Impact of violations and deviations in Hardy-Weinberg equilibrium on postulated gene-disease associations

Association of 10 Polymorphisms in PLA2R1 and HLA DQA1 Genes with Primary Membranous Nephropathy Risk: A Meta-Analysis and a Meta-Regression

Background

Although, several studies have assessed the association of the phospholipase A2 receptor (PLA2R) and HLA-DQA1 SNPs with primary membranous nephropathy (PMN), results were inconsistent and between-studies heterogeneity needs to be investigated.

Objectives

The aim of this review was to summarize existing data on the contribution of 10 SNPs in the PLA2R and HLA-DQA1 genes to PMN susceptibility and to investigate the between-studies heterogeneity by subgroup analyses and meta-regressions.

Design

This study was performed according to the PRISMA guidelines for systematic reviews and meta-analyses.

Data sources and methods

An electronic literature search for eligible studies among all papers published prior to January 10, 2024, was conducted through PubMed, EMBASE, Web of science and Scopus databases. Meta-analyses together with subgroup analyses and meta-regressions were performed for the 10 following SNPs: rs4664308, rs3749117, rs3749119, rs35771982, rs3828323, rs16844715, rs1511223, rs6757188, rs2715918, and rs2187668.

Results

Combined analyses revealed a significant increase in PMN risk conferred by the following alleles: rs4664308*A, rs3749117*T, rs3749119*C, rs35771982*G, rs3828323*C, rs16844715*C, rs1511223*A, rs2715918*A, and rs2187668*A, all P-values < .001. Moreover, the PLA2R-rs4664308/HLA-DQA1-rs2187668 interaction was significantly associated with an increased PMN risk, P < .001. However, there was a substantial between-studies heterogeneity for some SNPs. Subgroup analyses by ethnicity for the 9 PLA2R SNPs did not show any cross-ethnic disparity. Inversely, the risk conferred by the HLA-DQA1 rs2187668*A allele was significantly higher in Caucasians (OR [95% CI] = 3.929 [3.251-4.748]) than in Asians (OR [95% CI] = 2.537 [1.94-3.318], P = .007. Besides, meta-regressions revealed for the majority of investigated SNPs significant correlations of the effect size with albumin, 24-hours proteinuria, serum creatinine, and eGFR levels. Hence, the influence on PMN risk conferred by the PLA2R and HLA-DQA1 SNPs was rather noted in patients with a severe disease.

Conclusion

This meta-analysis showed that 9 out of the 10 investigated SNPs in PLA2R and HLA-DQA1 genes were associated with increased PMN risk. Heterogeneity could be due to disparate patient groups in terms of disease presentation for almost all SNPs, and ethnicity for the HLA-DQA1 rs2187668 SNP.

Registration

This review has been registered on PROSPERO: CRD42024506729. Available from: https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42024506729.

Toward Genetic Testing of Rivaroxaban? Insights from a Systematic Review on the Role of Genetic Polymorphism in Rivaroxaban Therapy

BACKGROUND

Investigations into the rivaroxaban response from the perspective of genetic variation have been relatively recent and wide in scope, whereas there is no consensus on the necessity of genetic testing of rivaroxaban. Thus, this systematic review aims to thoroughly evaluate the relationship between genetic polymorphisms and rivaroxaban outcomes.

METHODS

The PubMed, Embase, Cochrane Central Register of Controlled Trials (CENTRAL), and Chinese databases were searched to 23 October 2022. We included cohort studies reporting the pharmacogenetic correlation of rivaroxaban. Outcomes measured included efficacy (all-cause mortality, thromboembolic events and coagulation-related tests), safety (major bleeding, clinically relevant non-major bleeding [CRNMB] and any hemorrhage), and pharmacokinetic outcomes. A narrative synthesis was performed to summarize findings from individual studies according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses and the reporting guideline for Synthesis Without Meta-Analysis.

RESULTS

A total of 12 studies published between 2019 and 2022 involving 1364 patients were included. Ten, one, and six studies focused on the ABCB1, ABCG2, and CYP gene polymorphisms, respectively. Pharmacokinetic outcomes accounted for the majority of the outcomes reported (n = 11), followed by efficacy (n = 5) [including prothrombin time (PT) or international normalized ratio (n = 3), platelet inhibition rate (PIR) or platelet reactivity units (PRUs; n = 1), thromboembolic events (n = 1)], and safety (n = 5) [including major bleeding (n = 2), CRNMB (n = 2), any hemorrhage (n = 1)]. For ABCB1 gene polymorphism, the relationship between PT and ABCB1 rs1045642 was inconsistent across studies, however there was no pharmacogenetic relationship with other efficacy outcomes. Safety associations were found in ABCB1 rs4148738 and major bleeding, ABCB1 rs4148738 and CRNMB, ABCB1 rs1045642 and CRNMB, and ABCB1 rs2032582 and hemorrhage. Pharmacokinetic results were inconsistent among studies. For ABCG2 gene polymorphism, no correlation was observed between ABCG2 rs2231142 and dose-adjusted trough concentration (Cmin/D). For CYP gene polymorphisms, PIR or PRUs have a relationship with CYP2C19 rs12248560, however bleeding or pharmacokinetic effects did not show similar results.

CONCLUSIONS

Currently available data are insufficient to confirm the relationship between clinical or pharmacokinetic outcomes of rivaroxaban and gene polymorphisms. Proactive strategies are advised as a priority in clinical practice rather than detection of SNP genotyping.

CLINICAL TRIALS REGISTRATION

PROSPERO registration number CRD42022347907.

Impact of IL-10 gene promoter polymorphisms on treatment response in HCV patients: A systematic review, a meta-analysis, and a meta-regression

The impact of interleukin-10 (IL-10) gene promoter polymorphisms (SNPs) on treatment response in HCV patients was dissimilarly estimated. Hence, the aim of this meta-analysis was to robustly assess the effect of IL-10 SNPs on treatment response in HCV patients. An electronic literature search was carried out through PubMed, EMBASE, Web of science, and Scopus databases. Studies assessing the association between IL-10 polymorphisms and treatment response in HCV patients were included. Studies were excluded if genotype frequencies are not consistent with the Hardy-Weinberg Equilibrium (HWE) or in case of including patients with hepatitis B virus coinfection. Risk of bias in included studies was assessed using the Newcastle-Ottawa Scale. Meta-analyses were performed for the influence of IL-10 gene promoter SNPs (rs1800896 (-1082 A/G), rs1800871 (-819 C/T), and rs1800872 (-592 C/T)) and haplotypes on treatment response in HCV patients. Subgroup analyses, meta-regressions, publication bias assessment, and sensitivity analyses were also conducted. Overall, 32 studies with a total of 5943 HCV cases and 2697 controls were included in the present study. The -1082*G allele was significantly associated with increased risk of non-response (NR) to treatment, OR [95% CI] = 1.29 [1.1-1.51], p = .002. Besides, the rs1800872 -592*C allele was significantly associated with increased NR risk, OR [95% CI] = 1.22 [1.02-1.46], p = .03. Subgroup analysis showed that this association remained significant only in patients treated with PEG-IFN alone, p = .01. The -1082*G/-819*C/-592*C (GCC) haplotype was significantly associated with increased NR risk, OR [95% CI] = 1.62 [1.13-2.23], p = .009. Our results suggest that the IL-10 rs1800896 was associated with NR risk especially in North-African and Asian populations. Moreover, the IL-10 gene promoter -1082*G/-819*C/-592*C (GCC) haplotype which has been associated with higher production of IL-10, was significantly associated with increased NR risk.

Gene Polymorphisms and Expression of NRG1, DAOA, and DISC1 Genes in a Chinese Han Population with an Ultra-High Risk for Psychosis

Purpose

Although there is previous evidence supporting that ultra-high risk (UHR) for psychosis transformation is associated with NRG1, DAOA, and DISC1 genes, there have been no relevant studies in the Chinese population. The objective of the current study was to explore the gene polymorphism and expression of NRG1, DAOA, and DISC1 genes in a Han population with UHR for psychosis in China.

Methods

Eighteen UHR individuals, 61 first-degree relatives of patients with schizophrenia (FDR), 55 first-episode psychosis individuals (FEP), and 61 healthy controls (HC) were enrolled in the study. The genotypes at four loci of the NRG1 gene, four loci of the DAOA gene, and two loci of the DISC1 gene were tested for all subjects, and mRNAs of NRG1 and DISC1 were examined and analyzed in a pairwise comparison among the four groups. Statistical analysis of genetics was performed using snpStats software. For the case-control association analysis, a single site association study, epistatic effect analysis, and haplotype analysis were used to explore the association of the above genes.

Results

This study found that rs3918341 in the DAOA gene was associated with susceptibility to UHR by single site association analysis. Epistatic effect analysis results showed that the NRG1 gene interacted with the DAOA gene and DISC1 gene in the susceptibility to UHR. Haplotype association analysis showed that all haplotypes were not significantly associated with UHR. NRG1 mRNA was significantly downregulated in the UHR group compared with the HC group as well as the FEP group.

Conclusion

Our preliminary results show that NRG1, DAOA, and DISC1 genes may play a role in psychosis onset, opening the way to the identification of prognostic biomarkers.

