Association between ILMN_1689088 (<i>COLEC12</i>) expression and the main haplotypes derived from rs9966524, rs9960856, and rs2846666.

<p>See the first paragraph of legend in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003240#pgen-1003240-g002" target="_blank">Figure 2</a> for explanations. In CTS, the rs9966524 and rs2846666 were substituted by their corresponding proxies, rs3932728 (r² = 0.82) and rs2846667 (r² = 0.87). The original haplotypic association (dark grey bars) was due to two haplotypes associated with increased <i>COLEC12</i> expression, the TCA (β = +0.331 p = 3.07 10⁻¹⁰ and β = +0.111, p = 5.83 10⁻⁴, in CTS and GHS, respectively) and the CCA (β = +0.278 p = 5.96 10⁻¹⁸ and β = +0.204, p = 4.19 10⁻⁶⁰, in CTS and GHS, resp.). In GHS, the best imputed <i>cis</i> eSNP was rs11081136 whose minor allele was associated with increased <i>COLEC12</i> expression (β = +0.091, p = 1.02 10⁻²⁶). After adjustment for rs11081136 (light grey bars), the TCA (β = +0.092, p = 2.52 10⁻³) and CCA (β = +0.171, p = 1.39 10⁻⁴⁰) haplotypes were still associated with <i>COLEC12</i> expression. The rs11081136 effect also remained significant (β = +0.061, p = 1.12 10⁻¹³).</p

Association between ILMN_1726554 (<i>IREB2</i>) expression and the main haplotypes derived from rs1394371, rs13180, and rs950776.

<p>See the first paragraph of legend in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003240#pgen-1003240-g002" target="_blank">Figure 2</a> for explanations. In CTS, the rs950776 was substituted by its proxy rs1948 (r² = 0.96). The original haplotypic association (dark grey bars) was compatible with the effects of three common haplotypes associated with increased <i>IREB2</i> expression, CCT (β = +0.121, p = 1.75 10⁻¹² and β = +0.096, p = 2.40 10⁻²⁵ in CTS and GHS, respectively), CCC (β = +0.205, p = 2.69 10⁻²⁹ and β = +0.118, p = 1.10 10⁻³⁰, resp.) and CTC (β = +0.115, p = 7.87 10⁻¹⁰ and β = +0.059, p = 5.31 10⁻¹⁰, resp.). After adjusting for the best imputed <i>cis</i> eSNP rs12592111 in GHS (light grey), the effect of the CCT and CCC haplotypes were no longer significant (β = −0.026, p = 0.575 and β = +0.011, p = 0.302, respectively) while the effect of the CTC haplotype was barely modified (β = +0.051, p = 2.01 10⁻⁷). The CCT and CCC haplotypes are the only two haplotypes carrying the rs13180-C allele, suggesting that these haplotypes were reflecting an effect of rs13180. This is in accordance with the nearly complete association between rs13180 and the best <i>cis</i> eSNP rs12592111 (r² = 0.96).</p

Association between ILMN_1731596 (<i>AP3S2</i>) expression and the main haplotypes derived from rs7173483, rs3803536, and rs1269077.

<p>See the first paragraph of legend in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003240#pgen-1003240-g002" target="_blank">Figure 2</a> for explanations. In CTS, the rs7173483, rs3803536 and rs1269077 were substituted by their corresponding proxies, rs4932145 (r² = 1), rs10520684 (r² = 0.92) and rs1256854 (r² = 0.95), respectively. After imputation, the best <i>cis</i> eSNP in GHS was rs12148357 which was not among the associated htSNPs. Its minor allele was associated with decreased <i>AP3S2</i> expression (β = −0.146; p = 1.59 10⁻⁵⁴). However, in the conditional model adjusting for haplotype effects, its effect was no longer significant (β = −0.022, p = 0.420) suggesting that it was due to LD with haplotypes. The haplotypic association was compatible with the additive effects of three SNPs. The rs7173483-A allele was associated with decreased <i>AP3S2</i> expression (β = −0.147, p = 2.80 10⁻¹⁸ and β = −0.1500; p = 9.50 10⁻¹¹ in CTS and GHS, respectively), as were the rs3803536-G allele (β = −0.052, p = 5.03 10⁻⁴ and β = −0.065, p = 1.75 10⁻⁶, resp.) and the rs1269077-C allele (β = −0.067, p = 2.93 10⁻⁷ and β = −0.066, p = 9.49 10⁻¹⁷, resp.).</p

Association between ILMN_1757379 (<i>OPN1SW</i>) expression and the haplotypes derived from rs1109552, rs4731507, rs4731513, and rs339088.

