Meta-analysis of genetic association studies: methodologies, between-study heterogeneity and winner's curse

Genetics of child aggression, a systematic review

Excessive and persistent aggressiveness is the most common behavioral problem that leads to psychiatric referrals among children. While half of the variance in childhood aggression is attributed to genetic factors, the biological mechanism and the interplay between genes and environment that results in aggression remains elusive. The purpose of this systematic review is to provide an overview of studies examining the genetics of childhood aggression irrespective of psychiatric diagnosis. PubMed, PsycINFO, and MEDLINE databases were searched using predefined search terms for aggression, genes and the specific age group. From the 652 initially yielded studies, eighty-seven studies were systematically extracted for full-text review and for further quality assessment analyses. Findings show that (i) investigation of candidate genes, especially of MAOA (17 studies), DRD4 (13 studies), and COMT (12 studies) continue to dominate the field, although studies using other research designs and methods including genome-wide association and epigenetic studies are increasing, (ii) the published articles tend to be moderate in sizes, with variable methods of assessing aggressive behavior and inconsistent categorizations of tandem repeat variants, resulting in inconclusive findings of genetic main effects, gene-gene, and gene-environment interactions, (iii) the majority of studies are conducted on European, male-only or male-female mixed, participants. To our knowledge, this is the first study to systematically review the effects of genes on youth aggression. To understand the genetic underpinnings of childhood aggression, more research is required with larger, more diverse sample sets, consistent and reliable assessments and standardized definition of the aggression phenotypes. The search for the biological mechanisms underlying child aggression will also benefit from more varied research methods, including epigenetic studies, transcriptomic studies, gene system and genome-wide studies, longitudinal studies that track changes in risk/ameliorating factors and aggression-related outcomes, and studies examining causal mechanisms.

An alternative method of SNP inclusion to develop a generalized polygenic risk score analysis across Alzheimer's disease cohorts

Introduction

Polygenic risk scores (PRSs) have great clinical potential for detecting late-onset diseases such as Alzheimer's disease (AD), allowing the identification of those most at risk years before the symptoms present. Although many studies use various and complicated machine learning algorithms to determine the best discriminatory values for PRSs, few studies look at the commonality of the Single Nucleotide Polymorphisms (SNPs) utilized in these models.

Methods

This investigation focussed on identifying SNPs that tag blocks of linkage disequilibrium across the genome, allowing for a generalized PRS model across cohorts and genotyping panels. PRS modeling was conducted on five AD development cohorts, with the best discriminatory models exploring for a commonality of linkage disequilibrium clumps. Clumps that contributed to the discrimination of cases from controls that occurred in multiple cohorts were used to create a generalized model of PRS, which was then tested in the five development cohorts and three further AD cohorts.

Results

The model developed provided a discriminability accuracy average of over 70% in multiple AD cohorts and included variants of several well-known AD risk genes.

Discussion

A key element of devising a polygenic risk score that can be used in the clinical setting is one that has consistency in the SNPs that are used to calculate the score; this study demonstrates that using a model based on commonality of association findings rather than meta-analyses may prove useful.

Reproducibility of cerebellar involvement as quantified by consensus structural MRI biomarkers in advanced essential tremor

Essential tremor (ET) is the most prevalent movement disorder with poorly understood etiology. Some neuroimaging studies report cerebellar involvement whereas others do not. This discrepancy may stem from underpowered studies, differences in statistical modeling or variation in magnetic resonance imaging (MRI) acquisition and processing. To resolve this, we investigated the cerebellar structural differences using a local advanced ET dataset augmented by matched controls from PPMI and ADNI. We tested the hypothesis of cerebellar involvement using three neuroimaging biomarkers: VBM, gray/white matter volumetry and lobular volumetry. Furthermore, we assessed the impacts of statistical models and segmentation pipelines on results. Results indicate that the detected cerebellar structural changes vary with methodology. Significant reduction of right cerebellar gray matter and increase of the left cerebellar white matter were the only two biomarkers consistently identified by multiple methods. Results also show substantial volumetric overestimation from SUIT-based segmentation-partially explaining previous literature discrepancies. This study suggests that current estimation of cerebellar involvement in ET may be overemphasized in MRI studies and highlights the importance of methods sensitivity analysis on results interpretation. ET datasets with large sample size and replication studies are required to improve our understanding of regional specificity of cerebellum involvement in ET. PROTOCOL REGISTRATION: The stage 1 protocol for this Registered Report was accepted in principle on 21 March 2022. The protocol, as accepted by the journal, can be found at: https://doi.org/10.6084/m9.figshare.19697776 .

Risk of type 2 diabetes and KCNJ11 gene polymorphisms: a nested case-control study and meta-analysis

Due to the central role in insulin secretion, the potassium inwardly-rectifying channel subfamily J member 11 (KCNJ11) gene is one of the essential genes for type 2 diabetes (T2D) predisposition. However, the relevance of this gene to T2D development is not consistent among diverse populations. In the current study, we aim to capture the possible association of common KCNJ11 variants across Iranian adults, followed by a meta-analysis. We found that the tested variants of KCNJ11 have not contributed to T2D incidence in Iranian adults, consistent with similar insulin secretion levels among individuals with different genotypes. The integration of our results with 72 eligible published case-control studies (41,372 cases and 47,570 controls) as a meta-analysis demonstrated rs5219 and rs5215 are significantly associated with the increased T2D susceptibility under different genetic models. Nevertheless, the stratified analysis according to ethnicity showed rs5219 is involved in the T2D risk among disparate populations, including American, East Asian, European, and Greater Middle Eastern, but not South Asian. Additionally, the meta-regression analysis demonstrated that the sample size of both case and control groups was significantly associated with the magnitude of pooled genetic effect size. The present study can expand our knowledge about the KCNJ11 common variant's contributions to T2D incidence, which is valuable for designing SNP-based panels for potential clinical applications in precision medicine. It also highlights the importance of similar sample sizes for avoiding high heterogeneity and conducting a more precise meta-analysis.

The role of FTO variant rs1421085 in the relationship with obesity: a systematic review and meta-analysis

PURPOSE

Fat mass and obesity-associated (FTO) is considered the first locus associated with adiposity, a concerning health problem worldwide. Many studies have evaluated the relationship between the FTO variants and obesity susceptibility. While the strong association of FTO rs1421085 with the risk of obesity across populations was reported in different studies, some researchers found a lack of association of this variant with adiposity. This systematic review and meta-analysis aimed to assess the association between obesity and rs1421085 polymorphism.

METHODS

We systematically searched PubMed, Scopus, and Google Scholar up to June 2022 to find pertinent studies. To further assess this issue, we surveyed the probable association of rs1421085 with obesity development among Iranian adults using the logistic regression analysis, and the obtained results were used for doing meta-analysis. After selection, nine eligible studies were included in the meta-analysis through the random- and fixed-effect models to determine the combined odds ratios (OR) and 95% confidence intervals (CI).

RESULTS

According to our meta-analysis conducted on 5169 obese and 7772 non-obese individuals using different genetic models, including recessive, dominant, over-dominant, and additive, rs1421085 could positively increase the risk of obesity under all tested genetic models. Also, we detected a high to moderate level of heterogeneity among different studies under various genetic models.

CONCLUSION

This meta-analysis further verified the positive association of FTO rs1421085 with the risk of developing obesity.

STUDY REGISTRATION

This study is registered as PROSPERO CRD42021220092.

LEVEL OF EVIDENCE

Level I, systematic reviews and meta-analyses.

