Repeat polymorphisms underlie top genetic risk loci for glaucoma and colorectal cancer.

Many regions in the human genome vary in length among individuals due to variable numbers of tandem repeats (VNTRs). To assess the phenotypic impact of VNTRs genome-wide, we applied a statistical imputation approach to estimate the lengths of 9,561 autosomal VNTR loci in 418,136 unrelated UK Biobank participants and 838 GTEx participants. Association and statistical fine-mapping analyses identified 58 VNTRs that appeared to influence a complex trait in UK Biobank, 18 of which also appeared to modulate expression or splicing of a nearby gene. Non-coding VNTRs at TMCO1 and EIF3H appeared to generate the largest known contributions of common human genetic variation to risk of glaucoma and colorectal cancer, respectively. Each of these two VNTRs associated with a >2-fold range of risk across individuals. These results reveal a substantial and previously unappreciated role of non-coding VNTRs in human health and gene regulation.

Influences of rare copy-number variation on human complex traits.

The human genome contains hundreds of thousands of regions harboring copy-number variants (CNV). However, the phenotypic effects of most such polymorphisms are unknown because only larger CNVs have been ascertainable from SNP-array data generated by large biobanks. We developed a computational approach leveraging haplotype sharing in biobank cohorts to more sensitively detect CNVs. Applied to UK Biobank, this approach accounted for approximately half of all rare gene inactivation events produced by genomic structural variation. This CNV call set enabled a detailed analysis of associations between CNVs and 56 quantitative traits, identifying 269 independent associations (p < 5 × 10-8) likely to be causally driven by CNVs. Putative target genes were identifiable for nearly half of the loci, enabling insights into dosage sensitivity of these genes and uncovering several gene-trait relationships. These results demonstrate the ability of haplotype-informed analysis to provide insights into the genetic basis of human complex traits.

Associations with other cancer-related biomarkers might contribute to poor outcomes in RAS-altered, younger patients with colorectal cancer.

Colorectal cancer (CRC) is a common cancer in younger adults. In patients undergoing liver resection with RAS-altered CRCs, there is evidence suggesting younger patients have worse outcomes than older patients. To explain this pattern, differences in associations between RAS status and other cancer-related biomarkers in tumors from younger versus older patients with CRC were evaluated in a cohort of 925 patients with CRC, 277 (30.0%) of whom were ≤50 years old, and 454 (49.1%) who had RAS-altered tumors. For 3 biomarkers, RNF43, APC, and microsatellite instability (MSI), the association with RAS status was significantly modified by age after adjustment for multiple testing. Specifically, younger patients with RAS-altered tumors were more likely to be MSI-high, RNF43 mutated, and APC wild type. These differences might contribute to the observed pattern of diminished survival in younger versus older patients with CRC with RAS-mutated tumors undergoing liver metastasis resection.

NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's disease genetic and genomic knowledge.

INTRODUCTION: The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site Alzheimer's Genomics Database (GenomicsDB) is a public knowledge base of Alzheimer's disease (AD) genetic datasets and genomic annotations. METHODS: GenomicsDB uses a custom systems architecture to adopt and enforce rigorous standards that facilitate harmonization of AD-relevant genome-wide association study summary statistics datasets with functional annotations, including over 230 million annotated variants from the AD Sequencing Project. RESULTS: GenomicsDB generates interactive reports compiled from the harmonized datasets and annotations. These reports contextualize AD-risk associations in a broader functional genomic setting and summarize them in the context of functionally annotated genes and variants. DISCUSSION: Created to make AD-genetics knowledge more accessible to AD researchers, the GenomicsDB is designed to guide users unfamiliar with genetic data in not only exploring but also interpreting this ever-growing volume of data. Scalable and interoperable with other genomics resources using data technology standards, the GenomicsDB can serve as a central hub for research and data analysis on AD and related dementias. HIGHLIGHTS: The National Institute on Aging Genetics of Alzheimer's Disease Data Storage Site (NIAGADS) offers to the public a unique, disease-centric collection of AD-relevant GWAS summary statistics datasets. Interpreting these data is challenging and requires significant bioinformatics expertise to standardize datasets and harmonize them with functional annotations on genome-wide scales. The NIAGADS Alzheimer's GenomicsDB helps overcome these challenges by providing a user-friendly public knowledge base for AD-relevant genetics that shares harmonized, annotated summary statistics datasets from the NIAGADS repository in an interpretable, easily searchable format.