Strong Cumulative Evidence of Associations of 6 Single Nucleotide Polymorphisms with Ovarian Cancer Risk: An Umbrella Review

Background: An increasing number of studies have reported associations between single nucleotide polymorphisms (SNPs) and ovarian cancer (OC) risk. However, some of the findings were inconsistent. The objective of this umbrella review was to evaluate the associations comprehensively and quantitatively. Methods: The protocol of this review was registered in PROSPERO (No. CRD42022332222). We searched the PubMed, Web of Science, and Embase databases to identify related systematic reviews and meta-analyses from inception to 15 October 2021. In addition to estimating the summary effect size by using fixed and random effects models and calculating the 95% prediction interval, we evaluated the cumulative evidence for associations with nominally statistical significance based on the Venice criteria and false positive report probability (FPRP). Results: Forty articles were included in this umbrella review, which referred to a total of 54 SNPs. The median number of original studies per meta-analysis was four, while the median number of total subjects was 3455. All included articles had greater than moderate methodological quality. A total of 18 SNPs were nominally statistically associated with OC risk; 6 SNPs (8 genetic models), 5 SNPs (7 genetic models), and 16 SNPs (25 genetic models) were identified as strong, moderate, and weak cumulative evidence, respectively. Conclusion: This umbrella review revealed associations between SNPs and OC risk and suggested strong cumulative evidence of associations of six SNPs (eight genetic models) with OC risk.

Association between XRCC3 p.Thr241Met polymorphism and risk of glioma: A systematic review and meta-analysis

BACKGROUND

The XRCC3 p.Thr241Met (rs861539) polymorphism has been extensively studied for its association with glioma risk, but results remain conflicting. Therefore, we performed a systematic review and meta-analysis to resolve this inconsistency.

METHODS

Studies published up to June 10, 2022, were searched in PubMed, Web of Science, Scopus, VIP, Wanfang, and China National Knowledge Infrastructure databases and screened for eligibility. Then, the combined odds ratio (OR) of the included studies was estimated based on five genetic models, i.e., homozygous (Met/Met vs. Thr/Thr), heterozygous (Thr/Met vs. Thr/Thr), dominant (Thr/Met + Met/Met vs. Thr/Thr), recessive (Met/Met vs. Thr/Thr + Thr/Met) and allele (Met vs. Thr). The study protocol was preregistered at PROSPERO (registration number: CRD42021235704).

RESULTS

Overall, our meta-analysis of 14 eligible studies involving 12,905 subjects showed that the p.Thr241Met polymorphism was significantly associated with increased glioma risk in both homozygous and recessive models (homozygous, OR = 1.381, 95% CI = 1.081-1.764, P = 0.010; recessive, OR = 1.305, 95% CI = 1.140-1.493, P<0.001). Subgroup analyses by ethnicity also revealed a statistically significant association under the two aforementioned genetic models, but only in the Asian population and not in Caucasians (P>0.05).

CONCLUSION

We demonstrated that the XRCC3 p.Thr241Met polymorphism is associated with an increased risk of glioma only in the homozygous and recessive models.

Association between dietary acid load and cancer risk and prognosis: An updated systematic review and meta-analysis of observational studies

Epidemiological studies have suggested that dietary acid load (DAL) might be related to the risk and prognosis of cancer, whereas the evidence is contentious. Several high-quality observational studies have been published following a prior systematic review with only one study included. Consequently, we conducted an updated systematic review and meta-analysis to comprehensively investigate the relationship between DAL and cancer risk and prognosis. A systematic literature search was conducted in the PubMed, Embase, and Web of Science databases from inception to 26 October 2021. Summary relative risks (RRs) with 95% CIs were calculated using a random-effects model. Publication bias, subgroup, meta-regression, and sensitivity analyses were also conducted. Ten observational studies (six cohorts and four case–control studies) with 227,253 participants were included in this systematic review and meta-analysis. The summary RRs revealed a statistically significant associations between DAL and cancer risk (RR = 1.58, 95% CI = 1.23–2.05, I² = 71.9%, n = 7) and prognosis (RR = 1.53, 95% CI = 1.10–2.13, I² = 77.1%, n = 3). No evidence of publication bias was observed in the current analysis. Positive associations were observed in most subgroup analyses stratified by predefined factors, including region, study design, study quality, study population, participants’ gender, age of participants, cancer type, DAL assessment indicator, and adjustment of potential confounding parameters. No evidence of heterogeneity between subgroups was indicated by meta-regression analyses. The high DAL might be associated with an increased risk of cancer, as well as a poor prognosis of cancer. More high-quality prospective studies are warranted to further determine the associations between DAL and risk and prognosis for specific cancers.

The impact of angiotensin converting enzyme insertion/deletion gene polymorphism on diabetic kidney disease: A debatable issue

OBJECTIVE

The objective of this study was to evaluate the influence of ACE I/D gene polymorphisms on diabetic kidney disease (DKD) risk.

METHODS

All eligible investigations were identified, the number of various genotype in the case and control group were reviewed. The pooled analysis was performed using Stata software.

RESULTS

In overall subjects, 24,321 participants with 12,961 cases and 11,360 controls were included. the pooled analysis showed a significant link between D allele, DD or II genotype and DKD risk (D versus I: OR=1.316, 95% CI: 1.213-1.427, P=0.000; DD versus ID+II: OR=1.414, 95% CI: 1.253-1.595, P=0.000; II versus DD+ID: OR=0.750, 95% CI: 0.647-0.869, P=0.000). The subgroup pooled analysis showed that ACE I/D gene polymorphism was correlated with DKD both in Asian and in Chinese population. In addition, ACE I/D gene polymorphism was correlated with type 2 DKD (D versus I: OR=1.361, 95% CI: 1.243-1.490, P=0.000; DD versus ID+II: OR=1.503, 95% CI: 1.310-1.726, P=0.000; II versus DD+ID: OR=0.738, 95% CI: 0.626 -0.870, P=0.000). However, there was no obvious correlation in Caucasian subjects and type 1 diabetic patients.

CONCLUSION

ACE I/D polymorphisms were correlated with DKD in Asian and type 2 diabetic populations. ACE D allele/DD genotype might be a risk factor, while ACE II genotype might be a protective factor for DKD.

Ambient air pollution and COVID-19 risk: Evidence from 35 observational studies

BACKGROUND AND AIMS

The coronavirus disease 2019 (COVID-19) pandemic is severely threatening and challenging public health worldwide. Epidemiological studies focused on the influence of outdoor air pollution (AP) on COVID-19 risk have produced inconsistent conclusions. We aimed to quantitatively explore this association using a meta-analysis.

METHODS

We searched for studies related to outdoor AP and COVID-19 risk in the Embase, PubMed, and Web of Science databases. No language restriction was utilized. The search date entries were up to August 13, 2021. Pooled estimates and 95% confidence intervals (CIs) were obtained with random-/fixed-effects models. PROSPERO registration number: CRD42021244656.

RESULTS

A total of 35 articles were eligible for the meta-analysis. For long-term exposure to AP, COVID-19 incidence was positively associated with 1 μg/m3 increase in nitrogen dioxide (NO2; effect size = 1.042, 95% CI 1.017-1.068), particulate matter with diameter <2.5 μm (PM2.5; effect size = 1.056, 95% CI 1.039-1.072), and sulfur dioxide (SO2; effect size = 1.071, 95% CI 1.002-1.145). The COVID-19 mortality was positively associated with 1 μg/m3 increase in nitrogen dioxide (NO2; effect size = 1.034, 95% CI 1.006-1.063), PM2.5 (effect size = 1.047, 95% CI 1.025-1.1071). For short-term exposure to air pollutants, COVID-19 incidence was positively associated with 1 unit increase in air quality index (effect size = 1.001, 95% CI 1.001-1.002), 1 μg/m3 increase NO2 (effect size = 1.014, 95% CI 1.011-1.016), particulate matter with diameter <10 μm (PM10; effect size = 1.005, 95% CI 1.003-1.008), PM2.5 (effect size = 1.003, 95% CI 1.002-1.004), and SO2 (effect size = 1.015, 95% CI 1.007-1.023).

CONCLUSIONS

Outdoor air pollutants are detrimental factors to COVID-19 outcomes. Measurements beneficial to reducing pollutant levels might also reduce the burden of the pandemic.

Association of Insulin Receptor Substrate-1 Gene Polymorphism (rs1801278) with Alzheimer’s Disease

Background: Alzheimer’s disease (AD) is the most common form of dementia. AD is also the leading cause of morbidity and mortality due to dementia worldwide. It has been shown that AD is associated with type 2 diabetes mellitus (T2DM) and brain insulin resistance. Rs1801278 is a polymorphism in insulin receptor substrate-1 (IRS-1) gene which changes the amino acid Arg972. This polymorphism has been found to be associated with susceptibility to AD in some populations. Objective: In the present study, our aim was to investigate the association of Arg972 IRS-1 (rs1801278) gene polymorphism and late-onset Alzheimer’s disease (LOAD) in an Iranian population. Methods: In this case-control study, 150 patients with LOAD and 150 unrelated healthy controls were recruited. Polymerase chain reaction (PCR) was performed to amplify a DNA segment of 263 base-pair (bp) length containing the single nucleotide polymorphism (SNP). The PCR product was then incubated with MvaI restriction enzyme to undergo enzymatic cleavage. Electrophoresis was thereafter carried out using agarose gel and DNA safe stain. The gel was ultimately visualized under a UV trans-illuminator. Allelic and genotypic frequencies were then compared. Results: A allele (mutant) of the gene was significantly associated with the risk of AD after adjustment for sex and age (p = 0.04, adjusted OR:1.77, 95% CI:1.00–3.11). Only AA genotype (mutant homozygote) was significantly associated with the risk of AD after adjustment for sex and age (p = 0.01, adjusted OR:2.39, 95% CI:1.22–4.66). Conclusion: SNP rs1801278 is significantly associated with the risk of developing AD in the studied Iranian population.

