Integrated genetic and methylomic analyses identify shared biology between autism and autistic traits.

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Massrali, Aicha 
Brunel, Helena 
Hannon, Eilis 
Wong, Chloe 
iPSYCH-MINERvA Epigenetics Group 

Previous studies have identified differences in DNA methylation in autistic individuals compared to neurotypical individuals. Yet, it is unclear if this extends to autistic traits-subclinical manifestation of autism features in the general population. Here, we investigate the association between DNA methylation at birth (cord blood), and scores on the Social and Communication Disorders Checklist (SCDC), a measure of autistic traits, in 701 8-year-olds, by conducting a methylome-wide association study (MWAS). We did not identify significant CpGs associated with SCDC. The most significant CpG site was cg14379490, on chromosome 9 (MWAS beta = - 1.78 ± 0.35, p value = 5.34 × 10 -7 ). Using methylation data for autism in peripheral tissues, we did not identify a significant concordance in effect direction of CpGs with p value < 10-4 in the SCDC MWAS (binomial sign test, p value > 0.5). In contrast, using methylation data for autism from post-mortem brain tissues, we identify a significant concordance in effect direction of CpGs with a p value < 10-4 in the SCDC MWAS (binomial sign test, p value = 0.004). Supporting this, we observe an enrichment for genes that are dysregulated in the post-mortem autism brain (one-sided Wilcoxon rank-sum test, p value = 6.22 × 10-5). Finally, integrating genome-wide association study (GWAS) data for autism (n = 46,350) with mQTL maps from cord-blood (n = 771), we demonstrate that mQTLs of CpGs associated with SCDC scores at p value thresholds of 0.01 and 0.005 are significantly shifted toward lower p values in the GWAS for autism (p < 5 × 10-3). We provide additional support for this using a GWAS of SCDC, and demonstrate a lack of enrichment in a GWAS of Alzheimer's disease. Our results highlight the shared cross-tissue methylation architecture of autism and autistic traits, and demonstrate that mQTLs associated with differences in DNA methylation associated with childhood autistic traits are enriched for common genetic variants associated with autism and autistic traits.

Autistic Disorder, Brain, Child, CpG Islands, DNA Methylation, Gene Expression Regulation, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Postmortem Changes, Quantitative Trait Loci, Social Communication Disorder, Transcription, Genetic
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Mol Autism
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Springer Science and Business Media LLC
This study was funded by grants from the Medical Research Council, the Wellcome Trust, the Autism Research Trust, and the Templeton World Charity Foundation. The research was conducted in association with the National Institute for Health Research (NIHR) Collaboration for Leadership in Applied Health Research and Care East of England at Cambridgeshire and Peterborough NHS Foundation Trust. The UK Medical Research Council and Wellcome (grant ref: 102215/2/13/2) and the University of Bristol provide core support for ALSPAC. This study was supported by grant HD073978 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institute of Environmental Health Sciences, and National Institute of Neurological Disorders and Stroke; and by the Beatrice and Samuel A. Seaver Foundation. We acknowledge iPSYCH and The Lundbeck Foundation for providing samples and funding for the MINERvA dataset. The iPSYCH (The Lundbeck Foundation Initiative for Integrative Psychiatric Research) team acknowledges funding from The Lundbeck Foundation (grant numbers R102-A9118 and R155–2014-1724), the Stanley Medical Research Institute, the European Research Council (project number 294838), the Novo Nordisk Foundation for supporting the Danish National Biobank resource, and grants from Aarhus and Copenhagen Universities and University Hospitals, including support to the iSEQ Center, the GenomeDK HPC facility, and the CIRRAU Center. This research has been conducted using the Danish National Biobank resource, supported by the Novo Nordisk Foundation. The SEED study was supported by Centers for Disease Control and Prevention (CDC) Cooperative Agreements announced under the RFAs 01086, 02199, DD11–002, DD06–003, DD04–001, and DD09–002 and the SEED DNA methylation measurements were supported by Autism Speaks Award #7659 to MDF. The SSC was supported by Simons Foundation (SFARI) award and NIH grant MH089606. The project leading to this application has received funding from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 777394. The JU receives support from the European Union’s Horizon 2020 research and innovation programme and EFPIA and AUTISM SPEAKS, Autistica, SFARI.