QTLRel: an R Package for Genome-wide Association Studies in which Relatedness is a Concern

BACKGROUND Existing software for quantitative trait mapping is either not able to model polygenic variation or does not allow incorporation of more than one genetic variance component. Improperly modeling the genetic relatedness among subjects can result in excessive false positives. We have developed an R package, QTLRel, to enable more flexible modeling of genetic relatedness as well as covariates and non-genetic variance components. RESULTS We have successfully used the package to analyze many datasets, including F₃₄ body weight data that contains 688 individuals genotyped at 3105 SNP markers and identified 11 QTL. It took 295 seconds to estimate variance components and 70 seconds to perform the genome scan on an Linux machine equipped with a 2.40GHz Intel(R) Core(TM)2 Quad CPU. CONCLUSIONS QTLRel provides a toolkit for genome-wide association studies that is capable of calculating genetic incidence matrices from pedigrees, estimating variance components, performing genome scans, incorporating interactive covariates and genetic and non-genetic variance components, as well as other functionalities such as multiple-QTL mapping and genome-wide epistasis.This project was supported by NIH grants R01DA021336, R01MH079103 and R21DA024845

ANGPTL4 gene E40K variation protects against obesity-associated dyslipidemia in participants with obesity

Objective ANGPTL4 inhibits lipoprotein lipase in adipose tissue, regulating plasma triglycerides levels. In persons with obesity plasma ANGPTL4 levels have been positively correlated with body fat mass, TG levels and low HDL. A loss-of-function E40K mutation in ANGPTL4 prevents LPL inhibition, resulting in lower TGs and higher HDLc in the general population. Since obesity determines metabolic alterations and consequently is a major risk factor for cardiovascular disease, the aim was to explore if obesity-related metabolic abnormalities are modified by the ANGPTL4-E40K mutation. Methods ANGPTL4-E40K was screened in 1206 Italian participants, of which 863 (71.5%) with obesity. All subjects without diabetes underwent OGTT with calculation of indices of insulin-sensitivity. Results Participants with obesity carrying the E40K variant had significantly lower TG (p = 0.001) and higher HDLc levels (p = 0.024). Also in the whole population low TGs and high HDLc were confirmed in E40K carriers. In the obese subpopulation it was observed that almost all E40K carriers were within the lowest quartile of TGs (p = 1.1 x 10(-9)). E40K had no substantial effect of on glucose metabolism. Finally, none of the obese E40K carriers had T2D, and together with the favourable lipid profile, they resemble a metabolically healthy obese (MHO) phenotype, compared to 38% of E40E wild-type obese that had diabetes and/or dyslipidaemia (p = 0.0106). Conclusions In participants with obesity the ANGPTL4-E40K variant protects against dyslipidemia. The phenotype of obese E40K carriers is that of a patient with obesity without metabolic alterations, similar to the phenotype described as metabolic healthy obesity

Genome-wide study of association and interaction with maternal cytomegalovirus infection suggests new schizophrenia loci.

Genetic and environmental components as well as their interaction contribute to the risk of schizophrenia, making it highly relevant to include environmental factors in genetic studies of schizophrenia. This study comprises genome-wide association (GWA) and follow-up analyses of all individuals born in Denmark since 1981 and diagnosed with schizophrenia as well as controls from the same birth cohort. Furthermore, we present the first genome-wide interaction survey of single nucleotide polymorphisms (SNPs) and maternal cytomegalovirus (CMV) infection. The GWA analysis included 888 cases and 882 controls, and the follow-up investigation of the top GWA results was performed in independent Danish (1396 cases and 1803 controls) and German-Dutch (1169 cases, 3714 controls) samples. The SNPs most strongly associated in the single-marker analysis of the combined Danish samples were rs4757144 in ARNTL (P=3.78 × 10(-6)) and rs8057927 in CDH13 (P=1.39 × 10(-5)). Both genes have previously been linked to schizophrenia or other psychiatric disorders. The strongest associated SNP in the combined analysis, including Danish and German-Dutch samples, was rs12922317 in RUNDC2A (P=9.04 × 10(-7)). A region-based analysis summarizing independent signals in segments of 100 kb identified a new region-based genome-wide significant locus overlapping the gene ZEB1 (P=7.0 × 10(-7)). This signal was replicated in the follow-up analysis (P=2.3 × 10(-2)). Significant interaction with maternal CMV infection was found for rs7902091 (P(SNP × CMV)=7.3 × 10(-7)) in CTNNA3, a gene not previously implicated in schizophrenia, stressing the importance of including environmental factors in genetic studies

