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Heliyon Apr 2024Coronary artery disease (CAD) is the most common reason for mortality and disability-adjusted life years (DALYs) lost globally. This study aimed to suggest a new gene...
BACKGROUND
Coronary artery disease (CAD) is the most common reason for mortality and disability-adjusted life years (DALYs) lost globally. This study aimed to suggest a new gene list for the treatment of CAD by a systematic review of bioinformatics analyses of pharmacogenomics impacts of potential genes and variants.
METHODS
PubMed search was filtered by the title including Coronary Artery Disease during 2020-2023. To find the genes with pharmacogenetic impact on the CAD, additional filtrations were considered according to the variant annotations. Protein-Protein Interactions (PPIs), Gene-miRNA Interactions (GMIs), Protein-Drug Interactions (PDIs), and variant annotation assessments (VAAs) performed by STRING-MODEL (ver. 12), Cytoscape (ver. 3.10), miRTargetLink.2., NetworkAnalyst (ver 0.3.0), and PharmGKB.
RESULTS
Results revealed 5618 publications, 1290 papers were qualified, and finally, 650 papers were included. 4608 protein-coding genes were extracted, among them, 1432 unique genes were distinguished and 530 evidence-based repeated genes remained. 71 genes showed a pharmacogenetics-related variant annotation in at least (entirely 6331 annotations). Variant annotation assessment (VAA) showed 532 potential variants for the final report, and finally, the concluding PGs list represented 175 variants. Based on the function and MAF, 57 nonsynonymous variants of 29 Pharmacogenomics-related genes were associated with CAD.
CONCLUSION
Conclusively, evaluating circulating miR33a in individuals' plasma with CAD, and genotyping of rs2230806, rs2230808, rs2487032, rs12003906, rs2472507, rs2515629, and rs4149297 (ABCA1 variants) lead to precisely prescribing of well-known drugs. Also, the findings of this review can be used in both whole-genome sequencing (WGS) and whole-exome sequencing (WES) analysis in the prognosis and diagnosis of CAD.
PubMed: 38601677
DOI: 10.1016/j.heliyon.2024.e28983 -
Pathogens (Basel, Switzerland) Nov 2023Host genetic factors significantly influence susceptibility to SARS-CoV-2 infection and COVID-19 severity. Among these genetic factors are single-nucleotide variants... (Review)
Review
Host genetic factors significantly influence susceptibility to SARS-CoV-2 infection and COVID-19 severity. Among these genetic factors are single-nucleotide variants (SNVs). and genes have been associated with severe COVID-19 in populations from the United Kingdom, Africa, and Latin America. IFNAR1 and IFNAR2 are subunits forming the type I interferon receptor (IFNAR). SNVs in the genes impact protein function, affecting antiviral response and disease phenotypes. This systematic review aimed to describe and variants associated with COVID-19 susceptibility and severity. Accordingly, the current review focused on and studies published between January 2021 and February 2023, utilizing the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) protocol. The electronic search was conducted in PubMed databases using Boolean operators and inclusion and exclusion criteria. Of the 170 literature pieces, 11 studies were included. We include case reports of rare SNVs, defined by minor allele frequency (MAF) < 1%, and genome-wide associated studies (GWAS). Variants in and could potentially be new targets for therapies that limit the infection and the resulting inflammation by SARS-CoV-2 infection.
PubMed: 38003785
DOI: 10.3390/pathogens12111320 -
International Journal of Molecular... Apr 2023Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons in the spinal cord, brain stem, and... (Meta-Analysis)
Meta-Analysis Review
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by the progressive loss of motor neurons in the spinal cord, brain stem, and cerebral cortex. Biomarkers for ALS are essential for disease detection and to provide information on potential therapeutic targets. Aminopeptidases catalyze the cleavage of amino acids from the amino terminus of protein or substrates such as neuropeptides. Since certain aminopeptidases are known to increase the risk of neurodegeneration, such mechanisms may reveal new targets to determine their association with ALS risk and their interest as a diagnostic biomarker. The authors performed a systematic review and meta-analyses of genome-wide association studies (GWASs) to identify reported aminopeptidases genetic loci associated with the risk of ALS. PubMed, Scopus, CINAHL, ISI Web of Science, ProQuest, LILACS, and Cochrane databases were searched to retrieve eligible studies in English or Spanish, published up to 27 January 2023. A total of 16 studies were included in this systematic review, where a series of aminopeptidases could be related to ALS and could be promising biomarkers (DPP1, DPP2, DPP4, LeuAP, pGluAP, and PSA/NPEPPS). The literature reported the association of single-nucleotide polymorphisms (SNPs: rs10260404 and rs17174381) with the risk of ALS. The genetic variation rs10260404 in the DPP6 gene was identified to be highly associated with ALS susceptibility, but meta-analyses of genotypes in five studies in a matched cohort of different ancestry (1873 cases and 1861 control subjects) showed no ALS risk association. Meta-analyses of eight studies for minor allele frequency (MAF) also found no ALS association for the "C" allele. The systematic review identified aminopeptidases as possible biomarkers. However, the meta-analyses for rs1060404 of DPP6 do not show a risk associated with ALS.