The Molecular Comorbidity Network of Periodontal Disease.

Periodontal disease, a multifactorial inflammatory condition affecting the supporting structures of the teeth, has been increasingly recognized for its association with various systemic diseases. Understanding the molecular comorbidities of periodontal disease is crucial for elucidating shared pathogenic mechanisms and potential therapeutic targets. In this study, we conducted comprehensive literature and biological database mining by utilizing DisGeNET2R for extracting gene-disease associations, Romin for integrating and modeling molecular interaction networks, and Rentrez R libraries for accessing and retrieving relevant information from NCBI databases. This integrative bioinformatics approach enabled us to systematically identify diseases sharing associated genes, proteins, or molecular pathways with periodontitis. Our analysis revealed significant molecular overlaps between periodontal disease and several systemic conditions, including cardiovascular diseases, diabetes mellitus, rheumatoid arthritis, and inflammatory bowel diseases. Shared molecular mechanisms implicated in the pathogenesis of these diseases and periodontitis encompassed dysregulation of inflammatory mediators, immune response pathways, oxidative stress pathways, and alterations in the extracellular matrix. Furthermore, network analysis unveiled the key hub genes and proteins (such as TNF, IL6, PTGS2, IL10, NOS3, IL1B, VEGFA, BCL2, STAT3, LEP and TP53) that play pivotal roles in the crosstalk between periodontal disease and its comorbidities, offering potential targets for therapeutic intervention. Insights gained from this integrative approach shed light on the intricate interplay between periodontal health and systemic well-being, emphasizing the importance of interdisciplinary collaboration in developing personalized treatment strategies for patients with periodontal disease and associated comorbidities.

No Association of Polymorphisms in the Genes Encoding Interleukin-6 and Interleukin-6 Receptor Subunit Alpha with the Risk of Keloids in Polish Patients.

A keloid is a benign fibroproliferative hypertrophy of scar tissue that extends outside the original wound and invades adjacent healthy skin. Keloid formation is thought to be a complex process including overactivity of the interleukin-6 signaling pathway and genetic susceptibility. The aim of the study was to investigate possible associations between rs1800797, rs1800796, and rs1800795 polymorphisms in the promoter of the IL6 gene encoding interleukin-6 and the rs2228145 polymorphism in the IL6R gene encoding the interleukin-6 receptor subunit alpha with the predisposition to keloids in Polish patients. The genetic polymorphisms were identified either using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) or sequencing of samples of genomic DNA extracted from blood leukocytes of 86 adult patients with keloids and 100 newborns comprising a control group. No significant differences in the distributions of IL6 or IL6R alleles or genotypes were found between keloid patients and newborn controls. There were also no significant differences between both groups in the distribution of IL6 haplotypes. The IL6 rs1800797, rs1800796 and rs1800795 and IL6R rs2228145 polymorphisms were not found to predispose individuals in the study group to keloids. IL6 promoter haplotypes were not found to be associated with a higher risk of keloids in the studied group.

Identification of Putative Causal Relationships Between Type 2 Diabetes and Blood-Based Biomarkers in East Asians by Mendelian Randomization.

Observational studies have revealed phenotypic associations between type 2 diabetes (T2D) and many biomarkers. However, causality between these conditions in East Asians is unclear. We leveraged genome-wide association study (GWAS) summary statistics on T2D (n = 77,418 cases; n = 356,122 controls) from the Asian Genetic Epidemiology Network (sample recruited during 2001-2011) and GWAS summary statistics on 42 biomarkers (n = 12,303-143,658) from BioBank Japan (sample recruited during 2003-2008) to investigate causal relationships between T2D and biomarkers. Applications of Mendelian randomization approaches consistently revealed genetically instrumented associations of T2D with increased serum potassium levels (liability-scale ß = 0.04-0.10; P = 6.41 × 10-17-9.85 × 10-5) and decreased serum chloride levels (liability-scale ß = -0.16 to -0.06; P = 5.22 × 10-27-3.14 × 10-5), whereas these 2 biomarkers showed no causal effects on T2D. Heritability Estimation Using Summary Statistics (ρ-HESS) and summary-data-based Mendelian randomization highlighted 27 genomic regions and 3 genes (α-1,3-mannosyl-glycoprotein 2-ß-N-acetylglucosaminyltransferase (MGAT1), transducing-like enhancer (TLE) family member 1, transcriptional corepressor (TLE1), and 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMGCR)) that interactively associated with the shared genetics underlying T2D and the 2 biomarkers. Thus, T2D may causally affect serum potassium and chloride levels among East Asians. In contrast, the relationships of potassium and chloride with T2D are not causal, suggesting the importance of monitoring electrolyte disorders for T2D patients.

