstetrics and Gynecology Hospital, Capital Medical University, Beijing, China
| | | | | | | | | | | | - Karl-Oliver Kagan
- Department of Obstetrics and Gynecology, University of Tübingen, Tübingen, Germany
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Best S, Rosser E, Bajaj M. Fifteen years of genetic testing from a London developmental clinic. Arch Dis Child 2017; 102:1014-1018. [PMID: 28659270 DOI: 10.1136/archdischild-2017-312739] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/22/2017] [Accepted: 05/25/2017] [Indexed: 11/03/2022]
Abstract
OBJECTIVE To evaluate genetic disease among children referred to a community paediatric clinic. DESIGN Retrospective cohort study. SETTING Community paediatric clinic, Tower Hamlets, London. PATIENTS All patients seen for first time in the Child Development Team (CDT) clinic between 1999 and 2013. INTERVENTIONS Clinical notes were reviewed. Genetic test results were obtained. Exploratory Excel analysis was performed. Patients without an identified genetic disorder were labelled 'more likely genetic cause' if they had at least two out of three risk factors: developmental delay, congenital abnormality or parental consanguinity, and 'unlikely genetic cause' if they had one or no risk factors, or an obvious alternative cause. MAIN OUTCOME MEASURES Prevalence of genetic diagnoses and parental consanguinity, undertaking of genetic tests, predicted likelihood of a genetic cause among unsolved patients. RESULTS 749 patients were included. 404 (53.9%) had undergone genetic testing and 158 of those tested (39.1%) had a confirmed genetic diagnosis. Parental relatedness was documented in 461 patients, of which 128 (27.8%) had first-cousin parents. The number of patients undergoing genetic testing increased over time. Aneuploidies and syndromic/Mendelian disorders were most common. Of the 591 patients without a genetic diagnosis, 29.9% were classified 'more likely genetic cause'. Patients with consanguineous parents were significantly more likely to have a diagnosed genetic disorder than those with non-consanguineous parents (43/128 vs 72/333), particularly an autosomal recessive condition (27/43 vs 6/72). CONCLUSIONS Genetic disease was common and genetic testing is important in evaluating children in this clinic. Consanguinity increases the likelihood of autosomal recessive disease.
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Affiliation(s)
- Sunayna Best
- Community Paediatrics, Wellington Way Centre, Barts Health NHS Trust, London, UK.,Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Elisabeth Rosser
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Monika Bajaj
- Community Paediatrics, Wellington Way Centre, Barts Health NHS Trust, London, UK
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Futuristic Look at Genetic and Birth Defect Diagnoses and Treatments. Clin Obstet Gynecol 2017; 60:867-877. [PMID: 28990982 DOI: 10.1097/grf.0000000000000327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
One aim of prenatal care is to provide information to prospective parents. The information provided encompasses prenatal care, intrapartum and postpartum care. Learning the genetic constitution of the parents pre-conception or the ongoing pregnancy allows parents to make decisions and set expectations. Offering screening and diagnostic testing has been the main in satisfying the desire for prenatal genetic information. With rapid advances in genomics and genome sequencing, screening during an ongoing pregnancy may become obsolete. Preconception risk will be determined by whole exome sequencing and chromosomal microarray of prospective parents and a number of approaches to alter pregnancy outcome can be considered when genome variations are identified. Therapeutic approaches include mitochondrial transfer and gene editing, two technologies that are in early stages, but showing promise as tools to alter outcomes.