The Role of Genetic Polymorphisms in High-Dose Methotrexate Toxicity and Response in Hematological Malignancies: A Systematic Review and Meta-Analysis

Objective: High-dose methotrexate (HDMTX) is a mainstay therapeutic agent for the treatment of diverse hematological malignancies, and it plays a significant role in interindividual variability regarding the pharmacokinetics and toxicity. The genetic association of HDMTX has been widely investigated, but the conflicting results have complicated the clinical utility. Therefore, this systematic review aims to determine the role of gene variants within the HDMTX pathway and to fill the gap between knowledge and clinical practice. Methods: Databases including EMBASE, PubMed, Cochrane Central Register of Controlled Trials (CENTRAL), and the Clinical Trials.gov were searched from inception to November 2020. We included twelve single-nucleotide polymorphisms (SNPs) within the HDMTX pathway, involving RFC1, SLCO1B1, ABCB1, FPGS, GGH, MTHFR, DHFR, TYMS, and ATIC. Meta-analysis was conducted by using Cochrane Collaboration Review Manager software 5.3. The odds ratios (ORs) or hazard ratios (HRs) with 95% confidence interval (95% CI) were analyzed to evaluate the associations between SNPs and clinical outcomes. This study was performed according to the PRISMA guideline. Results: In total, 34 studies with 4102 subjects were identified for the association analysis. Nine SNPs involving MTHFR, RFC1, ABCB1, SLCO1B1, TYMS, FPGS, and ATIC genes were investigated, while none of studies reported the polymorphisms of GGH and DHFR yet. Two SNPs were statistically associated with the increased risk of HDMTX toxicity: MTHFR 677C>T and hepatotoxicity (dominant, OR=1.52, 95% CI=1.03-2.23; recessive, OR=1.68, 95% CI=1.10-2.55; allelic, OR=1.41, 95% CI=1.01-1.97), mucositis (dominant, OR=2.11, 95% CI=1.31-3.41; allelic, OR=1.91, 95% CI=1.28-2.85), and renal toxicity (recessive, OR=3.54, 95% CI=1.81-6.90; allelic, OR=1.89, 95% CI=1.18-3.02); ABCB1 3435C>T and hepatotoxicity (dominant, OR=3.80, 95% CI=1.68-8.61), whereas a tendency toward the decreased risk of HDMTX toxicity was present in three SNPs: TYMS 2R>3R and mucositis (dominant, OR=0.66, 95% CI=0.47-0.94); RFC1 80A>G and hepatotoxicity (recessive, OR=0.35, 95% CI=0.16-0.76); and MTHFR 1298A>C and renal toxicity (allelic, OR=0.41, 95% CI=0.18-0.97). Since the data of prognosis outcomes was substantially lacking, current studies were underpowered to investigate the genetic association. Conclusions: We conclude that genotyping of MTHFR and/or ABCB1 polymorphisms prior to treatment, MTHFR 677C>T particularly, is likely to be potentially useful with the aim of tailoring HDMTX therapy and thus reducing toxicity in patients with hematological malignancies.

Umbrella Review on Associations Between Single Nucleotide Polymorphisms and Lung Cancer Risk

The aim is to comprehensively and accurately assess potential relationships between single nucleotide polymorphisms (SNP) and lung cancer (LC) risk by summarizing the evidence in systematic reviews and meta-analyses. This umbrella review was registered with the PROSPERO international prospective register of systematic reviews under registration number CRD42020204685. The PubMed, Web of Science, and Embase databases were searched to identify eligible systematic reviews and meta-analyses from inception to August 14, 2020. The evaluation of cumulative evidence was conducted for associations with nominally statistical significance based on the Venice criteria and false positive report probability (FPRP). This umbrella review finally included 120 articles of a total of 190 SNP. The median number of studies and sample size included in the meta-analyses were five (range, 3–52) and 4 389 (range, 354–256 490), respectively. A total of 85 SNP (in 218 genetic models) were nominally statistically associated with LC risk. Based on the Venice criteria and FPRP, 13 SNP (in 22 genetic models), 47 SNP (in 99 genetic models), and 55 SNP (in 94 genetic models) had strong, moderate, and weak cumulative evidence of associations with LC risk, respectively. In conclusion, this umbrella review indicated that only 13 SNP (of 11 genes and one miRNA) were strongly correlated to LC risk. These findings can serve as a general and helpful reference for further genetic studies.

The impact of angiotensin converting enzyme insertion/deletion gene polymorphism on diabetic kidney disease: A debatable issue

OBJECTIVE

The objective of this study was to evaluate the influence of ACE I/D gene polymorphisms on diabetic kidney disease (DKD) risk.

METHODS

All eligible investigations were identified, the number of various genotype in the case and control group were reviewed. The pooled analysis was performed using Stata software.

RESULTS

In overall subjects, 24,321 participants with 12,961 cases and 11,360 controls were included. the pooled analysis showed a significant link between D allele, DD or II genotype and DKD risk (D versus I: OR=1.316, 95% CI: 1.213-1.427, P=0.000; DD versus ID+II: OR=1.414, 95% CI: 1.253-1.595, P=0.000; II versus DD+ID: OR=0.750, 95% CI: 0.647-0.869, P=0.000). The subgroup pooled analysis showed that ACE I/D gene polymorphism was correlated with DKD both in Asian and in Chinese population. In addition, ACE I/D gene polymorphism was correlated with type 2 DKD (D versus I: OR=1.361, 95% CI: 1.243-1.490, P=0.000; DD versus ID+II: OR=1.503, 95% CI: 1.310-1.726, P=0.000; II versus DD+ID: OR=0.738, 95% CI: 0.626 -0.870, P=0.000). However, there was no obvious correlation in Caucasian subjects and type 1 diabetic patients.

CONCLUSION

ACE I/D polymorphisms were correlated with DKD in Asian and type 2 diabetic populations. ACE D allele/DD genotype might be a risk factor, while ACE II genotype might be a protective factor for DKD.

Genetic variants of HOTAIR are associated with susceptibility to recurrent spontaneous abortion: A preliminary case-control study

AIM

To investigate the association between Hox transcript antisenses RNA (HOTAIR) polymorphisms, rs12826786 C/T, rs920778 T/C, rs4759314 A/G, and rs1899663 G/T, with recurrent spontaneous abortion (RSA) susceptibility in the Iranian women.

METHODS

We enrolled 161 patients diagnosed with RSA and 177 healthy women with at least one live birth without a history of abortion. Genotyping of HOTAIR polymorphisms was carried out using both restriction fragment length polymorphism-polymerase chain reaction and amplification refractory mutation system-polymerase chain reaction methods. Odds ratios (ORs) with 95% confidence intervals (CIs) were assessed to estimate the strength of association.

RESULTS

Different inheritance models of rs12826786 C/T, rs920778 T/C, and rs1899663 G/T polymorphisms significantly enhanced the risk of RSA (p < 0.05), whereas the rs4759314 A/G polymorphism was correlated with diminished risk of developing RSA under recessive AA versus GA + GG (OR 0.42 [95% CI = 0.19-0.91]), log-additive GG versus GA vs. GG (OR 0.67 [95% CI = 0.48-0.93]), and allelic A versus G (OR 0.65 [95% CI = 0.47-0.92]) models. Moreover, the TGTC, TTCT, TTTC, CGTC, CGTT, CTCC, CTCT, CTTC, and CTTT haplotypes of rs920778/rs1899663/rs12826786/ significantly increased the risk of RSA. The studied variants were not in strong linkage disequilibrium.

CONCLUSIONS

Our results indicated that variations in the HOTAIR gene might serve as beneficial biomarkers for determining susceptibility to RSA. To confirm these findings, replication studies with a larger population and different races are needed.

Post-Diagnostic Beta Blocker Use and Prognosis of Ovarian Cancer: A Systematic Review and Meta-Analysis of 11 Cohort Studies With 20,274 Patients

Objectives

Previous experimental studies have indicated that exposure to beta blocker provides protective effects against ovarian cancer (OC). However, findings from epidemiologic studies have still been controversial. Therefore, we carried out a meta-analysis to update and quantify the correlation between post-diagnostic beta blocker usage and OC prognosis.

Methods

The meta-analysis had been registered at PROSPEPO. The number of registration is CRD42020188806. A comprehensive search of available literatures in English prior to April 16, 2020, was conducted in PubMed, EMBASE, and the Web of Science databases. Random-effects models were used to calculate overall hazard ratios (HRs) and 95% confidence intervals (CIs). Publication bias assessments, and subgroup, sensitivity, and meta-regression analyses were also performed.

