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      The Role of Epigenetic Change in Autism Spectrum Disorders

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          Abstract

          Autism spectrum disorders (ASD) are a heterogeneous group of neurodevelopmental disorders characterized by problems with social communication, social interaction, and repetitive or restricted behaviors. ASD are comorbid with other disorders including attention deficit hyperactivity disorder, epilepsy, Rett syndrome, and Fragile X syndrome. Neither the genetic nor the environmental components have been characterized well enough to aid diagnosis or treatment of non-syndromic ASD. However, genome-wide association studies have amassed evidence suggesting involvement of hundreds of genes and a variety of associated genetic pathways. Recently, investigators have turned to epigenetics, a prime mediator of environmental effects on genomes and phenotype, to characterize changes in ASD that constitute a molecular level on top of DNA sequence. Though in their infancy, such studies have the potential to increase our understanding of the etiology of ASD and may assist in the development of biomarkers for its prediction, diagnosis, prognosis, and eventually in its prevention and intervention. This review focuses on the first few epigenome-wide association studies of ASD and discusses future directions.

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          Most cited references148

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          High density DNA methylation array with single CpG site resolution.

          We have developed a new generation of genome-wide DNA methylation BeadChip which allows high-throughput methylation profiling of the human genome. The new high density BeadChip can assay over 480K CpG sites and analyze twelve samples in parallel. The innovative content includes coverage of 99% of RefSeq genes with multiple probes per gene, 96% of CpG islands from the UCSC database, CpG island shores and additional content selected from whole-genome bisulfite sequencing data and input from DNA methylation experts. The well-characterized Infinium® Assay is used for analysis of CpG methylation using bisulfite-converted genomic DNA. We applied this technology to analyze DNA methylation in normal and tumor DNA samples and compared results with whole-genome bisulfite sequencing (WGBS) data obtained for the same samples. Highly comparable DNA methylation profiles were generated by the array and sequencing methods (average R2 of 0.95). The ability to determine genome-wide methylation patterns will rapidly advance methylation research. Copyright © 2011 Elsevier Inc. All rights reserved.
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            Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells.

            Cytosine methylation is required for mammalian development and is often perturbed in human cancer. To determine how this epigenetic modification is distributed in the genomes of primary and transformed cells, we used an immunocapturing approach followed by DNA microarray analysis to generate methylation profiles of all human chromosomes at 80-kb resolution and for a large set of CpG islands. In primary cells we identified broad genomic regions of differential methylation with higher levels in gene-rich neighborhoods. Female and male cells had indistinguishable profiles for autosomes but differences on the X chromosome. The inactive X chromosome (Xi) was hypermethylated at only a subset of gene-rich regions and, unexpectedly, overall hypomethylated relative to its active counterpart. The chromosomal methylation profile of transformed cells was similar to that of primary cells. Nevertheless, we detected large genomic segments with hypomethylation in the transformed cell residing in gene-poor areas. Furthermore, analysis of 6,000 CpG islands showed that only a small set of promoters was methylated differentially, suggesting that aberrant methylation of CpG island promoters in malignancy might be less frequent than previously hypothesized.
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              Epigenome-wide association studies for common human diseases.

              Despite the success of genome-wide association studies (GWASs) in identifying loci associated with common diseases, a substantial proportion of the causality remains unexplained. Recent advances in genomic technologies have placed us in a position to initiate large-scale studies of human disease-associated epigenetic variation, specifically variation in DNA methylation. Such epigenome-wide association studies (EWASs) present novel opportunities but also create new challenges that are not encountered in GWASs. We discuss EWAS design, cohort and sample selections, statistical significance and power, confounding factors and follow-up studies. We also discuss how integration of EWASs with GWASs can help to dissect complex GWAS haplotypes for functional analysis.
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                Author and article information

                Contributors
                URI : http://frontiersin.org/people/u/225424
                URI : http://frontiersin.org/people/u/2900
                URI : http://frontiersin.org/people/u/31131
                Journal
                Front Neurol
                Front Neurol
                Front. Neurol.
                Frontiers in Neurology
                Frontiers Media S.A.
                1664-2295
                26 May 2015
                2015
                : 6
                : 107
                Affiliations
                [1] 1Murdoch Childrens Research Institute, Royal Children’s Hospital and Department of Paediatrics, University of Melbourne , Parkville, VIC, Australia
                [2] 2Melbourne Brain Centre, Florey Institute of Neuroscience and Mental Health, The University of Melbourne , Parkville, VIC, Australia
                Author notes

                Edited by: Marnie Blewitt, Walter and Eliza Hall Institute of Medical Research, Australia

                Reviewed by: Claudio V. Mello, Oregon Health & Science University, USA; Claudia Vianna Maurer-Morelli, University of Campinas, Brazil

                *Correspondence: Jeffrey Mark Craig, Murdoch Childrens Research Institute, Royal Childrens Hospital, Flemington Road, Parkville, VIC, Australia, jeff.craig@ 123456mcri.edu.au

                Specialty section: This article was submitted to Neurogenomics, a section of the journal Frontiers in Neurology

                Article
                10.3389/fneur.2015.00107
                4443738
                26074864
                18f0569c-f133-4a54-bdb1-377c39239629
                Copyright © 2015 Loke, Hannan and Craig.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 28 February 2015
                : 28 April 2015
                Page count
                Figures: 1, Tables: 4, Equations: 0, References: 188, Pages: 18, Words: 15969
                Funding
                Funded by: Australian National Health and Medical Research Council
                Award ID: 437015
                Award ID: 607358
                Funded by: Financial Markets Foundation for Children
                Award ID: 032-2007
                Funded by: MCRI
                Funded by: Victorian Government’s Operational Infrastructure Support Program
                Categories
                Neuroscience
                Review

                Neurology
                epigenetics,methylation,autism spectrum disorders,epigenomics,gene expression
                Neurology
                epigenetics, methylation, autism spectrum disorders, epigenomics, gene expression

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