Recent genome-wide association studies (GWAS) have confirmed known risk mutations for venous thromboembolism (VTE) and identified a number of novel susceptibility loci in adults. Here we present a ...GWAS in 212 nuclear families with pediatric VTE followed by targeted next-generation sequencing (NGS) to identify causative mutations contributing to the association. Three single nucleotide polymorphisms (SNPs) exceeded the threshold for genome-wide significance as determined by permutation testing using 100 000 bootstrap permutations (P < 10−5). These SNPs reside in a region on chromosome 6q13 comprising the genes small ARF GAP1 (SMAP1), an ARF6 guanosine triphosphatase-activating protein that functions in clathrin-dependent endocytosis, and β-1,3-glucoronyltransferase 2 (B3GAT2), a member of the human natural killer 1 carbohydrate pathway. Rs1304029 and rs2748331 are associated with pediatric VTE with unpermuted/permuted values of P = 1.42 × 10−6/2.0 × 10−6 and P = 6.11 × 10−6/1.8 × 10−5, respectively. Rs2748331 was replicated (P = .00719) in an independent study sample coming from our GWAS on pediatric thromboembolic stroke (combined P = 7.88 × 10−7). Subsequent targeted NGS in 24 discordant sibling pairs identified 17 nonsynonymous coding variants, of which 1 located in SMAP1 and 3 in RIMS1, a member of the RIM family of active zone proteins, are predicted as damaging by Protein Variation Effect Analyzer and/or sorting intolerant from tolerant scores. Three SNPs curtly missed statistical significance in the transmission-disequilibrium test in the full cohort (rs112439957: P = .08326, SMAP1; rs767118962: P = .08326, RIMS1; and rs41265501: P = .05778, RIMS1). In conjunction, our data provide compelling evidence for SMAP1, B3GAT2, and RIMS1 as novel susceptibility loci for pediatric VTE and warrant future functional studies to unravel the underlying molecular mechanisms leading to VTE.
•Our study identified a region on chromosome 6 comprising the genes SMAP1, B3GAT2, and RIMS1 as novel susceptibility locus for pediatric VTE.•Nonsynonymous variants in SMAP1 and RIMS1 are predicted as deleterious and may influence vesicle processing in blood cells.
Purpose
Genetic factors contribute to the development and progression of age-related macular degeneration (AMD). We aimed to assess the association of drusen as phenotypic characteristics of early ...AMD and their progression with polymorphisms in the
CFH
,
ABCA1,
and
ARMS2
genes.
Methods
In the Münster Aging and Retina Study (MARS), drusen were detected in 406 patients with early AMD and 170 healthy controls according to the International Classification using fundus photographs, with a follow-up examination after 2.6 years (median). Six drusen features were assessed: drusen number (</≥20); confluence of drusen (</≥50 %), largest drusen size (</≥175 μm); area occupied by drusen (</≥10 %); most frequent drusen size (</≥175 μm), and presence of soft, indistinct drusen (no/yes). Based on these features, an unweighted summary drusen severity score (DSS; categorized in “low”, “intermediate” and “high”) was calculated. The relationship of each drusen feature and the DSS with
CFH
rs1061170,
ABCA1
rs1883025, and
ARMS2
rs10490924 at baseline and after 2.6 years was analyzed using multivariate logistic regression models.
Results
Cross-sectionally, each drusen feature was associated with a higher frequency of the
CFH
and
ARMS2
risk variants. Compared to healthy eyes, the
CFH
risk variant was more common in eyes with early as well as advanced drusen features, while the
ARMS2
variant was only associated with advanced drusen. After 2.6 years, 43 % of the eyes showed a progression of at least 1 unit in the DSS. The progression from low to higher DSS was inversely associated with
ABCA1
(OR = 0.54), and the progression from intermediate to high DSS was positively related to
CFH
rs1061170 (OR = 2.3;
p
< 0.05 for each).
Conclusions
Variants in
CFH
,
ABCA1
, and
ARMS2
genes are related to the presence and progression of drusen in early AMD.
