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Open Access Highly Accessed Research article

Identification of candidate intergenic risk loci in autism spectrum disorder

Susan Walker1 and Stephen W Scherer12*

Author Affiliations

1 Program in Genetics and Genome Biology, The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada

2 McLaughlin Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada

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BMC Genomics 2013, 14:499  doi:10.1186/1471-2164-14-499

Published: 24 July 2013



Copy number variations (CNVs) and DNA sequence alterations affecting specific neuronal genes are established risk factors for Autism Spectrum Disorder (ASD). In what is largely considered a genetic condition, so far, these mutations account for ~20% of individuals having an ASD diagnosis. However, non-coding genomic sequence also contains functional elements introducing additional disease risk loci for investigation.


We have performed genome-wide analyses and identified rare inherited CNVs affecting non-genic intervals in 41 of 1491 (3%) of ASD cases examined. Examples of such intergenic CNV regions include 16q21 and 2p16.3 near known ASD risk genes CDH8 and NRXN1 respectively, as well as novel loci contiguous with ZHX2, MOCS1, LRRC4C, SEMA3C, and other genes.


Rare variants in intergenic regions may implicate new risk loci and genes in ASD and also present useful data for comparison with coming whole genome sequence datasets.

Autism spectrum disorder; Copy number variation; Non-coding DNA