Topics: Humans; Amyotrophic Lateral Sclerosis; Aminopeptidases; Genome-Wide Association Study; Neurodegenerative Diseases; Prognosis; Biomarkers
PubMed: 37108335
DOI: 10.3390/ijms24087169 -
European Journal of Haematology Aug 2020Pyruvate kinase deficiency (PK deficiency) is a rare disorder caused by compound heterozygosity or homozygosity for > 300 mutations in the PKLR gene. To understand PK... (Meta-Analysis)
Meta-Analysis
OBJECTIVES
Pyruvate kinase deficiency (PK deficiency) is a rare disorder caused by compound heterozygosity or homozygosity for > 300 mutations in the PKLR gene. To understand PK deficiency prevalence, we conducted a systematic literature review.
METHODS
We queried Embase and Medline for peer-reviewed references reporting PK deficiency prevalence/incidence, PKLR mutant allele frequency (MAF) among the general population, or crude results from which these metrics could be derived.
RESULTS
Of 1390 references screened, 1296 were excluded after title/abstract review; 60 were excluded after full-text review. Four of the remaining 34 studies were considered high-quality for estimating PK deficiency prevalence. Two high-quality studies identified cases from source populations of known sizes, producing estimates of diagnosed PK deficiency prevalence of 3.2 and 8.5 per million. Another high-quality study derived an estimate of diagnosed PK deficiency prevalence of 6.5 per million by screening jaundiced newborns. The final high-quality study estimated total diagnosed and undiagnosed PK deficiency prevalence to be 51 per million through extrapolation from observed MAFs.
CONCLUSIONS
We conclude that prevalence of clinically diagnosed PK deficiency is likely between 3.2 and 8.5 per million in Western populations, while the prevalence of diagnosed and undiagnosed PK deficiency could possibly be as high as 51 per million.
Topics: Alleles; Anemia, Hemolytic, Congenital Nonspherocytic; Gene Frequency; Genetic Predisposition to Disease; Genotype; Humans; Mutation; Population Surveillance; Prevalence; Pyruvate Kinase; Pyruvate Metabolism, Inborn Errors
PubMed: 32279356
DOI: 10.1111/ejh.13424 -
International Journal of Environmental... Aug 2019Non-syndromic cleft lip/palate (NSCL/P) has an etiology, including both genetic and environmental factors. Herein, we evaluated the association of rs13041247 and... (Meta-Analysis)
Meta-Analysis
Polymorphic Variants of V-Maf Musculoaponeurotic Fibrosarcoma Oncogene Homolog B (rs13041247 and rs11696257) and Risk of Non-Syndromic Cleft Lip/Palate: Systematic Review and Meta-Analysis.
Non-syndromic cleft lip/palate (NSCL/P) has an etiology, including both genetic and environmental factors. Herein, we evaluated the association of rs13041247 and rs11696257 v-maf musculoaponeurotic fibrosarcoma oncogene homolog B () polymorphisms with the risk of NSCL/P in a meta-analysis. The PubMed/Medline, Scopus, Cochrane Library, Web of Science, and HuGE Navigator databases were systematically searched to retrieve relevant articles published up to January 2019. The Newcastle-Ottawa scale was applied for quality evaluation of retrieved articles. The 95% confidence interval (CI) and crude odds ratio (OR) were calculated for each study using the Review Manager 5.3 software to show the association between polymorphisms and risk of NSCL/P. The comprehensive meta-analysis 2.0 software was used to calculate the publication bias. In addition, sensitivity analysis was carried out to show the stability of results. Of 102 articles retrieved from the databases, 10 articles were analyzed in this meta-analysis. