Pairwise comparison of the number of cis-eQTLs with a nominal JLIM <i>P</i>-value < 0.01.

<p>Pairwise comparison of the number of cis-eQTLs with a nominal JLIM <i>P</i>-value < 0.01.</p

Examples of causal cis-eQTLs with systematic or heterogeneous effects on expression.

<p>This figure shows exon-level analysis using a modified test of heterogeneity to distinguish systematic causal <i>cis</i>-eQTLs and heterogeneous <i>cis</i>-eQTLs. It then stratifies these results based on whether the association is detected at gene-level or not. Each panel shows the gene-level association with <i>cis</i>-eQTL association <i>P</i>-value and RTC score (RTC > = 0.95 is deemed causal, highlighted in green), the exon-level association for each exon of the gene against the <i>cis</i>-eQTL, the heterogeneous model output from the likelihood ratio test with χ² statistic, degrees of freedom (DF), and model <i>P</i>-value (highlighted in red is heterogeneous, green is systematic), and finally the collapsed gene model underneath with labelled exons. N.B box-plots in a darker shade are those that are deemed to be causal associations (<i>P</i>_BF < 0.05 & RTC > = 0.95). (A) Systematic <i>cis</i>-eQTL detected at gene-level (B) systematic <i>cis</i>-eQTL not detected at gene-level (C) heterogeneous <i>cis</i>-eQTL detected at gene-level (D) heterogeneous <i>cis</i>-eQTL not detected at gene-level.</p

Breakdown of autoimmune associated causal cis-eQTLs using RNA-Seq.

<p>(A) Percentage and number of causal <i>cis</i>-eQTL associations detected per RNA-Seq quantification type, following LD pruning of associated SNPs from twenty autoimmune diseases to 560 independent susceptibly loci. The top chart shows the number of causal <i>cis</i>-eQTLs when combining all RNA-Seq profiling types together (20%). (B) Sharing of causal <i>cis</i>-eQTL associations per quantification type (110 detected in total). Percentage of causal <i>cis</i>-eQTLs captured are shown as a percentage of the 110 total. (C) Total causal <i>cis</i>-eQTLs per disease across all five levels of RNA-Seq quantification, using the 20 diseases of the ImmunoBase resource. In orange are disease-associated SNPs that show no shared association with expression across any quantification type. In blue are the disease-associated SNPs that are also causal <i>cis</i>-eQTLs. (D) Causal <i>cis</i>-eQTLs and candidate genes per disease broken down by quantification type.</p

Functional annotation of causal autoimmune cis-eQTLs.

<p>(A) We took the causal autoimmune <i>cis</i>-eQTLs detected for each RNA-Seq quantification type and performed enrichment testing for chromatin state segmentation and histone marks in LCLs taken from the NIH Roadmap Epigenomics Project. We used the GoShifter algorithm to do this (see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007071#sec014" target="_blank">methods</a>); which takes all SNPs in strong LD (<i>r</i>²>0.8) with the causal <i>cis</i>-eQTLs and calculates the proportion of SNPs overlapping chromatin marks, the positions of the marks are then shuffled whilst retaining the SNP positions, and the fraction of overlap recalculated over 1,000 permutations. A permutation <i>P</i>-value is then generated–which is annotated in each box (<i>P</i><0.05 deemed significant). The heat colour is representative of the permutation <i>P</i>-value. Significant enrichment tests are highlighted in bold. The total number of causal <i>cis</i>-eQTLs per quantification type are annotated at the bottom of the heatmap. (B) The percentage of causal <i>cis</i>-eQTLs in chromatin regulatory marks per quantification type. An asterisk shows that this level of enrichment is deemed to be significant as shown in panel A. (C) The percentage of causal <i>cis</i>-eQTLs in chromatin regulatory marks per quantification type that are or are highly correlated (<i>r</i>²>0.8) with SNPs that alter splice site consensus sequences of the target genes (assessed by Sequence Ontology for the hg19 GENCODE v12 reference annotation).</p

Pairwise comparison of cis-eQTL and JLIM P-values for matched SNP-gene pairs.

