Genetic influence of a STAU2 frameshift mutation and RELN regulatory elements on performance in Icelandic horses

Equine protozoal encephalomyelitis

Genome-wide association studies (GWAS) have identified thousands of single nucleotide polymorphisms (SNPs) that are associated with complex traits. GWAS data allows us to investigate the shared genetic etiologies among different traits. However, linkage disequilibrium (LD) between the SNPs complicates the detection and identification of shared genetic effects. In this paper we model the LD by dividing the genome into LD blocks and linking the genetic variants within a block to a possible latent causal variant. An eigenvector-projected score statistic that leverages the set of variants in LD and a maxtype test statistic (Max-block) are proposed to detect the existence of cross-trait genetic association. The Max-block is easy to calculate and is shown to control the genome-wide error rate. After the detection a stepwise procedure is proposed to identify the significant blocks that explain the genetic sharing between two traits. Simulation experiments show that Max-block is more powerful than standard approaches in the sparse settings and is robust to different signal strengths or levels of sparsity. The method is applied to study shared cross-trait associations in 10 pediatric autoimmune diseases and identified several regions that explain the genetic sharing between juvenile idiopathic arthritis (JIA) and ulcerative colitis (UC) and between UC and Crohn’s disease (CD). In addition, our analysis also indicates the genetic sharing in the MHC region among systemic lupus (SLE), celiac disease (CEL) and common variable immunodeficiency (CVID). Results from real data and simulation studies show that Max-block provides an important alternative to commonly used genetic correlation estimation in understanding genetic correlation among complex diseases.

Background and ObjectiveGenetic markers associated with disease are often non-functional and generally tag one or more functional “causative” variants in linkage disequilibrium. Markers may not show tight linkage to the causative variants across multiple ethnicities due to evolutionary divergence, and therefore may not be informative across different population groups. Validated markers of disease suggest causative variants exist in the gene and, if the causative variants can be identified, it is reasonable to hypothesize that such variants will be informative across diverse populations. The aim of this study was to test that hypothesis using functional interleukin-1 gene variations across multiple ethnic populations to replace the non-functional markers originally associated with chronic adult periodontitis in Caucasians.Material and MethodsAdult chronic periodontitis cases and controls from 4 ethnic groups (Caucasians, African Americans, Hispanics and Asians) were recruited in the U.S., Chile and China. Genotypes of IL1B gene SNPs, including 3 functional SNPs (rs16944, rs1143623, rs4848306) in the promoter and 1 intronic SNP (rs1143633), were determined using single base extension method or TaqMan 5′ nuclease assay. Logistic regression and other statistical analyses were used to examine the association between moderate to severe periodontitis and IL1B gene variations, including SNPs, haplotypes, and composite genotypes. Genotype patterns associated with disease in the discovery study were then evaluated in independent validation studies.ResultsSignificant associations were identified in the discovery study, consisting of Caucasians and African Americans, between moderate to severe adult chronic periodontitis and functional variations in the IL1B gene, including a pattern of 4 IL1B SNPs (OR=1.87, P-value<0.0001). The association between the disease and this IL1B composite genotype pattern was validated in two additional studies consisting of Hispanics (OR=1.95, P-value=0.04) or Asians (OR=3.27, P-value=0.01). A meta-analysis of the 3 populations supported the association between the IL-1 genotype pattern and moderate to severe periodontitis (OR 1.95; P-value <0.001). Our analysis also demonstrated that IL1B gene variations had added value to conventional risk factors in predicting chronic periodontitis.ConclusionThis study validated the influence of IL-1 genetic factors on the severity of chronic periodontitis in four different ethnicities.