Improved Minimum Cost and Maximum Power Two Stage Genome-Wide Association Study Designs

In a two stage genome-wide association study (2S-GWAS), a sample of cases and controls is allocated into two groups, and genetic markers are analyzed sequentially with respect to these groups. For such studies, experimental design considerations have primarily focused on minimizing study cost as a function of the allocation of cases and controls to stages, subject to a constraint on the power to detect an associated marker. However, most treatments of this problem implicitly restrict the set of feasible designs to only those that allocate the same proportions of cases and controls to each stage. In this paper, we demonstrate that removing this restriction can improve the cost advantages demonstrated by previous 2S-GWAS designs by up to 40%. Additionally, we consider designs that maximize study power with respect to a cost constraint, and show that recalculated power maximizing designs can recover a substantial amount of the planned study power that might otherwise be lost if study funding is reduced. We provide open source software for calculating cost minimizing or power maximizing 2S-GWAS designs.</p

Trait-stratified genome-wide association study identifies novel and diverse genetic associations with serologic and cytokine phenotypes in systemic lupus erythematosus

INTRODUCTION: Systemic lupus erythematosus (SLE) is a highly heterogeneous disorder, characterized by differences in autoantibody profile, serum cytokines, and clinical manifestations. SLE-associated autoantibodies and high serum interferon alpha (IFN-α) are important heritable phenotypes in SLE which are correlated with each other, and play a role in disease pathogenesis. These two heritable risk factors are shared between ancestral backgrounds. The aim of the study was to detect genetic factors associated with autoantibody profiles and serum IFN-α in SLE. METHODS: We undertook a case-case genome-wide association study of SLE patients stratified by ancestry and extremes of phenotype in serology and serum IFN-α. Single nucleotide polymorphisms (SNPs) in seven loci were selected for follow-up in a large independent cohort of 538 SLE patients and 522 controls using a multi-step screening approach based on novel metrics and expert database review. The seven loci were: leucine-rich repeat containing 20 (LRRC20); protein phosphatase 1 H (PPM1H); lysophosphatidic acid receptor 1 (LPAR1); ankyrin repeat and sterile alpha motif domain 1A (ANKS1A); protein tyrosine phosphatase, receptor type M (PTPRM); ephrin A5 (EFNA5); and V-set and immunoglobulin domain containing 2 (VSIG2). RESULTS: SNPs in the LRRC20, PPM1H, LPAR1, ANKS1A, and VSIG2 loci each demonstrated strong association with a particular serologic profile (all odds ratios > 2.2 and P < 3.5 × 10(-4)). Each of these serologic profiles was associated with increased serum IFN-α. SNPs in both PTPRM and LRRC20 were associated with increased serum IFN-α independent of serologic profile (P = 2.2 × 10(-6 )and P = 2.6 × 10(-3 )respectively). None of the SNPs were strongly associated with SLE in case-control analysis, suggesting that the major impact of these variants will be upon subphenotypes in SLE. CONCLUSIONS: This study demonstrates the power of using serologic and cytokine subphenotypes to elucidate genetic factors involved in complex autoimmune disease. The distinct associations observed emphasize the heterogeneity of molecular pathogenesis in SLE, and the need for stratification by subphenotypes in genetic studies. We hypothesize that these genetic variants play a role in disease manifestations and severity in SLE

The influence of mindfulness, resilience, and self-efficacy on foreign language anxiety among chinese college students