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Castells-Sarret N, Cueto-González AM, Borregan M, López-Grondona F, Miró R, Tizzano E, Plaja A. [Comparative genomic hybridisation as a first option in genetic diagnosis: 1,000 cases and a cost-benefit analysis]. An Pediatr (Barc) 2017; 89:3-11. [PMID: 28958749 DOI: 10.1016/j.anpedi.2017.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/18/2017] [Accepted: 07/19/2017] [Indexed: 01/28/2023] Open
Abstract
BACKGROUND AND OBJECTIVE Conventional cytogenetics diagnoses 3-5% of patients with unexplained developmental delay/intellectual disability and/or multiple congenital anomalies. The Multiplex Ligation-dependent Probe Amplification increases diagnostic rates from between 2.4 to 5.8%. Currently the comparative genomic hybridisation array or aCGH is the highest performing diagnostic tool in patients with developmental delay/intellectual disability, congenital anomalies and autism spectrum disorders. Our aim is to evaluate the efficiency of the use of aCGH as first-line test in these and other indications (epilepsy, short stature). PATIENTS AND METHOD A total of 1000 patients referred due to one or more of the abovementioned disorders were analysed by aCGH. RESULTS Pathogenic genomic imbalances were detected in 14% of the cases, with a variable distribution of diagnosis according to the phenotypes: 18.9% of patients with developmental delay/intellectual disability; 13.7% of multiple congenital anomalies, 9.76% of psychiatric pathologies, 7.02% of patients with epilepsy, and 13.3% of patients with short stature. Within the multiple congenital anomalies, central nervous system abnormalities and congenital heart diseases accounted for 14.9% and 10.6% of diagnoses, respectively. Among the psychiatric disorders, patients with autism spectrum disorders accounted for 8.9% of the diagnoses. CONCLUSIONS Our results demonstrate the effectiveness and efficiency of the use of aCGH as the first line test in genetic diagnosis of patients suspected of genomic imbalances, supporting its inclusion within the National Health System.
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Affiliation(s)
- Neus Castells-Sarret
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España.
| | - Anna M Cueto-González
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; Facultat de Medicina, Departament de Ciències Morfològiques, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
| | - Mar Borregan
- Facultat de Medicina, Departament de Ciències Morfològiques, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
| | | | - Rosa Miró
- Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
| | - Eduardo Tizzano
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; CIBERER, Barcelona, España
| | - Alberto Plaja
- Àrea de Genètica Clínica i Molecular, Hospital Vall d'Hebron, Barcelona, España; Departament de Biologia Cel·lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, España
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Sansović I, Ivankov AM, Bobinec A, Kero M, Barišić I. Chromosomal microarray in clinical diagnosis: a study of 337 patients with congenital anomalies and developmental delays or intellectual disability. Croat Med J 2017; 58:231-238. [PMID: 28613040 PMCID: PMC5470123 DOI: 10.3325/cmj.2017.58.231] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Aim To determine the diagnostic yield and criteria that could help to classify and interpret the copy number variations (CNVs) detected by chromosomal microarray (CMA) technique in patients with congenital and developmental abnormalities including dysmorphia, developmental delay (DD) or intellectual disability (ID), autism spectrum disorders (ASD) and congenital anomalies (CA). Method CMA analysis was performed in 337 patients with DD/ID with or without dysmorphism, ASD, and/or CA. In 30 of 337 patients, chromosomal imbalances had previously been detected by classical cytogenetic and molecular cytogenetic methods. Results In 73 of 337 patients, clinically relevant variants were detected and better characterized. Most of them were >1 Mb. Variants of unknown clinical significance (VOUS) were discovered in 35 patients. The most common VOUS size category was <300 kb (40.5%). Deletions and de novo imbalances were more frequent in pathogenic CNV than in VOUS category. CMA had a high diagnostic yield of 43/307, excluding patients previously detected by other methods. Conclusion CMA was valuable in establishing the diagnosis in a high proportion of patients. Criteria for classification and interpretation of CNVs include CNV size and type, mode of inheritance, and genotype-phenotype correlation. Agilent ISCA v2 Human Genome 8x60 K oligonucleotide microarray format proved to be reasonable resolution for clinical use, particularly in the regions that are recommended by the International Standard Cytogenomic Array (ISCA) Consortium and associated with well-established syndromes.