<p>The top panel shows the results in the discovery cohort CTS and the bottom panel in the replication cohort GHS. Each bar corresponds to the expected mean of gene expression associated with one dose of the corresponding haplotype under the assumption of additive haplotype effects. According to this model, the expression level of an individual is the sum of the levels of his (her) two haplotypes. Haplotype frequencies are indicated under each haplotype label. In CTS, the rs4731507 and rs339088 were substituted by their perfect proxies (r² = 1) rs4283986 and rs339085, respectively. The original haplotypic association (dark grey bars) was due to a unique rare haplotype derived from 4 common htSNPs. This rare haplotype, GGGG, was associated with a strong increase in <i>OPN1SW</i> expression (β = +0.240, p = 8.12 10⁻²⁶ and β = +0.341, p<10⁻³⁰⁷ in CTS and GHS, respectively). After adjusting in GHS for the best imputed <i>cis</i> eSNP rs142976957 (light grey bars), the effect of this rare haplotype was still highly significant (β = +0.208, p = 4.78 10⁻¹³⁵).</p

Association between ILMN_2367638 (<i>CAMKK2</i>) expression and the main haplotypes derived from rs1140886, rs1063843, and rs11065504.

<p>The left panel shows the results in the discovery cohort CTS and the right panel in the replication cohort GHS. Each bar corresponds to the expected mean of gene expression associated with one dose of the corresponding haplotype under the assumption of additive haplotype effects. According to this model, the expression level of an individual is the sum of the levels of his (her) two haplotypes. Haplotype frequencies are indicated under each haplotype label. For ease of presentation, mean expression for the most frequent haplotype in CTS was set to be the same as that observed in GHS. In CTS, the rs11065504 was substituted by its proxy rs3794207 (r² = 0.96). After imputation, the best <i>cis</i> eSNP in GHS was rs11065504 whose allele C was carried by an unique haplotype, TCC, which was associated with increased <i>CAMKK2</i> expression (β = +0.338, p = 9.05 10⁻¹⁵⁶ and β = +0.217, p = 5.69 10⁻¹⁵¹ in CTS and GHS, respectively) compared to the TCT haplotype. In addition, the less common CCG haplotype was associated with an even stronger increase in <i>CAMKK2</i> expression (β = +0.386, p = 5.09 10⁻⁵⁶ and β = +0.269, p = 4.00 10⁻⁵³, resp.).</p

List of identified <i>LRRK2</i> eQTLs in three gene expression datasets: brain (n = 134), liver (n = 970) and monocytes (n = 1,490).

<p>For the P-value computations in brain samples, <i>LRRK2</i> expression values are averaged across all 10 brain regions. MAF: minor allele frequency. ^a: See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070724#pone.0070724.s002" target="_blank">Figure S2</a>. ^b: See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070724#pone.0070724.s001" target="_blank">Figure S1</a>.</p

Common variant associations in the <i>LRRK2</i> region for PD, CD and leprosy.

<p>The CD GWAS results indicate a minimum of two independent associations. For each disease association we list the P-values in the expression datasets. NS: not-significant (<i>P</i>>0.001). (a): See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0070724#pone.0070724.s003" target="_blank">Figure S3</a>.</p

RT-PCR results showing evidence of amplifiable splice forms across exons 32–33 of LRRK2 in selected brain regions, occipital cortex (OCTX), substantia nigra (SNIG), medulla (MEDU) and cerebellum (CRBL).

<p>(<b>A</b>) RT-PCR results confirming the splicing out of exons 32–33 in SNIG, compared with the other brain regions tested. The expected band size for the isoform with exon 32–33 included is 470 bps, whereas that for the isoform with exon 32 alone spliced out is 270 bps. These results show splicing out of exons 32–33 in substantia nigra and the existence of an isoform with exon 32 alone spliced out in OCTX, MEDU and CRBL. (<b>B</b>) RT-PCR results further confirm the splicing out of exon 33 in SNIG. While OCTX, MEDU and CRBL show the expected band size of 195 bps suggesting that exon 32–33 is not spliced out in these regions, SNIG does not.</p

Regional variability in LRRK2 expression.

<p>(<b>A</b>) Box plot of mRNA expression levels for <i>LRRK2</i> in 10 brain regions, based on microarray experiments and plotted on a log2 scale (y axis). Whiskers extend from the box to 1.5 times the inter-quartile range. (<b>B</b>) Box plot of mRNA expression levels for <i>LRRK2</i> in 4 brain regions, based on QuantiGene experiments. Whiskers extend to the maximum and minimum values. Stars indicate significant differences in expression between brain regions (p-value <0.01, Wilcoxon signed rank testing). (<b>C</b>) Dot plot of mRNA expression levels for <i>LRRK2</i> in 3 brain regions based on TaqMan Real Time PCR experiments. The expression levels were normalized to the geometric mean of 3 housekeeping genes. The graph shows higher expression in OCTX compared with other regions. Abbreviations: frontal cortex (FCTX), occipital cortex (specifically primary visual cortex, OCTX), temporal cortex (TCTX), intralobular white matter (WHMT), thalamus (THAL), putamen (PUTM), substantia nigra (SNIG), hippocampus (HIPP), medulla (specifically inferior olivary nucleus, MEDU) and cerebellum (CRBL).</p

Gene-level association analysis of genes identified in the SNP-level analysis

<p>Gene-level association analysis of genes identified in the SNP-level analysis</p