This study explores the effects of mindfulness, resilience, and self-efficacy on foreign language anxiety among Chinese college students and identifies the most significant predictor of foreign language anxiety. Employing a quantitative approach, data were collected from 323 English as a foreign language students using validated scales measuring these variables. Pearson correlation analyses revealed significant negative correlations of self-efficacy (r=-0.538, p0.01), resilience (r=-0.372, p0.01), and mindfulness (r=-0.331, p0.01) with foreign language anxiety. Multiple regression analysis indicated that self-efficacy was the most impactful variable for predicting foreign language anxiety, while mindfulness also significantly predicted foreign language anxiety, but resilience did not. These findings underscore the pivotal part played by self-efficacy in reducing foreign language anxiety and suggest that enhancing self-efficacy can improve language study experiences. The research offers meaningful understandings regarding the mechanisms of foreign language anxiety and offers practical recommendations for educators to implement strategies aimed at boosting students’ self-efficacy, with implications for future research and practice

Atmospheric Deposition of Inorganic Elements and Organic Compounds at the Inlets of the Venice Lagoon

The Venice Lagoon is subjected to long-range transport of contaminants via aerosol from the near Po Valley. Moreover, it is an area with significant local anthropogenic emissions due to the industrial area of Porto Marghera, the urban centres, and the glass factories and with emissions by ships traffic within the Lagoon. Furthermore, since 2005, the Lagoon has also been affected by the construction of the MOSE (Modulo Sperimentale Elettromeccanico—Electromechanical Experimental Module) mobile dams, as a barrier against the high tide. This work presents and discusses the results from chemical analyses of bulk depositions, carried out in different sites of the Venice Lagoon. Fluxes of pollutants were also statistically analysed on PCA with the aim of investigating the spatial variability of depositions and their correlation with precipitations. Fluxes of inorganic pollutants depend differently on precipitations, while organic compounds show a more seasonal trend. The statistical analysis showed that the site in the northern Lagoon has lower and almost homogeneous fluxes of pollutants, while the other sites registered more variable concentrations. The study also provided important information about the annual trend of pollutants and their evolution over a period of about five years, from 2005 to 2010

Rondas interprofesionales de heridas antes y después de Best Practice Spotlight Organization (BPSO)

Introduction. The patient care model at the Salvation Army Toronto Grace Health Centre Hospital is based on principles of patient- and family-centered care provided by the interprofessional team. In this framework, different programs are designed and implemented to constantly improve and keep a good level of care and quality of life of the patients, within the limitations involved in hospitalization, once they have become a Best Practice Spotlight. Objective. Present the experience of the interprofessional wound rounds before and after being recognized as a Best Practice Spotlight. Summary. Before becoming a BPSO, the policy and procedure documents guiding the hospital’s practices on ulcers or pressure wounds used as reference the evidence-based guidelines of the Registered Nurses' Association of Ontario (RNAO). However, the implementation or application of these practices had not been formalized directly at the point of patient care. This article presents the transition and the relevant aspects for making patient- and family-centered care a reality for the interprofessional team in the component of interprofessional wound rounds. Conclusions. The success in the effective implementation of the guidelines of the BPSO program has become a collective identity for the organizations that work towards the best results in healthcare organizations — in national and international institutions.Introducción. El modelo de cuidado a pacientes en el Salvation Army Toronto Grace Health Centre Hospital está basado en los principios de cuidado centrado en el paciente y la familia como parte integral del equipo interprofesional. Dentro de este marco se diseñan y se implementan diferentes programas para que se mejore constantemente y se mantenga un buen nivel de cuidados y calidad de vida de los pacientes, dentro de las limitaciones que conlleva el estar hospitalizado, esto después de convertirse en Best Practice Spotlight. Objetivo. Presentar la experiencia de las rondas interprofesionales de heridas antes y después de Best Practice Spotlight. Síntesis. Antes de ser BPSO los documentos de pólizas y procedimientos que guiaban las prácticas alrededor de úlceras o heridas por presión, en el hospital se utilizaban como referencia las guías basadas en las evidencias de la Asociación de Enfermeras de Ontario (RNAO). Sin embargo, no estaba formalizada la ejecución o aplicación de estas prácticas al punto de cuidado directo al paciente. En este artículo se presenta la transición y los aspectos relevantes para que sea una realidad el cuidado centrado en el paciente y la familia como parte del equipo interprofesional en el componente de las rondas interprofesionales de heridas. Conclusiones. El éxito de la implementación efectiva de las guías ha sido el programa BPSO, que se ha convertido en una identidad colectiva de organizaciones que trabajan en pro de los mejores resultados en las organizaciones de salud en instituciones nacionales e internacionales