Background/Introduction Genome-wide association studies (GWAS) have identified two novel coronary artery disease (CAD) risk variants, rs17087335 [1] and rs72627509 [2], located near the REST gene, which encodes the RE-1 silencing transcription factor. While REST is recognised as a transcriptional regulator of neuronal genes, its role in atherosclerosis and CAD is poorly understood. Purpose To investigate the molecular mechanisms by which the CAD risk variants rs17087335 and rs72627509 influence REST gene expression and contribute to atherosclerotic phenotypes. Methods In silico analyses were performed to identify variants in linkage disequilibrium with rs17087335 and rs72627509. Reporter gene assays were used to assess regulatory activity at these loci. Mass spectrometry was employed to examine transcription factor binding to variant alleles. Expression quantitative trait loci (eQTL) data were obtained from the GTEx database, and VSMC siRNA knockdown studies were conducted to evaluate cellular effects. Results Linkage disequilibrium (LD) analysis revealed that rs17087335 and rs72627509 are in LD with 14 other variants. To narrow the number of putative causal variants, we performed reporter gene assays that confirmed regulatory activity specifically at rs17087335 and rs72627509, as well as at rs3796529. Mass spectrometry analysis revealed differential transcription factor binding to the alleles of these variants, potentially influencing REST transcription. Indeed, eQTL data demonstrated that CAD patients carrying the risk alleles of rs17087335, rs72627509, and rs3796529, respectively, had significantly decreased REST mRNA levels in the aorta. Functional studies on vascular smooth muscle cells (VSMCs) showed that REST siRNA knockdown increased cell migration and lipid accumulation under inflammatory conditions. RNA sequencing revealed ATF6 and PLA2G4C as potential downstream targets of REST, potentially mediating the observed changes in VSMC migration and lipid accumulation. Conclusion(s) This study provides the first insights into the role of REST in atherosclerosis. The CAD risk variants rs17087335, rs72627509, and rs3796529 influence REST expression, and decreased REST levels promote atherosclerotic phenotypes in VSMCs. These effects are likely mediated through altered lipid metabolism and cell migration, driven by REST targets such as ATF6 and PLA2G4C. Our findings suggest that targeting REST could offer new therapeutic strategies for CAD prevention and treatment.

We recently identified a locus on chromosome 18q11.2 for high serum triglycerides in Mexicans. We hypothesize that the lead genome-wide association study single-nucleotide polymorphism rs9949617, or its linkage disequilibrium proxies, regulates 1 of the 5 genes in the triglyceride-associated region. We performed a linkage disequilibrium analysis and found 9 additional variants in linkage disequilibrium (r(2)>0.7) with the lead single-nucleotide polymorphism. To select the variants for functional analyses, we annotated the 10 variants using DNase I hypersensitive sites, transcription factor and chromatin states and identified rs17259126 as the lead candidate variant for functional in vitro validation. Using luciferase transcriptional reporter assay in liver HepG2 cells, we found that the G allele exhibits a significantly lower effect on transcription (P<0.05). The electrophoretic mobility shift and ChIPqPCR (chromatin immunoprecipitation coupled with quantitative polymerase chain reaction) assays confirmed that the minor G allele of rs17259126 disrupts an hepatocyte nuclear factor 4 α-binding site. To find the regional candidate gene, we performed a local expression quantitative trait locus analysis and found that rs17259126 and its linkage disequilibrium proxies alter expression of the regional transmembrane protein 241 (TMEM241) gene in 795 adipose RNAs from the Metabolic Syndrome In Men (METSIM) cohort (P=6.11×10(-07)-5.80×10(-04)). These results were replicated in expression profiles of TMEM241 from the Multiple Tissue Human Expression Resource (MuTHER; n=856). The Mexican genome-wide association study signal for high serum triglycerides on chromosome 18q11.2 harbors a regulatory single-nucleotide polymorphism, rs17259126, which disrupts normal hepatocyte nuclear factor 4 α binding and decreases the expression of the regional TMEM241 gene. Our data suggest that decreased transcript levels of TMEM241 contribute to increased triglyceride levels in Mexicans.

There is strong and consistent evidence that a genetic component contributes to the etiology of chronic lymphocytic leukemia (CLL). A recent genome-wide association study of CLL identified seven genetic variants that increased the risk of CLL within a European population. We evaluated the association of these variants, or variants in linkage disequilibrium with these variants, with CLL risk in an independent sample of 438 CLL cases and 328 controls. Of these seven single nucleotide polymorphisms (SNP), six had P trend < 0.05 and had estimated odds ratios (OR) that were strikingly comparable to those of the previous study. Associations were seen for rs9378805 [OR, 1.47; 95% confidence intervals (CI), 1.19-1.80; P trend = 0.0003] near IRF4 and rs735665 near GRAMD1B (OR, 1.47; 95% CI, 1.14-1.89; P trend = 0.003). However, no associations (P > 0.05) were found for rs11083846, nor were any found for any SNP in linkage disequilibrium with rs11083846. Our results confirm the previous findings and further support the role of a genetic basis in the etiology of CLL; however, more research is needed to elucidate the causal SNP(s) and the potential manner in which these SNPs or linked SNPs function in CLL pathogenesis.

