-
Reviews in Medical Virology Sep 2023Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) associated with susceptibility and severity of coronavirus disease 2019... (Meta-Analysis)
Meta-Analysis Review
Genome-wide association studies (GWASs) have identified single nucleotide polymorphisms (SNPs) associated with susceptibility and severity of coronavirus disease 2019 (COVID-19). However, identified SNPs are inconsistent across studies, and there is no compelling consensus that COVID-19 status is determined by genetic factors. Here, we conducted a systematic review and meta-analysis to determine the effect of genetic factors on COVID-19. A random-effect meta-analysis was performed to estimate pooled odds ratios (ORs) of SNP effects, and SNP-based heritability (SNP-h ) of COVID-19. The analyses were performed using meta-R package, and Stata version 17. The meta-analysis included a total of 96,817 COVID-19 cases and 6,414,916 negative controls. The meta-analysis showed that a cluster of highly correlated 9 SNPs (R > 0.9) at 3p21.31 gene locus covering LZTFL1 and SLC6A20 genes was significantly associated with COVID-19 severity, with a pooled OR of 1.8 [1.5-2.0]. Meanwhile, another 3 SNPs (rs2531743-G, rs2271616-T, and rs73062389-A) within the locus was associated with COVID-19 susceptibility, with pooled estimates of 0.95 [0.93-0.96], 1.23 [1.19-1.27] and 1.15 [1.13-1.17], respectively. Interestingly, SNPs associated with susceptibility and SNPs associated with severity in this locus are in linkage equilibrium (R < 0.026). The SNP-h on the liability scale for severity and susceptibility was estimated at 7.6% (Se = 3.2%) and 4.6% (Se = 1.5%), respectively. Genetic factors contribute to COVID-19 susceptibility and severity. In the 3p21.31 locus, SNPs that are associated with susceptibility are not in linkage disequilibrium (LD) with SNPs that are associated with severity, indicating within-locus heterogeneity.
Topics: Humans; Genetic Predisposition to Disease; Genome-Wide Association Study; COVID-19; Linkage Disequilibrium; Polymorphism, Single Nucleotide; Membrane Transport Proteins
PubMed: 37303119
DOI: 10.1002/rmv.2466 -
The Lancet. Infectious Diseases Jan 2009Streptococcus pneumoniae and Neisseria meningitidis can cause sepsis and meningitis. Several risk factors for pneumococcal and meningococcal disease have been... (Meta-Analysis)
Meta-Analysis Review
Streptococcus pneumoniae and Neisseria meningitidis can cause sepsis and meningitis. Several risk factors for pneumococcal and meningococcal disease have been identified, but the cause of basic differences in susceptibility between individuals and populations is unknown. Single-nucleotide polymorphisms are thought to explain interindividual differences in susceptibility. New technologies provide the opportunity to study the genetic basis of susceptibility to these diseases. In recent years, several studies have been published on these polymorphisms in pneumococcal and meningococcal disease, many with apparently conflicting results. Herein we provide a systematic overview of all polymorphisms studied for a relation with susceptibility to pneumococcal and meningococcal disease. We also propose an initiative to pool genetic data on pneumococcal and meningococcal meningitis in one biobank.