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Affiliation(s)
- Ivona Sansović
- Ivona Sansović, Department of Medical Genetics and Reproductive Health, Children's Hospital Zagreb, Klaićeva 16, 10000 Zagreb, Croatia,
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Quintela I, Eirís J, Gómez-Lado C, Pérez-Gay L, Dacruz D, Cruz R, Castro-Gago M, Míguez L, Carracedo Á, Barros F. Copy number variation analysis of patients with intellectual disability from North-West Spain. Gene 2017; 626:189-199. [PMID: 28506748 DOI: 10.1016/j.gene.2017.05.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 04/07/2017] [Accepted: 05/11/2017] [Indexed: 10/19/2022]
Abstract
Intellectual disability (ID) is a complex and phenotypically heterogeneous neurodevelopmental disorder characterized by significant deficits in cognitive and adaptive skills, debuting during the developmental period. In the last decade, microarray-based copy number variation (CNV) analysis has been proved as a strategy particularly useful in the discovery of loci and candidate genes associated with these phenotypes and is widely used in the clinics with a diagnostic purpose. In this study, we evaluated the usefulness of two genome-wide high density SNP microarrays -Cytogenetics Whole-Genome 2.7M SNP array (n=126 patients; Group 1) and CytoScan High-Density SNP array (n=447 patients; Group 2)- in the detection of clinically relevant CNVs in a cohort of ID patients from Galicia (NW Spain). In 159 (27.7%) patients, we detected 186 rare exonic chromosomal imbalances, that were grouped into the following classes: Clinically relevant (67/186; 36.0%), of unknown clinical significance (93/186; 50.0%) and benign (26/186; 14.0%). The 67 pathogenic CNVs were identified in 64 patients, which means an overall diagnostic yield of 11.2%. Overall, we confirmed that ID is a genetically heterogeneous condition and emphasized the importance of using genome-wide high density SNP microarrays in the detection of its genetic causes. Additionally, we provided clinical and molecular data of patients with pathogenic or likely pathogenic CNVs and discussed the potential implication in neurodevelopmental disorders of genes located within these variants.
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Affiliation(s)
- Inés Quintela
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain
| | - Jesús Eirís
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Carmen Gómez-Lado
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Laura Pérez-Gay
- Hospital Universitario Lucus Augusti, Unidad de Neurología Pediátrica, Departamento de Pediatría, Lugo, Spain
| | - David Dacruz
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Raquel Cruz
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, CIBER de Enfermedades Raras (CIBERER)-Instituto de Salud Carlos III, Santiago de Compostela, Spain
| | - Manuel Castro-Gago
- Complexo Hospitalario Universitario de Santiago de Compostela, Unidad de Neurología Pediátrica, Departamento de Pediatría, Santiago de Compostela, Spain
| | - Luz Míguez
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain
| | - Ángel Carracedo
- Grupo de Medicina Xenómica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado - Plataforma de Recursos Biomoleculares y Bioinformáticos - Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain; Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain; King Abdulaziz University, Center of Excellence in Genomic Medicine Research, Jeddah, Saudi Arabia
| | - Francisco Barros
- Grupo de Medicina Xenómica, CIBERER, Fundación Pública Galega de Medicina Xenómica - SERGAS, Santiago de Compostela, Spain.
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Wu XL, Li R, Fu F, Pan M, Han J, Yang X, Zhang YL, Li FT, Liao C. Chromosome microarray analysis in the investigation of children with congenital heart disease. BMC Pediatr 2017; 17:117. [PMID: 28472932 PMCID: PMC5418813 DOI: 10.1186/s12887-017-0863-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 04/11/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Our study was aimed to explore the clinical implication of chromosome microarray analysis (CMA) in genetically etiological diagnosis of children with congenital heart disease (CHD). METHODS A total of 104 children with CHD with or without multiple congenital anomalies (MCA) or intellectual disabilities/developmental delay (ID/DD) but normal karyotype were investigated using Affymetrix CytoScan HD array. RESULT Pathogenic copy number variations (PCNVs) were identified in 29 children (27.9%). The detection rates in children with simple CHD and complex CHD were 31.1% (19/61) and 23.2% (10/43), respectively. The detection rates of PCNVs were 17.9% (7/39), 20% (5/25), 63.2% (12/19) and 23.8% (5/21) in isolated CHD, CHD plus MCA, CHD plus ID/DD, CHD plus MCA and ID/DD, respectively. The PCNVs rate of CHD plus ID/DD was significantly higher than that of isolated CHD. Two genomic loci including 15q11.2 deletion and 1q43-q44 deletion were considered as CHD locus. The DVL1, SKI, STIM1, CTNNA3 and PLN were identified as candidate genes associated with CHD phenotypes. CONCLUSION CMA can increase the diagnostic rate and improve the etiological diagnosis in children with CHD. We suggest CMA as a first-tier test in children with CHD, especially in children with CHD plus ID/DD.