Significant Association of the Catechol-O-Methyltransferase Gene Polymorphism (rs4680) and Opioid Use Disorder in Asian Populations, but not Caucasian Populations: A Meta-analysis

Objective: Previous studies have reported on the association between the rs4680 polymorphism in the Catechol-O-methyltransferase (COMT) gene and opioid use disorder (OUD) with inconsistent outcomes. The goal of this study was to examine the correlation of the rs4680 polymorphism and OUD using a meta-analysis approach. Methods: Six electronic databases, including PubMed, Web of Science, Cochrane Library, EMBASE, Wanfang and CNKI, were searched thoroughly for relevant studies on the association of the rs4680 polymorphism and OUD up to September, 2021. Summary odds ratios (ORs) with 95% confidence intervals (CIs) were utilized to test the association. Statistical analyses was performed using RevMan 5.3 software. Results: Eleven studies with 13 independent cohorts encompassing 2538 cases and 2519 controls were included in this study. In the overall analysis, the rs4680 polymorphism was not associated with OUD susceptibility. Subgroup analyses suggested that rs4680 was significantly correlated with OUD in Asian populations: VV vs. MM, OR = 1.46, 95% CI 1.05-2.02, p = 0.02; VM vs. MM, OR = 1.44, 95% CI 1.04-2.00, p = 0.03; VV+VM vs. MM, OR = 1.45, 95% CI 1.07-1.99, p = 0.02. However, the pooled data did not suggest any significant association in the Caucasian population. Conclusion: This meta-analysis supports a significant association between the rs4680 polymorphism and predisposition to OUD in Asians, carriers of VV and VM genotypes appear to have an increased susceptibility to OUD. However, the association does not exist in Caucasians.

"Association of MTHFR and MS/MTR gene polymorphisms with congenital heart defects in North Indian population (Jammu and Kashmir): a case-control study encompassing meta-analysis and trial sequential analysis"

Background

The risk of Congenital Heart Defects (CHD) is greatly influenced by variants within the genes involved in folate-homocysteine metabolism. Polymorphism in MTHFR (C677T and G1793A) and MS/MTR (A2756G) genes increases the risk of developing CHD risk, but results are controversial. Therefore, we conducted a case–control association pilot study followed by an up-dated meta-analysis with trial sequential analysis (TSA) to obtain more precise estimate of the associations of these two gene variants with the CHD risk.

Methods

For case–control study, we enrolled 50 CHD patients and 100 unrelated healthy controls. Genotyping was done by PCR–RFLP method and meta-analysis was performed by MetaGenyo online Statistical Analysis System software. For meta-analysis total number of individuals was as follows: for MTHFR C677T 3450 CHD patients and 4447 controls whereas for MS A2756G 697 CHD patients and 777 controls.

Results

Results of the original pilot study suggested lack of association for MTHFR C677T and MS A2756G polymorphism with risk of CHD whereas MTHFR G1793A was significantly associated with the disease. On performing meta-analysis, a significant association was observed with MTHFR C677T polymorphism but not with MS A2756G. Trial sequential Analysis also confirmed the sufficient sample size requirement for findings of meta-analysis.

Conclusions

The results of the meta-analysis suggested a significant role of MTHFR in increased risk of CHD.

Systematic review of host genetic association with Covid-19 prognosis and susceptibility: What have we learned in 2020?

Biomarker identification may provide strategic opportunities to understand disease pathophysiology, predict outcomes, improve human health, and reduce healthcare costs. The highly heterogeneous Covid-19 clinical manifestation suggests a complex interaction of several different human, viral and environmental factors. Here, we systematically reviewed genetic association studies evaluating Covid-19 severity or susceptibility to SARS-CoV-2 infection following PRISMA recommendations. Our research comprised papers published until December 31st , 2020, in PubMed and BioRXiv databases focusing on genetic association studies with Covid-19 prognosis or susceptibility. We found 20 eligible genetic association studies, of which 11 assessed Covid-19 outcome and 14 evaluated infection susceptibility (five analyzed both effects). Q-genie assessment indicated moderate quality. Five large-scale association studies (GWAS, whole-genome, or exome sequencing) were reported with no consistent replication to date. Promising hits were found on the 3p21.31 region and ABO locus. Candidate gene studies examined ACE1, ACE2, TMPRSS2, IFITM3, APOE, Furin, IFNL3, IFNL4, HLA, TNF-ɑ genes, and ABO system. The most evaluated single locus was the ABO, and the most sampled region was the HLA with three and five candidate gene studies, respectively. Meta-analysis could not be performed. Available data showed the need for further reports to replicate claimed associations.

A meta-analysis of salivary cortisol responses in the Trier Social Stress Test to evaluate the effects of speech topics, sex, and sample size

Background

The Trier Social Stress Test (TSST) is one of the most widely used laboratory-based psychological stress paradigms. Previous studies have shown that males have a more robust cortisol response than females in the TSST. However, the effects of sample size, speech topic, and interaction between sex and speech topic on cortisol responses in TSST remain elusive. Our goal was to evaluate these influencing factors in the TSST using salivary cortisol reactivity as an objective measure.

Methods

We collected TSST research articles in Web of Science, PubMed, PsycNet, and CNKI. We only included TSST studies that had measures of salivary cortisol both before and after task completion. A total of 65 articles involving 76 sub-studies met our inclusion criteria, with a total of 5171 participants (2040 females and 3131 males). The effects of sample sizes were assessed to determine if results of studies with various sample sizes were stable. We performed multivariate meta-regression to determine the effects of speech topic, sex, and the interaction between sex and speech topic after controlling their confounding effects. Subgroup analysis of sex was conducted to detect inter-group differences. We further evaluated the baseline and peak salivary cortisol concentrations for males and females independently to detect the sources of sex differences.

Results

The average effect size (i.e., Cohen's d) of salivary cortisol reactivity was 0.93, 95% CI = 0.82 to 1.04, p < .001. The small studies produced larger variations in the reported effect sizes than the large-sample studies (r = -0.24, p = .041). A sample size of 40 was necessary to provide sufficient statistical power to detect significant changes of salivary cortisol in TSST. Speech topics, sex, and sex-speech topic interaction could predict salivary cortisol responses (F(df1 = 3, df2 = 72) = 11.98, p < .001) and explained 42.68% of the total experimental variation. Sex was the only significant contributing factor (p < .00025) in the regression model. Salivary cortisol responses in males were significantly higher than in females (Q_B = 42.89, df = 1, p < .001). Further, significant differences between males and females were detected at baseline (t = -2.03, df = 74, p = .046) and peak (t = -4.96, df = 74, p < .001).

Conclusions

The TSST effectively induces stress response as measured by salivary cortisol change. Forty samples is the minimum sample size for detecting the robust salivary cortisol responses. We confirmed that males have more robust salivary cortisol reactivity than females in TSST. Speech topics that we tested did not significantly contribute to differences in salivary cortisol responses. No significant interaction between sex and speech topic on salivary cortisol responses was detected.

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Forty samples is the minimum for detecting robust salivary cortisol responses.

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The speech topics tested did not significantly alter salivary cortisol responses.

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Males have higher salivary cortisol responses than females in the TSST.

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Males had higher salivary cortisol levels than females in the TSST at both baseline and peak.

VEGFA rs3025039 and biliary atresia susceptibility in Chinese population: a systematic review and meta-analysis

Background

Previous studies have suggested an association between vascular endothelial growth factor A (VEGFA) rs3025039 polymorphism and biliary atresia (BA). However, this conclusion is controversial and there is no published pooled evidence of this association.