Association of HMOX-1 rs2071747 with sporadic Parkinson's disease in southern Han Chinese.

STUDY OBJECTIVES: To discover the associations between HMOX-1 and sporadic Parkinson's disease (PD). METHODS: Five hundred sporadic PD patients and 500 healthy controls were recruited in this study. Polymerase chain reaction (PCR) was used. RESULTS: The dominant model of HMOX-1 rs2071747 was shown statistically significant between PD patients and control after adjustment of age and gender (dominant model: p value: 0.045, OR: 1.51, 95% CI: 1.01-2.27, adjusted). The associations of additive model and dominant model of rs2071747 were also found (additive model: p value: 0.047; dominant model: p value: 0.035, OR: 1.55, 95% CI: 1.03, 2.34). CONCLUSIONS: We found the association of the dominant of HMOX1 rs2071747 with PD. We also found the associations of additive model and dominant model of HMOX1 rs2071747 with late onset PD (LOPD) patients. HIGHLIGHTS: • The dominant model of HMOX1 rs2071747 was associated with PD. • The additive model of HMOX1 rs2071747 was associated with LOPD. • The dominant model of HMOX1 rs2071747 was associated with LOPD.

Combined Analysis of the Metabolome and Transcriptome to Explore Heat Stress Responses and Adaptation Mechanisms in Celery (Apium graveolens L.).

Celery is an important leafy vegetable that can grow during the cool season and does not tolerate high temperatures. Heat stress is widely acknowledged as one of the main abiotic stresses affecting the growth and yield of celery. The morphological and physiological indices of celery were investigated in the present study to explore the physiological mechanisms in response to high temperatures. Results showed that the antioxidant enzyme activity, proline, relative conductivity, and malondialdehyde were increased, while chlorophyll and the water content of leaves decreased under high-temperature conditions. Short-term heat treatment increased the stomatal conductance to cool off the leaves by transpiration; however, long-term heat treatment led to stomatal closure to prevent leaf dehydration. In addition, high temperature caused a disordered arrangement of palisade tissue and a loose arrangement of spongy tissue in celery leaves. Combined metabolomic and transcriptomic analyses were further used to reveal the regulatory mechanisms in response to heat stress at the molecular level in celery. A total of 1003 differential metabolites were identified and significantly enriched in amino acid metabolism and the tricarboxilic acid (TCA) cycle. Transcriptome sequencing detected 24,264 different genes, including multiple transcription factor families such as HSF, WRKY, MYB, AP2, bZIP, and bHLH family members that were significantly upregulated in response to heat stress, suggesting that these genes were involved in the response to heat stress. In addition, transcriptional and metabolic pathway analyses showed that heat stress inhibited the glycolysis pathway and delayed the TCA cycle but increased the expression of most amino acid synthesis pathways such as proline, arginine, and serine, consistent with the results of physiological indicators. qRT-PCR further showed that the expression pattern was similar to the expression abundance in the transcriptome. The important metabolites and genes in celery that significantly contributed to the response to high temperatures were identified in the present study, which provided the theoretical basis for breeding heat-resistant celery.

A Systematic Review of Candidate Genes for Major Depression.