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Affiliation(s)
- Xiao-li Wu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Ru Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Fang Fu
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Min Pan
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Jin Han
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Xin Yang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Yong-ling Zhang
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Fa-tao Li
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
| | - Can Liao
- Prenatal Diagnostic Center, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, No. 9 Jinsui Road, Guangdong, China
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Chen Y, Bartanus J, Liang D, Zhu H, Breman AM, Smith JL, Wang H, Ren Z, Patel A, Stankiewicz P, Cram DS, Cheung SW, Wu L, Yu F. Characterization of chromosomal abnormalities in pregnancy losses reveals critical genes and loci for human early development. Hum Mutat 2017; 38:669-677. [PMID: 28247551 DOI: 10.1002/humu.23207] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 02/19/2017] [Accepted: 02/21/2017] [Indexed: 11/09/2022]
Abstract
Detailed characterization of chromosomal abnormalities, a common cause for congenital abnormalities and pregnancy loss, is critical for elucidating genes for human fetal development. Here, 2,186 product-of-conception samples were tested for copy-number variations (CNVs) at two clinical diagnostic centers using whole-genome sequencing and high-resolution chromosomal microarray analysis. We developed a new gene discovery approach to predict potential developmental genes and identified 275 candidate genes from CNVs detected from both datasets. Based on Mouse Genome Informatics (MGI) and Zebrafish model organism database (ZFIN), 75% of identified genes could lead to developmental defects when mutated. Genes involved in embryonic development, gene transcription, and regulation of biological processes were significantly enriched. Especially, transcription factors and gene families sharing specific protein domains predominated, which included known developmental genes such as HOX, NKX homeodomain genes, and helix-loop-helix containing HAND2, NEUROG2, and NEUROD1 as well as potential novel developmental genes. We observed that developmental genes were denser in certain chromosomal regions, enabling identification of 31 potential genomic loci with clustered genes associated with development.
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Affiliation(s)
- Yiyun Chen
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Justin Bartanus
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Desheng Liang
- State Key Lab of Medical Genetics of China Central South University, Changsha, Hunan, China
| | | | - Amy M Breman
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Janice L Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Hua Wang
- Hunan Maternal and Child Health Care Hospital, Changsha, Hunan, China
| | - Zhilin Ren
- Berry Genomics Corporation, Beijing, China
| | - Ankita Patel
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Pawel Stankiewicz
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | | | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Cytogenetics Laboratory, Baylor Miraca Genetics Laboratories, Houston, Texas
| | - Lingqian Wu
- State Key Lab of Medical Genetics of China Central South University, Changsha, Hunan, China
| | - Fuli Yu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas.,Berry Genomics Corporation, Beijing, China
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43
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Reiner J, Karger L, Cohen N, Mehta L, Edelmann L, Scott SA. Chromosomal Microarray Detection of Constitutional Copy Number Variation Using Saliva DNA. J Mol Diagn 2017; 19:397-403. [PMID: 28315673 DOI: 10.1016/j.jmoldx.2016.11.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Revised: 10/27/2016] [Accepted: 11/16/2016] [Indexed: 01/10/2023] Open
Abstract
Chromosomal microarray (CMA) testing to detect copy number aberrations among individuals with multiple congenital anomalies and/or developmental delay is typically performed on peripheral blood DNA. However, the use of saliva DNA may be preferred for some patients, which prompted our validation study using six saliva DNA samples with a range of bacterial content (approximately 3% to 21%) and 20 paired blood and saliva specimens on the Agilent Technologies, Illumina, and Affymetrix CMA platforms. Ten of the 20 paired specimens were previously determined to carry clinically significant copy number aberrations by clinical CMA testing on blood DNA (100 kb to 2.56 Mb; five deletions, eight duplications). Notably, the quality of saliva DNA (DNA Genotek) was equivalent to blood DNA regardless of bacterial content, as was CMA quality and single-nucleotide polymorphism genotyping quality with all CMA platforms. The number of copy number variants and absence of heterozygosity regions detected by CMA were comparable between paired blood and saliva DNA and, more important, all 13 clinically significant copy number aberrations were detected in saliva DNA by all CMA platforms. These data confirm that the quality of saliva DNA is comparable to blood DNA regardless of bacterial content, including important CMA and single-nucleotide polymorphism quality metrics, and that saliva DNA is a reliable alternative for the detection of clinically significant copy number aberrations by clinical CMA testing.
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Affiliation(s)
- Jennifer Reiner
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lisa Karger
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Ninette Cohen
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lakshmi Mehta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Lisa Edelmann
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Stuart A Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.