Methods

This study was conducted and reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. The protocol was registered with PROSPERO (International Prospective Register of Systematic Reviews). A thorough search was performed on databases including PubMed, Embase, and Chinese Biomedical Database up to August 2020. This study included 846 cases of BA and 2821 controls concerning VEGFA rs3025039 polymorphism. We selected relevant studies based on the following inclusion criteria: (1) the study design was case–control and cohort and (2) the patients carried standard clinical diagnoses of BA, etc. The exclusion criteria were as follows: (1) patients with other related diseases, (2) lack of requisite information and (3) duplicate data. The OR (odd ratio) and the corresponding 95% CI (confidence interval) were calculated to estimate the association.

Results

This study on VEGFA rs3025039 polymorphism in the Chinese population included 846 cases and 2821 controls. The results showed that there was no significant association between rs3025039 and susceptibility to BA under four genetic models. The results of the subgroup analysis were similar to the overall results.

Conclusions

This meta-analysis shows that rs3025039 was not associated with susceptibility to BA in the Chinese population. Further validation may entail additional research.

PROSPERO registration number

CRD42020203812.

Genome-Wide Association Study Statistical Models: A Review

Statistical models are at the core of the genome-wide association study (GWAS). In this chapter, we provide an overview of single- and multilocus statistical models, Bayesian, and machine learning approaches for association studies in plants. These models are discussed based on their basic methodology, cofactors adjustment accounted for, statistical power and computational efficiency. New statistical models and machine learning algorithms are both showing improved performance in detecting missed signals, rare mutations and prioritizing causal genetic variants; nevertheless, further optimization and validation studies are required to maximize the power of GWAS.

The association between polymorphisms near TMEM18 and the risk of obesity: a meta-analysis

BACKGROUND

Many studies have proposed that the pathogenesis of obesity has a genetic basis, with an important risk factor being the presence of polymorphisms in the region of the TMEM18 gene, which plays a significant role in feeding behaviour; however, subsequent studies among different ethnic populations and age groups have shown inconsistent results. Therefore, this present meta-analysis examines the relationship between TMEM18 polymorphisms with the risk of obesity with regard to age group and ethnic population.

METHODS

A literature database search was conducted for available relevant studies investigating the association between obesity risk and the presence of rs6548238, rs4854344, rs11127485, rs2867125 and rs7561317 polymorphisms in TMEM18. Pooled odds ratio (OR) and 95% confidence intervals (95% CI) were calculated by either a fixed-effects model or random effect model based on a heterogeneity test. The meta-analysis of rs6548238 and its surrogates examined the relationships between 53 395 obesity cases and 123 972 healthy controls from 27 studies and published data from the POPULOUS collection (Poland).

RESULTS

A significant association is observed between rs6548238 (and surrogate) and obesity risk, with OR = 1.25 (95% CI: 1.08-1.45). Regarding population type, a significant association was revealed among groups of Europeans with OR = 1.32 (1.10-1.59) and Mexicans with OR = 1.39 (1.13-1.73). However, a lack of statistical significance was noticed in groups in Asia with OR = 1.11 (95% CI: 0.86-1.42). Regarding age, a significant association was observed among children with OR = 1.28 (95% CI: 1.18-1.39) but not in adults OR = 1.21 (95% CI: 0.92-1.58).

CONCLUSIONS

The polymorphisms near TMEM18 appear to play a role in the development of obesity. Our findings indicate that differences exist between ethnic populations and age groups, supporting those of a previous study showing the various effects of genetic factors on age and ethnic groups.

Apolipoprotein E4 Polymorphism and Outcomes from Traumatic Brain Injury: A Living Systematic Review and Meta-Analysis

The mortality of traumatic brain injury (TBI) has been largely static despite advances in monitoring and imaging techniques. Substantial variance exists in outcome, not fully accounted for by baseline characteristics or injury severity, and genetic factors likely play a role in this variance. The aims of this systematic review were to examine the evidence for a link between the apolipoprotein E4 (APOE4) polymorphism and TBI outcomes and where possible, to quantify the effect size via meta-analysis. We searched EMBASE, MEDLINE, CINAHL, and gray literature in December 2017. We included studies of APOE genotype in relation to functional adult TBI outcomes. Methodological quality was assessed using the Quality in Prognostic Studies Risk of Bias Assessment Instrument and the prognostic studies adaptation of the Grading of Recommendations Assessment, Development and Evaluation tool. In addition, we contacted investigators and included an additional 160 patients whose data had not been made available for previous analyses, giving a total sample size of 2593 patients. Meta-analysis demonstrated higher odds of a favorable outcome following TBI in those not possessing an ApoE ɛ4 allele compared with ɛ4 carriers and homozygotes (odds ratio 1.39, 95% confidence interval 1.05 to 1.84; p = 0.02). The influence of APOE4 on neuropsychological functioning following TBI remained uncertain, with multiple conflicting studies. We conclude that the ApoE ɛ4 allele confers a small risk of poor outcome following TBI, with analysis by TBI severity not possible based on the currently available published data. Further research into the long-term neuropsychological impact and risk of dementia is warranted.

Genetic factors contributing to skeletal class III malocclusion: a systematic review and meta-analysis

OBJECTIVES

The present systematic review aims to report and critically assess the findings of the available scientific evidence from genetic association studies examining the genetic variants underlying skeletal class III malocclusion and its sub-phenotypes.

MATERIAL AND METHODS

A pre-piloted protocol was registered and followed. The PubMed, Scopus, WOS, Cochrane Library, Gray Open literature, and CADTH databases were explored for genetic association studies following PICOS-based selection criteria. The research was reported in accordance with PRISMA statement and HuGE guidelines. The Q-genie tool was applied to assess the quality of genetic studies. Meta-analysis of genetic association studies was done by means of Meta-Genyo tool.

RESULTS

A total of 8258 articles were retrieved, of which 22 were selected for in-depth analysis. Most of the studies did not differentiate between sub-phenotypes, and the cohorts were heterogeneous regarding ethnicity. Four to five principal components of class III malocclusion explained the phenotypic variation, and gene variants at MYO1H(rs10850110), BMP3(rs1390319), GHR (rs2973015,rs6184, rs2973015), FGF7(rs372127537), FGF10(rs593307), and SNAI3(rs4287555) (p < .05) explained most of the variation across the studies, associated to vertical, horizontal, or combined skeletal discrepancies. Meta-analysis results identified a statistically significant association between risk of class III malocclusion of A allele of the FBN3 rs7351083 [OR 2.13; 95% CI 1.1-4.1; p 0.02; recessive model].

CONCLUSION

Skeletal class III is a polygenic trait substantially modulated by ethnicity. A multicentric approach should be considered in future studies to increase sample sizes, applying multivariate analysis such as PCA and cluster analysis to characterize existing sub-phenotypes warranting a deeper analysis of genetic variants contributing to skeletal class III craniofacial disharmony.

CLINICAL RELEVANCE

Grasping the underlying mechanisms of this pathology is critical for a fuller understanding of its etiology, allowing generation of preventive strategies, new individualized therapeutic approaches and more accurate treatment planification strategies.

Revisiting genome-wide association studies from statistical modelling to machine learning

Over the last decade, genome-wide association studies (GWAS) have discovered thousands of genetic variants underlying complex human diseases and agriculturally important traits. These findings have been utilized to dissect the biological basis of diseases, to develop new drugs, to advance precision medicine and to boost breeding. However, the potential of GWAS is still underexploited due to methodological limitations. Many challenges have emerged, including detecting epistasis and single-nucleotide polymorphisms (SNPs) with small effects and distinguishing causal variants from other SNPs associated through linkage disequilibrium. These issues have motivated advancements in GWAS analyses in two contrasting cultures-statistical modelling and machine learning. In this review, we systematically present the basic concepts and the benefits and limitations in both methods. We further discuss recent efforts to mitigate their weaknesses. Additionally, we summarize the state-of-the-art tools for detecting the missed signals, ultrarare mutations and gene-gene interactions and for prioritizing SNPs. Our work can offer both theoretical and practical guidelines for performing GWAS analyses and for developing further new robust methods to fully exploit the potential of GWAS.