CFH
and, inversely,
ABCA1
seem to be involved in early drusen development, while the role of
ARMS2
is more pronounced in advanced stages of early AMD.
Recently, we reported a gene network of ADAMTS (A Disintegrin-like and Metalloprotease with Thrombospondin motifs) genes as central component of the genetic risk contributing to pediatric stroke. ...ADAMTS13 is a prime example for such a key component as it cleaves von Willebrand factor multimers, reduces platelet adhesion and aggregation, and downregulates thrombus formation and inflammation.
We characterized the genetic architecture of ADAMTS13 through targeted next-generation sequencing of 48 affected children and their unaffected siblings and identified in total 241 variants (single nucleotide polymorphisms or insertions/deletions) in the ADAMTS13 gene. From these, based on significance in the sibship disequilibrium test (P<0.05) or protein-altering properties, we selected 21 common variants covering the complete ADAMTS13 gene for genotyping in 270 trios and subsequent association analyses. Transmission disequilibrium testing was performed for affection status and ADAMTS13 activity levels using PLINK and FBAT, respectively. Ten single nucleotide polymorphisms were significantly associated with pediatric stroke (P<0.05 to P<0.001), 2 of which (rs2285489 and rs28793911) were also significantly associated with ADAMTS13 levels (P=0.0004 and P=0.0092). The resulting protective haplotype H1.1. (T:U 95.5: 144.4; P=0.0016) is associated with increased ADAMTS13 levels (age-adjusted P=0.0108). Haplotype association using a sliding window approach assigns this association to the ADAMTS13 von Willebrand factor-binding domain (P=1.2×10(-4)).
Our data provide a link between the genetic architecture of ADAMTS13, ADAMTS13 levels, and stroke susceptibility. Altogether, these studies render ADAMTS13 an attractive candidate for functional studies and may contribute to personalized diagnosis and treatment options in future.
Pediatric stroke is a rare but highly penetrant disease with a strong genetic background. Although there are an increasing number of genome-wide association studies (GWASs) for stroke in adults, such ...studies for stroke of pediatric onset are lacking. Here we report the results of the first GWAS on pediatric stroke using a large cohort of 270 family-based trios. GWAS was performed using the Illumina 370 CNV single nucleotide polymorphisms array and analyzed using the transmission disequilibrium test as implemented in PLINK. An enrichment analysis was performed to identify additional true association signals among lower P value signals and searched for cumulatively associated genes within protein interaction data using dmGWAS. We observed clustering of association signals in 4 genes belonging to one family of metalloproteinases at high (ADAMTS12, P = 2.9 × 10−6; ADAMTS2, P = 8.0 × 10−6) and moderate (ADAMTS13, P = 9.3 × 10−4; ADAMTS17, P = 8.5 × 10−4) significance levels. Over-representation and gene-network analyses highlight the importance of the extracellular matrix in conjunction with members of the phosphoinositide and calcium signaling pathways in the susceptibility for pediatric stroke. Associated extracellular matrix components, such as ADAMTS proteins, in combination with misbalanced coagulation signals as unveiled by gene network analysis suggest a major role of postnatal vascular injury with subsequent thrombus formation as the leading cause of pediatric stroke.
OBJECTIVE Cerebral aneurysms (CAs) affect 2%-5% of the population, and familial predisposition plays a significant role in CA pathogenesis. Several lines of evidence suggest that genetic variations ...in matrix metalloproteinase genes (MMP) are involved in the etiopathology of CAs. The authors performed a case-control study to investigate the effect of 4 MMP variants from the ADAMTS family on the pathogenesis of CAs. METHODS To identify susceptible genetic variants, the authors investigated 8 single nucleotide polymorphisms (SNPs) in 4 genes from the ADAMTS family (ADAMTS2, -7, -12, and -13) known to be associated with vascular diseases. The study included 353 patients with CAs and 1055 healthy adults. RESULTS The authors found significant associations between CA susceptibility and genetic variations in 3 members of the ADAMTS family. The largest risk for CA (OR 1.32, p = 0.006) was observed in carriers of the ADAMTS2 variant rs11750568, which has been previously associated with pediatric stroke. Three SNPs under investigation are associated with a protective effect in CA pathogenesis (ADAMTS12 variant rs1364044: OR 0.65, p = 0.0001; and ADAMTS13 variants rs739469 and rs4962153: OR 0.77 and 0.63, p = 0.02 and 0.0006, respectively), while 2 other ADAMTS13 variants may confer a significant risk (rs2301612: OR 1.26, p = 0.011; rs2285489: OR 1.24, p = 0.02). CONCLUSIONS These results suggest that reduced integrity of the endothelial wall, as conferred by ADAMTS variants, together with inflammatory processes and defective vascular remodeling plays an important role in CA pathogenesis, although the mechanism of action remains unknown. The authors' findings may lead to specific screening of at-risk populations in the future.