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Abstract
The genomes of individuals with severe, undiagnosed developmental disorders are enriched in damaging de novo mutations (DNMs) in developmentally important genes. Here we have sequenced the exomes of 4,293 families containing individuals with developmental disorders, and meta-analysed these data with data from another 3,287 individuals with similar disorders. We show that the most important factors influencing the diagnostic yield of DNMs are the sex of the affected individual, the relatedness of their parents, whether close relatives are affected and the parental ages. We identified 94 genes enriched in damaging DNMs, including 14 that previously lacked compelling evidence of involvement in developmental disorders. We have also characterized the phenotypic diversity among these disorders. We estimate that 42% of our cohort carry pathogenic DNMs in coding sequences; approximately half of these DNMs disrupt gene function and the remainder result in altered protein function. We estimate that developmental disorders caused by DNMs have an average prevalence of 1 in 213 to 1 in 448 births, depending on parental age. Given current global demographics, this equates to almost 400,000 children born per year.
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Romaniello R, Marelli S, Giorda R, Bedeschi MF, Bonaglia MC, Arrigoni F, Triulzi F, Bassi MT, Borgatti R. Clinical Characterization, Genetics, and Long-Term Follow-up of a Large Cohort of Patients With Agenesis of the Corpus Callosum. J Child Neurol 2017; 32:60-71. [PMID: 27683483 DOI: 10.1177/0883073816664668] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
To gain a better understanding of the clinical and genetic features associated with agenesis of corpus callosum, we enrolled and characterized 162 patients with complete or partial agenesis of corpus callosum. Clinical and genetic protocols allowed us to categorize patients as syndromic subjects, affected by complex extra-brain malformations, and nonsyndromic subjects without any additional anomalies. We observed slight differences in sex ratio (56% males) and agenesis type (52% complete). Syndromic agenesis of corpus callosum subjects were prevalent (69%). We detected associated cerebral malformations in 48% of patients. Neuromotor impairment, cognitive and language disorders, and epilepsy were frequently present, regardless of the agenesis of corpus callosum subtype. Long-term follow-up allowed us to define additional indicators: syndromic agenesis of corpus callosum plus patients showed the most severe clinical features while isolated complete agenesis of corpus callosum patients had the mildest symptoms, although we observed intellectual disability (64%) and epilepsy (15%) in both categories. We achieved a definitive (clinical and/or genetic) diagnosis in 42% of subjects.
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Affiliation(s)
- Romina Romaniello
- 1 Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Susan Marelli
- 1 Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Roberto Giorda
- 2 Laboratory of Molecular Biology, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Maria F Bedeschi
- 3 Medical Genetic Unit, Department of Obstetrics and Pediatrics, University of Milan, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Mangiagalli e Regina Elena, Milan, Italy
| | - Maria C Bonaglia
- 4 Laboratory of Cytogenetics, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Filippo Arrigoni
- 5 Neuroimaging Lab, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Fabio Triulzi
- 5 Neuroimaging Lab, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Maria T Bassi
- 2 Laboratory of Molecular Biology, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
| | - Renato Borgatti
- 1 Neuropsychiatry and Neurorehabilitation Unit, Scientific Institute, IRCCS Eugenio Medea, Bosisio Parini, Lecco, Italy
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Szczałuba K, Jakubiuk-Tomaszuk A, Kędzior M, Bernaciak J, Zdrodowska J, Kurzątkowski W, Radkowski M, Demkow U. Cytogenomic Evaluation of Children with Congenital Anomalies: Critical Implications for Diagnostic Testing and Genetic Counseling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 912:11-9. [PMID: 26987321 DOI: 10.1007/5584_2016_234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Identification of submicroscopic chromosomal aberrations, as a cause of structural malformations, is currently performed by MLPA (multiplex ligation-dependent probe amplification) or array CGH (array comparative genomic hybridization) techniques. The aim of this study was the evaluation of diagnostic usefulness of MLPA and array CGH in patients with congenital malformations or abnormalities (at least one major or minor birth defect, including dysmorphism) with or without intellectual disability or developmental delay and the optimization of genetic counseling in the context of the results obtained. The MLPA and array CGH were performed in 91 patients diagnosed with developmental disorders and major or minor congenital anomalies. A total of 49 MLPA tests toward common microdeletion syndromes, 42 MLPA tests for subtelomeric regions of chromosomes, two tests for common aberrations in autism, and five array CGH tests were performed. Eight (9 %) patients were diagnosed with microdeletion MLPA, four (4 %) patients with subtelomeric MLPA, one (1 %) patient with autism MLPA. Further three (3 %) individuals had rearrangements diagnosed by array CGH. Altogether, chromosomal microaberrations were found in 16 patients (17 %). All the MLPA-detected rearrangements were found to be pathogenic, but none detected with array CGH could unequivocally be interpreted as pathogenic. In patients with congenital anomalies, the application of MLPA and array CGH techniques is efficient in detecting syndromic and unique microrearrangements. Consistent pre-MLPA test phenotyping leads to better post-test genetic counseling. Incomplete penetrance and unknown inheritance of detected variants are major issues in clinical interpretation of array CGH data.