Associations between vitamin D receptor gene polymorphisms and spinal degenerative disease: evidence from a meta-analysis based on 35 case-control studies

OBJECTIVE

Dozens of reports on the associations of vitamin D receptor (VDR) gene polymorphisms and susceptibility to spinal degenerative disease (SDD) were conducted with inconsistent findings. This study aimed to elucidate the associations through a meta-analysis approach.

METHODS

Databases of PubMed, EMBASE, Web of Science, CNKI, and Wanfang were searched until July 10, 2020. Study quality was evaluated by using Newcastle-Ottawa Scale (NOS). Odds ratios (ORs) and 95% confidence intervals (95%CIs) were calculated to evaluate the associations under allelic model (1 vs. 2), homozygous model (11 vs. 22), heterozygous model (12 vs. 22), dominant model (11 + 12 vs. 22), and recessive model (11 vs. 12 + 22).

RESULTS

A total of 5021 cases and 5746 controls from 35 studies were eligible to this meta-analysis. According to NOS, the included studies were in excellent quality. In the overall population, the pooled data indicated that ApaI was associated with a reduced SDD susceptibility (AA vs. Aa + aa, OR = 0.83, 95%CI 0.71 - 0.96, P = 0.010). But the association was not observed in FokI, TaqI, and BsmI polymorphisms. Subgroup analysis suggested that TaqI polymorphism was correlated to an elevated SDD risk in Asians (TT + Tt vs. tt, OR = 2.55, 95%CI 1.90 - 3.44, P < 0.001).

CONCLUSION

The present study indicates that ApaI polymorphism may contribute to a reduced risk to SDD in the overall population, and TaqI polymorphism confers an elevated susceptibility to SDD in Asians. While, BsmI and FokI polymorphisms appear to have no significant association with SDD.

HLA-B*39:01:01 is a novel risk factor for antithyroid drug-induced agranulocytosis in Japanese population

Antithyroid drug (ATD) is a mainstay of Graves' disease (GD). About 0.1-0.5% of patients with GD treated with ATD exhibit ATD-induced agranulocytosis, which is characterized by severe reduction of circulating neutrophils. Immune-mediated responses have been proposed as a possible mechanism for the pathogenesis of ATD-induced agranulocytosis. Although it has been reported that the HLA class II allele (HLA-DRB1*08:03) was associated with ATD-induced agranulocytosis in multiple populations, the entire HLA region have not been explored in Japanese. Therefore, we performed HLA sequencing for 10 class I and 11 class II genes in 87 patients with ATD-induced agranulocytosis and 384 patients with GD who did not show ATD-induced agranulocytosis. By conducting case-control association studies at the HLA allele and haplotype levels, we replicated the association between HLA-DRB1*08:03:02 and ATD-induced agranulocytosis (P = 5.2 × 10^-7, odds ratio = 2.80), and identified HLA-B*39:01:01 as an independent risk factor (P = 1.4 × 10^-3, odds ratio = 3.35). To verify reproducibility of the novel association of HLA-B*39:01:01, we reanalyzed allele frequency data for HLA-B*39:01:01 from previous case-control association studies. The association of HLA-B*39:01:01 was significantly replicated in Chinese (P = 9.0 × 10^-3), Taiwanese (P = 1.1 × 10^-3), and European populations (P = 5.2 × 10^-4). A meta-analysis combining results from the previous and current studies reinforced evidence of the association between HLA-B*39:01:01 and ATD-induced agranulocytosis (P_meta = 1.2 × 10^-9, pooled OR = 3.66, 95% CI; 2.41-5.57). The results of this study will provide a better understanding of the pathogenesis of ATD-induced agranulocytosis in the context of HLA-mediated hypersensitivity reactions.

Sources of bias in genomics research of oral and dental traits

Evidence regarding the genomic basis of oral/dental traits and diseases is a fundamental pillar of the emerging notion of precision health. During the last decade, technological advances have improved the feasibility and affordability of conducting genome-wide association studies (GWAS) and studying the associations of emanating data with both common and rare oral conditions. Most evidence thus far emanates from GWAS of dental caries and periodontal disease that have tested the associations of several million single nucleotide polymorphisms (SNPs) with typically binary, health vs. disease phenotypes. GWAS offer advantages over the previous candidate-gene studies, mainly owing to their agnostic (i.e., unbiased, or hypothesis-free) nature. Nevertheless, GWAS are prone to virtually all sources of random and systematic error. Here, we review common sources of bias in genomics research with focus on GWAS including: type I and II errors, population stratification and heterogeneity, selection bias, adjustment for heritable covariates, appropriate reference panels for imputation, and gene annotation. We argue that valid and precise phenotype measurement is a key requirement, as GWAS sample sizes and thus statistical power increase. Finally, we stress that the lack of diversity of populations with phenotypes and genotypes is a major limitation for the generalizability and ultimate translation of the emerging genomics evidence-base into oral health promotion for all.

Long-term outcomes of macrovascular diseases and metabolic indicators of bariatric surgery for severe obesity type 2 diabetes patients with a meta-analysis

There is currently no detailed evidence for the long-term effects of bariatric surgery on severely obese with type 2 diabetes, such as the risk of myocardial infarction and stroke. In order to provide evidence on the risks of macrovascular diseases and metabolic indicators of bariatric surgery follow-up for more than five years, we searched in the Cochrane library, Pubmed, and EMBASE databases from the earliest studies to January 31, 2019. Randomized clinical trials or cohort studies compared bariatric surgery and conventional medical therapy for long-term incidence of macrovascular events and metabolic outcomes in severely obese patients with T2DM. Fixed-effects and random-effects meta-analyses were performed to pool the relative risks (RRs), hazard ratios (HRs) and weighted mean difference (WMD). Publication bias and heterogeneity were examined. Four RCTs and six cohort studies were finally involved in this review. Patients in the bariatric surgery group as compared to the conventional treatment group had lower incidence of macrovascular complications (RR = 0.43, 95%CI = 0.27~0.70), cardiovascular events (CVEs) (HR = 0.52, 95%CI = 0.39~0.71), and myocardial infarction (MI) (RR = 0.40, 95%CI = 0.26~0.61). At the same time, the results demonstrate that bariatric surgery is associated with better weight and better glycemic control over the long-term than non-surgical therapies, and reveal that different surgical methods have different effects on various metabolic indicators. Bariatric surgery significantly decreases macrovascular complications over the long term and is associated with greater weight loss and better intermediate glucose outcomes among T2DM patients with severe obesity as compared to patients receiving only conservative medical measures.

Combining multi-population datasets for joint genome-wide association and meta-analyses: The case of bovine milk fat composition traits

In genome-wide association studies (GWAS), sample size is the most important factor affecting statistical power that is under control of the investigator, posing a major challenge in understanding the genetics underlying difficult-to-measure traits. Combining data sets available from different populations for joint or meta-analysis is a promising alternative to increasing sample sizes available for GWAS. Simulation studies indicate statistical advantages from combining raw data or GWAS summaries in enhancing quantitative trait loci (QTL) detection power. However, the complexity of genetics underlying most quantitative traits, which itself is not fully understood, is difficult to fully capture in simulated data sets. In this study, population-specific and combined-population GWAS as well as a meta-analysis of the population-specific GWAS summaries were carried out with the objective of assessing the advantages and challenges of different data-combining strategies in enhancing detection power of GWAS using milk fatty acid (FA) traits as examples. Gas chromatography (GC) quantified milk FA samples and high-density (HD) genotypes were available from 1,566 Dutch, 614 Danish, and 700 Chinese Holstein Friesian cows. Using the joint GWAS, 28 additional genomic regions were detected, with significant associations to at least 1 FA, compared with the population-specific analyses. Some of these additional regions were also detected using the implemented meta-analysis. Furthermore, using the frequently reported variants of the diacylglycerol acyltransferase 1 (DGAT1) and stearoyl-CoA desaturase (SCD1) genes, we show that significant associations were established with more FA traits in the joint GWAS than the remaining scenarios. However, there were few regions detected in the population-specific analyses that were not detected using the joint GWAS or the meta-analyses. Our results show that combining multi-population data set can be a powerful tool to enhance detection power in GWAS for seldom-recorded traits. Detection of a higher number of regions using the meta-analysis, compared with any of the population-specific analyses also emphasizes the utility of these methods in the absence of raw multi-population data sets to undertake joint GWAS.

