Trans-effects of cis-eQTLs.

<p>(A) Histogram of the proportion of probes (π1) affected in trans by each cis-eQTL that could be detected with a very large sample size. The cis-eQTLs of several genes is highlighted in black. (B) Histogram of the number of genes significantly affected in trans by cis-eQTLs (5% FDR) detected with 869 individuals.</p

Causal directed relationships between variation in level of expression of the cis gene and variation in the level of expression of the trans gene.

<p>Causal directed relationships between variation in level of expression of the cis gene and variation in the level of expression of the trans gene.</p

Tissue sharing (π1) of cis-eQTLs between ALSPAC LCLs and cis-eQTLs detected by the MUTHER cohort in LCLs (black), skin (red) and adipose tissues (green) tissues in function of the ALSPAC sample size.

<p>Error bars represent the 5% and 95% confidence interval and lines show the best polynomial fit of the data.</p

Enrichment of eQTLs and mQTLs in distinct genomic regions.

<p>For distinct genomic regions, the proportion of overlapping eQTLs (A) and mQTLs (B) (both in red) was compared to the proportion of overlapping null SNPs (black, see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#sec004" target="_blank">Methods</a> for details). We found significant enrichment of eQTLs in CpG islands, exons and DNase I hypersensitive sites (HSs), and significant enrichment of mQTLs in enhancer and insulator marks, as well as significant depletion in last exons and introns. One star indicates <i>P</i> < 0.05, two stars indicate <i>P</i> < 5E-04, Fisher’s exact test.</p

Summary of associations and allele-specific expression analyses in GenCord.

<p>Number of significant genes, methylation sites or assayable heterozygous sites in fibroblasts (F), LCLs (L) and T-cells (T). The association analyses on eQTL, mQTLs and eQTMs were previously reported [<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#pgen.1004958.ref037" target="_blank">37</a>].</p><p>* FDR calculated as number of expected over number of observed based on the nominal P-value threshold.</p><p>Summary of associations and allele-specific expression analyses in GenCord.</p

Properties of DNA methylation when associated to gene expression.

<p>(A) Number of all significant positive (pos-eQTMs) and negative (neg-eQTMs) correlations between DNA methylation and gene expression in fibroblasts (F), LCLs (L) and T-cells (T). A larger number of neg-eQTMs is found in all three cell-types, but an important part is composed of pos-eQTMs. (B) Percent of pos-eQTMs, neg-eQTMs and null sites that overlap with promoters, CpG island shores, CpG islands, gene bodies and enhancers. Pos-eQTMs are significantly depleted in promoter proximal regions in all cell-types. In most cases both positive and negative eQTMs are enriched for CpG island shores, gene bodies and enhancers, and depleted for CpG islands. One star indicates <i>P</i> < 0.05, two stars indicate <i>P</i> < 5E-04, Fisher’s exact test. (C) Correlation coefficients of eQTMs significant in both cell-types compared for all pair wise combinations of the three cell-types are plotted. The percentage of discordant cases (associations with opposite sign between any pair of cell-types) is indicated in the top left corner of each panel. Most eQTMs that are significant in any pair of cell-types have the same sign of association. (D) eQTM effect sizes are measured as the slope of the linear regression of expression given methylation on scaled values, and compared between cell-types for union of eQTMs. Black dots are significant eQTMs (same CpG-exon pair) in both the cell-types compared; orange, blue and purple dots are eQTMs significant only in fibroblast, LCL and T-cell, respectively, within the pair compared. Coefficient of determination <i>R</i>², reflecting the proportion of effect size variance in one cell-type explained by the other cell-type, is shown in the top left corner of each plot (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#pgen.1004958.s001" target="_blank">S1 Table</a>). This shows that there is a large amount of tissue-specific effects for correlations between DNA methylation and gene expression.</p

Genetic effects on alternative splicing.