Results

Of the 637 initially identified articles, 11 retrospective cohort studies with 20,274 OC patients were included. The summary HRs did not reveal any statistically significant associations between post-diagnostic beta blocker use and OC prognosis characteristics, such as total mortality (HR = 1.08, 95% CI = 0.92–1.27, I² = 76.5%, n = 9), cancer-specific mortality (HR = 1.22, 95% CI = 0.89–1.67, I² = 88.1%, n=3), and progression-free survival (HR = 0.88, 95% CI = 0.75–1.05, I² = 0, n = 4). No evidence of publication bias was observed in current analysis. In our subgroup analyses, the majority of results were consistent with the main findings. However, several positive correlations were detected in studies with ≥800 cases (HR = 1.20, 95% CI = 1.05–1.37), no immortal time bias (HR = 1.28, 95% CI = 1.10–1.49), and adjustment for comorbidity (HR = 1.20, 95% CI = 1.05–1.37). In the meta-regression analysis, no evidence of heterogeneity was detected in the subgroups according to study characteristics and confounding factors.

Conclusions

Post-diagnostic beta blocker use has no statistical correlation with OC prognosis. More prospective cohort studies are necessary to further verify our results.

Systematic Review Registration

Identifier (CRD42020188806).

Association between FAS gene -670 A/G and -1377 G/A polymorphisms and the risk of autoimmune diseases: a meta-analysis

Objectives: FAS plays a critical role in the extrinsic apoptosis pathway in autoimmune diseases. Previous studies investigating the association between FAS gene −670 A/G and −1377 G/A polymorphisms and the risk of autoimmune diseases reported controversial results. We performed the meta-analysis to evaluate the possible association. Methods: Relevant studies were identified by searching the PubMed, Embase, CNKI, and Wanfang databases up to December 2018. Odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were calculated to determine the association. Results: A total of 43 articles including 67 studies (52 studies for FAS −670 A/G and 15 studies for −1377 G/A) were included in the meta-analysis. Our meta-analysis showed that the FAS −670 A/G polymorphism was associated with the risk of autoimmune diseases (GG vs. GA: OR = 1.079, 95% CI = 1.004–1.160, P=0.038), especially in Caucasians (GG vs. GA: OR = 1.12, 95% CI = 1.03–1.23, P=0.012), Asians (G vs. A: OR = 0.89, 95% CI = 0.83–0.96, P=0.002), systemic lupus erythematosus (SLE) (G vs. A: OR = 0.85, 95% CI = 0.77–0.94, P=0.001), multiple sclerosis (MS) (GG+GA vs. AA: OR = 0.83, 95% CI = 0.70–0.99, P=0.043), systemic sclerosis (SSc) (GG vs. GA: OR = 1.20, 95% CI = 1.07–1.36, P=0.003) and Hashimoto’s thyroiditis (HT) (G vs. A: OR = 1.45, 95% CI = 1.10–1.90, P=0.008); the FAS −1377 G/A polymorphism was associated with the risk of autoimmune diseases (A vs. G: OR = 1.11, 95% CI = 1.03–1.20, P=0.008), especially in Asians (A vs. G: OR = 1.15, 95% CI = 1.05–1.25, P=0.002) and high quality studies (A vs. G: OR = 1.14, 95% CI = 1.05–1.24, P=0.002). Conclusion: This meta-analysis demonstrated that the FAS –670A/G and –1377 G/A polymorphisms were associated with the risk of autoimmune diseases.

Paraoxonase single nucleotide variants show associations with polycystic ovary syndrome: a meta-analysis

BACKGROUND

Etiology of polycystic ovary syndrome (PCOS) is attributed to genetic and environmental factors. One environmental factor is oxidative stress. Paraoxonase 1 (PON1) is an antioxidant high-density lipoprotein-associated enzyme encoded by the PON1 gene. The PON1 gene has been implicated in the risk for PCOS, the influence of which appears to come from single nucleotide variants (SNVs) at multiple genetic loci. However, association study reports have been inconsistent which compels a meta-analysis to obtain more precise estimates.

METHODS

From 12 publications, extracted genotype data were used in two genetic procedures. First, linkage disequilibrium (LD) was used to group eight PON SNVs into three: LD1, LD2 and LD3. Second, frequencies of the variant (var), wild-type (wt) and heterozygous (het) genotypes were used for genetic modeling (allele-genotype for LD1 and standard for LD2 and LD3). Risk associations were expressed in terms of pooled odds ratios (ORs), 95% confidence intervals (CIs) and P^a-values. Evidence was considered strong when significance was high (P^a < 0.0001) and heterogeneity absent (I² = 0%). Pooled effects were subjected to modifier (power), subgroup (Asian/Caucasian), outlier, sensitivity and publication bias treatments. Multiple comparisons were Bonferroni-corrected.

RESULTS

This meta-analysis generated 11 significant outcomes, five in LD1, six in LD2 and none in LD3. All six LD2 outcomes did not survive the Bonferroni-correction but two of the five in LD1 did. These two core LD1 findings conferred greater odds of PCOS to the var allele in the highly significant (P^a < 0.0001) overall (OR 1.44, 95% CI 1.24-1.67) and Asian (OR 1.41, 95% CI 1.20-1.65) outcomes. Of these two core outcomes, the Asian effect was homogeneous (I² = 0%) but not the overall (I² = 29%).

CONCLUSIONS

Of the eight PON SNVs examined, two (rs854560 and rs662) were associated with PCOS risk. These 1.4-fold increased risk effects rendered Asians susceptible to PCOS. High statistical power, high significance, zero to low-level heterogeneity, robustness and lack of bias in the core outcomes underpinned the strong evidence for association.

Infertility and ovarian cancer risk: Evidence from nine prospective cohort studies

Epidemiological studies have investigated the relationship between infertility and the risk of ovarian cancer (OC); however, the results have been inconsistent. We therefore conducted the first meta-analysis to update and quantify the aforementioned association based on prospective cohort studies. Studies were identified by searching PubMed, EMBASE and Web of Science databases up to January 8, 2020. We extracted data from the studies and performed quality assessments. Summary relative risks (RRs) with 95% confidence intervals (CIs) were calculated using a random-effects model. Publication bias, and subgroup, meta-regression and sensitivity analyses were also conducted. Nine prospective cohort studies with a total of 10 383 OC cases and 6 278 830 participants were included in the present study. The summary RR of the association between infertility and the risk of OC was 1.51 (95% CI: 1.35-1.69), with low heterogeneity. Positive associations were observed in most subgroup analyses stratified by predefined factors, including region, duration of follow-up, study quality, causes of infertility, invasiveness of OC, infertility treatment status and adjustment of potential confounding parameters. No significant publication bias was detected. Our findings suggest that infertility in women were associated with an increased risk of OC.

Relationship between legume consumption and metabolic syndrome: A systematic review and meta-analysis of observational studies

AIMS

The prevalence of metabolic syndrome (MetS) has been increasing in recent years. Investigation of whether consumption of legumes as a part of healthy diet could reduce the odds of MetS has led to inconsistent conclusions. Here, we performed the first meta-analysis of observational studies to analyze the association between legume consumption and prevalence of MetS.

DATA SYNTHESIS

PubMed, EMBASE, and Web of Science databases were searched to identify observational studies up to June 1, 2019. We extracted data from the studies included and performed quality assessments. Summary odds ratios (ORs) with 95% confidence intervals (CIs) were calculated using a random-effects model. Publication bias and subgroup and sensitivity analyses were also performed. We finally included four cross-sectional studies, two cohort studies, and one case-control study involving 56,028 participants. The summary OR revealed no statistically significant association between legume consumption and odds of MetS (OR = 0.93, 95% CI = 0.76-1.12, I² = 73.5%). Subgroup analysis of study characteristics and adjustment for confounding along with sensitivity analyses revealed no statistically significant differences. No evidence of publication bias was detected.

CONCLUSION

Legume consumption is not associated with the odds of MetS. These findings require validation in well-designed cohort studies and randomized clinical trials with accurate measurement of legume intake and strict control of confounders.

REGISTRATION

This study was registered with the International Prospective Register of Systematic Reviews (registration number: CRD42019131777).

Role of CD226 Rs763361 Polymorphism in Susceptibility to Multiple Autoimmune Diseases

Background: Gly307Ser (rs763361) polymorphism in Cluster of Differentiation 226 (CD226) gene has been implicated in susceptibility to autoimmune diseases (ADs) with controversial results. This study aimed to conduct a meta-analysis for examining the relationship between CD226 rs763361 polymorphism and ADs risk. Methods: a literature search was performed to identify relevant studies published in Embase, PubMed, Wanfang, and China National Knowledge Infrastructure. In the most appropriate genetic models, pooled odds ratio (OR) with 95% confidence interval (CI) was calculated for evaluating the strength of the associations. Besides standard meta-analysis, cumulative meta-analysis was also conducted to assess the trend in OR over time. Also, we performed subgroup and sensitivity analysis, and checked for the heterogeneity and publication bias. Results: Twenty-nine reports with 51 independent studies, comprising 18157 cases and 29904 controls, were enrolled in this meta-analysis. Among overall and various ethnic populations (Europeans, Asians, Africans, and South Americans), CD226 rs763361 polymorphism was significantly associated with ADs susceptibility; in the subgroup analysis by disease type, rs763361 polymorphism revealed significant associations with the risk of RA, SLE, T1D, and MS. The sensitivity analysis and cumulative meta-analysis confirmed the stability and robustness of these significant results. However, no evidence of stable significant association emerged in the subgroup analysis of SSc. Conclusion: These findings demonstrate that CD226 rs763361 polymorphism confers susceptibility to ADs in the overall population, Europeans, Asians, Africans, and South Americans. rs763361 polymorphism in CD226 gene may be a potential susceptible predictor of ADs especially RA, SLE, T1D, and MS.

