31673
Rare Epigenic Variations in Autism Spectrum Disorder

Poster Presentation
Friday, May 3, 2019: 11:30 AM-1:30 PM
Room: 710 (Palais des congres de Montreal)
M. Janecka1, E. Hannon2, P. Garg3, A. Starnawska4, N. H. Staunstrup4, D. Schendel4, J. Mill5, A. Reichenberg1, A. Sharp3 and J. Buxbaum6, (1)Seaver Autism Center, Department of Psychiatry, Icahn School of Medicine at Mount Sinai Hospital, New York, NY, (2)Exeter Medical School, University of Exeter, Exeter, United Kingdom, (3)Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, (4)Aarhus University, Aarhus, Denmark, (5)University of Exeter Medical School, University of Exeter, Exeter, United Kingdom, (6)Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY
Background: To date, epigenome-wide association studies have found few significant associations between the levels of DNA methylation and autism spectrum disorder (ASD). Identifying further case-control differences could be challenging in an etiologically heterogeneous disorder.

Objectives: Our study tests if ASD is associated with loci showing extreme DNA methylation levels in a small fraction of cases, akin to the observations of the role of rare genetic mutations in ASD etiology.

Methods: As described in our previous work, DNA was isolated from dried blood spot samples (Guthrie cards) collected early postnatally from all newborns in Denmark, and archived in the Danish Neonatal Screening Biobank. The DNA extraction and subsequent DNA methylation profiling was performed at Statens Serum Institut, using a previously established method. Quality control steps included removal of samples with low signal intensities, low bisulfite conversion, or low detection P value, and probes within 5bp of known single nucleotide polymorphism. We also excluded all probes on the sex chromosomes. Data were normalized using the wateRmelon package.

Subsequently, a sliding-window approach was used to identify “epivariation”, i.e. regions where DNA methylation levels in cases or controls were outside the 99% confidence intervals in the set of independent, reference control samples, at a minimum of 3 consecutive probes within 1kb, with at least one of those probes deviating a minimum of 10% from the most extreme reference control.

Using permutation testing, we investigated the overall enrichment of such regions in cases compared to controls, as well as the differences in the characteristics of the underlying genomic regions (i.e., enrichment of either ASD-associated genes derived from the Autism Sequencing Consortium) or genes intolerant to mutation, defined as pLI >0.9.

Results: After quality control, there were 629 ASD and 634 control samples (both ~50% female) used in the analyses, with 456,725 autosomal probes analyzed. There were no significant differences in the rates of epivariation between cases and controls (p=0.084). However, cases had significantly more instances of epivariation in ASD FDR 0.1 genes (respectively, 0.003 and 0.001 per individual, p=0.015) and FDR 0.5 genes (respectively, 0.020 and 0.004, p=2.3x10-8), and genes intolerant to mutation (0.074 and 0.059, p=0.035).

Conclusions: Our data indicate that ASD cases show a significant enrichment of epivariations in both genes previously linked with ASD, and genes intolerant to mutation, when compared to controls. Future studies will establish whether such epivariations could be causal in some cases of ASD, rather than marking other genomic alterations, e.g. copy number variations or aberrations of imprinting.

See more of: Epigenetics
See more of: Epigenetics