Common genetic risk variants identified in the SPARK cohort support DDHD2 as a candidate risk gene for autism

Abstract

Autism spectrum disorder (ASD) is a highly heritable neurodevelopmental disorder. Large genetically informative cohorts of individuals with ASD have led to the identification of a limited number of common genome-wide significant (GWS) risk loci to date. However, many more common genetic variants are expected to contribute to ASD risk given the high heritability. Here, we performed a genome-wide association study (GWAS) on 6222 case-pseudocontrol pairs from the Simons Foundation Powering Autism Research for Knowledge (SPARK) dataset to identify additional common genetic risk factors and molecular mechanisms underlying risk for ASD. We identified one novel GWS locus from the SPARK GWAS and four significant loci, including an additional novel locus from meta-analysis with a previous GWAS. We replicated the previous observation of significant enrichment of ASD heritability within regulatory regions of the developing cortex, indicating that disruption of gene regulation during neurodevelopment is critical for ASD risk. We further employed a massively parallel reporter assay (MPRA) and identified a putative causal variant at the novel locus from SPARK GWAS with strong impacts on gene regulation (rs7001340). Expression quantitative trait loci data demonstrated an association between the risk allele and decreased expression of DDHD2 (DDHD domain containing 2) in both adult and prenatal brains. In conclusion, by integrating genetic association data with multi-omic gene regulatory annotations and experimental validation, we fine-mapped a causal risk variant and demonstrated that DDHD2 is a novel gene associated with ASD risk.

Fig. 1. Genome-wide association of ASD in the SPARK dataset.

a GWAS result from SPARK full dataset (N_{case+pseudocontrol} = 12,444). b Genetic correlations across ASD GWAS. From left to right, iPSYCH versus PGC, SPARK EUR versus iPSYCH, SPARK EUR versus PGC and SPARK EUR versus iPSYCH-PGC study. c GWAS results from the meta-analysis (SPARK European population and iPSYCH-PGC, N_{max_case+control} = 55,420). For Manhattan plots (a, c), the x-axes indicate the chromosomal position and y-axes indicate the significance of associations. The blue and red lines denote the significance threshold at suggestive (P < 1 × 10^–6) and significant (P < 5 × 10^–8) levels. SNPs with P < 1 × 10^–6 are shown as a filled circle. Rs number indicates index SNPs from independent loci (1 MB apart from each other) at P < 1 × 10^–8). Index SNPs at P < 5 × 10^–8 are shown as diamonds. d Common variant risk burden is higher in cases compared to pseudocontrols. e Comparison of PRS across family types (from left to right, families with multiple affected children with affected parent(s), multiple affected children with unaffected parents, one affected child with affected parent(s), and one affected child with unaffected parents) shows no evidence for a higher common variant burden in multiplex families. f Comparison of PRS between male and female probands shows no evidence of enrichment of common variants impacting risk for ASD in females. g There is no evidence for a difference in the transmission of common variant risk burden from mother versus father.

Fig. 2. H-MAGMA identified 263 protein-coding genes linked to ASD.

a Schematic diagram of H-MAGMA. SNP based association P-values were aggregated to gene-based P-values using positional information, as well as chromatin interaction in the fetal brain. b Gene-based association results from H-MAGMA. The x-axis indicates the start position of genes (hg19). c Overlap of ASD risk genes harboring common and rare variants. d Overlapped genes with differential expression from post-mortem brains in individuals with ASD patients and neurotypical controls. e Gene ontologies enriched for ASD linked genes (top 20). f Developmental expression pattern of ASD risk genes.

Fig. 3. Genetic correlation of ASD against twelve brain and behavioral phenotypes.

The x-axis represents an estimate of the genetic correlation (r_g). Error bars represent the 95% confidence interval. P-values at FDR < 0.05 are shown in bold. MDD major depressive disorder, ADHD attention-deficit/hyperactivity disorder.

Fig. 4. Identification of putative causal variant and gene impacting risk for ASD.

a Annotated locus plot near rs60527016 ASD risk index variant, from top panel to bottom, ASD associations within SPARK full dataset (n = 6222 case-pseudocontrol pairs), eQTL for DDHD2 in fetal brains (n = 235) and adult brain (n = 1387), MPRA expression (n = 6), ATAC-seq averaged depth in neuron (n = 61) and progenitor (n = 73). Differential open chromatin accessibility peaks from ATAC-seq, and gene model (NCBI Refseq). LD was calculated to rs7001340 within SPARK parents of cases, fetal brain donors, or 1 KG EUR and colored accordingly. b The barcoded expression level of mRNA based from each allele at rs7001340 from the MPRA experiment. c The expression level of DDHD2 by rs7001340 genotypes in the fetal brain. d The expression level of DDHD2 by rs7001340 genotypes in adult brain. Individuals with allele dosage (0–0.1 as C/C, 0.9–1.1 as C/T, 1.9–2.0 as T/T) are shown. For b to d, ASD risk allele for rs7001340 is T and protective allele is C.