AimsThe aim of this study was to identify risk variants and haplotypes that impair dihydropyrimidine dehydrogenase (DPD) activity and are, therefore, candidate risk variants for severe toxicity to 5‐fluorouracil (5‐FU) chemotherapy.MethodsPlasma dihydrouracil/uracil (UH2/U) ratios were measured as a population marker for DPD activity in a total of 1382 subjects from 4 independent studies. Genotype and haplotype correlations with UH2/U ratios were assessed.ResultsSignificantly lower UH2/U ratios (panova < 2 × 10−16) were observed in carriers of the 4 well‐studied 5‐FU toxicity risk variants with mean differences (MD) of −43.7% for DPYD c.1905 + 1G > A (rs3918290), −46.0% for DPYD c.1679T > G (rs55886062), −37.1%, for DPYD c.2846A > T (rs67376798), and −13.2% for DPYD c.1129‐5923C > G (rs75017182). An additional variant, DPYD c.496A > G (rs2297595), was also associated with lower UH2/U ratios (P < .0001, MD: −12.6%). A haplotype analysis was performed for variants in linkage disequilibrium with c.496A > G, which consisted of the common variant c.85T > C (rs1801265) and the risk variant c.1129‐5923C > G. Both haplotypes carrying c.496A > G were associated with decreased UH2/U ratios (H3, P = .003, MD: −9.6%; H5, P = .002, MD: −16.9%). A haplotype carrying only the variant c.85T > C (H2) was associated with elevated ratios (P = .004, MD: +8.6%).ConclusionsBased on our data, DPYD‐c.496A > G is a strong candidate risk allele for 5‐FU toxicity. Our data suggest that DPYD‐c.85T > C might be protective; however, the deleterious impacts of the linked alleles c.496A > G and c.1129‐5923C > G likely limit this effect in patients. The possible protective effect of c.85T > C and linkage disequilibrium with c.496A > G and c.1129‐5923C > G may have hampered prior association studies and should be considered in future clinical studies.

BackgroundColocalization is a statistical method used in genetics to determine whether the same variant is causal for multiple phenotypes, for example, complex traits and gene expression. It provides stronger mechanistic evidence than shared significance, which can be produced through separate causal variants in linkage disequilibrium. Current colocalization methods require full summary statistics for both traits, limiting their use with the majority of reported GWAS associations (e.g. GWAS Catalog). We propose a new approximation to the popular coloc method that can be applied when limited summary statistics are available.Our method (POint EstiMation of Colocalization, POEMColoc) imputes missing summary statistics for one or both traits using LD structure in a reference panel, and performs colocalization using the imputed summary statistics.ResultsWe evaluate the performance of POEMColoc using real (UK Biobank phenotypes and GTEx eQTL) and simulated datasets. We show good correlation between posterior probabilities of colocalization computed from imputed and observed datasets and similar accuracy in simulation. We evaluate scenarios that might reduce performance and show that multiple independent causal variants in a region and imputation from a limited subset of typed variants have a larger effect while mismatched ancestry in the reference panel has a modest effect. Further, we find that POEMColoc is a better approximation of coloc when the imputed association statistics are from a well powered study (e.g., relatively larger sample size or effect size). Applying POEMColoc to estimate colocalization of GWAS Catalog entries and GTEx eQTL, we find evidence for colocalization of 150,000 trait-gene-tissue triplets.ConclusionsWe find that colocalization analysis performed with full summary statistics can be closely approximated when only the summary statistics of the top SNP are available for one or both traits. When applied to the full GWAS Catalog and GTEx eQTL, we find that colocalized trait-gene pairs are enriched in tissues relevant to disease etiology and for matches to approved drug mechanisms. POEMColoc R package is available at https://github.com/AbbVie-ComputationalGenomics/POEMColoc.

Understanding the determinants of healthy mental ageing is a priority for society today. So far, we know that intelligence differences show high stability from childhood to old age and there are estimates of the genetic contribution to intelligence at different ages. However, attempts to discover whether genetic causes contribute to differences in cognitive ageing have been relatively uninformative. Here we provide an estimate of the genetic and environmental contributions to stability and change in intelligence across most of the human lifetime. We used genome-wide single nucleotide polymorphism (SNP) data from 1,940 unrelated individuals whose intelligence was measured in childhood (age 11 years) and again in old age (age 65, 70 or 79 years). We use a statistical method that allows genetic (co)variance to be estimated from SNP data on unrelated individuals. We estimate that causal genetic variants in linkage disequilibrium with common SNPs account for 0.24 of the variation in cognitive ability change from childhood to old age. Using bivariate analysis, we estimate a genetic correlation between intelligence at age 11 years and in old age of 0.62. These estimates, derived from rarely available data on lifetime cognitive measures, warrant the search for genetic causes of cognitive stability and change.

