Stroke has multiple etiologies, but the underlying genes and pathways are largely unknown. We conducted a multiancestry genome-wide-association meta-analysis in 521,612 individuals (67,162 cases and 454,450 controls) and discovered 22 new stroke risk loci, bringing the total to 32. We further found shared genetic variation with related vascular traits, including blood pressure, cardiac traits, and venous thromboembolism, at individual loci (n = 18), and using genetic risk scores and linkage-disequilibrium-score regression. Several loci exhibited distinct association and pleiotropy patterns for etiological stroke subtypes. Eleven new susceptibility loci indicate mechanisms not previously implicated in stroke pathophysiology, with prioritization of risk variants and genes accomplished through bioinformatics analyses using extensive functional datasets. Stroke risk loci were significantly enriched in drug targets for antithrombotic therapy.

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Body fat distribution is a risk factor for adverse cardiovascular health consequences. We analyzed the association of body fat distribution, assessed by waist-to-hip ratio adjusted for body mass index, with 228,985 predicted coding and splice site variants available on exome arrays in up to 344,369 individuals from five major ancestries (discovery) and 132,177 European-ancestry individuals (validation). We identified 15 common (minor allele frequency, MAF ≥ 5%) and 9 low frequency or rare (MAF < 5%) coding novel variants. Pathway/gene set enrichment analyses identified lipid particle, adiponectin, abnormal white adipose tissue physiology, and bone development and morphology as important contributors to fat distribution, while cross-trait associations highlight cardiometabolic traits. In functional follow-up analyses, specifically in Drosophila RNAi-knockdowns, we observed a significant increase in the total body triglyceride levels for two genes ( DNAH10 and PLXND1 ). We implicate novel genes in fat distribution, stressing the importance of interrogating low-frequency and protein-coding variants.

Carotid intima media thickness (cIMT) is a biomarker of subclinical atherosclerosis and a predictor of future cardiovascular events. Identifying associations between gene expression levels and cIMT may provide insight to atherosclerosis etiology. Here, we use two approaches to identify associations between mRNA levels and cIMT: differential gene expression analysis in whole blood and S-PrediXcan. We used microarrays to measure genome-wide whole blood mRNA levels of 5647 European individuals from four studies. We examined the association of mRNA levels with cIMT adjusted for various potential confounders. Significant associations were tested for replication in three studies totaling 3943 participants. Next, we applied S-PrediXcan to summary statistics from a cIMT genome-wide association study (GWAS) of 71 128 individuals to estimate the association between genetically determined mRNA levels and cIMT and replicated these analyses using S-PrediXcan on an independent GWAS on cIMT that included 22 179 individuals from the UK Biobank. mRNA levels of TNFAIP3, CEBPD and METRNL were inversely associated with cIMT, but these associations were not significant in the replication analysis. S-PrediXcan identified associations between cIMT and genetically determined mRNA levels for 36 genes, of which six were significant in the replication analysis, including TLN2, which had not been previously reported for cIMT. There was weak correlation between our results using differential gene expression analysis and S-PrediXcan. Differential expression analysis and S-PrediXcan represent complementary approaches for the discovery of associations between phenotypes and gene expression. Using these approaches, we prioritize TNFAIP3, CEBPD, METRNL and TLN2 as new candidate genes whose differential expression might modulate cIMT.

Introduction: Common variants in the gene encoding insulin receptor substrate 1 ( IRS1 ) and nearby on 2q36.3 have been associated with levels of fasting insulin (FI). We hypothesized that a greater burden of rare variants in these regions is associated with higher FI. Methods: CHARGE-S sequenced (average coverage >60x) the IRS1 and 2q36.6 regions (totaling 185 kb) in 3,539 individuals on the SOLiD platform. FI information among non-diabetics was available in 3 studies: Framingham Heart Study ( N =811), Cardiovascular Heart Study ( N =967) and Atherosclerosis Risk in Communities Study ( N =1761). We analyzed rare variants (MAF < 1%) using a weighted sum test, similar to Madsen-Browning (powerful to detect an association if effects of casual rare variants are in the same direction), and the SKAT test (preferred method if variant effects are in opposite directions). Meta-analyses of weighted rare variants results used the inverse-variance method while SKAT results used a similar approach. For multi-variant tests, the threshold for significance was considered to be α = 0.05. Coding annotation predictions were obtained from the dbNSFP database which includes functional predictions from SIFT, MutationTaster, Polyphen-2, Phylo-P and LRT. Non-coding annotation information (protein binding regions, transcription factor binding sites, DNase hypersensitivity sites, conservation scores) was obtained from ENCODE and ORegAnno databases. From these annotations, we grouped different types of variants together (possible loss of function; possibly regulatory) in order to determine specific variants contributing most to the effect. Results: Sequencing found 4,534 variants in two regions, 86.7% of which were rare and novel, not seen in 1000 genomes or dbSNP. Approximately 20% of variants had annotation information available; of these, 34 variants were possibly damaging. We found suggestive association with FI ( p =0.03) for all rare variants in the meta-analysis of weighted-sum tests at 2q36.3 but not at IRS1 . At IRS1 (but not at 2q36.3), SKAT meta-analysis tests showed evidence for all rare variants associated with FI ( p =0.03). SKAT tests restricted to N =365 possibly damaging variants at IRS1 suggested an association with FI in coding ( p =0.06) and in non-coding ( p =0.02) variants. Conclusion: Large scale deep sequencing in the IRS1 and 2q36.3 regions found very large numbers of new, rare variants. Multi-variant tests suggest that rare variation in these regions influence FI levels, with individuals with more and rarer variants having higher FI. Further investigation is warranted to address why weighted sum and SKAT tests provide different levels of evidence for association in the two regions. Also, conditional analyses will test whether new rare variants at IRS1 or 2q36 explain observed GWAS associations.

Introduction: Fibrinogen is a key component of the coagulation cascade, and variation in its circulating levels may contribute to thrombotic diseases, such as venous thromboembolism (VTE) and ischemic stroke. Methods: Two-sample Mendelian randomization (MR) was applied to estimate the causal effect of circulating fibrinogen and its isoform, gamma prime fibrinogen, on risk of VTE and ischemic stroke subtypes using summary statistics from published genome-wide association studies of fibrinogen, VTE, and ischemic stroke, and an unpublished study of gamma prime fibrinogen. Genetic instruments for fibrinogen and gamma prime fibrinogen were selected by pruning genome-wide significant variants to linkage disequilibrium r 2 < 0.1. The inverse variance weighted MR approach was used to estimate effects in the main analysis, with additional approaches that are more robust to the inclusion of pleiotropic variants applied in sensitivity analyses, including MR-Egger, weighted median MR, and weighted mode MR. Results: The main inverse variance weighted MR estimates ( Table ) based on 85 genetic instruments for fibrinogen and 27 genetic instruments for gamma prime fibrinogen indicated a protective effect of both fibrinogen and gamma prime fibrinogen levels on VTE risk. Higher fibrinogen levels decreased the risk of cardioembolic stroke but increased the risk of large artery and small vessel stroke. Higher gamma prime fibrinogen levels decreased the risk of all ischemic stroke, cardioembolic stroke, and large artery stroke. Effect estimates were consistent across sensitivity analyses, indicating that the results are unlikely to be attributable to the inclusion of pleiotropic variants. Conclusion: Our results are consistent with effects of genetically determined fibrinogen and gamma prime fibrinogen on VTE and ischemic stroke. The identified protective effects may reflect the diverse roles of the fibrinogen, beyond the formation of fibrin clots, in thrombotic diseases with different etiologies.