The systemic lupus erythematosus IRF5 risk haplotype is associated with systemic sclerosis

Systemic sclerosis (SSc) is a fibrotic autoimmune disease in which the genetic component plays an important role. One of the strongest SSc association signals outside the human leukocyte antigen (HLA) region corresponds to interferon (IFN) regulatory factor 5 (IRF5), a major regulator of the type I IFN pathway. In this study we aimed to evaluate whether three different haplotypic blocks within this locus, which have been shown to alter the protein function influencing systemic lupus erythematosus (SLE) susceptibility, are involved in SSc susceptibility and clinical phenotypes. For that purpose, we genotyped one representative single-nucleotide polymorphism (SNP) of each block (rs10488631, rs2004640, and rs4728142) in a total of 3,361 SSc patients and 4,012 unaffected controls of Caucasian origin from Spain, Germany, The Netherlands, Italy and United Kingdom. A meta-analysis of the allele frequencies was performed to analyse the overall effect of these IRF5 genetic variants on SSc. Allelic combination and dependency tests were also carried out. The three SNPs showed strong associations with the global disease (rs4728142: P = 1.34×10&lt;sup&gt;−8&lt;/sup&gt;, OR = 1.22, CI 95% = 1.14–1.30; rs2004640: P = 4.60×10&lt;sup&gt;−7&lt;/sup&gt;, OR = 0.84, CI 95% = 0.78–0.90; rs10488631: P = 7.53×10&lt;sup&gt;−20&lt;/sup&gt;, OR = 1.63, CI 95% = 1.47–1.81). However, the association of rs2004640 with SSc was not independent of rs4728142 (conditioned P = 0.598). The haplotype containing the risk alleles (rs4728142*A-rs2004640*T-rs10488631*C: P = 9.04×10&lt;sup&gt;−22&lt;/sup&gt;, OR = 1.75, CI 95% = 1.56–1.97) better explained the observed association (likelihood P-value = 1.48×10&lt;sup&gt;−4&lt;/sup&gt;), suggesting an additive effect of the three haplotypic blocks. No statistical significance was observed in the comparisons amongst SSc patients with and without the main clinical characteristics. Our data clearly indicate that the SLE risk haplotype also influences SSc predisposition, and that this association is not sub-phenotype-specific

A Genome-Wide Association Study Finds Genetic Associations with Broadly-Defined Headache in UK Biobank (N = 223,773)

Background: Headache is the most common neurological symptom and a leading cause of years lived with disability. We sought to identify the genetic variants associated with a broadly-defined headache phenotype in 223,773 subjects from the UK Biobank cohort. Methods: We defined headache based on a specific question answered by the UK Biobank participants. We performed a genome-wide association study of headache as a single entity, using 74,461 cases and 149,312 controls. Results: We identified 3343 SNPs which reached the genome-wide significance level of P < 5 × 10−8. The SNPs were located in 28 loci, with the top SNP of rs11172113 in the LRP1 gene having a P value of 4.92 × 10−47. Of the 28 loci, 14 have previously been associated with migraine. Among 14 new loci, rs77804065 with a P value of 5.87 × 10−15 in the LINC02210-CRHR1 gene was the top SNP. Significant relationships between multiple brain tissues and genetic associations were identified through tissue expression analysis. We also identified significant positive genetic correlations between headache and many psychological traits. Conclusions: Our results suggest that brain function is closely related to broadly-defined headache. In addition, we found that many psychological traits have genetic correlations with headache