Association of Toll-Like Receptor Polymorphisms With Nasal Polyposis

Nasal polyposis is a disease characterized with chronic inflammation of the nasal mucosa. Toll-like receptors (TLRs) are defined as essential receptors of the innate immune system and may play in the development of nasal polyposis. A total of 71 patients with nasal polyposis and 74 healthy controls were included in this study. Three single-nucleotide polymorphisms (SNPs); TLR2 (2258 A>G), TLR4 (896 A>G), and TLR4 (1196 C>T) were analyzed in all patients. The degree of pair-wise linkage disequilibrium and the genotype and haplotype analyses were conducted using regression in this logistic model and the Multifactor Dimensionality Reduction (MDR) software package was used to construct all possible interactions among different genotype variants belonging to the TLR gene. There was significant difference in genotype and allele frequencies of the TLR4 (1196 C>T) polymorphism between the nasal polyposis and control groups (0.017). Also, it was observed that the probability of nasal polyposis was 62.7% in the presence of TLR4 (1196 C>T) polymorphism with asthma (P = .007). As a conclusion, this study showed that TLR4 and TLR2 polymorphisms were predisposing factors for nasal polyposis. Further functional studies investigating the consequences of loss of TLR function are needed.

Susceptibility to leishmaniasis is affected by host SLC11A1 gene polymorphisms: a systematic review and meta-analysis

Leishmaniases are cutaneous, mucocutaneous, and visceral diseases affecting humans and domesticated animals mostly in the tropical and subtropical areas of the planet. Host genetics have been widely investigated for their role in developing various infectious diseases. The SLC11A1 gene has been reported to play a role in neutrophil function and is associated with susceptibility to infectious and inflammatory diseases such as tuberculosis or rheumatoid arthritis. In the present meta-analysis, we investigate the genetic association of SLC11A1 polymorphisms with susceptibility to leishmaniasis. Genotypes and other risk-related data were collected from 13 case-control and family-based studies (after literature search). Conventional random-effects meta-analysis was performed using STATA 13. To pool case-control and family-based data, the weighted Stouffer's method was also applied. Eight polymorphisms were investigated: rs2276631, rs3731865, rs3731864, rs17221959, rs201565523, rs2279015, rs17235409, and rs17235416. We found that rs17235409 (D543N) and rs17235416 (1729 + 55del4) are significantly associated with a risk for cutaneous leishmaniasis (CL), whereas rs17221959, rs2279015, and rs17235409 are associated with visceral leishmaniasis (VL). Our results suggest that polymorphisms in SLC11A1 affect susceptibility to CL and VL. These findings open new pathways in understanding macrophage response to Leishmania infection and the genetic factors predisposing to symptomatic CL or VL that can lead to the usage of predictive biomarkers in populations at risk.

PRL -1149T allele (rs1341239) is associated with decreased risk of rheumatoid arthritis in population from southern Mexico: analysis of mRNA expression and PRL serum levels

INTRODUCTION

Prolactin (PRL) is a sex hormone with immunomodulatory properties, and it is associated with the clinical activity of rheumatoid arthritis (RA). The -1149G>T polymorphism at the prolactin (PRL) gene has been associated with autoimmune diseases, but its functional effect is unclear.

OBJECTIVE

To analyze the association of the PRL -1149G>T polymorphism with disease susceptibility, mRNA, and protein expression of PRL in RA patients from Southern Mexico.

METHODS

We included 300 RA patients and 300 control subjects (CS). Genotypes were identified by the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique, the PRL mRNA expression was determined by real-time PCR, and PRL serum levels were measured by enzyme-linked immunosorbent assay.

RESULTS

Applying genetic models of inheritance (dominant, recessive, and additive), we found an association between the T allele and decreased RA susceptibility (OR = 0.55, 95% CI 0.35-0.87, p = 0.009; OR = 0.09, 95% CI 0.012-0.76, p = 0.011; OR = 0.49, 95% CI 0.32-0.76, p = 0.001, respectively). RA patients had higher mRNA expression and soluble levels of PRL than CS (p < 0.05). The PRL serum levels were similar in RA and CS according to genotypes. However, in CS, carriers of GT and TT genotypes showed lower PRL mRNA expression than GG genotype carriers (7.1-fold and 20-fold respectively, p = 0.006).

CONCLUSIONS

This study demonstrated that the PRL -1149T allele is a genetic marker of decrease risk to RA in population from Southern Mexico, and it is associated with low PRL mRNA.

KEY POINTS

• PRL -1149T allele is a marker of decreased RA susceptibility in population from southern Mexico. • PRL -1149TT genotype is associated with low PRL mRNA expression. • RA patients have higher mRNA expression and soluble levels of PRL than healthy subjects. • PRL serum levels are higher in those RA patients with < 2 years of disease evolution.

Association of mir-196a-2 rs11614913 and mir-149 rs2292832 Polymorphisms With Risk of Cancer: An Updated Meta-Analysis

Background: Accumulating evidence suggests that functional dysregulations of miRNAs, especially miR-196a-2 and miR-149, in cancers could be attributed to polymorphisms in miRNA sequences. This study was aimed at clarifying the association of mir-196a-2 rs11614913 and mir-149 rs2292832 with cancer risk by performing an updated meta-analysis of genetic association studies. Methods: PubMed, Embase, Scopus, and ScienceDirect databases were searched until 9 April 2018 to identify eligible studies. Studies should meet the following criteria to be included in the meta-analysis: evaluation of genetic association between rs11614913 and/or rs2292832 and susceptibility to cancer; A case-control design; Written in English; Availability of sufficient data for estimating odds ratio (OR) and its 95% confidence interval (95%CI). Studies that met the following criteria were excluded: review articles, meta-analysis, abstracts or conference papers; duplicate publications; studies on animals or cell-lines; studies without a case-control design; studies that did not report genotype frequencies. Pooled ORs and 95% CIs were estimated using a total of 111 studies (41,673 cases and 49,570 controls) for mir-196a rs11614913 and 44 studies (15,954 cases and 19,594 controls) for mir-149 rs2292832. Stratified analysis according to quality scores, genotyping method, ethnicity, broad cancer category and cancer type was also performed. Results: Mir-196a-2 rs11614913 T allele was associated with decreased cancer risk in overall population. The association was only significant in Asians but not Caucasians. In subgroup analysis, significant associations were found in high quality studies, gynecological cancers, ovarian, breast, and hepatocellular cancer. Mir-149 rs2292832 was not associated with cancer risk in overall population and there were no differences between Asians and Caucasians. However, the T allele was associated with a decrease risk of gastrointestinal tract cancers under the heterozygote model and an increased risk of colorectal cancer under the recessive model. Conclusions: The present meta-analysis suggests that mir-196a-2 rs11614913 may contribute to the risk of cancer especially in Asians. Mir-149 rs2292832 may modulate the risk of gastrointestinal tract cancers especially colorectal cancer. This study had some limitations such as significant heterogeneity in most contrasts, limited number of studies enrolling Africans or Caucasians ancestry and lack of adjustment for covariates and environmental interactions.

The Role of Stressful Parenting and Mineralocorticoid Receptor Haplotypes on Social Development During Adolescence and Young Adulthood

The development of social behavior could be affected by stressful parenting. The mineralocorticoid receptor, one of the two main receptors for the stress hormone cortisol, plays a vital role in adequate responses to stress. Therefore, the effects of stressful parenting on social development (i.e., empathic concern, perspective taking and prosocial behavior) may be moderated by functional genetic variation in mineralocorticoid receptor haplotypes (a combination of alleles). A group of 343 adolescents (44.3% females) was followed from the age of 13 until 24 years. Growth curve analyses showed lower levels of prosocial behaviors and a slower increase in empathic concern and perspective taking in adolescents who reported more stressful parenting. In contrast, relatively higher levels of prosocial behavior, empathic concern and perspective taking were present in combination with stress resilient mineralocorticoid receptor haplotypes. Despite sex differences in social development with earlier social development for girls, no consistent sex differences were found with regard to mineralocorticoid receptor haplotypes. The current study showed that genetic variation in mineralocorticoid receptor impacts the social development during adolescence and young adulthood.

