Abstract
BackgroundDe novo loss-of-function (dnLoF) mutations are found twofold more often in autism spectrum disorder (ASD) probands than their unaffected siblings. Multiple independent dnLoF mutations in the same gene implicate the gene in risk and hence provide a systematic, albeit arduous, path forward for ASD genetics. It is likely that using additional non-genetic data will enhance the ability to identify ASD genes.MethodsTo accelerate the search for ASD genes, we developed a novel algorithm, DAWN, to model two kinds of data: rare variations from exome sequencing and gene co-expression in the mid-fetal prefrontal and motor-somatosensory neocortex, a critical nexus for risk. The algorithm casts the ensemble data as a hidden Markov random field in which the graph structure is determined by gene co-expression and it combines these interrelationships with node-specific observations, namely gene identity, expression, genetic data and the estimated effect on risk.ResultsUsing currently available genetic data and a specific developmental time period for gene co-expression, DAWN identified 127 genes that plausibly affect risk, and a set of likely ASD subnetworks. Validation experiments making use of published targeted resequencing results demonstrate its efficacy in reliably predicting ASD genes. DAWN also successfully predicts known ASD genes, not included in the genetic data used to create the model.ConclusionsValidation studies demonstrate that DAWN is effective in predicting ASD genes and subnetworks by leveraging genetic and gene expression data. The findings reported here implicate neurite extension and neuronal arborization as risks for ASD. Using DAWN on emerging ASD sequence data and gene expression data from other brain regions and tissues would likely identify novel ASD genes. DAWN can also be used for other complex disorders to identify genes and subnetworks in those disorders.
Highlights
De novo loss-of-function mutations are found twofold more often in autism spectrum disorder (ASD) probands than their unaffected siblings
Discovering network and risk genes using detecting association with networks (DAWN) To search for clusters of possible risk genes embedded in the entire expression network, DAWN models the interrelationships amongst nodes of a network, in terms of risk status, and combines such interrelationships with nodespecific genetic signals for association (Figure 1)
The distribution of these scores demonstrates that network ASD (nASD) genes are significantly more connected to other genes potentially affecting risk when compared to genes not in this set (Methods, Additional file 3: Table S2; and Additional file 8: Figure S3; Wilcoxon rank test, P < 10−16)
Summary
De novo loss-of-function (dnLoF) mutations are found twofold more often in autism spectrum disorder (ASD) probands than their unaffected siblings. It is likely that using additional non-genetic data will enhance the ability to identify ASD genes. That genetic variation affects the risk for autism spectrum disorders (ASDs) has been known for decades, yet only recently has the complexity of its architecture come into focus [1]. Analysis of 1,043 ASD trios has identified a handful of the genes involved in the ASD risk. Extrapolating from these data would require exome analysis of tens of thousands of families to identify even half of the risk genes, an infeasible short-term goal with regard to sample collection and funding. There is an urgent need to advance ASD gene discovery through the integration of complementary biologically relevant datasets
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