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Affiliation(s)
- Krzysztof Szczałuba
- MedGen Medical Center, Warsaw, Poland.
- Medical Genetics Unit, Mastermed Medical Center, Białystok, Poland.
| | | | - Marta Kędzior
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Joanna Bernaciak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Warsaw Medical University, Warsaw, Poland
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Detection of clinically relevant copy-number variants by exome sequencing in a large cohort of genetic disorders. Genet Med 2016; 19:667-675. [PMID: 28574513 PMCID: PMC5460076 DOI: 10.1038/gim.2016.163] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/31/2016] [Indexed: 01/08/2023] Open
Abstract
Purpose: Copy-number variation is a common source of genomic variation and an important genetic cause of disease. Microarray-based analysis of copy-number variants (CNVs) has become a first-tier diagnostic test for patients with neurodevelopmental disorders, with a diagnostic yield of 10–20%. However, for most other genetic disorders, the role of CNVs is less clear and most diagnostic genetic studies are generally limited to the study of single-nucleotide variants (SNVs) and other small variants. With the introduction of exome and genome sequencing, it is now possible to detect both SNVs and CNVs using an exome- or genome-wide approach with a single test. Methods: We performed exome-based read-depth CNV screening on data from 2,603 patients affected by a range of genetic disorders for which exome sequencing was performed in a diagnostic setting. Results: In total, 123 clinically relevant CNVs ranging in size from 727 bp to 15.3 Mb were detected, which resulted in 51 conclusive diagnoses and an overall increase in diagnostic yield of ~2% (ranging from 0 to –5.8% per disorder). Conclusions: This study shows that CNVs play an important role in a broad range of genetic disorders and that detection via exome-based CNV profiling results in an increase in the diagnostic yield without additional testing, bringing us closer to single-test genomics. Genet Med advance online publication 27 October 2016
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D'Antonio F, Pagani G, Familiari A, Khalil A, Sagies TL, Malinger G, Leibovitz Z, Garel C, Moutard ML, Pilu G, Bhide A, Acharya G, Leombroni M, Manzoli L, Papageorghiou A, Prefumo F. Outcomes Associated With Isolated Agenesis of the Corpus Callosum: A Meta-analysis. Pediatrics 2016; 138:peds.2016-0445. [PMID: 27581855 DOI: 10.1542/peds.2016-0445] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/16/2016] [Indexed: 11/24/2022] Open
Abstract
CONTEXT Antenatal counseling in cases of agenesis of the corpus callosum (ACC) is challenging. OBJECTIVES To ascertain the outcome in fetuses with isolated complete ACC and partial ACC. DATA SOURCES Medline, Embase, CINAHL, and Cochrane databases. STUDY SELECTION Studies reporting a prenatal diagnosis of ACC. The outcomes observed were: chromosomal abnormalities at standard karyotype and chromosomal microarray (CMA) analysis, additional anomalies detected only at prenatal MRI and at postnatal imaging or clinical evaluation, concordance between prenatal and postnatal diagnosis and neurodevelopmental outcome. DATA EXTRACTION Meta-analyses of proportions were used to combine data. RESULTS Twenty-seven studies were included. In cACC, chromosomal anomalies occurred in 4.81% (95% confidence interval [CI], 2.2-8.4) of the cases. Gross and fine motor control were abnormal in 4.40% (95% CI, 0.6-11.3) and 10.98% (95% CI, 4.1-20.6) of the cases, respectively, whereas 6.80% (95% CI, 1.7-14.9) presented with epilepsy. Abnormal cognitive status occurred in 15.16% (95% CI, 6.9-25.9) of cases. In partial ACC, the rate of chromosomal anomalies was 7.45% (95% CI, 2.0-15.9). Fine motor control was affected in 11.74% (95% CI, 0.9-32.1) of the cases, and 16.11% (95% CI, 2.5-38.2) presented with epilepsy. Cognitive status was affected in 17.25% (95% CI, 3.0-39.7) of cases. LIMITATIONS Different neurodevelopmental tools and time of follow-up of the included studies. CONCLUSIONS Children wih a prenatal diagnosis of isolated ACC show several degrees of impairment in motor control, coordination, language, and cognitive status. However, in view of the large heterogeneity in outcomes measures, time at follow-up, and neurodevelopmental tools used, large prospective studies are needed to ascertain the actual occurrence of neuropsychological morbidity of children with isolated ACC.