Topics: Genetic Predisposition to Disease; Humans; Meningococcal Infections; Pneumococcal Infections; Polymorphism, Genetic
PubMed: 19036641
DOI: 10.1016/S1473-3099(08)70261-5 -
Journal of Autoimmunity Mar 2017Psoriasis is an inflammatory disease of the skin that is sometimes accompanied by an auto-inflammatory arthritis called psoriatic arthritis (PsA). Psoriasis and PsA are... (Meta-Analysis)
Meta-Analysis Review
Psoriasis is an inflammatory disease of the skin that is sometimes accompanied by an auto-inflammatory arthritis called psoriatic arthritis (PsA). Psoriasis and PsA are multifactorial diseases that result from complex interactions of environmental and genetic risk factors. Epigenetic marks, which are labile chemical marks with diverse functions, form a layer of biological information that sits at the interface of genetics and the environment. Aberrant epigenetic regulation has been previously implicated in other rheumatological disorders. The purpose of this review is to summarize and critically evaluate the nascent literature on epigenetics in psoriasis and PsA. A systematic review yielded 52 primary articles after applying inclusion and exclusion criteria. Data were extracted using a standardized template and study quality assessed using a methodological quality checklist. Studies reflect a broad range of epigenetic sub-disciplines, the most common being DNA methylation, followed by the parent of origin effect or genomic imprinting, expression or activity of epigenetic modifying enzymes, and histone modifications. Epidemiological studies demonstrating excessive paternal transmission provided the earliest evidence of epigenetic deregulation in psoriatic disease, however few studies have examined its molecular mechanisms. Methylation studies evolved rapidly from low resolution global to targeted analyses of known psoriatic disease susceptibility loci such as HLA-C*0602. The recent explosion of epigenome-wide association studies has provided us with novel insights into psoriasis pathogenesis, and the mechanism of action of UVB, methotrexate, and anti-TNF therapies, as well as molecular signatures of psoriasis that may have clinical relevance. Finally, recent studies of pharmacological inhibitors of epigenetic modifier enzymes demonstrate their potential applicability as novel treatment modalities for psoriasis. Challenges of epigenetics research in psoriasis and PsA were identified and future perspectives are discussed herein.
Topics: Arthritis, Psoriatic; DNA Methylation; Epigenesis, Genetic; Epigenomics; Genetic Association Studies; Genetic Predisposition to Disease; Genomic Imprinting; Histones; Humans; Organ Specificity; Psoriasis
PubMed: 27965059
DOI: 10.1016/j.jaut.2016.12.002 -
Rheumatology (Oxford, England) Sep 2014Vitamin D appears to have significant effects on both innate and acquired immunity and deficiency may be associated with both susceptibility and disease severity in some... (Review)
Review
OBJECTIVES
Vitamin D appears to have significant effects on both innate and acquired immunity and deficiency may be associated with both susceptibility and disease severity in some autoimmune conditions. There has been little focus on the potential immunomodulatory role of vitamin D in AS. This study systematically reviews the evidence for an association between vitamin D deficiency and disease susceptibility and severity in AS.
METHODS
A systematic review was conducted using Medline, EMBASE, Web of Science and conference abstracts of the European League Against Rheumatism (2002-13), British Society for Rheumatology (1993-2013) and ACR (2006-13).
RESULTS
Fifteen original articles and five conference abstracts met the criteria for inclusion. All were cross-sectional in design. Seven of 11 studies identified lower concentrations of 25-hydroxyvitamin D (25OHD) in AS patients compared with healthy controls. A significant inverse correlation between 25OHD and disease activity was observed in 5 of 11 studies. The majority of studies that failed to demonstrate significant findings used inappropriate statistical methods.
CONCLUSION
Cross-sectional studies using appropriate statistical analyses have highlighted that AS is associated with lower vitamin D concentrations. Within groups of AS patients there is some evidence that low vitamin D concentrations are associated with higher disease activity. However, there are insufficient published data to support an immunomodulatory role for vitamin D in AS. Further study with a longitudinal design is required to understand whether optimizing vitamin D in AS has potential as a disease-modifying intervention.
Topics: Cross-Sectional Studies; Disease Susceptibility; Humans; Spondylitis, Ankylosing; Vitamin D; Vitamin D Deficiency
PubMed: 24706990
DOI: 10.1093/rheumatology/keu042 -
Clinical Infectious Diseases : An... Jan 2016Norovirus and rotavirus are prominent enteric viruses responsible for severe acute gastroenteritis disease burden around the world. Both viruses recognize and bind to... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Norovirus and rotavirus are prominent enteric viruses responsible for severe acute gastroenteritis disease burden around the world. Both viruses recognize and bind to histo-blood group antigens, which are expressed by the fucosyltransferase 2 (FUT2) gene. Individuals with a functional FUT2 gene are termed "secretors." FUT2 polymorphisms may influence viral binding patterns and, therefore, may influence host susceptibility to infection by these viruses.
METHODS
We performed a systematic review of the published literature on this topic. Data were abstracted and compiled for descriptive analyses and metaanalyses. We estimated pooled odds ratios (ORs) for infection using random-effects models.
RESULTS
We found that secretors were 9.9 times (95% confidence interval [CI], 3.9-24.8) as likely to be infected with genogroup II.4 noroviruses and 2.2 times as likely to be infected with genogroup II non-4 noroviruses (95% CI, 1.2-4.2) compared with nonsecretors. Secretors were also 26.6 times more susceptible to infections from P[8]-type rotaviruses compared with nonsecretors (95% CI, 8.3-85.0).
CONCLUSIONS
Our analyses indicate that host genetic susceptibility to norovirus and rotavirus infection may be strain specific. As strain distribution and the proportion of genetic phenotypes vary in different countries, future studies should focus on differences in susceptibility among various ethnicities. Knowledge of innate susceptibility to rotavirus and norovirus can lead to improved understanding of both vaccine performance and individual risk of disease.
Topics: Caliciviridae Infections; Fucosyltransferases; Genetic Predisposition to Disease; Humans; Norovirus; Rotavirus; Rotavirus Infections; Galactoside 2-alpha-L-fucosyltransferase
PubMed: 26508510
DOI: 10.1093/cid/civ873 -
Neurology India 2013Recent genome-wide and locus-specific association studies identified RNF213 as an important Moyamoya disease (MMD) susceptibility gene. But the results of these studies... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Recent genome-wide and locus-specific association studies identified RNF213 as an important Moyamoya disease (MMD) susceptibility gene. But the results of these studies are limited by the few subjects, different methodologies and ethnicities.
AIMS
To investigate the association between p.R4810K (rs 112735431, ss179362673; G > A) and p.R4859K (c.14576 G > A) polymorphisms of the RNF213 gene and MMD susceptibility.
SETTINGS AND DESIGN
We conducted a meta-analysis to evaluate the association.
MATERIALS AND METHODS
Two investigators independently searched the PubMed, Medline, and Embase databases for studies published before October 2012. For included studies, we performed meta-analyses using Cochrane RevMan software.
STATISTICAL ANALYSIS
Summary odds ratios (ORs) and 95% confidence intervals (CIs) for RNF213 p.R4810K and p.R4859K polymorphisms; MMD were calculated in a fixed-effects model and a random effects model whenever appropriate.
RESULTS
Five eligible studies were reviewed and analyzed, which included two studies for p.R4810K polymorphisms (421 cases and 1214 controls) and three studies for p.R4859K polymorphisms (398 cases and 765 controls). Overall, the pooled results indicated that both p.R4810K polymorphisms and p.R4859K polymorphisms were associated with MMD risk (OR 92.03, 95% CI 54.06-156.65, P < 0.00001 and OR 157.53, 95% CI 85.37-290.7, P < 0.00001, respectively). Stratified analyses by ethnicity revealed the population attributable risks in the Japanese and Korean populations were larger than that in the Chinese population (P =0.0006).
CONCLUSIONS
This meta-analysis demonstrated that there are strong associations between p.R4859K and p.R4810K polymorphisms of the RNF213 gene and MMD. The discoveries of its association with MMD may help in early diagnosis and prevention of this disease. Further study is still necessary to clarify the biochemical function and pathological role of RNF213 in MMD.
Topics: Adenosine Triphosphatases; Asian People; Genetic Predisposition to Disease; Humans; Moyamoya Disease; Polymorphism, Genetic; Ubiquitin-Protein Ligases
PubMed: 23466837
DOI: 10.4103/0028-3886.107927 -
Gene Aug 2020The goal of our study is to investigate the contribution of the 13 single-nucleotide polymorphisms to inflammatory bowel disease (IBD), including Crohn's disease (CD)... (Meta-Analysis)
Meta-Analysis
AIMS
The goal of our study is to investigate the contribution of the 13 single-nucleotide polymorphisms to inflammatory bowel disease (IBD), including Crohn's disease (CD) and Ulcerative colitis (UC).