Genome-wide association study revealed novel loci which aggravate asymptomatic hyperuricaemia into gout

Objective

The first ever genome-wide association study (GWAS) of clinically defined gout cases and asymptomatic hyperuricaemia (AHUA) controls was performed to identify novel gout loci that aggravate AHUA into gout.

Methods

We carried out a GWAS of 945 clinically defined gout cases and 1003 AHUA controls followed by 2 replication studies. In total, 2860 gout cases and 3149 AHUA controls (all Japanese men) were analysed. We also compared the ORs for each locus in the present GWAS (gout vs AHUA) with those in the previous GWAS (gout vs normouricaemia).

Results

This new approach enabled us to identify two novel gout loci (rs7927466 of CNTN5 and rs9952962 of MIR302F) and one suggestive locus (rs12980365 of ZNF724) at the genome-wide significance level (p<5.0×10^–8). The present study also identified the loci of ABCG2, ALDH2 and SLC2A9. One of them, rs671 of ALDH2, was identified as a gout locus by GWAS for the first time. Comparing ORs for each locus in the present versus the previous GWAS revealed three ‘gout vs AHUA GWAS’-specific loci (CNTN5, MIR302F and ZNF724) to be clearly associated with mechanisms of gout development which distinctly differ from the known gout risk loci that basically elevate serum uric acid level.

Conclusions

This meta-analysis is the first to reveal the loci associated with crystal-induced inflammation, the last step in gout development that aggravates AHUA into gout. Our findings should help to elucidate the molecular mechanisms of gout development and assist the prevention of gout attacks in high-risk AHUA individuals.

5-HTTLPR and COMT Val158Met are not associated with alexithymia: New evidence and meta-analyses

BACKGROUNDS

Alexithymia refers to the difficulties in identifying and describing one's own emotions, lacking of imagination, and an externally oriented thinking style. Studies up to date have examined the associations of 5-HTTLPR and COMT Val158Met polymorphisms with alexithymia. However, the previous findings were mixed.

METHODS

We replicated the associations by scoring on alexithymia with the 20-item Toronto Alexithymia Scale and genotyping the polymorphisms of 5-HTTLPR and COMT Val158Met in a large population of college students (N = 1698). Moreover, we also meta-analyzed the associations with five samples (N = 7517) for the 5-HTTLPR and with five samples (N = 2186) for the COMT Val158Met.

RESULTS

Neither the replicated study nor the meta-analyses indicated the 5-HTTLPR and COMT Val158Met were associated with alexithymia.

CONCLUSIONS

The findings suggest that the 5-HTTLPR and COMT Val158Met polymorphisms are not associated with alexithymia. However, genetic-environmental studies with different ethnicity and psychopathology should be carried in future.

Quality of methods and reporting in association studies of chronic periodontitis and IL1A -889 and IL1B +3953/4 SNPs: A systematic review

OBJECTIVE

The aim of this systematic review was to evaluate the quality of reporting and methodology in genetic association studies between IL1A -889 and IL1B +3954 polymorphisms and chronic periodontitis.

BACKGROUND

Evidence provided by periodontal research on genetic risk factors is of uttermost importance in clinical practice as a possible diagnostic and prognostic tool for periodontitis. Inadequate reporting of results as well as high risk of bias due to methodological inconsistency hampers the integration of evidence in terms of clinical applicability.

METHODS

This review includes case-control studies in humans published between 1997 and July 2017. Searching was conducted through MEDLINE, EMBASE, and search handing. Specific scoring systems have been developed to evaluate the quality of methods and reporting. Each article was scored according to its adequacy, and then, the total number and the percentage of items positively qualified for both methods and reporting were calculated. The quality of methods in studies scoring 0-6, 7-12, and 13-16 was, respectively, considered poor, moderate, and good. For reporting, scores of 0-9, 10-18, and 19-26 were deemed of poor, moderate, and good quality, respectively. Pearson's correlation coefficient was calculated to explore the correlation between the year of publication and the quality in terms of methods and reporting.

RESULTS

From the 531 screened studies, 52 met the inclusion criteria and were thus included in the study. The quality of methods and reporting of published genetic association papers on IL1 and chronic periodontitis is moderate. On a scale from 0 to 16, the mean score for methods of the reviewed studies was 8.19 ± 1.93. The items more frequently considered inadequate concerned the handling of confounders in statistical analysis, especially oral hygiene habits, socioeconomic status, subgingival colonization of specific periodontal pathogens, and stress. A significant positive correlation was found between the year of publication and the quality scores in terms of method (r = 0.401, P = 0.003). In terms of reporting, the mean score was 14.83 ± 3.04 on a scale from 0 to 26 and it was considered overall moderate. No statistically significant correlation was found between the year of publication and the quality of reporting (P = 0.266).

CONCLUSIONS

The association between IL1A -889 and IL1B +3954 polymorphisms and chronic periodontitis is questionable due to methodological inconsistency. Evidence arising from meta-analysis is unreliable due to high risk of bias and moderate quality in terms of reporting.

Adjustment for covariates using summary statistics of genome-wide association studies

Linear regression is a standard approach to identify genetic variants associated with continuous traits in genome-wide association studies (GWAS). In a standard epidemiology study, linear regression is often performed with adjustment for covariates to estimate the independent effect of a predictor variable or to improve statistical power by reducing residual variability. However, it is problematic to adjust for heritable covariates in genetic association analysis. Here, we propose a new method that utilizes summary statistics of the covariate from additional samples for reducing the residual variability and hence improves statistical power. Our simulation study showed that the proposed methodology can maintain a good control of Type I error and can achieve much higher power than a simple linear regression. The method is illustrated by an application to the GWAS results from the Genetic Investigation of Anthropometric Traits consortium.

Systematic reviews and cancer research: a suggested stepwise approach

Systematic reviews, with or without meta-analysis, play an important role today in synthesizing cancer research and are frequently used to guide decision-making. However, there is now an increase in the number of systematic reviews on the same topic, thereby necessitating a systematic review of previous systematic reviews. With a focus on cancer, the purpose of this article is to provide a practical, stepwise approach for systematically reviewing the literature and publishing the results. This starts with the registration of a protocol for a systematic review of previous systematic reviews and ends with the publication of an original or updated systematic review, with or without meta-analysis, in a peer-reviewed journal. Future directions as well as potential limitations of the approach are also discussed. It is hoped that the stepwise approach presented in this article will be helpful to both producers and consumers of cancer-related systematic reviews and will contribute to the ultimate goal of preventing and treating cancer.

The role of radical prostatectomy for the treatment of metastatic prostate cancer: a systematic review and meta-analysis

The recommended therapy by EAU guidelines for metastatic prostate cancer (mPCa) is androgen deprivation therapy (ADT) with or without chemotherapy. The role of radical prostatectomy (RP) in the treatment of mPCa is still controversial. Hence, a meta-analysis was conducted by comprehensively searching the databases PubMed, EMBASE and Web of Science for the relevant studies published before September 1st, 2017. Our results successfully shed light on the relationship that RP for mPCa was associated with decreased cancer-specific mortality (CSM) (pooled HR = 0.41, 95%CI = 0.36–0.47) and enhanced overall survival (OS) (pooled HR = 0.49, 95%CI = 0.44–0.55). Subsequent stratified analysis demonstrated that no matter how RP compared with no local therapy (NLT) or radiation therapy (RT), it was linked to a lower CSM (pooled HR = 0.36, 95%CI = 0.30–0.43 and pooled HR = 0.56, 95%CI 0.43–0.73, respectively) and a higher OS (pooled HR = 0.49, 95%CI = 0.44–0.56 and pooled HR = 0.46, 95%CI 0.33–0.65, separately). When comparing different levels of Gleason score, M-stage or N-stage, our results indicated that high level of Gleason score, M-stage or N-stage was associated with increased CSM. In summary, the outcomes of the present meta-analysis demonstrated that RP for mPCa was correlated with decreased CSM and enhanced OS in eligible patients of involved studies. In addition, patients with less aggressive tumors and good general health seemed to benefit the most. Moreover, no matter compared with NLT or RT, RP showed significant superiority in OS or CSM. Upcoming prospective randomized controlled trials were warranted to provide more high-quality data.

Association Between the Estrogen Receptor Beta (ESR2) Rs1256120 Single Nucleotide Polymorphism and Adolescent Idiopathic Scoliosis: A Systematic Review and Meta-Analysis

STUDY DESIGN

A systematic review and meta-analysis.

OBJECTIVE

The aim of this study was to assess and synthesize the current evidence on the association between the rs1256120 single nucleotide polymorphism (SNP) of the estrogen receptor beta gene (ESR2) and adolescent idiopathic scoliosis (AIS).

SUMMARY OF BACKGROUND DATA

Hormonal disturbance has been postulated as a potential etiological factor in the development of AIS. As estrogen receptors are important mediators of estrogen response, mutations in these genes, including rs1256120 of ESR2, have been chosen as susceptibility candidates for AIS predisposition. The association of rs1256120 with AIS has been investigated in several recent studies, but showed conflicting evidence. We conducted a systematic review to evaluate the strength of this body of evidence and quantitative synthesis to examine sources of heterogeneity.

METHODS

This study conformed to PRISMA guidelines. Using a sensitive search strategy, PubMed (MEDLINE), EMBASE, and HuGE Literature Finder databases were searched to identify relevant studies for inclusion in the systematic review and meta-analysis. Risk of bias was assessed using a modified Newcastle-Ottawa Scale. The inverse variance model was used to calculate summary odds ratios (ORs) and corresponding 95% confidence intervals (CIs) for the allelic (C vs. T) and genotypic comparisons. Planned subgroup and sensitivity analyses were performed.

RESULTS

Three studies were included for systematic review and meta-analysis (n = 1264 AIS cases and n=1020 controls). A null relationship was found between rs1256120 and AIS (allelic OR = 1.20, 95% CI: 0.81-1.78, P = 0.36, I = 84.9%), with the first reported association likely to be false-positive and contributing substantially to heterogeneity.

CONCLUSION

Findings from the systematic review and meta-analysis suggest that rs1256120 of ESR2 is unlikely to be a predisposing or disease-modifying genetic risk factor for AIS.

LEVEL OF EVIDENCE

2.

Comparison between transrectal and transperineal prostate biopsy for detection of prostate cancer: a meta-analysis and trial sequential analysis

To systematically assess the efficacy and complications of transrectal (TR) versus transperineal (TP) prostate biopsy in the detection of prostate cancer (PCa). A meta-analysis was performed by searching the databases Pubmed, Embase and Web of science for the relevant available studies until September 1st, 2016, and thirteen studies met the inclusion criteria. The pooled odds ratios with 95% confidence intervals were calculated to evaluate the differences of TR and TP groups in PCa detection rate. Then, trial sequential analysis was performed to reduce the risk of type I error and estimated whether the evidence of the results was reliable. Overall, this meta-analysis included a total of 4280 patients, who had been accrued between April 2000 and Aug 2014 and randomly divided into TR group and TP group. Prostate biopsies included sextant, extensive and saturation biopsy procedures. Patients who received TP prostate biopsy had no significant improvement in PCa detection rate, comparing TR group. Moreover, when comparing TR and TP studies, no significant difference was found in abnormal DRE findings, serum PSA level measurement, Gleason score, prostate volume. Besides, this meta-analysis showed no obvious differences between these two groups in terms of relevant complications. Therefore, this meta-analysis revealed that no significant differences were found in PCa detection rate between TP and TR approaches for prostate biopsy. However, with regard to pain relief and additional anesthesia, TR prostate needle biopsy was relatively preferable, compared to TP prostate biopsy.

Methods to increase reproducibility in differential gene expression via meta-analysis

Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size.

Association between Toll-Like Receptor 9-1237T/C Polymorphism and the Susceptibility of Inflammatory Bowel Diseases: A Meta-Analysis

PURPOSE

The -1237T/C polymorphism of the Toll-like receptor 9 (TLR9) gene has been implicated in the susceptibility of inflammatory bowel diseases (IBDs), but the results remain conflicting. We further investigated this association via meta-analysis.

MATERIALS AND METHODS

Multiple electronic databases were extensively searched until February, 2015. The strength of association was evaluated by calculating the pooled odds ratios (ORs) and 95% confidence intervals (CIs).

RESULTS

A total of 2987 cases and 2388 controls from eight studies were analyzed. Overall, association was found between TLR9 -1237T/C polymorphism and the risk of IBDs when all the studies were pooled (recessive model, OR: 1.59, 95% CI: 1.02-2.47, p=0.04; homozygote comparison, OR: 1.62, 95% CI: 1.04-2.52, p=0.03; allele model, OR: 1.13, 95% CI: 1.00-1.27, p=0.05). Stratification by ethnicity indicated an association between TLR9 -1237T/C polymorphism and IBDs risk in Caucasians (recessive model, OR: 1.59, 95% CI: 1.02-2.47, p=0.04; homozygote comparison, OR: 1.62, 95% CI: 1.04-2.52, p=0.03; allele model, OR: 1.12, 95% CI: 1.00-1.27, p=0.05). When stratified by disease type, significant correlation were only found in the Crohn's disease subgroup (recessive model, OR: 1.69, 95% CI: 1.05-2.73, p=0.03; homozygote model, OR: 1.74, 95% CI: 1.07-2.82, p=0.02; allele model, OR: 1.15, 95% CI: 1.01-1.32, p=0.04).

CONCLUSION

The present study suggested that the TLR9 -1237T/C polymorphism might act as a risk factor in the development of IBDs, particularly in Caucasians.

iWAS--A novel approach to analyzing Next Generation Sequence data for immunology

In this communication we describe a novel way to use Next Generation Sequence from the receptors expressed on T and B cells. This informatics methodology is named iWAS, for immunonome Wide Association Study, where we use the immune receptor sequences derived from T and B cells and the features of those receptors (sequences themselves, V/J gene usage, length and character each of the CDR3 sub-regions) to define biomarkers of health and disease, as well as responses to therapies. Unlike GWAS, which do not provide immediate access to mechanism, the associations with immune receptors immediately suggest possible and plausible entrée's into disease pathogenesis and treatment.