Multivariate Methods for Meta-Analysis of Genetic Association Studies

Multivariate meta-analysis of genetic association studies and genome-wide association studies has received a remarkable attention as it improves the precision of the analysis. Here, we review, summarize and present in a unified framework methods for multivariate meta-analysis of genetic association studies and genome-wide association studies. Starting with the statistical methods used for robust analysis and genetic model selection, we present in brief univariate methods for meta-analysis and we then scrutinize multivariate methodologies. Multivariate models of meta-analysis for a single gene-disease association studies, including models for haplotype association studies, multiple linked polymorphisms and multiple outcomes are discussed. The popular Mendelian randomization approach and special cases of meta-analysis addressing issues such as the assumption of the mode of inheritance, deviation from Hardy-Weinberg Equilibrium and gene-environment interactions are also presented. All available methods are enriched with practical applications and methodologies that could be developed in the future are discussed. Links for all available software implementing multivariate meta-analysis methods are also provided.

miRNA Polymorphisms and Risk of Cardio-Cerebrovascular Diseases: A Systematic Review and Meta-Analysis

Recently extensive focus has been concentrated on the role of miRNAs in the initiation and progression of cardio-cerebrovascular diseases (CCDs) which constitute a range of conditions including cardiovascular diseases (CVDs, especially coronary artery disease (CAD)), congenital heart disease (CHD) and cerebrovascular diseases (CBVDs, especially the ischemic stroke (IS)). An increasing number of studies are evaluating the association between different miRNA polymorphisms and risk of CCDs, but results have been inconclusive. This study represents a comprehensive systematic review and meta-analysis of the association between miRNA polymorphisms and risk of CCDs. PubMed, Embase, Scopus, and Web of Science were queried to identify eligible articles. Odds ratios and 95% confidence intervals were used to assess the association of miRNA polymorphisms with CCD susceptibility. A total of 51 eligible articles evaluating the association of 31 miRNA polymorphisms were identified. Meta-analysis was performed for six miRNA polymorphisms. miR-146a rs2910164 (30 studies: 13,186 cases/14,497 controls), miR-149 rs2292832 (Nine studies: 4116 cases/3511 controls), miR-149 rs71428439 (Three studies: 1556 cases/1567 controls), miR-196a2 rs11614913 (20 studies: 10,144 cases/10,433 controls), miR-218 rs11134527 (Three studies: 2,322 cases/2,754 controls) were not associated with overall CCD. miR-499 rs3746444 was associated with CCD (20 studies: 9564 cases/8876 controls). In the subgroups, rs2910164 and rs3746444 were only associated with CVDs, especially CAD. In conclusion, the results support the existence of a role for miR-146a rs2910164 and miR-499 rs3746444 in determining susceptibility to CCDs, especially CAD.

Association of Ugrp2 gene polymorphisms with adenoid hypertrophy in the pediatric population

INTRODUCTION

Adenoid hypertrophy is a condition that presents itself as the chronic enlargement of adenoid tissues; it is frequently observed in the pediatric population. The Ugrp2 gene, a member of the secretoglobin superfamily, encodes a low-molecular weight protein that functions in the differentiation of upper airway epithelial cells. However, little is known about the association of Ugrp2 genetic variations with adenoid hypertrophy.

OBJECTIVE

The aim of this study is to investigate the association of single nucleotide polymorphisms in the Ugrp2 gene with adenoid hypertrophy and its related phenotypes.

METHODS

A total of 219 children, comprising 114 patients suffering from adenoid hypertrophy and 105 healthy patients without adenoid hypertrophy, were enrolled in this study. Genotypes of the Ugrp2 gene were determined by DNA sequencing.

RESULTS

We identified four single nucleotide polymorphisms (IVS1-189G>A, IVS1-89T>G, c.201delC, and IVS2-15G>A) in the Ugrp2 gene. Our genotype analysis showed that the Ugrp2 (IVS1-89T>G) TG and (c.201delC) CdelC genotypes and their minor alleles were associated with a considerable increase in the risk of adenoid hypertrophy compared with the controls (p=0.012, p=0.009, p=0.013, and p=0.037, respectively). Furthermore, Ugrp2 (GTdelCG, GTdelCA) haplotypes were significantly associated with adenoid hypertrophy (four single nucleotide polymorphisms ordered from 5' to 3'; p=0.0001). Polymorfism-Polymorfism interaction analysis indicated a strong interaction between combined genotypes of the Ugrp2 gene contributing to adenoid hypertrophy, as well as an increased chance of its diagnosis (p<0.0001). In addition, diplotypes carrying the mutant Ugrp2 (c.201delC) allele were strongly associated with an increased risk of adenoid hypertrophy with asthma and with allergies (p=0.003 and p=0.0007, respectively).

CONCLUSION

Some single nucleotide polymorphisms and their combinations in the Ugrp2 gene are associated with an increased risk of developing adenoid hypertrophy. Therefore, we tried to underline the importance of genetic factors associated with adenoid hypertrophy and its related clinical phenotypes.

Response to commentary article: "The association between Interleukin-1β gene rs1143634 polymorphism and the risk of breast cancer by Bei Wang, Fenlai Yuan"

This a response to the commentary article entitled "The association between Interleukin-1β gene rs1143634 polymorphism and the risk of breast cancer" by Bei Wang, Fenlai Yuan. We completely agree with Wang and Yuan that there is significant deviation of HWE in control subjects for IL-1beta exon 5 +3954 polymorphism. Therefore, the apparent genetic association in IL-1beta exon 5 +3954 polymorphism must be used cautiously for further interpretation.

Association between Dietary Isoflavones in Soy and Legumes and Endometrial Cancer: A Systematic Review and Meta-Analysis

BACKGROUND

Epidemiologic studies have reported conflicting findings between soy- and legume-derived dietary isoflavones and risk of endometrial cancer.

OBJECTIVE

The aim of the present meta-analysis was to quantitatively investigate the association between daily intake of soy- and legume-derived isoflavones and risk of endometrial cancer.

DESIGN

A broad search was conducted in the following electronic databases: PubMed, EMBASE, Google Scholar, the Cochrane Library, the China Knowledge Resource Integrated Database, and the Chinese Biomedical Database based on combinations of the key words endometrial cancer, isoflavone, soy, and legume for epidemiologic studies that focused on relationships between dietary isoflavones and endometrial cancer risk. A fixed-effect or random-effect model was used to pool study-specific risk estimates.

RESULTS

A total of 13 epidemiologic studies were included in the present meta-analysis, consisting of three prospective cohort studies and 10 population-based case-control studies. The final results indicated that higher dietary isoflavone levels from soy products and legumes were associated with a reduced risk of endometrial cancer (odds ratio [OR] 0.81, 95% CI 0.74 to 0.89). Low heterogeneous bias was observed (I2=11.7%; P=0.327). Subgroup analyses were conducted based on study design, source of dietary isoflavones, and study region. When restricted to study design, dietary isoflavones from soy and legumes played a role in prevention of endometrial cancer in case-control studies (OR 0.81, 95% CI 0.73 to 0.90). However, there did not appear to be an association between dietary isoflavones and endometrial cancer in cohort studies (OR 0.81, 95% CI 0.66 to 1.00). Significant associations were found between dietary isoflavones from soy products (OR 0.82, 95% CI 0.72 to 0.92) and legumes (OR 0.84, 95% CI 0.74 to 0.96) and endometrial cancer. Dietary isoflavones were associated with reduced incidence of endometrial cancer, both in Asian countries (OR 0.78, 95% CI 0.66 to 0.93) and non-Asian countries (OR 0.82, 95% CI 0.73 to 0.92).

CONCLUSIONS

The findings suggest a weak inverse association between higher consumption of dietary isoflavones from soy products and legumes and endometrial cancer risk. However, there is still a need for large, prospective epidemiologic studies that provide a higher level of evidence to verify these findings.

Gene-environment interaction for polymorphisms in ataxia telangiectasia-mutated gene and radiation exposure in carcinogenesis: results from two literature-based meta-analyses of 27120 participants

Purpose

We conducted two meta-analyses of ATM genetic polymorphisms and cancer risk in individuals with or without radiation exposure to determine whether there was a joint effect between the ATM gene and radiation exposure in carcinogenesis.

Results

rs1801516, which was the only ATM polymorphism investigated by more than 3 studies of radiation exposure, was eligible for the present study. The meta-analysis of 23333 individuals without radiation exposure from 24 studies showed no association between the rs1801516 polymorphism and cancer risk, without heterogeneity across studies. The meta-analysis of 3787 individuals with radiation exposure from 6 studies showed a significant association between the rs1801516 polymorphism and a decreased cancer risk, with heterogeneity across studies. There was a borderline-significant difference between the ORs of the two meta-analyses (P = 0.066), and the difference was significant when only Caucasians were included (P = 0.011).

Materials and methods

Publications were identified by searching PubMed, EMBASE, Web of Science, and CNKI databases. Odds ratios (ORs) were calculated to estimate the association between ATM genetic polymorphisms and cancer risk. Tests of interaction were used to compare differences between the ORs of the two meta-analyses.

Conclusions

Our meta-analyses confirmed the presence of a gene-environment interaction between the rs1801516 polymorphism and radiation exposure in carcinogenesis, whereas no association was found between the rs1801516 polymorphism and cancer risk for individuals without radiation exposure. The heterogeneity observed in the meta-analysis of individuals with radiation exposure might be due to gene-ethnicity or gene-gene interactions. Further studies are needed to elucidate sources of the heterogeneity.