METHODS
A total of 44 articles were retrieved from bibliographic databases including PubMed, Embase, SpingerLink, Web of Science, Chinese National Knowledge Infrastructure (CNKI), and Wanfang. Through a comprehensive filtering procedure, 13 single-nucleotide polymorphisms were collected in the meta-analysis, which was done by Review Manager 5.0.
RESULTS
After a systematic filtration, there were 13 single-nucleotide polymorphisms (SNPs) from 44 articles involved in our meta-analysis. Our results demonstrated that 3 SNPs were found to be significantly associated with CD/UC/IBD: IRF5 rs4728142 (UC: OR = 1.21, 95% CI = 1.09-1.35, P = 0.0003; OR = 1.30, 95% CI = 1.08-1.57, P = 0.006 in Asian), PTGER4 rs4613763 (CD: the overall OR = 1.28, 95% CI = 1.01-1.64, P = 0.04; IBD: OR = 1.31, 95% CI = 1.04-1.65, P = 0.02), IL12B rs6887695 (CD: the overall OR = 1.17, 95% CI = 1.06-1.30, P = 0.002; UC: the overall OR = 1.13, 95% CI = 1.01-1.26, P = 0.03; IBD: the overall OR = 1.15, 95% CI = 1.06-1.24, P = 0.0009).
CONCLUSION
Our meta-analyses have indicated the significant associations between SNPs (IRF5 rs4728142, PTGER4 rs4613763, and IL12B rs6887695) and CD/UC/IBD.
Topics: Asian People; Case-Control Studies; Colitis, Ulcerative; Crohn Disease; Disease Susceptibility; Genetic Association Studies; Genetic Predisposition to Disease; Genotype; Humans; Inflammatory Bowel Diseases; Interferon Regulatory Factors; Interleukin-12 Subunit p40; Phenotype; Polymorphism, Single Nucleotide; Receptors, Prostaglandin E, EP4 Subtype; White People
PubMed: 32464244
DOI: 10.1016/j.gene.2020.144814 -
International Journal of Molecular... Dec 2022Aim: The single-nucleotide polymorphism (SNP) rs713041, located in the regulatory region, is required to incorporate selenium into the selenoprotein glutathione... (Meta-Analysis)
Meta-Analysis Review
Aim: The single-nucleotide polymorphism (SNP) rs713041, located in the regulatory region, is required to incorporate selenium into the selenoprotein glutathione peroxidase 4 (GPX4) and has been found to have functional consequences. This systematic review aimed to conduct a meta-analysis to determine whether there is an association between GPX4 (rs713041) SNP and the risk of diseases in humans and its correlation with selenium status. Material and methods: A systematic search for English-language manuscripts published between January 1990 and November 2022 was carried out using six databases: CINAHL, Cochrane, Medline, PubMed, Scopus and Web of Science. Odds ratios (ORs) and 95% confidence intervals (CIs) were applied to assess a relationship between GPX4 (rs713041) SNP and the risk of different diseases based on three genetic models. Review Manager 5.4 and Comprehensive Meta-Analysis 4 software were used to perform the meta-analysis and carry out Egger’s test for publication bias. Results: Data from 21 articles were included in the systematic review. Diseases were clustered according to the physiological system affected to understand better the role of GPX4 (rs713041) SNP in developing different diseases. Carriers of the GPX4 (rs173041) T allele were associated with an increased risk of developing colorectal cancer in additive and dominant models (p = 0.02 and p = 0.004, respectively). In addition, carriers of the T allele were associated with an increased risk of developing stroke and hypertension in the additive, dominant and recessive models (p = 0.002, p = 0.004 and p = 0.01, respectively). On the other hand, the GPX4 (rs713041) T allele was associated with a decreased risk of developing pre-eclampsia in the additive, dominant and recessive models (p < 0.0001, p = 0.002 and p = 0.0005, respectively). Moreover, selenium levels presented lower mean values in cancer patients relative to control groups (SMD = −0.39 µg/L; 95% CI: −0.64, −0.14; p = 0.002, I2 = 85%). Conclusion: GPX4 (rs713041) T allele may influence colorectal cancer risk, stroke, hypertension and pre-eclampsia. In addition, low selenium levels may play a role in the increased risk of cancer.