The Association between HMGA1 rs146052672 Variant and Type 2 Diabetes: A Transethnic Meta-Analysis

The high-mobility group A1 (HMGA1) gene has been previously identified as a potential novel candidate gene for susceptibility to insulin resistance and type 2 diabetes (T2D) mellitus. For this reason, several studies have been conducted in recent years examining the association of the HMGA1 gene variant rs146052672 (also designated IVS5-13insC) with T2D. Because of non-univocal data and non-overlapping results among laboratories, we conducted the current meta-analysis with the aim to yield a more precise and reliable conclusion for this association. Using predetermined inclusion criteria, MEDLINE, PubMed, Web of Science, Scopus, Google Scholar and Embase were searched for all relevant available literature published until November 2014. Two of the authors independently evaluated the quality of the included studies and extracted the data. Values from the single studies were combined to determine the meta-analysis pooled estimates. Heterogeneity and publication bias were also examined. Among the articles reviewed, five studies (for a total of 13,789 cases and 13,460 controls) met the predetermined criteria for inclusion in this meta-analysis. The combined adjusted odds ratio estimates revealed that the rs146052672 variant genotype had an overall statistically significant effect on increasing the risk of development of T2D. As most of the study subjects were Caucasian, further studies are needed to establish whether the association of this variant with an increased risk of T2D is generalizable to other populations. Also, in the light of this result, it would appear to be highly desirable that further in-depth investigations should be undertaken to elucidate the biological significance of the HMGA1 rs146052672 variant.

Distribution of HLA haplotypes across Japanese Archipelago: similarity, difference and admixture

The human leukocyte antigen (HLA) region is the most polymorphic region in the human genome. The polymorphic nature of the HLA region is thought to have been shaped from balancing selection. The complex migration events during the Out-of-Africa expansion have influenced geographic patterns of HLA allele frequencies and diversities across present-day human populations. Differences in the HLA allele frequency may contribute geographic differences in the susceptibility to many diseases, such as infectious, autoimmune and metabolic diseases. Here we briefly reviewed characteristics of frequency distribution of HLA alleles and haplotypes in Japanese population. A large part of HLA alleles and haplotypes that are common in Japanese are shared with neighboring Asian populations. The differentiations in HLA alleles and haplotypes across Japanese regional populations may provide clues to model for peopling of Japanese Archipelago and for design of genetic association studies. Finally, we introduce recent topics that new HLA alleles derived from ancient admixtures with Neanderthals and Denisovans are thought to have played an important role in the adaptation of modern humans to local pathogens during Out-of-Africa expansion.

Genome-wide association study of clinically defined gout identifies multiple risk loci and its association with clinical subtypes

OBJECTIVE

Gout, caused by hyperuricaemia, is a multifactorial disease. Although genome-wide association studies (GWASs) of gout have been reported, they included self-reported gout cases in which clinical information was insufficient. Therefore, the relationship between genetic variation and clinical subtypes of gout remains unclear. Here, we first performed a GWAS of clinically defined gout cases only.

METHODS

A GWAS was conducted with 945 patients with clinically defined gout and 1213 controls in a Japanese male population, followed by replication study of 1048 clinically defined cases and 1334 controls.

RESULTS

Five gout susceptibility loci were identified at the genome-wide significance level (p<5.0×10(-8)), which contained well-known urate transporter genes (ABCG2 and SLC2A9) and additional genes: rs1260326 (p=1.9×10(-12); OR=1.36) of GCKR (a gene for glucose and lipid metabolism), rs2188380 (p=1.6×10(-23); OR=1.75) of MYL2-CUX2 (genes associated with cholesterol and diabetes mellitus) and rs4073582 (p=6.4×10(-9); OR=1.66) of CNIH-2 (a gene for regulation of glutamate signalling). The latter two are identified as novel gout loci. Furthermore, among the identified single-nucleotide polymorphisms (SNPs), we demonstrated that the SNPs of ABCG2 and SLC2A9 were differentially associated with types of gout and clinical parameters underlying specific subtypes (renal underexcretion type and renal overload type). The effect of the risk allele of each SNP on clinical parameters showed significant linear relationships with the ratio of the case-control ORs for two distinct types of gout (r=0.96 [p=4.8×10(-4)] for urate clearance and r=0.96 [p=5.0×10(-4)] for urinary urate excretion).

CONCLUSIONS

Our findings provide clues to better understand the pathogenesis of gout and will be useful for development of companion diagnostics.

Endothelial nitric oxide synthase (eNOS) 4b/a polymorphism and the risk of diabetic nephropathy in type 2 diabetes mellitus: A meta-analysis

Many studies have accessed the association between eNOS-4b/a polymorphism and the risk of diabetic nephropathy (DN) among type 2 diabetic subjects. However, the results are conflicting and inconclusive. The aim of current meta-analysis was to more precisely estimate the relationship. Pubmed, Embase, the China National Knowledge Infrastructure and the Wanfang Database were searched for articles published up to May 26th, 2013 that addressed eNOS-4b/a polymorphism and the risk of DN among type 2 diabetic subjects. 18 studies were included in this meta-analysis. eNOS-4b/a polymorphisms were associated with an overall significantly increased risk of DN (allele model: OR = 1.44, 95% CI = 1.14-1.82; additive model: OR = 2.03, 95% CI = 1.14-3.62; dominant model: OR = 1.34, 95% CI = 1.07-1.68; recessive model: OR = 2.01, 95% CI = 1.12-3.61). Subgroup analysis revealed a significant association between the eNOS-4b/a polymorphism and DN in Asian population, especially in Chinese population, but not in non Asian populations. Our meta-analysis supported an association between the 4b/a polymorphism of eNOS gene and increased risk of DN in type 2 diabetes among Asians, especially in Chinese population.

Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases

Regulatory and coding variants are known to be enriched with associations identified by genome-wide association studies (GWASs) of complex disease, but their contributions to trait heritability are currently unknown. We applied variance-component methods to imputed genotype data for 11 common diseases to partition the heritability explained by genotyped SNPs (hg(2)) across functional categories (while accounting for shared variance due to linkage disequilibrium). Extensive simulations showed that in contrast to current estimates from GWAS summary statistics, the variance-component approach partitions heritability accurately under a wide range of complex-disease architectures. Across the 11 diseases DNaseI hypersensitivity sites (DHSs) from 217 cell types spanned 16% of imputed SNPs (and 24% of genotyped SNPs) but explained an average of 79% (SE = 8%) of hg(2) from imputed SNPs (5.1× enrichment; p = 3.7 × 10(-17)) and 38% (SE = 4%) of hg(2) from genotyped SNPs (1.6× enrichment, p = 1.0 × 10(-4)). Further enrichment was observed at enhancer DHSs and cell-type-specific DHSs. In contrast, coding variants, which span 1% of the genome, explained <10% of hg(2) despite having the highest enrichment. We replicated these findings but found no significant contribution from rare coding variants in independent schizophrenia cohorts genotyped on GWAS and exome chips. Our results highlight the value of analyzing components of heritability to unravel the functional architecture of common disease.

FTO genetic variants and risk of obesity and type 2 diabetes: a meta-analysis of 28,394 Indians

OBJECTIVE

To investigate the magnitude of association of FTO variants with obesity, type 2 diabetes (T2DM), and related traits among Asian Indians.

METHODS

Random-effect meta-analysis was performed on pooled data from eight studies (n = 28,394) for obesity and related traits and six studies (n = 24,987) for assessment of T2DM risk in Indians where FTO variants were reported.

