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Akter H, Rahman MM, Sarker S, Basiruzzaman M, Islam MM, Rahaman MA, Rahaman MA, Eshaque TB, Dity NJ, Sarker S, Amin MR, Hossain MM, Lopa M, Jahan N, Hossain S, Islam A, Mondol A, Faruk MO, Saha N, Kundu GK, Kanta SI, Kazal RK, Fatema K, Rahman MA, Hasan M, Hossain Mollah MA, Hosen MI, Karuvantevida N, Begum G, Zehra B, Nassir N, Nabi AHMN, Uddin KMF, Uddin M. Construction of copy number variation landscape and characterization of associated genes in a Bangladeshi cohort of neurodevelopmental disorders. Front Genet 2023; 14:955631. [PMID: 36959829 PMCID: PMC10028086 DOI: 10.3389/fgene.2023.955631] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 02/14/2023] [Indexed: 03/09/2023] Open
Abstract
Introduction: Copy number variations (CNVs) play a critical role in the pathogenesis of neurodevelopmental disorders (NDD) among children. In this study, we aim to identify clinically relevant CNVs, genes and their phenotypic characteristics in an ethnically underrepresented homogenous population of Bangladesh. Methods: We have conducted chromosomal microarray analysis (CMA) for 212 NDD patients with male to female ratio of 2.2:1.0 to identify rare CNVs. To identify candidate genes within the rare CNVs, gene constraint metrics [i.e., "Critical-Exon Genes (CEGs)"] were applied to the population data. Autism Diagnostic Observation Schedule-Second Edition (ADOS-2) was followed in a subset of 95 NDD patients to assess the severity of autism and all statistical tests were performed using the R package. Results: Of all the samples assayed, 12.26% (26/212) and 57.08% (121/212) patients carried pathogenic and variant of uncertain significance (VOUS) CNVs, respectively. While 2.83% (6/212) patients' pathogenic CNVs were found to be located in the subtelomeric regions. Further burden test identified females are significant carriers of pathogenic CNVs compared to males (OR = 4.2; p = 0.0007). We have observed an increased number of Loss of heterozygosity (LOH) within cases with 23.85% (26/109) consanguineous parents. Our analyses on imprinting genes show, 36 LOH variants disrupting 69 unique imprinted genes and classified these variants as VOUS. ADOS-2 subset shows severe social communication deficit (p = 0.014) and overall ASD symptoms severity (p = 0.026) among the patients carrying duplication CNV compared to the CNV negative group. Candidate gene analysis identified 153 unique CEGs in pathogenic CNVs and 31 in VOUS. Of the unique genes, 18 genes were found to be in smaller (<1 MB) focal CNVs in our NDD cohort and we identified PSMC3 gene as a strong candidate gene for Autism Spectrum Disorder (ASD). Moreover, we hypothesized that KMT2B gene duplication might be associated with intellectual disability. Conclusion: Our results show the utility of CMA for precise genetic diagnosis and its integration into the diagnosis, therapy and management of NDD patients.
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Affiliation(s)
- Hosneara Akter
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Muhammad Mizanur Rahman
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shaoli Sarker
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Mohammed Basiruzzaman
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Mazharul Islam
- Department of Child Neurology, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Neurology, National Institute of Neurosciences and Hospital, Dhaka, Bangladesh
| | - Md. Atikur Rahaman
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | | | | | - Nushrat Jahan Dity
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shouvik Sarker
- Institute of Plant Genetics, Department of Plant Biotechnology, Leibniz University Hannover, Hanover, Germany
| | - Md. Robed Amin
- Department of Medicine, Dhaka Medical College, Dhaka, Bangladesh
| | - Mohammad Monir Hossain
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Maksuda Lopa
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Nargis Jahan
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Shafaat Hossain
- Department of Biology and Biochemistry, University of Houston, Houston, TX, United States
| | - Amirul Islam
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Cellular Intelligence Lab, GenomeArc Inc, Toronto, ON, Canada
| | | | - Md Omar Faruk
- Centre for Precision Therapeutics, NeuroGen Healthcare, Dhaka, Bangladesh
| | - Narayan Saha
- Department of Paediatric Neurology, National Institute of Neuroscience and Hospital, Dhaka, Bangladesh
| | - Gopen kumar Kundu
- Department of Child Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Shayla Imam Kanta
- Department of Paediatric Neuroscience, Dhaka Shishu Hospital, Dhaka, Bangladesh
| | - Rezaul Karim Kazal
- Department of Obstetrics and Gynaecology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Kanij Fatema
- Department of Paediatric Neurology, Bangabandhu Sheikh Mujib Medical University, Dhaka, Bangladesh
| | - Md. Ashrafur Rahman
- Department of Pharmaceutical Sciences, Wilkes University, Pennsylvania, PA, United States
| | - Maruf Hasan
- Department of Biomedical Engineering, Military Institute of Science and Technology, Dhaka, Bangladesh
| | | | - Md. Ismail Hosen
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Ghausia Begum
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Binte Zehra
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - Nasna Nassir
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | - A. H. M. Nurun Nabi
- Department of Biochemistry and Molecular Biology, University of Dhaka, Dhaka, Bangladesh
| | - K. M. Furkan Uddin
- Genetics and Genomic Medicine Centre, NeuroGen Healthcare, Dhaka, Bangladesh
- Department of Biochemistry, Holy Family Red Crescent Medical College, Dhaka, Bangladesh
| | - Mohammed Uddin
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
- Cellular Intelligence (Ci) Lab, GenomeArc Inc, Toronto, ON, Canada
- *Correspondence: Mohammed Uddin,