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Affiliation(s)
- Francesco D'Antonio
- Department of Clinical Medicine, Faculty of Health Sciences, UiT - The Artic University of Norway, Tromsø, Norway;
| | - Giorgio Pagani
- Department of Obstetrics and Gynecology, Fondazione Poliambulanza, Brescia, Italy
| | - Alessandra Familiari
- Department of Maternal-Fetal Medicine, Catholic University of the Sacred Heart, Rome, Italy
| | - Asma Khalil
- Fetal Medicine Unit, Division of Developmental Sciences, St. George's University of London, London, United Kingdom
| | - Tally-Lerman Sagies
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Fetal Neurology Clinic and Paediatric Neurology Unit, Wolfson Medical Centre, Holon, Israel
| | - Gustavo Malinger
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; GYN Ultrasound Division, Tel Aviv Medical Center, Tel Aviv, Israel
| | - Zvi Leibovitz
- Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel; Fetal Neurology Clinic and Institute of Medical Genetics, Wolfson Medical Center, Holon, Israel
| | - Catherine Garel
- Service de Radiologie, Hôpital d'Enfants Armand-Trousseau, Paris, France
| | - Marie Laure Moutard
- Service de Neuropédiatrie, Hôpital Trousseau, Hôpitaux Universitaires de l'Est Parisien, Université Pierre et Marie Curie, Paris, France
| | - Gianluigi Pilu
- Department of Obstetrics and Gynaecology, Sant'Orsola-Malpighi Hospital, University of Bologna, Bologna, Italy
| | - Amar Bhide
- Fetal Medicine Unit, Division of Developmental Sciences, St. George's University of London, London, United Kingdom
| | - Ganesh Acharya
- Department of Clinical Medicine, Faculty of Health Sciences, UiT - The Artic University of Norway, Tromsø, Norway
| | - Martina Leombroni
- Department of Obstetrics and Gynecology, University of Chieti-Pescara, Chieti, Italy
| | - Lamberto Manzoli
- Department of Medicine and Aging Sciences, University of Chieti-Pescara, Chieti, Italy; EMISAC, Ce.S.I. Biotech, Chieti, Italy; and
| | - Aris Papageorghiou
- Fetal Medicine Unit, Division of Developmental Sciences, St. George's University of London, London, United Kingdom
| | - Federico Prefumo
- Department of Obstetrics and Gynaecology, University of Brescia, Brescia, Italy
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Tong X, Ma Y, Niu X, Yan Z, Liu S, Peng B, Peng S, Fan H. The BTNL2 G16071A gene polymorphism increases granulomatous disease susceptibility: A meta-analysis including FPRP test of 8710 participants. Medicine (Baltimore) 2016; 95:e4325. [PMID: 27472712 PMCID: PMC5265849 DOI: 10.1097/md.0000000000004325] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
OBJECTIVE The butyrophilin-like 2 (BTNL2) G16071A gene polymorphism has been implicated in the susceptibility to granulomatous diseases, but the results were inconclusive. The objective of the current study was to precisely explore the relationship between BTNL2 G16071A gene polymorphism and granulomatous disease susceptibility by the meta-analysis including false-positive report probability (FPRP) test. METHODS A systematic literature search in the PubMed, Embase, and Wanfang databases, China National Knowledge Internet, and commercial Internet search engines was conducted to identify studies published up to April 1, 2016. The odds ratio (OR) with 95% confidence interval (CI) was used to assess the effect size. Statistical analysis was conducted using the STATA 12.0 software and FPRP test sheet. RESULTS In total, all 4324 cases and 4386 controls from 14 eligible studies were included in the current meta-analysis. By the overall meta-analysis, we found a significant association between BTNL2 G16071A gene polymorphism and granulomatous disease susceptibility (A vs G: OR = 1.25, 95% CI = 1.07-1.45, P = 0.005). The meta-regression analyses showed that a large proportion of the between-study heterogeneity was significantly attributed to the ethnicity (A vs G, P = 0.013) and the types of