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Khan H, Harripaul R, Mikhailov A, Herzi S, Bowers S, Ayub M, Shabbir MI, Vincent JB. Biallelic variants identified in 36 Pakistani families and trios with autism spectrum disorder. Sci Rep 2024; 14:9230. [PMID: 38649688 PMCID: PMC11035605 DOI: 10.1038/s41598-024-57942-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 03/22/2024] [Indexed: 04/25/2024] Open
Abstract
With its high rate of consanguineous marriages and diverse ethnic population, little is currently understood about the genetic architecture of autism spectrum disorder (ASD) in Pakistan. Pakistan has a highly ethnically diverse population, yet with a high proportion of endogamous marriages, and is therefore anticipated to be enriched for biallelic disease-relate variants. Here, we attempt to determine the underlying genetic abnormalities causing ASD in thirty-six small simplex or multiplex families from Pakistan. Microarray genotyping followed by homozygosity mapping, copy number variation analysis, and whole exome sequencing were used to identify candidate. Given the high levels of consanguineous marriages among these families, autosomal recessively inherited variants were prioritized, however de novo/dominant and X-linked variants were also identified. The selected variants were validated using Sanger sequencing. Here we report the identification of sixteen rare or novel coding variants in fifteen genes (ARAP1, CDKL5, CSMD2, EFCAB12, EIF3H, GML, NEDD4, PDZD4, POLR3G, SLC35A2, TMEM214, TMEM232, TRANK1, TTC19, and ZNF292) in affected members in eight of the families, including ten homozygous variants in four families (nine missense, one loss of function). Three heterozygous de novo mutations were also identified (in ARAP1, CSMD2, and NEDD4), and variants in known X-linked neurodevelopmental disorder genes CDKL5 and SLC35A2. The current study offers information on the genetic variability associated with ASD in Pakistan, and demonstrates a marked enrichment for biallelic variants over that reported in outbreeding populations. This information will be useful for improving approaches for studying ASD in populations where endogamy is commonly practiced.
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Affiliation(s)
- Hamid Khan
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - Ricardo Harripaul
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
| | - Anna Mikhailov
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | - Sumayah Herzi
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | - Sonya Bowers
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada
| | | | - Muhammad Imran Shabbir
- Department of Biological Sciences, International Islamic University Islamabad, Islamabad, Pakistan
| | - John B Vincent
- Molecular Neuropsychiatry and Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Centre for Addiction and Mental Health, 250 College St, Toronto, ON, M5T 1R8, Canada.
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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