Background and Objectives: The aim of this systematic review was to analyse which candidate genes were examined in genetic association studies and their association with major depressive disorder (MDD). Materials and Methods: We searched PUBMED for relevant studies published between 1 July 2012 and 31 March 2019, using combinations of keywords: "major depressive disorder" OR "major depression" AND "gene candidate", "major depressive disorder" OR "major depression" AND "polymorphism". Synthesis focused on assessing the likelihood of bias and investigating factors that may explain differences between the results of studies. For selected gene list after literature overview, functional enrichment analysis and gene ontology term enrichment analysis were conducted. Results: 141 studies were included in the qualitative review of gene association studies focusing on MDD. 86 studies declared significant results (p < 0.05) for 172 SNPs in 85 genes. The 13 SNPs associations were confirmed by at least two studies. The 18 genetic polymorphism associations were confirmed in both the previous and this systematic analysis by at least one study. The majority of the studies (68.79 %) did not use or describe power analysis, which may have had an impact over the significance of their results. Almost a third of studies (N = 54) were conducted in Chinese Han population. Conclusion: Unfortunately, there is still insufficient data on the links between genes and depression. Despite the reported genetic associations, most studies were lacking in statistical power analysis, research samples were small, and most gene polymorphisms have been confirmed in only one study. Further genetic research with larger research samples is needed to discern whether the relationship is random or causal. Summations: This systematic review had summarized all reported genetic associations and has highlighted the genetic associations that have been replicated. Limitations: Unfortunately, most gene polymorphisms have been confirmed only once, so further studies are warranted for replicating these genetic associations. In addition, most studies included a small number of MDD cases that could be indicative for false positive. Considering that polymorphism loci and associations with MDD is also vastly dependent on interpersonal variation, extensive studies of gene interaction pathways could provide more answers to the complexity of MDD.

Genetic-Driven Druggable Target Identification and Validation.

Choosing the right biological target is the critical primary decision for the development of new drugs. Systematic genetic association testing of both human diseases and quantitative traits, along with resultant findings of coincident associations between them, is becoming a powerful approach to infer drug targetable candidates and generate in vitro tests to identify compounds that can modulate them therapeutically. Here, we discuss opportunities and challenges, and infer criteria for the optimal use of genetic findings in the drug discovery pipeline.

Evaluation of Primary Angle-Closure Glaucoma Susceptibility Loci for Estimating Angle Closure Disease Severity.

PURPOSE: To investigate whether recently identified genetic loci for primary angle-closure glaucoma (PACG) are associated with disease severity. DESIGN: Case-control study. PARTICIPANTS: Eight hundred four PACG patients and 943 control participants of Chinese ethnicity from Singapore. METHODS: The 8 PACG-associated single nucleotide polymorphisms (SNPs; rs11024102 at PLEKHA7, rs3753841 at COL11A1, rs1015213 located between PCMTD1 and ST18 on chromosome 8q, rs3816415 at EPDR1, rs1258267 at CHAT, rs736893 at GLIS3, rs7494379 at FERMT2, and rs3739821 mapping in between DPM2 and FAM102A) identified from genome-wide association studies were tested for association with disease severity using logistic regression adjusted for age and gender. A P value of 0.006 was set as significant after Bonferroni correction for testing of 8 loci. We also calculated the weighted genetic risk score (GRS) weighted by the estimated individual SNP effect size on PACG calculated as logarithm of the odds ratio (OR). Disease severity was based on the visual field mean deviation (MD) and classified as early to moderate (MD, >-12 dB) and severe (MD, <-20 dB). MAIN OUTCOME MEASURES: Association of PACG loci with severe disease. RESULTS: Of the 804 PACG patients, genotyping data were available for 768 individuals and included 436 with mild-to-moderate PACG and 206 with severe PACG. The PACG patients were significantly older (mean age, 64.3 ± 9.1 years vs. 56.4 ± 8.9 years; P < 0.001) and there were proportionately more women compared with control participants (58.4% vs. 49.0%; P < 0.001). Of the 8 loci investigated, we observed significant evidence of association with severe PACG at 1 SNP, namely rs3816415 in EPDR1 (OR, 2.03; 95% confidence interval [CI], 1.49-2.78; P = 1 × 10-5). A higher-weighted GRS was associated significantly with severe PACG, with an OR of 3.11 (95% CI, 1.95-4.96) comparing the lowest quartile with the highest quartile. CONCLUSIONS: Our results show that EPDR1 is associated significantly with severe PACG, suggesting that it may predispose patients to more aggressive disease development. Individuals with PACG with a higher GRS were associated with a higher risk of severe PACG.

Association of HMOX-1 with sporadic Alzheimer's disease in southern Han Chinese.