One of the neurotransmitter serotonin's receptors, HTR1B, is of interest for many neuropsychiatric traits, illnesses and treatments for multiple reasons, especially its tissue distribution, pharmacological profile and findings from mice lacking the receptor, along with reasons generally implicating serotonin. Eight mutation scans have uncovered sixteen polymorphisms in the coding sequence and surrounding 5'- and 3'-untranslated regions and much is now known of the distribution of these polymorphisms in various ethnic groups and their linkage disequilibrium relationships. Thus far, evidence exists that the uncommon missense T371G (Phe124Cys) and the common promoter region A-161T polymorphisms may exhibit functional effects and possibly that the common synonymous G861C (or more likely a variant in linkage disequilibrium with G861C) does as well. From the eighteen reported population-based case control studies of HTR1B to multiple disorders, several facts stand out. There exists preliminary evidence for association of G861C with i) antisocial alcoholism in the Finnish; ii) alcoholism in the presence of inactive aldehyde dehydrogenase 2 in the Japanese; iii) a history of suicide attempts in European-American personality disorder patients; and iv) minimum lifetime body mass index in Canadian bulimia nervosa patients. From the three reported family-based case control studies of HTR1B to various disorders, one provides preliminary evidence for association of G861C with obsessive compulsive disorder. Although many association studies have been completed, positive results should still be considered preliminary. As these preliminary reports are tested for replication with larger, more powerful samples, there should be increased clarity as to which findings remain robust; in some cases this will require the application of meta-analytic techniques.

OBJECTIVE—A recent meta-analysis demonstrated a nominal association of the ectonucleotide pyrophosphatase phosphodiesterase 1 (ENPP1) K→Q missense single nucleotide polymorphism (SNP) at position 121 with type 2 diabetes. We set out to confirm the association of ENPP1 K121Q with hyperglycemia, expand this association to insulin resistance traits, and determine whether the association stems from K121Q or another variant in linkage disequilibrium with it.RESEARCH DESIGN AND METHODS—We characterized the haplotype structure of ENPP1 and selected 39 tag SNPs that captured 96% of common variation in the region (minor allele frequency ≥5%) with an r2 value ≥0.80. We genotyped the SNPs in 2,511 Framingham Heart Study participants and used age- and sex-adjusted linear mixed effects (LME) models to test for association with quantitative metabolic traits. We also examined whether interaction between K121Q and BMI affected glycemic trait levels.RESULTS—The Q allele of K121Q (rs1044498) was associated with increased fasting plasma glucose (FPG), A1C, fasting insulin, and insulin resistance by homeostasis model assessment (HOMA-IR; all P = 0.01–0.006). Two noncoding SNPs (rs7775386 and rs7773477) demonstrated similar associations, but LME models indicated that their effects were not independent from K121Q. We found no association of K121Q with obesity, but interaction models suggested that the effect of the Q allele on FPG and HOMA-IR was stronger in those with a higher BMI (P = 0.008 and 0.01 for interaction, respectively).CONCLUSIONS—The Q allele of ENPP1 K121Q is associated with hyperglycemia and insulin resistance in whites. We found an adiposity-SNP interaction, with a stronger association of K121Q with diabetes-related quantitative traits in people with a higher BMI.