RESULTS

The minor A-allele of the FTO variant rs9939609 was associated with increased risk of obesity (OR 1.15, 95% CI 1.08-1.21, p = 2.14 × 10(-) (5) ), BMI (β = 0.30 kg/m2, 95% CI 0.21-0.38, p = 4.78 × 10(-) (11) ) and other regional adiposity measurements [waist (β = 0.74 cm, 95% CI 0.49-0.99), HC (β = 0.52, 95% CI 0.26-0.78), and waist-hip ratio (WHR) (β = 0.002, 95% CI 0.001-0.004)] in Indians (p ≤ 0.001). An increased risk for T2DM (OR 1.11; 95% CI 1.04-1.19, p = 0.002) was observed, which attenuated when adjusted for age, gender, and BMI (OR 1.09; 95%CI 1.02-1.16, p = 0.01).

CONCLUSIONS

Our study provides evidence of association between common FTO variant and obesity risk among Indians with comparable effect sizes as in Caucasians. The attenuation of FTO-T2DM risk on BMI adjustment reinforces that BMI does not fully account for the adiposity effects among Asian Indians who are more centrally obese.

Association of KCNQ1 and KLF14 polymorphisms and risk of type 2 diabetes mellitus: A global meta-analysis

rs151290 in KCNQ1 and rs972283 in KLF14 have been evaluated in terms of risk of type 2 diabetes mellitus (T2DM), but the results are inconsistent. We performed an meta-analysis to assess the contributions of rs151290 in KCNQ1 and rs972283 in KLF14 to risk of T2DM. We searched the worldwide literature published from 2008 to 2013 in MEDLINE via PubMed, EMBASE, Cochrane CENTRAL and Chinese databases. Two reviewers extracted data independently using a standardized protocol, and any discrepancies were resolved by a third reviewer. Fixed- and random-effects meta-analyses were performed to pool the odds ratios (ORs). Publication bias and heterogeneity were examined. A total of 11 articles were included in the meta-analysis: 6 studies with 6696 cases and 7151 controls investigated rs151290 in KCNQ1, and 5 studies with 50,552 cases and 106,535 controls investigated rs972283 in KLF14. We obtained highly significant ORs for the risk allele C for rs151290 and the risk allele G for rs972283. The population attributable risk percentage for rs151290 and rs972283 was 6.83% and 4.18%, respectively. The risk allele C of rs151290 in KCNQ1 and risk allele G of rs972283 in KLF14 were both associated with increased risk of T2DM in a global population.

Epistatic effects of multiple receptor genes on pathophysiology of asthma - its limits and potential for clinical application

To date, genome-wide association studies (GWAS) permit a comprehensive scan of the genome in an unbiased manner, with high sensitivity, and thereby have the potential to identify candidate genes for the prevalence or development of multifactorial diseases such as bronchial asthma. However, most studies have only managed to explain a small additional percentage of hereditability estimates, and often fail to show consistent results among studies despite large sample sizes. Epistasis is defined as the interaction between multiple different genes affecting phenotypes. By applying epistatic analysis to clinical genetic research, we can analyze interactions among more than 2 molecules (genes) considering the whole system of the human body, illuminating dynamic molecular mechanisms. An increasing number of genetic studies have investigated epistatic effects on the risk for development of asthma. The present review highlights a concept of epistasis to overcome traditional genetic studies in humans and provides an update of evidence on epistatic effects on asthma. Furthermore, we review concerns regarding recent trends in epistatic analyses from the perspective of clinical physicians. These concerns include biological plausibility of genes identified by computational statistics, and definition of the diagnostic label of 'physician-diagnosed asthma'. In terms of these issues, further application of epistatic analysis will prompt identification of susceptibility of diseases and lead to the development of a new generation of pharmacological strategies to treat asthma.

The Val66Met polymorphism of the BDNF gene in anorexia nervosa: new data and a meta-analysis

OBJECTIVES

The Val66Met polymorphism (rs6265) of the BDNF gene is a non-synonymous polymorphism, previously associated with anorexia nervosa (AN).

METHODS

We genotyped rs6265 in 235 patients with AN and 643 controls. Furthermore, we performed a systematic review of all case-control and family-based studies testing this SNP in AN, and combined the results in a meta-analysis.

RESULTS

The results of the case-control study were non-significant. For the meta-analysis, nine studies were identified (ncases = 2,767; ncontrols = 3,322, ntrios = 53) and included. Primarily, the analyses indicated an association with OR of 1.11 (P = 0.024) in the allelic contrast, and OR of 1.14 (P = 0.025) for the dominant effect of the Met allele. However, additional analyses revealed that the first published study (from those included in the meta-analysis) overly influenced the pooled effect size (possibly due to a phenomenon known as a winner's curse). When this case-control study was replaced by a trio study (ntrios = 293) performed on a largely overlapping sample, the effect size became smaller and non-significant, both for the allelic contrast (OR = 1.07, P = 0.156) and the dominant effect (OR = 1.07, P = 0.319). The quality of included studies was good and there was no significant heterogeneity across the effect sizes.

CONCLUSIONS

Our analyses indicate that the BDNF Val66Met variant is not associated with AN at detectable levels.

The -173 G/C polymorphism of the MIF gene and inflammatory bowel disease risk: a meta-analysis

The -173 G/C polymorphism in the macrophage migration inhibitory factor (MIF) gene has been implicated in susceptibility to inflammatory bowel disease (IBD), but the results are inconclusive. The present meta-analysis aimed to investigate the overall association between the -173 G/C polymorphism and IBD risk. We searched in Pubmed, and Embase for studies evaluating the association between the -173G/C gene polymorphism and IBD risk. Data were extracted and statistical analysis was performed using Revman 5.1 and STATA 12.0 software. A total of seven publications involving 4729 subjects (2282 IBD cases and 2447 controls) were included in this meta-analysis. Combined analysis revealed a clear association between this polymorphism and IBD susceptibility (OR = 1.48, 95% CI: 1.10-2.00, p = 0.009 for CC vs. CG + GG). Subgroup analysis by ethnicity showed that the IBD risk associated with the -173G/C gene polymorphism was significantly elevated among Asians (OR = 1.79, 95% CI: 1.08-2.96, p = 0.02), but not among Caucasians. Subgroup analysis by disease suggested that the -173G/C gene polymorphism is a risk factor for ulcerative colitis (OR = 1.62, 95% CI: 1.10-2.37, p = 0.01), but that it was not associated with Crohn's disease. This meta-analysis suggests that the -173 G/C polymorphism in the macrophage MIF gene contributes to IBD susceptibility, specifically in Asian populations. Further studies are needed to validate these findings.

A nonsynonymous variant of IL1A is associated with endometriosis in Japanese population

Our previous genome-wide association study has demonstrated that single-nucleotide polymorphisms (SNPs) located in intronic and downstream regions of IL1A (interleukin 1α) were associated with the risk of endometriosis. These SNPs on the genome-wide association study platform could be only surrogates for the true causal variant. Thus, we resequenced all the exons of IL1A in 377 patients with endometriosis and 457 healthy controls. We detected seven rare variants (minor allele frequency <0.01) and four common variants. All the rare variants were not associated with endometriosis. The four common variants (rs17561, rs1304037, rs2856836 and rs3783553) in IL1A were significantly associated with endometriosis (P=0.0024, 0.0024, 0.0014 and 0.0061, respectively). All the four SNPs were within a linkage disequilibrium block. Among them, only rs17561 was nonsynonymous (p.A114S), which has been reported to be associated with susceptibility to ovarian cancer. Taken together, we examined association between rs17561 and endometriosis in an independent validation data set (524 patients and 533 healthy controls) replicating significant association (P=4.0 × 10(-5); odds ratio (OR), 1.91; 95% confidence interval (CI), 1.41-2.61). Meta-analysis by combining results from the two stages strengthened the evidence of association (P=2.5 × 10(-7); OR, 1.90; 95% CI, 1.49-2.43). Our findings demonstrated that the nonsynonymous variant of IL1A might confer genetic susceptibility to endometriosis in Japanese population.