BACKGROUND AND PURPOSE: The aim of this study was to discover the associations between HMOX-1 and Alzheimer's disease (AD). METHODS: A total of 500 AD patients and 500 healthy controls were recruited in this study. Polymer chain reaction was used. RESULTS: There was a statistically significant difference between AD patients and controls in both the dominant and recessive models of HMOX-1 rs2071746 after adjustment for age, gender and education (dominant model: p = 0.047, odds ratio [OR] 1.34, 95% confidence interval [CI] 1.00-1.78, adjusted; recessive model: p = 0.049, OR 1.34, 95% CI 1.00-1.80, adjusted). There was also a trend for an association between the dominant model and late-onset AD after adjustment for age, gender and education (dominant model: p = 0.084, OR 1.37, 95% CI 0.96-1.95, adjusted). CONCLUSIONS: We found an association between the dominant and recessive models of HMOX1 rs2071746 and AD.

GATE: an efficient procedure in study of pleiotropic genetic associations.

BACKGROUND: The association studies on human complex traits are admittedly propitious to identify deleterious genetic markers. Compared to single-trait analyses, multiple-trait analyses can arguably make better use of the information on both traits and markers, and thus improve statistical power of association tests prominently. Principal component analysis (PCA) is a well-known useful tool in multivariate analysis and can be applied to this task. Generally, PCA is first performed on all traits and then a certain number of top principal components (PCs) that explain most of the trait variations are selected to construct the test statistics. However, under some situations, only utilizing these top PCs would lead to a loss of important evidences from discarded PCs and thus makes the capability compromised. METHODS: To overcome this drawback while keeping the advantages of using the top PCs, we propose a group accumulated test evidence (GATE) procedure. By dividing the PCs which is sorted in the descending order according to the corresponding eigenvalues into a few groups, GATE integrates the information of traits at the group level. RESULTS: Simulation studies demonstrate the superiority of the proposed approach over several existing methods in terms of statistical power. Sometimes, the increase of power can reach 25%. These methods are further illustrated using the Heterogeneous Stock Mice data which is collected from a quantitative genome-wide association study. CONCLUSIONS: Overall, GATE provides a powerful test for pleiotropic genetic associations.

Statistical controversies in clinical research: overlap and errors in the meta-analyses of microRNA genetic association studies in cancers.

BACKGROUND: Various errors in the design, conduct, and analysis of medical and public health research studies can produce false results and waste valuable resources. While systematic reviews and meta-analyses are arguably considered the most dependable source of evidence-based medicine, increasing numbers of studies are indicating that, on the contrary to the public's belief, many of these investigations are redundant, erroneous, and even biased. METHODS: Ninety-four meta-analyses on microRNA polymorphism and risk of cancer were extracted from Pubmed database on August 2016. Two investigators independently extracted data (i.e. number of studies, ethnicity, number of cases/controls, bias, etc.) from each meta-analysis. PROSPERO registration status and reference status were also recorded. RESULTS: Among the 217 microRNA gene-variant cancer associations reported by 94 published meta-analyses, 37% had overlapping results and were extracted from the exact identical case-control studies. However, not one meta-analysis was registered into PROSPERO. Thirty-one percent of the overlapping associations referenced a previous meta-analysis investigating the same association; although only 36% of these overlapping associations referenced earlier meta-analysis that had the same overlapping results. Seventy-four percent of these references were limited to mere citations. Twenty-six percent of the overlapping associations from 16 meta-analyses showed discordant results, and of these, 87% of the genotype comparisons were found significant, contrary to the initial reports of being non-significant. However, no association was noteworthy in regards to false positive rate probability calculations at a given prior probability of 0.001 and 0.000001 and statistical power to detect an odds ratio (OR) of 1.1 and 1.5. CONCLUSIONS: Genetic association meta-analyses were by far more redundant, erroneous, and lacking references than initially expected. Careful search of similar studies, attention to small details, and inclination to reference previous works are needed. This paper proposes potential solutions for these problems in hopes of standardizing research efforts and in improving the quality of medical research.

Genetic relationships among female fertility disorders, female fertility traits and productivity of Holstein dairy cows in the early lactation period.

