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Whole Genome Analysis of Dizygotic Twins With Autism Reveals Prevalent Transposon Insertion Within Neuronal Regulatory Elements: Potential Implications for Disease Etiology and Clinical Assessment. J Autism Dev Disord 2023; 53:1091-1106. [PMID: 35759154 DOI: 10.1007/s10803-022-05636-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/03/2022] [Indexed: 10/17/2022]
Abstract
Transposable elements (TEs) have been implicated in autism spectrum disorder (ASD). However, our understanding of their roles is far from complete. Herein, we explored de novo TE insertions (dnTEIs) and de novo variants (DNVs) across the genomes of dizygotic twins with ASD and their parents. The neuronal regulatory elements had a tendency to harbor dnTEIs that were shared between twins, but ASD-risk genes had dnTEIs that were unique to each twin. The dnTEIs were 4.6-fold enriched in enhancers that are active in embryonic stem cell (ESC)-neurons (p < 0.001), but DNVs were 1.5-fold enriched in active enhancers of astrocytes (p = 0.0051). Our findings suggest that dnTEIs and DNVs play a role in ASD etiology by disrupting enhancers of neurons and astrocytes.
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Increased Diagnostic Yield of Array Comparative Genomic Hybridization for Autism Spectrum Disorder in One Institution in Taiwan. Medicina (B Aires) 2021; 58:medicina58010015. [PMID: 35056323 PMCID: PMC8779646 DOI: 10.3390/medicina58010015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/31/2022] Open
Abstract
Background and Objectives: Chromosomal microarray offers superior sensitivity for identification of submicroscopic copy number variants (CNVs) and is recommended for the initial genetic testing of patients with autism spectrum disorder (ASD). This study aims to determine the diagnostic yield of array comparative genomic hybridization (array-CGH) in ASD patients from a cohort of Chinese patients in Taiwan. Materials and Methods: Enrolled in this study were 80 ASD children (49 males and 31 females; 2–16 years old) followed up at Taipei MacKay Memorial Hospital between January 2010 and December 2020. The genomic DNA extracted from blood samples was analyzed by array-CGH via the Affymetrix GeneChip Genome-Wide Human single nucleotide polymorphism (SNP) and NimbleGen International Standards for Cytogenomic Arrays (ISCA) Plus Cytogenetic Arrays. The CNVs were classified into five groups: pathogenic (pathologic variant), likely pathogenic (potential pathologic variant), likely benign (potential normal genomic variant), benign (normal genomic variant), and uncertain clinical significance (variance of uncertain significance), according to the American College of Medical Genetics (ACMG) guidelines. Results: We identified 47 CNVs, 31 of which in 27 patients were clinically significant. The overall diagnostic yield was 33.8%. The most frequently clinically significant CNV was 15q11.2 deletion, which was present in 4 (5.0%) patients. Conclusions: In this study, a satisfactory diagnostic yield of array-CGH was demonstrated in a Taiwanese ASD patient cohort, supporting the clinical usefulness of array-CGH as the first-line testing of ASD in Taiwan.
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Williams SM, An JY, Edson J, Watts M, Murigneux V, Whitehouse AJO, Jackson CJ, Bellgrove MA, Cristino AS, Claudianos C. An integrative analysis of non-coding regulatory DNA variations associated with autism spectrum disorder. Mol Psychiatry 2019; 24:1707-1719. [PMID: 29703944 DOI: 10.1038/s41380-018-0049-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 01/16/2018] [Accepted: 02/19/2018] [Indexed: 01/09/2023]
Abstract
A number of genetic studies have identified rare protein-coding DNA variations associated with autism spectrum disorder (ASD), a neurodevelopmental disorder with significant genetic etiology and heterogeneity. In contrast, the contributions of functional, regulatory genetic variations that occur in the extensive non-protein-coding regions of the genome remain poorly understood. Here we developed a genome-wide analysis to identify the rare single nucleotide variants (SNVs) that occur in non-coding regions and determined the regulatory function and evolutionary conservation of these variants. Using publicly available datasets and computational predictions, we identified SNVs within putative regulatory regions in promoters, transcription factor binding sites, and microRNA genes and their target sites. Overall, we found that the regulatory variants in ASD cases were enriched in ASD-risk genes and genes involved in fetal neurodevelopment. As with previously reported coding mutations, we found an enrichment of the regulatory variants associated with dysregulation of neurodevelopmental and synaptic signaling pathways. Among these were several rare inherited SNVs found in the mature sequence of microRNAs predicted to affect the regulation of ASD-risk genes. We show a paternally inherited miR-873-5p variant with altered binding affinity for several risk-genes including NRXN2 and CNTNAP2 putatively overlay maternally inherited loss-of-function coding variations in NRXN1 and CNTNAP2 to likely increase the genetic liability in an idiopathic ASD case. Our analysis pipeline provides a new resource for identifying loss-of-function regulatory DNA variations that may contribute to the genetic etiology of complex disorders.
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Affiliation(s)
- Sarah M Williams
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia.,Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Joon Yong An
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Department of Psychiatry, University of California San Francisco, San Francisco, USA.,Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, USA
| | - Janette Edson
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Michelle Watts
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Valentine Murigneux
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia
| | - Andrew J O Whitehouse
- Telethon Kids Institute, University of Western Australia, Perth, Australia.,Cooperative Research Centre for Living with Autism, Brisbane, Australia
| | - Colin J Jackson
- Research School of Chemistry, Australian National University, Canberra, Australia
| | - Mark A Bellgrove
- Monash Institute of Cognitive and Clinical Neuroscience, Monash University, Melbourne, Australia
| | - Alexandre S Cristino
- University of Queensland Diamantina Institute, University of Queensland, Brisbane, Australia.
| | - Charles Claudianos
- Queensland Brain Institute, University of Queensland, Brisbane, Australia. .,Centre for Mental Health Research CMHR, Australian National University, Canberra, Australia.
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