Genome-wide investigation of DNA methylation marks associated with FV Leiden mutation.

In order to investigate whether DNA methylation marks could contribute to the incomplete penetrance of the FV Leiden mutation, a major genetic risk factor for venous thrombosis (VT), we measured genome-wide DNA methylation levels in peripheral blood samples of 98 VT patients carrying the mutation and 251 VT patients without the mutation using the dedicated Illumina HumanMethylation450 array. The genome-wide analysis of 388,120 CpG probes identified three sites mapping to the SLC19A2 locus whose DNA methylation levels differed significantly (p<3 10-8) between carriers and non-carriers. The three sites replicated (p<2 10-7) in an independent sample of 214 individuals from five large families ascertained on VT and FV Leiden mutation among which 53 were carriers and 161 were non-carriers of the mutation. In both studies, these three CpG sites were also associated (2.33 10-11<p<3.02 10-4) with biomarkers of the Protein C pathway known to be influenced by the FV Leiden mutation. A comprehensive linkage disequilibrium (LD) analysis of the whole locus revealed that the original associations were due to LD between the FV Leiden mutation and a block of single nucleotide polymorphisms (SNP) located in SLC19A2. After adjusting for this block of SNPs, the FV Leiden mutation was no longer associated with any CpG site (p>0.05). In conclusion, our work clearly illustrates some promises and pitfalls of DNA methylation investigations on peripheral blood DNA in large epidemiological cohorts. DNA methylation levels at SLC19A2 are influenced by SNPs in LD with FV Leiden, but these DNA methylation marks do not explain the incomplete penetrance of the FV Leiden mutation

Manhattan plot of the MWAS results at 388,120 CpG sites.

<p>Manhattan plot of the MWAS results at 388,120 CpG sites.</p

Association of rs970740 with <i>SLC19A2</i> cg1658605, cg0483076 and cg09671955 levels.

<p>p-values were adjusted for age, sex, batch, chip and cell type composition.</p><p>In the F5L-families study, the rs970740 was not genotyped but substituted by the proxy rs2420371 that is in complete association (r² = 1) with it.</p><p>Association of rs970740 with <i>SLC19A2</i> cg1658605, cg0483076 and cg09671955 levels.</p

Association⁽¹⁾ of <i>SLC19A2</i> CpG sites with ACVn (MARTHA) and APCR (F5L-families) phenotypes.

(1)<p> Association is expressed as % change in phenotype (95% Confidence Interval) for every 0.1 unit increase in methylation β-value.</p>(2)<p> Analysis were adjusted for age, sex, batch, chip and cell type composition.</p><p>Association^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0108087#nt105" target="_blank">(1)</a>} of <i>SLC19A2</i> CpG sites with ACVn (MARTHA) and APCR (F5L-families) phenotypes.</p

Characteristics of the studied populations.

(1)<p> In MARTHA, ACVn ratio was significantly (p = 1.63 10⁻³⁸) decreased in <i>F5</i> rs6025 carriers compared to non-carriers.</p>(2)<p> In families, APCR ratio was significantly (p = 9.98 10⁻⁴⁷) decreased in <i>F5</i> rs6205 carriers compared to non-carriers.</p><p>Characteristics of the studied populations.</p

Meta-analysis of 65,734 Individuals Identifies TSPAN15 and SLC44A2 as Two Susceptibility Loci for Venous Thromboembolism

Molecular Epidemiolog

Meta-analysis of 65,734 individuals identifies TSPAN15 and SLC44A2 as two susceptibility loci for venous thromboembolism.

International audienceVenous thromboembolism (VTE), the third leading cause of cardiovascular mortality, is a complex thrombotic disorder with environmental and genetic determinants. Although several genetic variants have been found associated with VTE, they explain a minor proportion of VTE risk in cases. We undertook a meta-analysis of genome-wide association studies (GWASs) to identify additional VTE susceptibility genes. Twelve GWASs totaling 7,507 VTE case subjects and 52,632 control subjects formed our discovery stage where 6,751,884 SNPs were tested for association with VTE. Nine loci reached the genome-wide significance level of 5 × 10(-8) including six already known to associate with VTE (ABO, F2, F5, F11, FGG, and PROCR) and three unsuspected loci. SNPs mapping to these latter were selected for replication in three independent case-control studies totaling 3,009 VTE-affected individuals and 2,586 control subjects. This strategy led to the identification and replication of two VTE-associated loci, TSPAN15 and SLC44A2, with lead risk alleles associated with odds ratio for disease of 1.31 (p = 1.67 × 10(-16)) and 1.21 (p = 2.75 × 10(-15)), respectively. The lead SNP at the TSPAN15 locus is the intronic rs78707713 and the lead SLC44A2 SNP is the non-synonymous rs2288904 previously shown to associate with transfusion-related acute lung injury. We further showed that these two variants did not associate with known hemostatic plasma markers. TSPAN15 and SLC44A2 do not belong to conventional pathways for thrombosis and have not been associated to other cardiovascular diseases nor related quantitative biomarkers. Our findings uncovered unexpected actors of VTE etiology and pave the way for novel mechanistic concepts of VTE pathophysiology