The authors performed a systematic review of the association of complement component 2(C2)/complement factor B (CFB) gene polymorphisms with age-related macular degeneration (AMD). In total, data ...from 19 studies published between 2006 and 2011 were pooled for 4 polymorphisms: rs9332739 and rs547154 in the C2 gene and rs4151667 and rs641153 in the CFB gene. Data extraction and assessments for risk of bias were independently performed by 2 reviewers. Allele frequencies and allele and genotypic effects were pooled. Heterogeneity and publication bias were explored. Pooled minor allele frequencies for all 4 SNPs were between 4.7% and 9.6% for all polymorphisms, except for an Indian population in which the C allele at rs9332739 was the major allele. For the C2 polymorphisms, the minor C allele at rs9332739 and the minor T allele at rs547154 carried estimated relative risks (odds ratios) of 0.55 (95% confidence interval (CI): 0.46, 0.65) and 0.47 (95% CI: 0.39, 0.57), respectively. For the CFB polymorphisms, the minor A alleles at rs4151667 and rs614153 carried estimated risks of 0.54 (95% CI: 0.45, 0.64) and 0.41 (95% CI: 0.34, 0.51), respectively. These allele effects contributed to an absolute lowering of the risk of all AMD in Caucasian populations by 2.0%-6.0%. This meta-analysis provides a robust estimate of the protective association of C2/CFB with AMD.
Abstract 3336
Genome wide association studies (GWAS) are the current method of choice to dissect the genetic basis of common complex diseases. Up-to-date, studies in families with a known first onset ...of symptomatic arterial or venous thrombosis (VT) in early childhood are lacking. Methods: Here, we performed a GWAS in a large family-based study sample comprising 241 nuclear families with pediatric VT using the Illumina 660W Infinium SNP array. The average genotype call rate was >99.5%, and the genomic inflation factor was a= 1.012. Single point and haplotype association was assessed using the Transmission Disequilibrium Test (TDT) as implemented in PLINK and FBAT, respectively, and corrected for multiple testing using permutation testing. In addition, associations were corrected for age, gender, and in a subsequent analysis for Factor VLeiden. Results and Conclusion: Four SNPs exceeded the threshold for genome wide significance in this dataset as determined by permutation testing using 100.000 bootstrap permutations (p<10−5), and are likely true associations. Among these, 2 SNPs reside in a region on chromosome 6q13 comprising the gene for beta-1,3-glucoronyltransferase 2 (B3GAT2), a member of the human natural killer 1 (HNK1) carbohydrate pathway are associated with pediatric VT with p-values for rs1304029 (p=3.42×10−6) and rs2748331 (p=6.92×10−6). The corresponding haplotype association test resulted in a p=5.37×10−6 for the GA-haplotype, further underlining the robustness of the association. The SNPs rs636434 on chromosome 6q12 and rs1565242 on chromosome 15 both reside within hypothetical genes and are associated with VT with a p=2.70×10−6 and p=8.24×10−6, respectively. Additional SNPs exceeding a p<10−5 are included in subsequent analyses looking at gene networks and replication in independent study samples including our second GWAS on pediatric thromboembolic stroke (TS). Future studies using larger study samples are warranted to validate these findings and to characterize the genetic architecture underlying VT and TS in children.
No relevant conflicts of interest to declare.
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