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Chisholm AK, Haebich KM, Pride NA, Walsh KS, Lami F, Ure A, Maloof T, Brignell A, Rouel M, Granader Y, Maier A, Barton B, Darke H, Dabscheck G, Anderson VA, Williams K, North KN, Payne JM. Delineating the autistic phenotype in children with neurofibromatosis type 1. Mol Autism 2022; 13:3. [PMID: 34983638 PMCID: PMC8729013 DOI: 10.1186/s13229-021-00481-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/14/2021] [Indexed: 12/15/2022] Open
Abstract
Background Existing research has demonstrated elevated autistic behaviours in children with neurofibromatosis type 1 (NF1), but the autistic phenotype and its relationship to other neurodevelopmental manifestations of NF1 remains unclear. To address this gap, we performed detailed characterisation of autistic behaviours in children with NF1 and investigated their association with other common NF1 child characteristics. Methods Participants were drawn from a larger cross-sectional study examining autism in children with NF1. The population analysed in this study scored above threshold on the Social Responsiveness Scale-Second Edition (T-score ≥ 60; 51% larger cohort) and completed the Autism Diagnostic Interview-Revised (ADI-R) and/or the Autism Diagnostic Observation Schedule-Second Edition (ADOS-2). All participants underwent evaluation of their intellectual function, and behavioural data were collected via parent questionnaires. Results The study cohort comprised 68 children (3–15 years). Sixty-three per cent met the ADOS-2 ‘autism spectrum’ cut-off, and 34% exceeded the more stringent threshold for ‘autistic disorder’ on the ADI-R. Social communication symptoms were common and wide-ranging, while restricted and repetitive behaviours (RRBs) were most commonly characterised by ‘insistence on sameness’ (IS) behaviours such as circumscribed interests and difficulties with minor changes. Autistic behaviours were weakly correlated with hyperactive/impulsive attention deficit hyperactivity disorder (ADHD) symptoms but not with inattentive ADHD or other behavioural characteristics. Language and verbal IQ were weakly related to social communication behaviours but not to RRBs. Limitations Lack of genetic validation of NF1, no clinical diagnosis of autism, and a retrospective assessment of autistic behaviours in early childhood. Conclusions Findings provide strong support for elevated autistic behaviours in children with NF1. While these behaviours were relatively independent of other NF1 comorbidities, the importance of taking broader child characteristics into consideration when interpreting data from autism-specific measures in this population is highlighted. Social communication deficits appear similar to those observed in idiopathic autism and are coupled with a unique RRB profile comprising prominent IS behaviours. This autistic phenotype and its relationship to common NF1 comorbidities such as anxiety and executive dysfunction will be important to examine in future research. Current findings have important implications for the early identification of autism in NF1 and clinical management. Supplementary Information The online version contains supplementary material available at 10.1186/s13229-021-00481-3.
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Affiliation(s)
- Anita K Chisholm
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.,The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Kristina M Haebich
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Natalie A Pride
- Kids Neuroscience Centre, The Children's Hospital at Westmead, 178A Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Karin S Walsh
- Center for Neuroscience and Behavioral Medicine, Children's National Hospital, Michigan Avenue NW, Washington, DC, 20310, USA
| | - Francesca Lami
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Alex Ure
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, School of Clinical Sciences, Monash University, 246 Clayton Road, Clayton, VIC, 3168, Australia.,Developmental Paediatrics, Monash Children's Hospital, 246 Clayton Road, Clayton, VIC, 3168, Australia
| | - Tiba Maloof
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.,The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Amanda Brignell
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, School of Clinical Sciences, Monash University, 246 Clayton Road, Clayton, VIC, 3168, Australia
| | - Melissa Rouel
- Kids Neuroscience Centre, The Children's Hospital at Westmead, 178A Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Yael Granader
- Center for Neuroscience and Behavioral Medicine, Children's National Hospital, Michigan Avenue NW, Washington, DC, 20310, USA
| | - Alice Maier
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Belinda Barton
- Kids Neuroscience Centre, The Children's Hospital at Westmead, 178A Hawkesbury Road, Westmead, NSW, 2145, Australia.,Sydney Medical School, University of Sydney, Camperdown, NSW, 2050, Australia.,Children's Hospital Education Research Institute, The Children's Hospital at Westmead, 178A Hawkesbury Road, Westmead, NSW, 2145, Australia
| | - Hayley Darke
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Gabriel Dabscheck
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.,The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Vicki A Anderson
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.,The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia
| | - Katrina Williams
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia.,Department of Paediatrics, School of Clinical Sciences, Monash University, 246 Clayton Road, Clayton, VIC, 3168, Australia.,Developmental Paediatrics, Monash Children's Hospital, 246 Clayton Road, Clayton, VIC, 3168, Australia
| | - Kathryn N North
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia.,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Jonathan M Payne
- Murdoch Children's Research Institute, 50 Flemington Road, Parkville, VIC, 3052, Australia. .,Department of Paediatrics, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC, 3010, Australia. .,The Royal Children's Hospital, 50 Flemington Road, Parkville, VIC, 3052, Australia.
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