The social genome of friends and schoolmates in the National Longitudinal Study of Adolescent to Adult Health

Humans tend to form social relationships with others who resemble them. Whether this sorting of like with like arises from historical patterns of migration, meso-level social structures in modern society, or individual-level selection of similar peers remains unsettled. Recent research has evaluated the possibility that unobserved genotypes may play an important role in the creation of homophilous relationships. We extend this work by using data from 5,500 adolescents from the National Longitudinal Study of Adolescent to Adult Health (Add Health) to examine genetic similarities among pairs of friends. Although there is some evidence that friends have correlated genotypes, both at the whole-genome level as well as at trait-associated loci (via polygenic scores), further analysis suggests that meso-level forces, such as school assignment, are a principal source of genetic similarity between friends. We also observe apparent social-genetic effects in which polygenic scores of an individual's friends and schoolmates predict the individual's own educational attainment. In contrast, an individual's height is unassociated with the height genetics of peers.

Is PMI the Hypothesis or the Null Hypothesis?

Over the past several decades, there have been several strident exchanges regarding whether forensic entomologists estimate the postmortem interval (PMI), minimum PMI, or something else. During that time, there has been a proliferation of terminology reflecting this concern regarding "what we do." This has been a frustrating conversation for some in the community because much of this debate appears to be centered on what assumptions are acknowledged directly and which are embedded within a list of assumptions (or ignored altogether) in the literature and in case reports. An additional component of the conversation centers on a concern that moving away from the use of certain terminology like PMI acknowledges limitations and problems that would make the application of entomology appear less useful in court-a problem for lawyers, but one that should not be problematic for scientists in the forensic entomology community, as uncertainty is part of science that should and can be presented effectively in the courtroom (e.g., population genetic concepts in forensics). Unfortunately, a consequence of the way this conversation is conducted is that even as all involved in the debate acknowledge the concerns of their colleagues, parties continue to talk past one another advocating their preferred terminology. Progress will not be made until the community recognizes that all of the terms under consideration take the form of null hypothesis statements and that thinking about "what we do" as a null hypothesis has useful legal and scientific ramifications that transcend arguments over the usage of preferred terminology.

Estimating the prevalence of heterozygous familial hypercholesterolaemia: a systematic review and meta-analysis

OBJECTIVES

Heterozygous familial hypercholesterolaemia (FH) confers a significant risk for premature cardiovascular disease (CVD). However, the estimated prevalence of FH varies substantially among studies. We aimed to provide a summary estimate of FH prevalence in the general population and assess variations in frequency across different sociodemographic characteristics.

SETTING, PARTICIPANTS AND OUTCOME MEASURES

We searched MEDLINE, EMBASE, Global Health, the Cochrane Library, PsycINFO and PubMed for peer-reviewed literature using validated strategies. Results were limited to studies published in English between January 1990 and January 2017. Studies were eligible if they determined FH prevalence using clinical criteria or DNA-based analyses. We determined a pooled point prevalence of FH in adults and children and assessed the variation of the pooled frequency by age, sex, geographical location, diagnostic method, study quality and year of publication. Estimates were pooled using random-effects meta-analysis. Differences by study-level characteristics were investigated through subgroups, meta-regression and sensitivity analyses.

RESULTS

The pooled prevalence of FH from 19 studies including 2 458 456 unique individuals was 0.40% (95% CI 0.29% to 0.52%) which corresponds to a frequency of 1 in 250 individuals. FH prevalence was found to vary by age and geographical location but not by any other covariates. Results were consistent in sensitivity analyses.

CONCLUSIONS

Our systematic review suggests that FH is a common disorder, affecting 1 in 250 individuals. These findings underscore the need for early detection and management to decrease CVD risk.

SMAD7 rs4939827 variant contributes to colorectal cancer risk in Chinese population

A genome-wide association study identified a common genetic variant rs4939827 at 18q21 in SMAD7 to be related with colorectal cancer (CRC) risk with OR=1.2 and P =7.80E-28. Until recently, several meta-analysis studies have been conducted, and reported significant association between rs4939827 and CRC risk. However none of these studies evaluated the potential association between rs4939827 and CRC risk in Chinese population. In this study, we evaluated this association by a meta-analysis using 12077 samples including 5816 CRC cases and 6261 controls. In the end, we identified the T allele of rs4939827 to be significantly related with an increase CRC risk (P=2.22E-05, OR=1.14, 95% CI 1.07-1.21) in Chinese population.

Pharmacogenetics of Ketamine-Induced Emergence Phenomena: A Pilot Study

BACKGROUND

Up to 55% of patients who are administered ketamine experience an emergence phenomena (EP) that closely mimics schizophrenia and increases their risk of injury; however, to date, no studies have investigated genetic association of ketamine-induced EP in healthy patients.

OBJECTIVES

The aim of the study was to investigate the feasibility and sample sizes required to explore the relationship between CYP2B6*6 and GRIN2B single-nucleotide polymorphisms and ketamine-induced EP.

METHODS

This cross-sectional, pharmacogenetic candidate, gene pilot study recruited 75 patients having minor elective outpatient surgeries. EP was measured with the Clinician Administered Dissociative State Scale. Genetic association of CYP2B6*6 and GRIN2B (rs1019385 and rs1806191) single-nucleotide polymorphisms and ketamine-induced EP occurrence and severity were tested using logistic and linear regression.

RESULTS

Forty-seven patients (63%) received ketamine and were genotyped, and 40% of them experienced EP. Occurrence and severity of EP were not associated with CYP2B6*6 or GRIN2B (p > .10). Exploratory analysis of nongenotype models containing age, ketamine dose, duration of anesthesia, and time from ketamine administration to assessment for EP significantly predicted EP occurrence (p = .001) and severity (p = .007). This pilot study demonstrates feasibility for implementing a pharmacogenetic study in a clinical setting, and we estimate that between 380 and 570 cases will be needed to adequately power future genetic association studies.

DISCUSSION

Younger age, higher dose, and longer duration of anesthesia significantly predicted EP occurrence and severity among our pilot sample. Although the small sample size limited our ability to demonstrate significant genotype differences, we generated effect sizes, sample size estimates, and nongenetic covariates information in order to support future pharmacogenetic study design for evaluating this adverse event.

Reappraisal of XRCC1 Arg194Trp polymorphism and glioma risk: a cumulative meta-analysis

The association between XRCC1 Arg194Trp polymorphism and glioma risk were inconsistent from published meta-analyses and epidemiological studies. Hence, we performed this updated and cumulative meta-analysis to reappraisal this relationship. PubMed, Embase, CBM (Chinese Biomedical Database), and CNKI (China National Knowledge Internet) databases were comprehensively searched up to August 13, 2016 (updated on December 22, 2016). After study selection and data extraction from eligible studies, the association was evaluated by odds ratios (ORs) and its 95% confidence intervals (95%CIs) using Comprehensive Meta-Analysis software. Finally 16 case-control studies involving 7011 patients and 9519 healthy controls were yielded. The results indicated that XRCC1 Arg194Trp polymorphism was significantly correlated with the increased risk of glioma [Trp vs. Arg: OR = 1.18(1.05-1.34); TrpTrp vs. ArgArg: OR = 1.66(1.31-2.12); ArgTrp vs. ArgArg: OR = 1.34(1.02-1.77); TrpTrp vs. ArgArg+ArgTrp: OR = 1.47(1.26-1.72); TrpTrp+ArgTrp vs. ArgArg: OR = 1.17(1.01-1.35)]. Cumulative analysis showed the results changed from non-significant to significant when new studies accumulated, and sensitivity analysis indicated the results were stable. Subgroup analysis showed the significant association existed in Asians but not in Caucasians. Current evidence indicated that XRCC1 Arg194Trp polymorphism was associated with increased risk for glioma, especially in Asians; however, relevant studies involving other ethnic groups are required to validate our findings in further.

Candidate Gene Association Studies of Anthracycline-induced Cardiotoxicity: A Systematic Review and Meta-analysis

Anthracyclines play an important role in the management of patients with cancer but the development of anthracycline-induced cardiotoxicity (ACT) remains a significant concern for most clinicians. Recently, genetic approach has been used to identify patients at increased risk of ACT. This systematic review assessed the association between genomic markers and ACT. A systematic literature search was performed in Medline, PubMed, Cochrane Central Register of Controlled Studies, CINAHL Plus, AMED, EMBASE and HuGE Navigator from inception until May 2016. Twenty-eight studies examining the association of genetic variants and ACT were identified. These studies examined 84 different genes and 147 single nucleotide polymorphisms. Meta-analyses showed 3 risk variants significantly increased the risk for ACT; namely ABCC2 rs8187710 (pooled odds ratio: 2.20; 95% CI: 1.36-3.54), CYBA rs4673 (1.55; 1.05-2.30) and RAC2 rs13058338 (1.79; 1.27-2.52). The current evidence remains unclear on the potential role of pharmacogenomic screening prior to anthracycline therapy. Further research is needed to improve the diagnostic and prognostic role in predicting ACT.

Significant association between SCGB1D4 gene polymorphisms and susceptibility to adenoid hypertrophy in a pediatric population

BACKGROUND/AIM

Adenoid hypertrophy (AH) is chronic enlargement of the adenoid tissue. The pathophysiology of the disease is unclear. We analyzed SCGB1D4 gene polymorphisms in order to determine the effect of the variants or their genetic combinations on AH.