<p>This figure is complementary to the data in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007071#pgen.1007071.t002" target="_blank">Table 2</a> and is derived from <i>cis</i>-eQTL analysis of the 38 SLE associated SNPs using RNA-Seq and implementation of the JLIM method to assess evidence of a shared causal variant. (A) We measured the Pearson’s correlation separately of all <i>cis</i>-eQTL and JLIM <i>P</i>-values between matched SNP-gene <i>cis</i>-eQTL pairs across the five RNA-Seq quantification types. We only considered matched SNP-gene <i>cis</i>-eQTL association pairs that had a nominal <i>cis</i>-eQTL association <i>P</i>-value < 0.01 in both quantification types, and to be conservative, when multiple transcripts, exons, junctions, and introns were annotated with the same gene symbol, we selected the associations that minimized the difference in JLIM <i>P</i>-value between matched SNP-gene <i>cis</i>-eQTLs across RNA-Seq quantification types. Note the weak JLIM <i>P</i>-value correlation of matched transcript-level and junction-level <i>cis</i>-eQTLs suggesting they stem from independent causal variants. (B) Correlation plots of matches SNP-gene <i>cis</i>-eQTL pairs as described above (red: <i>cis</i>-eQTL <i>P</i>-value; blue: JLIM <i>P</i>-value). Note that JLIM <i>P</i>-values often aggregate on the axis rather than on the diagonal suggesting independent causal variants across different quantification types. (C) An example of the sensitivity of exon-level analysis relative to gene-level. The majority of nominally significant JLIM <i>P</i>-values (<0.01) for matched SNP-gene pairs are captured by exon-level analysis and concealed at gene-level (green box: 9%).</p

Nine SLE loci contain cis-eQTLs driven by the same variant as the disease association.

<p>Nine SLE loci contain cis-eQTLs driven by the same variant as the disease association.</p

Isolation of potential causal molecular mechanism in <i>TYK2</i> by SLE cis-eQTL rs2304256.

<p>(A) SLE GWAS association plot and <i>cis</i>-eQTL association plot around the 19p13.2 susceptibility locus tagged by rs2304256. The top panel shows the association plot with SLE that spans the gene body and 3′ region of <i>TYK2</i> (Tyrosine Kinase 2). The haplotype block composed of highly correlated SNPs is highlighted in the red block. The second panel shows the <i>cis</i>-eQTL association plot at gene-level of all proximal SNPs to <i>TYK2</i> (no significant association with rs2304256 is detected). The third panel shows the same regional association but at exon-level for the most associated exon of <i>TYK2</i> with rs2304256 –the bottom panel is at intron-level for <i>TYK2</i> (both are highly associated). (B) Correlation of SLE GWAS <i>P</i>-value and <i>cis</i>-eQTL association <i>P</i>-value for all SNPs in <i>cis</i> to <i>TYK2</i>. We show at gene-level the most associated SLE SNPs are not <i>cis</i>-eQTLs (top panel). The middle and bottom panels show the same correlation at exon-level and intron-level and reveal the most associated SNPs to SLE are also the most associated <i>cis</i>-eQTLs to <i>TYK2</i>. (C) The direction of effect of <i>cis</i>-eQTL rs2304256 with <i>TYK2</i> at gene-level (top), exon-level (middle), and intron-level (bottom panel). The risk allele is rs2304256 [C]. (D) The top panel shows <i>cis</i>-eQTL association and JLIM <i>P</i>-values for all exons of <i>TYK2</i> against rs2304256. Exon 8 (marked by an asterisk) is defined as having a causal association with rs2304256. The bottom panel shows the intron-level <i>cis</i>-eQTL of <i>TYK2</i> against rs2304256. Note many introns are <i>cis</i>-eQTLs but are not causal with rs2304256. Exons and introns are numbered consecutively from start to end of gene if they are expressed (note some are not and therefore not included). (E) The genomic location of the single exon and single intron of <i>TYK2</i> that are modulated by rs2304256 are highlighted (rs2304256 is marked by an asterisk in red). The bottom two panels show the transcription levels assayed by RNA-Seq on LCLs assayed by ENCODE. Note intron 9–10 of <i>TYK2</i> is clearly expressed. The alignability of 75-mers by GEM is also shown to show the mapability of reads around rs2304256.</p

Meta-analysis for risk alleles in SLE-associated <i>MECP2</i> SNPs in Korean and European-derived cohorts

<p>OR, odds ratio; CI, confidence interval</p

Allelic association results and linkage disequilibrium (LD) plot of the chromosome Xq28 region around the <i>MECP2</i> gene.

<p>The allelic association p values of the SNPs analyzed are shown in the European-derived cohort included in this study.</p

Frequencies of homozygous risk allele genotypes in Korean SLE patients compared to controls.

<p>OR, odds ratio; CI, confidence interval.</p>*<p>A total of 628 independent female SLE patients and 736 healthy unrelated female controls were genotyped</p