The female protective effect in autism spectrum disorder is not mediated by a single genetic locus

Abstract

Background: A 4:1 male to female sex bias has consistently been observed in autism spectrum disorder (ASD). Epidemiological and genetic studies suggest a female protective effect (FPE) may account for part of this bias; however, the mechanism of such protection is unknown. Quantitative assessment of ASD symptoms using the Social Responsiveness Scale (SRS) shows a bimodal distribution unique to females in multiplex families. This leads to the hypothesis that a single, common genetic locus on chromosome X might mediate the FPE and produce the ASD sex bias. Such a locus would represent a major therapeutic target and is likely to have been missed by conventional genome-wide association study (GWAS) analysis.

Methods: To explore this possibility, we performed an association study in affected versus unaffected females, considering three tiers of single nucleotide polymorphisms (SNPs) as follows: 1) regions of chromosome X that escape X-inactivation, 2) all of chromosome X, and 3) genome-wide.

Results: No evidence of a SNP meeting the criteria for a single FPE locus was observed, despite the analysis being well powered to detect this effect.

Conclusions: The results do not support the hypothesis that the FPE is mediated by a single genetic locus; however, this does not exclude the possibility of multiple genetic loci playing a role in the FPE.

Keywords: Autism spectrum disorder; Female protective effect; GWAS; Sex bias.

Figure 1

Expected and observed Social Responsiveness Scale (SRS) scores in multiplex AGRE families. Children in multiplex families are assumed to have inherited a high degree of ASD risk. Under a threshold model, a quantitative measure of ASD severity, such as the SRS, would be expected to follow a normal distribution with unaffected individuals at the lower end. (A) The observed SRS scores for 927 male children (95 unaffected in blue, 832 affected in red) with each bar showing the sum of the number of unaffected and affected males. The black line shows the kernel density of the data, which approximates a normal distribution. (B) The corresponding plot is shown for 394 female children (151 unaffected, 243 affected). The SRS scores produce a bimodal distribution, as noted previously [22,23]. (C) To assess the expected distribution under quantitative trait model, we estimated the mean and standard deviation of the male observed data ‘A’ and used these characteristics to simulate a normal distribution for the same number of individuals. The scores were sorted, and a threshold for affected status was chosen to give the same number of affected and unaffected males as in ‘A’. Each bar shows the sum of the number of unaffected and affected simulated males, while the black line shows the kernel density. (D) The expected distribution under quantitative trait model is shown using the same method as in ‘C’ but for 394 females based on the female data in ‘B’. The expected distribution differs markedly from the observed in females, but not in males. (E) If multiple factors contribute to the presence of the FPE, then their combined effect is likely to produce a unimodal distribution. (F) As the number of factors contributing to the presence of the FPE decreases, the unimodal distribution in ‘E’ develops distinct distributions based on the number of factors present. (G) If only one factor contributes, then a bimodal distribution should be observed. (H) Finally, if there are no factors and the FPE is universally present in females, a unimodal distribution will arise based on the distribution of risk rather than protection.

Figure 2

GWAS power estimate for a single factor mediating the FPE. (A) In females exposed to high ASD risk, the protective factor will be enriched in unaffected individuals (green) and largely absent in cases (purple). We estimate a distinct difference in the frequency of the protective allele in these two cohorts (Additional file 1: Supplementary Methods) for an analysis based only on females (red line). Conversely, the protective allele has no effect in males and will be observed at an equal frequency in male cases and controls. Including males in a GWAS analysis will therefore add noise (blue line, representing the observed 5.25:1 ratio of males to females in Anney et al. [27]) resulting in a reduction in power. (B) An estimate of GWAS power to detect a single FPE allele in females only (red) and females and males (blue) under a model where protection contributes 50% of the observed 5.25:1 sex bias. The vertical lines represent the sample size in this study (red) and the Anney et al. [27] GWAS study (blue).

Figure 3

Identification of chromosome X SNPs that escape X-inactivation for tier 1 analysis. This Circos plot shows the length of chromosome X proceeding clockwise with position 0 on the short arm at twelve o’clock. Adjacent to the chromosome position, the innermost ring indicates chromosome banding by the depth of shading; two opposing black arrows indicate the centromere. Regions of chromosome Y homology are shown in purple in the middle ring; SNPs in these regions were excluded from the tier 1 analysis leaving the SNPs unique to chromosome X indicated in green. The outermost ring shows SNP density based on the genotyping array (see ‘Methods’ section) by the height of the bars. Regions that are inactivated on one copy of chromosome X are shown in gray [32] and SNPs in these regions were excluded from the tier 1 analysis, leaving only SNPs that escape X-inactivation, shown in red (Additional file 2: Table S4). Of the 6,955 SNPs on chromosome X, 451 (6.5%) were included in the tier 1 analysis.

Figure 4

Manhattan plots of association study results. Results of association studies comparing 208 affected females and 151 unaffected females from AGRE. To maximize the ability to identify a candidate variant for the FPE the association test was performed on three tiers of SNPs, based on the a priori probability of mediating the FPE. (A) Tier 1: 451 SNPs unique to chromosome X that escape X-inactivation. No SNPs are significant after multiple comparisons (horizontal red line). The top five SNPs (red) are labeled (Table 1). (B) Tier 2: all 6,955 SNPs on chromosome X. No SNPs are significant after multiple comparisons (horizontal red line). The top five SNPs (red) are labeled (Table 2). (C) Tier 3: all 317,574 SNPs across the genome. No SNPs are significant after multiple comparisons (horizontal red line). The top five SNPs (red) are labeled (Table 3).