Fertility health disorders from the early lactation period including retained placenta (REPLA), metritis (MET), corpus luteum persistence (CLP), anoestria/acyclia (AOEAC) and ovarial cysts (OC), as well as overall disease categories (disorders during the postpartal period (DPP), ovary infertility (OINF), overall trait definition "fertility disorders" (FD)), were used to estimate genetic (co)variance components with female fertility and test-day traits. The disease data set comprised 25,142 Holstein cows from parities 1, 2 and 3 resulting in 43,584 lactations. For disease traits, we used the binary trait definition (sick or healthy) and disease count data reflecting the sum of treatments for the same disease within lactation or within lactation periods. Statistical modelling included single and multiple trait repeatability animal models for all trait combinations within a Bayesian framework. Heritabilities for binary disease traits ranged from 0.04 (OC) to 0.10 (REPLA) and were slightly lower for the corresponding sum trait definitions. Correlations between both trait definitions were almost one, for genetic as well as for permanent environmental effects. Moderate to high genetic correlations were found among puerperal disorders DPP, REPLA and MET (0.45-0.98) and among the ovarian disorders OINF, AOEAC, CLP and OC (0.59-0.99). Genetic correlations between puerperal and ovarian disorders were close to zero, apart from the REPLA-OC association (0.55). With regard to fertility disorders and productivity in early lactation, a pronounced genetic antagonistic relationship was only identified between OC and protein yield. Genetic correlations between fertility disorders and test-day SCS were close to zero. OINF and all diseases contributing to OINF were strongly correlated with the female fertility traits "interval from calving to first service," "interval from service to pregnancy" and "interval from calving to pregnancy." The strong correlations imply that fertility disorders could be included in genetic evaluations of economic fertility traits as correlated predictors. Vice versa, a breeding focus on female fertility traits will reduce genetic susceptibility to OC, CLP and AOEAC.

The impact of HLA class I and EBV latency-II antigen-specific CD8(+) T cells on the pathogenesis of EBV(+) Hodgkin lymphoma.

In 40% of cases of classical Hodgkin lymphoma (cHL), Epstein-Barr virus (EBV) latency-II antigens [EBV nuclear antigen 1 (EBNA1)/latent membrane protein (LMP)1/LMP2A] are present (EBV(+) cHL) in the malignant cells and antigen presentation is intact. Previous studies have shown consistently that HLA-A*02 is protective in EBV(+) cHL, yet its role in disease pathogenesis is unknown. To explore the basis for this observation, gene expression was assessed in 33 cHL nodes. Interestingly, CD8 and LMP2A expression were correlated strongly and, for a given LMP2A level, CD8 was elevated markedly in HLA-A*02(-) versus HLA-A*02(+) EBV(+) cHL patients, suggesting that LMP2A-specific CD8(+) T cell anti-tumoral immunity may be relatively ineffective in HLA-A*02(-) EBV(+) cHL. To ascertain the impact of HLA class I on EBV latency antigen-specific immunodominance, we used a stepwise functional T cell approach. In newly diagnosed EBV(+) cHL, the magnitude of ex-vivo LMP1/2A-specific CD8(+) T cell responses was elevated in HLA-A*02(+) patients. Furthermore, in a controlled in-vitro assay, LMP2A-specific CD8(+) T cells from healthy HLA-A*02 heterozygotes expanded to a greater extent with HLA-A*02-restricted compared to non-HLA-A*02-restricted cell lines. In an extensive analysis of HLA class I-restricted immunity, immunodominant EBNA3A/3B/3C-specific CD8(+) T cell responses were stimulated by numerous HLA class I molecules, whereas the subdominant LMP1/2A-specific responses were confined largely to HLA-A*02. Our results demonstrate that HLA-A*02 mediates a modest, but none the less stronger, EBV-specific CD8(+) T cell response than non-HLA-A*02 alleles, an effect confined to EBV latency-II antigens. Thus, the protective effect of HLA-A*02 against EBV(+) cHL is not a surrogate association, but reflects the impact of HLA class I on EBV latency-II antigen-specific CD8(+) T cell hierarchies.

A systematic appraisal of field synopses in genetic epidemiology: a HuGE review.