BackgroundMacrophage stimulating protein (MSP) is a serum growth factor that binds to and activates the receptor tyrosine kinase, Recepteur d'Origine Nantais (RON). A non-synonymous coding variant in MSP (689C) has been associated with genetic susceptibility to both Crohn's disease and ulcerative colitis, two major types of inflammatory bowel disease (IBD) characterized by chronic inflammation of the digestive tract. We investigated the consequences of this polymorphism for MSP-RON pathway activity and IBD pathogenesis.MethodsRON expression patterns were examined on mouse and human cells and tissues under normal and disease conditions to identify cell types regulated by MSP-RON. Recombinant MSP variants were tested for their ability to bind and stimulate RON and undergo proteolytic activation. MSP concentrations were quantified in the serum of individuals carrying the MSP 689R and 689C alleles.ResultsIn intestinal tissue, RON was primarily expressed by epithelial cells under normal and disease conditions. The 689C polymorphism had no impact on the ability of MSP to bind to or signal through RON. In a cohort of normal individuals and IBD patients, carriers of the 689C polymorphism had lower concentrations of MSP in their serum.ConclusionsBy reducing the quantities of circulating MSP, the 689C polymorphism, or a variant in linkage disequilibrium with this polymorphism, may impact RON ligand availability and thus receptor activity. Given the known functions of RON in regulating wound healing and our analysis of RON expression patterns in human intestinal tissue, these data suggest that decreased RON activity may impact the efficiency of epithelial repair and thus underlie the increased IBD susceptibility associated with the MSP 689C allele.

CCL2/Monocyte Chemoattractant Protein (MCP)-1 and other chemokines sharing a similar sequence, including CCL8/MCP-2, are involved in neurodegeneration. A few Single Nucleotide Polymorphisms (SNPs) have been reported in CCL8/MCP-2, all of which are located in the same linkage block. One of them (rs1163763) leads to an aminoacidic substitution, implying a potential impact on the function of the protein. rs1133763 was tested for association in 219 patients with Alzheimer's disease (AD) and 209 with Frontotemporal Lobar Degeneration (FTLD) as compared with 231 age-matched controls. The distribution of CCL8/MCP-2 rs1133763 was not significantly different among patients with AD or FTLD and controls, even stratifying according to gender. CCL8/MCP rs1133763 SNP, or other variants in linkage disequilibrium with this variant, likely do not influence the susceptibility to AD or FTLD in Caucasians.

Multiple myeloma (MM) is caused by the uncontrolled, clonal expansion of plasma cells. While there is epidemiological evidence for inherited susceptibility, the molecular basis remains incompletely understood. We report a genome-wide association study totalling 5,320 cases and 422,289 controls from four Nordic populations, and find a novel MM risk variant at SOHLH2 at 13q13.3 (risk allele frequency = 3.5%; odds ratio = 1.38; P = 2.2 × 10−14). This gene encodes a transcription factor involved in gametogenesis that is normally only weakly expressed in plasma cells. The association is represented by 14 variants in linkage disequilibrium. Among these, rs75712673 maps to a genomic region with open chromatin in plasma cells, and upregulates SOHLH2 in this cell type. Moreover, rs75712673 influences transcriptional activity in luciferase assays, and shows a chromatin looping interaction with the SOHLH2 promoter. Our work provides novel insight into MM susceptibility.

Previous studies have suggested that the Trp460 allele of the Gly460Trp polymorphism in the alpha-adducin gene is associated with salt sensitivity and primary hypertension. The present study was undertaken to evaluate if the Trp460 allele of this polymorphism is associated with primary hypertension in Scandinavians. To address this issue, 294 patients with primary hypertension and 265 normotensive control subjects from Sweden were examined and genotyped for the Gly460Trp polymorphism using polymerase chain reaction and restriction fragment length polymorphism methods. We then used a population of 80 patients with primary hypertension and 154 normotensive control subjects from Finland to replicate the findings. The frequency of the Trp460 allele was lower in hypertensive patients than in normotensive controls in the Swedish population (17.7% vs 23.0%; P = 0.03) and in the Finnish population (14.4% vs 19.5%; NS). Therefore we also performed a pooled analysis in which the frequency of the Trp460 allele was significantly lower in hypertensive patients than in normotensive controls (17.0% vs 21. 7%; P = 0.02). In subjects who did not receive antihypertensive medication (n = 447) there was no difference between carriers of the three different codon 460 genotypes (Trp-Trp; Trp-Gly and Gly-Gly) either for systolic (128 +/- 18; 127 +/- 15 and 129 +/- 17 mm Hg, NS) or for diastolic blood pressure (75.6 +/- 12.1; 74.7 +/- 9.3 and 75.0 +/- 10.4 mm Hg, NS). In conclusion, the lower frequency of the Trp460 allele in hypertensive patients than in normotensive controls strongly argues against a pathogenic role of this allele in primary hypertension. The results rather suggest that another variant in linkage disequilibrium with the Gly460Trp polymorphism increases susceptibility for hypertension. Journal of Human Hypertension (2000) 14, 43-46.