granulomatous diseases (A vs G, P = 0.002). By the subgroup meta-analysis, the BTNL2 G16071A gene polymorphism was associated with granulomatous disease susceptibility in Caucasians (A vs G: OR = 1.37, 95% CI = 1.18-1.58, P < 0.001). Moreover, a significant relationship between the BTNL2 G16071A gene polymorphism and sarcoidosis susceptibility (A vs G: OR = 1.52, 95% CI = 1.39-1.66, P < 0.001) was found. However, to avoid the "false-positive report," we further investigated the significant associations observed in the present meta-analysis by the FPRP test. Interestingly, the results of FPRP test indicated that the BTNL2 G16071A gene polymorphism was truly associated with sarcoidosis susceptibility (A vs G, FPRP < 0.001). Additionally, the FPRP test confirmed that the BTNL2 G16071A gene polymorphism was associated only with granulomatous disease susceptibility among Caucasians (A vs G, FPRP < 0.001) at the level of a prior probability, which was 0.001. CONCLUSION The meta-analysis indicated that BTNL2 G16071A gene polymorphism may as a likelihood factor contributed to granulomatous disease susceptibility, especially increasing the sarcoidosis susceptibility. In addition, the polymorphism may be greatly associated with likelihood of granulomatous diseases among Caucasians.
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Affiliation(s)
- Xiang Tong
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Yao Ma
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Xundong Niu
- Department of Endocrinology, The Second Affiliated Hospital of Ningxia Medical University, Yinchuan, Ningxia
| | - Zhipeng Yan
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Sitong Liu
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Bo Peng
- Department of Internal Medicine, Leshan Traditional Chinese Medicine Hospital, Leshan, Sichuan, China
| | - Shifeng Peng
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
| | - Hong Fan
- Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Chengdu, Sichuan
- Correspondence: Hong Fan, Department of Respiratory and Critical Care Medicine, West China Hospital/West China School of Medicine, Sichuan University, Guoxuexiang 37, Chengdu, Sichuan 610041, China (e-mail: fanhongfanscu@.sina.cn, )
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50
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A novel de novo microdeletion at 17q11.2 adjacent to NF1 gene associated with developmental delay, short stature, microcephaly and dysmorphic features. Mol Cytogenet 2016; 9:41. [PMID: 27247625 PMCID: PMC4886423 DOI: 10.1186/s13039-016-0251-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/18/2016] [Indexed: 11/24/2022] Open
Abstract
Background Microdeletions at 17q11.2 often encompass NF1 gene, is the cause for NF1 microdeletion syndrome. Microdeletion at 17q11.2 without the involvement of NF1 gene is rarely reported. Case presentation Here we reported a patient carrying a novel de novo deletion at 17q11.2 adjacent to NF1 gene, who presented with developmental delay, short stature, postnatal microcephaly, underweight and dysmorphic features including flat facial profile, dolicocephaly, hypertelorism, short philtrum, flat nasal bridge and posteriorly rotated and low set ears. Chromosomal microarray analysis revealed a 1.69 Mb de novo deletion at 17q11.2 adjacent to NF1 gene, which involves 43 RefSeq genes. We compared this with four overlapping deletions at this interval. Conclusions A rare de novo microdeletion at 17q11.2 not involving NF1 gene is associated with developmental delay and dysmorphic features. Seven genes, TAOK1, PHF12, NUFIP2, SLC26A4, SEZ6, GIT1 and TRAF4 are possible candidates for the clinical features of our patient. The delineation of this rare deletion and description of associated clinical phenotypes will help to understand the genotype-phenotype correlation of genomic imbalances at this locus.
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