Evidence from genetic association studies is accumulating rapidly. Field synopses have recently arisen as an unbiased way of systematically synthesizing this evidence. We performed a systematic review and appraisal of published field synopses in genetic epidemiology and assessed their main findings and methodological characteristics. We identified 61 eligible field synopses, published between January 1, 2007, and October 31, 2013, on 52 outcomes reporting 734 significant associations at the P < 0.05 level. The median odds ratio for these associations was 1.25 (interquartile range, 1.15-1.43). Egger's test was the most common method (n = 30 synopses) of assessing publication bias. Only 12 synopses (20%) used the Venice criteria to evaluate the epidemiologic credibility of their findings (n = 449 variants). Eleven synopses (18%) were accompanied by an online database that has been regularly updated. These synopses received more citations (P = 0.01) and needed a larger research team (P = 0.02) than synopses without an online database. Overall, field synopses are becoming a valuable tool for the identification of common genetic variants, especially when researchers follow relevant methodological guidelines. Our work provides a summary of the current status of the field synopses published to date and may help interested readers efficiently identify the online resources containing the relevant genetic evidence.

Direct, indirect and pleiotropic effects of candidate genes on internalizing disorder psychopathology.

BACKGROUND: Twin studies of internalizing disorders suggest that their high co-morbidity is partially explained by shared genetic risk. Few studies have investigated pleiotropic effects of well-validated candidate genes across phenotypes. METHOD: Subjects were 928 Caucasian patients who presented to an out-patient clinic specializing in the assessment and treatment of anxiety and mood disorders. We constructed latent dimensional phenotypes across the internalizing spectrum (neuroticism, extraversion, depression, generalized anxiety, panic/agoraphobia, social phobia, post-traumatic stress, and obsessions-compulsions) by combining diagnostic criteria with other clinical indicators. We selected multiple variants in four evidence-based candidate genes (SLC6A4, COMT, GAD1, RGS2) with previously reported effects on several of these phenotypes. We conducted genetic association testing of their direct and indirect effects as well as gene × stress interactions (G × E). RESULTS: We detected 19 nominally significant main effect associations for the 10 polymorphisms tested among the eight phenotypes (24%). These were generally phenotype non-specific, showing pleiotropic effects across multiple domains. The majority of observed sharing was between depression, panic disorder, and post-traumatic stress disorder. Some of these were best explained by mediational models in which genes increase liability for disorders indirectly via their effects on temperament. Limited G × E effects were detected between variants in SLC6A4 and both panic/agoraphobia and post-traumatic stress. CONCLUSIONS: Examining just a few candidate genes for their potential roles in internalizing phenotypes, we found moderate support for the shared effects of several polymorphisms. These findings highlight the richness and complexity by which genes potentially contribute to psychopathology via pleiotropy, moderation by stress, and mediation by temperament.

TOR1A polymorphisms in a Russian cohort with primary focal/segmental dystonia.

PURPOSE/AIM OF THE STUDY: To analyze contribution of rs3842225 and rs1182 single nucleotide polymorphisms (SNP) in TOR1A gene, the causative gene for the DYT1 form of hereditary early-onset generalized dystonia, to the development of focal and segmental dystonia in Russian patients. MATERIALS AND METHODS: We analyzed associations between rs3842225 and rs1182 polymorphisms in TOR1A and focal/segmental dystonia in 254 patients from Russian population, including 218 Slavic patients and 36 patients of mixed ethnic background. RESULTS: Stratification of patients based on age at the disease onset (≤ 30 years and > 30 years) showed statistically significant prevalence of the del-allele at the rs3842225 locus in Slavic patients with earlier age of onset of dystonia (36.96% vs. 21.39% in patients with late age of onset, p = 0.002) and an overrepresentation of the T-allele at the rs1182 locus (36.96% vs. 21.69%, p = 0.003). In Slavs, we also observed an overrepresentation of the homozygous genotypes, T/T (general sample of dystonia, 9.17% and focal dystonia, 10.28%) or G/G (general sample of dystonia, 60.55% and focal dystonia, 58.86%), compared to controls (T/T, 4.27% and G/G, 55.49%). In non-Slavic patients, we revealed neither significant associations, nor statistical tendencies regarding any of the clinical features. CONCLUSIONS: Our data in an Eastern Slavic (Russian) population correspond well to results of other studies from different countries and confirm that certain TOR1A genotypes may be regarded as factors predisposing to focal and segmental dystonia.