Genome-Wide Investigation of DNA Methylation Marks Associated with FV Leiden Mutation

PLOS ONE, Dec 2019

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.

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Genome-Wide Investigation of DNA Methylation Marks Associated with FV Leiden Mutation

et al. (2014) Genome-Wide Investigation of DNA Methylation Marks Associated with FV Leiden Mutation. PLoS ONE 9(9): e108087. doi:10.1371/journal.pone.0108087 Genome-Wide Investigation of DNA Methylation Marks Associated with FV Leiden Mutation Dylan Assi 0 Jessica Dennis 0 Martin Ladouceur 0 Vinh Truong 0 Nora Zwingerman 0 Ares Rocanin-Arjo 0 Marine Germain 0 Tara A. Paton 0 Pierre-Emmanuel Morange 0 France Gagnon 0 David-Alexandre Tre goue t 0 Tanja Zeller, Medical University Hamburg, University Heart Center, Germany 0 1 Sorbonne Universite s, UPMC Univ Paris 06, UMR_S 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases , Paris, France, 2 INSERM, UMR_S 1166 , Team Genomics & Pathophysiology of Cardiovascular Diseases , Paris , France , 3 ICAN Institute for Cardiometabolism and Nutrition, Paris, France, 4 Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto , Toronto , Canada , 5 Centre de Recherches du CHUM , Montre al , Canada , 6 The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children , Toronto, Ontario , Canada , 7 Aix-Marseille University, UMR_S 1062, Nutrition Obesity and Risk of Thrombosis , Marseille, France, 8 INSERM, UMR_S 1062 , Nutrition Obesity and Risk of Thrombosis , Marseille , France , 9 Laboratory of Haematology, La Timone Hospital , Marseille , France 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 1028) between carriers and noncarriers. The three sites replicated (p,2 1027) 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 10211,p,3.02 1024) 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. - Funding: DA and ARA were supported by a PhD grant from the Region Ile de France (CORDDIM). JD holds a Vanier Canada Graduate Scholarship, ML holds a fellowship from the Canadian Institutes of Health Research (CIHR), and FG holds a Canada Research Chair. JD, ML and NZ are fellows of the CIHR Strategic Training for Advanced Genetic Epidemiology Training Grant (STAGE) in Genetic Epidemiology and Statistical Genetics (GET-101831). The MARTHA project was supported by a grant from the Program Hospitalier de Recherche Clinique. The H450M epityping was partially funded by the Canadian Institutes of Health Research (grant MOP 86466) and by the Heart and Stroke Foundation of Canada (grant T6484). Statistical analyses of the MARTHA datasets was performed using the C2BIG computing cluster funded by the Region Ile de France, Pierre and Marie Curie University, and the Institute for Cardiometabolism and Nutrition (ANR-10-IAHU-05). The F5L Thrombophilia French-Canadian Pedigree study was supported by grants from the Canadian Institutes of Health Research (MOP86466) and by the Heart and Stroke Foundation of Canada (T6484). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Venous thrombosis (VT) is a common complex disease characterized by a sibling relative risk of ,3 [1] and heritability estimates ranging from 30% to 60% [2,3]. Contrary to other complex diseases, few new VT susceptibility genes were discovered by the recent waves of Genome-Wide Association Studies (GWAS) [4]. Established VT-associated genes collectively explain only about 5% of the disease heritability [2] and family history of VT remains an important risk factor despite adjustment for known variants [5,6]. In addition, marked clinical variability is observed even in affected individuals fro (...truncated)


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Dylan Aïssi, Jessica Dennis, Martin Ladouceur, Vinh Truong, Nora Zwingerman, Ares Rocanin-Arjo, Marine Germain, Tara A. Paton, Pierre-Emmanuel Morange, France Gagnon, David-Alexandre Trégouët. Genome-Wide Investigation of DNA Methylation Marks Associated with FV Leiden Mutation, PLOS ONE, 2014, Volume 9, Issue 9, DOI: 10.1371/journal.pone.0108087