<p>(A) Highly significant associations between genetic variation and alternative splicing (asQTLs) cluster close to the transcription start site (TSS). The top asQTL per exon-exon link is plotted showing its relative distance to the TSS by the level of significance—log(P-value). Additionally, we observe that associations called significant in three cell-types are closer to the TSS than associations significant in two cell-types and these are closer than associations significant in only one cell-type. A great part of the genetic control on splicing appears to occur in promoter proximal regions, and cell-type specific distant asQTLs could reflect that distant regulatory elements are involved in tissue-specific splicing. (B) For distinct genomic regions, the percent of overlapping asQTLs (top SNP per link) in comparison to the proportion of overlapping null SNPs in fibroblasts (F), LCLs (L) and T-cells (T). We found significant enrichment of asQTLs in splice region variants, active promoters, enhancers, DNase I hypersensitive sites (HSs), middle exons, CpG islands, elongation marks, CpG island shores and CTCF peaks (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#pgen.1004958.s005" target="_blank">S5 Table</a>). One star indicates <i>P</i> < 0.05, two stars indicate <i>P</i> < 5E-04, Fisher’s exact test. (C) Effect sizes of the union of asQTLs (best SNP per exon-exon link) for each pair of cell-types are plotted. Effect size is measured as the difference in medians of scaled alternative splicing levels between heterozygous individuals and the homozygous individuals for the major allele. Hence, effect sizes are quantified in terms of number of standard deviations on the alternative splicing levels modified by an allele change. Black dots depict associations significant in both cell-types compared; orange, blue and purple dots are associations significant in only fibroblasts, LCLs and T-cells, respectively, within the pair compared. Coefficient of determination R², reflecting the proportion of effect size variance in one cell-type explained by the other cell-type, is shown in the top left corner of each plot (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#pgen.1004958.s001" target="_blank">S1 Table</a>).</p

Allele-specific expression cell-type and individual effects.

<p>(A) Overlap of Allele-Specific Expression (ASE) across cell-types illustrated by the relative amount of ASE sites (<i>P</i> < 0.005) in each cell-type (x-axis) found in one, two or three cell-types within each individual (y-axis), requiring at least 30 reads per site and further sampling to exactly 30 reads. Number of ASE sites falling in each category is indicated in the squares. F, L and T stand for fibroblasts, LCLs and T-cells, respectively. 33–40% of the assayable heterozygous sites in the three cell-types of an individual are in ASE in at least two cell-types (see also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#pgen.1004958.s020" target="_blank">S13E Fig.</a>). (B) Distributions of allelic ratio distance (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#sec004" target="_blank">Materials and Methods</a>) between samples of different (DIFF) or same cell-types (Cell-tp) or individual (Indivl). All the pair wise differences between distributions have <i>P</i> < 2.2E-16 (Wilcoxon test). Allelic ratio distances between two cell-types of an individual are smaller than those between two individuals within one cell-type, and these are smaller than those between different individuals and different cell-types. This indicates a strong genetic load at the individual level, but also an important cell-type specific effect.</p

Cell-type specific genetic effects on gene expression and DNA methylation.

<p>Effect sizes of expression Quantitative Trait Locus (eQTL) (A) and methylation QTLs (mQTL) (B) unions for each pair of cell-types. Effect size is measured as the difference in medians of scaled expression or scaled methylation level (β-value) between heterozygous individuals and the homozygous individuals for the major allele. Hence, effect sizes are quantified in terms of number of expression or methylation standard deviations changed by an allele modification for eQTLs and mQTLs, respectively. Effect sizes are significantly correlated among all cell-types (Pearson’s correlation <i>P</i> < 2.2E-16). Coefficient of determination <i>R</i>², reflecting the proportion of effect size variance in one cell-type explained by the other cell-type, is shown in the top left corner of each plot (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1004958#pgen.1004958.s001" target="_blank">S1 Table</a>). SNP-exon pairs or SNP-CpG pairs that are significant in both tissues at 10% FDR are depicted in black, whereas associations significant in only one of the two cell-types compared are in orange (fibroblasts), blue (LCLs) and purple (T-cells). The <i>R</i>² and the spread of the scatter plots show there is a large amount of tissue-specific genetic effects on gene expression and DNA methylation.</p

Additional file 2 of Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

Supplementary Tables. This file consists of long supplementary tables. (XLSX 13200 KB