Topics: Female; Humans; Pregnancy; Colorectal Neoplasms; Genetic Predisposition to Disease; Glutathione Peroxidase; Hypertension; Phospholipid Hydroperoxide Glutathione Peroxidase; Polymorphism, Single Nucleotide; Pre-Eclampsia; Selenium; Stroke
PubMed: 36555402
DOI: 10.3390/ijms232415762 -
Gene Jun 2024Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease that is closely linked to genetic factors. Previous studies have revealed numerous single... (Meta-Analysis)
Meta-Analysis Review
AIM
Atopic dermatitis (AD) is a chronic pruritic inflammatory skin disease that is closely linked to genetic factors. Previous studies have revealed numerous single nucleotide polymorphisms (SNPs) that been related to susceptibility to AD; however, the results are conflicting. Therefore, a meta-analysis was conducted to assess the associations of these polymorphisms and AD risk.
MATERIAL AND METHODS
PubMed, Web of Science, Embase, Cochrane Library, and China National Knowledge Infrastructure databases were retrieved to identify eligible studies, with selected polymorphisms being reported in a minimum of three separate studies. The Newcastle-Ottawa Scale (NOS) was used to evaluate study quality. Review Manager 5.3 and STATA 14.0 were used to perform the meta-analysis.
RESULTS
After screening, 64 studies involving 13 genes (24 SNPs) were selected for inclusion in the meta-analysis. Nine SNPs were positively correlated with AD susceptibility [filaggrin (FLG) R501X, FLG 2282del4, chromosome 11q13.5 rs7927894, interleukin (IL)-17A rs2275913, IL-18 -137 G/C, Toll-like receptor 2 (TLR2) rs5743708, TLR2 A-16934 T, serine protease inhibitor Kazal type-5 (SPINK5) Asn368Ser, interferon-γ (IFN-γ) T874A] and one was negatively associated with AD susceptibility (IL-4 -1098 T/G). The 14 remaining SNPs were not significantly associated with AD susceptibility.
CONCLUSIONS
Nine SNPs that may be risk factors and one SNP that may be a protective factor for AD were identified, providing a reference for AD prediction, prevention, and therapy.
Topics: Humans; Dermatitis, Atopic; Genetic Predisposition to Disease; Toll-Like Receptor 2; Polymorphism, Single Nucleotide; Skin; Intermediate Filament Proteins
PubMed: 38513928
DOI: 10.1016/j.gene.2024.148397 -
PloS One Jan 2011Natural resistance associated macrophage protein 1 (NRAMP1), encoded by the SLC11A1 gene, has been described to regulate macrophage activation and be associated with... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Natural resistance associated macrophage protein 1 (NRAMP1), encoded by the SLC11A1 gene, has been described to regulate macrophage activation and be associated with infectious and autoimmune diseases. The relation between SLC11A1 polymorphisms and tuberculosis susceptibility has been studied in different populations.
METHODS
We systematically reviewed published studies on SLC11A1 polymorphisms and tuberculosis susceptibility until September 15, 2010 and quantitatively summarized associations of the most widely studied polymorphisms using meta-analysis.
RESULTS
In total, 36 eligible articles were included in this review. In Meta-analysis, significant associations were observed between tuberculosis risk and widely studied SLC11A1 polymorphisms with summarized odds ratio of 1.35 (95%CI, 1.17-1.54), 1.25 (95% CI, 1.04-1.50), 1.23 (95% CI, 1.04-1.44), 1.31 (95%CI, 1.08-1.59) for 3' UTR, D543N, INT4, and 5' (GT)n, respectively. Heterogeneity between studies was not pronounced, and the associations did not remarkably vary in the stratified analysis with respect to study population and study base.
CONCLUSIONS
The association between SLC11A1 polymorphisms and tuberculosis susceptibility observed in our analyses supports the hypothesis that NRAMP1 might play an important role in the host defense to the development of tuberculosis.
Topics: Cation Transport Proteins; Genetic Predisposition to Disease; Humans; Polymorphism, Genetic; Tuberculosis
PubMed: 21283567
DOI: 10.1371/journal.pone.0015831