MATERIALS AND METHODS

We genotyped the SCGB1D4 (IIS) gene in 167 participants (95 children with AH and 72 controls) by performing DNA sequencing in blood samples.

RESULTS

We genotyped three single nucleotide polymorphisms (SNPs). In the analysis, we found that in the presence of those SNPs and the minor alleles of individual SNPs four haplotypes were associated with an increased risk of AH. In addition, those SNPs were significantly associated with asthma, allergy, sleep-disordered breathing, AH grade +4, and a high level of IgE. As indicated on multifactor dimensionality reduction analysis, single-locus (rs35328961), two-locus (rs35328961_rs56196602), and three-locus models (rs200327820_rs35328961_rs56196602) had the highest synergistic interaction effect on AH. The three-factor model was also significantly associated with some genotypes of rs35328961 and allergic-asthmatic AH.

CONCLUSION

SNPs of SCGB1D4 and their combinations are associated with an increased risk for developing AH. We highlighted the importance of genetic factors on AH and AH-related clinical phenotypes.

The -174 G>C Interleukin-6 Gene Polymorphism is Associated with Angiographic Progression of Coronary Artery Disease over a 4-Year Period

BACKGROUND

Inflammation is a key process underlying the clinical course of coronary artery disease (CAD). C-reactive protein (CRP) and interleukin-6 (IL-6) contribute to its pathophysiology and act as biomarkers. We sought to examine whether known single nucleotide polymorphisms (SNPs) impact CAD progression, reflecting increased inflammation.

METHODS

We retrospectively evaluated coronary angiographies of patients with established CAD who were re-investigated for stable/unstable angina after a time interval of >12 months. We defined progression of CAD as the emergence of a new plaque or a ≥20 % increase of a formerly non-significant lesion. We genotyped patients for the 1846 C>T CRP and -174 G>C IL-6 SNPs. The probability of CAD progression among the Mendelian randomization groups was evaluated using the Kaplan-Meier method. Data were analyzed using a Cox model that included relevant clinical factors.

RESULTS

A total of 157 patients were included. The serum levels of CRP and IL-6 differed significantly between genotypes. The genotype frequencies of IL-6 were consistent with Hardy-Weinberg equilibrium, whereas those for CRP were excluded from our conclusions. At 48 months, 83 patients (52.9 %) with the IL-6 C allele versus 74 (47.1 %) with the G allele exhibited CAD progression. Patients with the IL-6 C allele had a 52.8 % probability for progression versus 13.3 % for those with the G allele (p=0.005). The results were confirmed by multivariate analysis; dyslipidemia, family history, and IL-6 SNP emerged as significant factors.

CONCLUSION

Patients with established CAD who carried the -174 C allele of the IL-6 gene demonstrated an increased risk for the progression of coronary plaques over a four-year period. Further studies will be needed to validate these findings.

Associations between AT-rich interactive domain 5B gene polymorphisms and risk of childhood acute lymphoblastic leukemia: a meta-analysis

Previous genome-wide association studies (GWAS) have implicated several single nucleotide polymorphisms (SNPs) in the AT-rich interactive domain 5B (ARID5B) gene with childhood acute lymphoblastic leukemia (ALL). However, replicated studies reported some inconsistent results in different populations. Using meta-analysis, we here aimed to clarify the nature of the genetic risks contributed by the two polymorphisms (rs10994982, rs7089424) for developing childhood ALL. Through searches of PubMed, EMBASE, and manually searching relevant references, a total of 14 articles with 16 independent studies were included. Odds ratios (ORs) with 95% confidence intervals (95%CI) were calculated to assess the associations. Both SNPs rs10994982 and rs7089424 showed significant associations with childhood ALL risk in all genetic models after Bonferroni correction. Furthermore, subtype analyses of B-lineage ALL provided strong evidence that SNP rs10994982 is highly associated with the risk of developing B-hyperdiploid ALL. These results indicate that SNPs rs10994982 and rs7089424 are indeed significantly associated with increased risk of childhood ALL.

Polymorphisms in HTR2A and DRD4 Predispose to Smoking and Smoking Quantity

BACKGROUND

Genes encoding the receptors involved in the dopaminergic and serotonergic pathways are potential candidates in the mechanisms of nicotine addiction.

AIMS

To identify genetic variants in the promoter regions and exons of the DRD4 and HTR2A genes associated with tobacco smoking and the degree of nicotine addiction in Mexican mestizos.

METHODS

The study included 438 non-smokers (NS) and 1,157 current smokers, ranked based on their consumption of cigarettes per day (cpd): 574 heavy smokers (HS, >20 cpd) and 583 light smokers (LS, 1-10 cpd). Genotyping was performed for 4 and 8 single nucleotide polymorphisms (SNPs) in the DRD4 and HTR2A genes, respectively.

RESULTS

The C allele of rs1800955 in DRD4 was found to be associated with cigarette smoking in the HS vs. NS and LS vs. NS comparisons (p = 2.34E-03 and p = 1.13E-03, respectively); the association was maintained in the homozygous CC genotype (p = 5.00E-04 and p = 2.00E-04, respectively). The T allele of rs6313 in HTR2A was significantly associated with cigarette smoking and a greater degree of nicotine addiction (p = 4.77E-03, OR = 1.55); the association was maintained in the homozygous genotype (TT) (p = 4.90E-03, OR = 1.96). The A allele of rs6313 was associated with cigarette smoking in the HS vs. NS comparison (p = 1.53E-02, OR = 1.36); the risk was nearly doubled in the homozygous AA genotype (p = 1.30E-03, OR = 1.83) compared with the heterozygous GA genotype (OR = 1.38).

CONCLUSIONS

Among Mexican mestizos, the C allele of rs1800955 in the DRD4 gene and the A allele of rs6311 in the HTR2A gene are associated with cigarette smoking, whereas the T allele of rs6313 in HTR2A is associated with cigarette smoking and the degree of nicotine addiction.

Angiotensin-Converting Enzyme Insertion/Deletion Polymorphism and Susceptibility to Osteoarthritis of the Knee: A Case-Control Study and Meta-Analysis

Background

Studies of angiotensin-converting enzyme insertion/deletion (ACE I/D) polymorphisms and the risks of knee osteoarthritis (OA) have yielded conflicting results.

Objective

To determine the association between ACE I/D and knee OA, we conducted a combined case-control study and meta-analysis.

Methods

For the case-control study, 447 knee OA cases and 423 healthy controls were recruited between March 2010 and July 2011. Knee OA cases were defined using the Kellgren-Lawrence grading system, and the ACE I/D genotype was determined using a standard polymerase chain reaction. The association between ACE I/D and knee OA was detected using allele, genotype, dominant, and recessive models. For the meta-analysis, PubMed and Embase databases were systematically searched for prospective observational studies published up until August 2015. Studies of ACE I/D and knee OA with sufficient data were selected. Pooled results were expressed as odds ratios (ORs) with corresponding 95% confidence intervals (CI) for the D versus I allele with regard to knee OA risk.

Results

We found no significant association between the D allele and knee OA [OR: 1.09 (95% CI: 0.76–1.89)] in the present case-control study, and the results of other genetic models were also nonsignificant. Five current studies were included, and there were a total of six study populations after including our case-control study (1165 cases and 1029 controls). In the meta-analysis, the allele model also yielded nonsignificant results [OR: 1.37 (95% CI: 0.95–1.99)] and a high heterogeneity (I²: 87.2%).

Conclusions

The association between ACE I/D and knee OA tended to yield negative results. High heterogeneity suggests a complex, multifactorial mechanism, and an epistasis analysis of ACE I/D and knee OA should therefore be conducted.

Apolipoprotein C3 gene variants and the risk of coronary heart disease: A meta-analysis

BACKGROUND

It has been reported that three common loci, SstI, C-482T, and T-455C, in the apolipoprotein C3 (APOC3) gene might be associated with an increased risk of coronary heart disease (CHD). Considering the inconsistent results and ethnicity variations, we performed a systematic meta-analysis to evaluate the association between three single nucleotide polymorphisms (SNPs) and the risk of CHD.

METHODS

We searched HuGE Navigator and PubMed databases to screen for the related literature published before 25 September, 2015. Two independent reviewers extracted the data and assessed the study quality. A random-effect model was used to pool the effect size.

RESULTS

A total of 29 studies met inclusion criteria. Nineteen studies, including 11,186 subjects relative to SstI, five studies comprising 3727 subjects relative to C-482T, and nine studies with 6753 subjects relative to T-455C were included in the final analysis. A significant increase in CHD risk was observed in the SstI polymorphism (S2 versus S1: odds ratio [OR] = 1.30, 95% confidence interval [CI] 1.10-1.55. There was also a significant increasing trend of CHD risk in the T-455C polymorphism (C versus T: OR = 1.28, 95% CI 1.16-1.41. However, no associations between C-482T and CHD risk were found in this meta-analysis.

CONCLUSIONS

The pooled evidence suggests that two SNPs (SstI and T-455C) are associated with an increased risk of CHD. However, because of the limited sample size and heterogeneity, further large-scale and well-designed studies are needed to validate our findings.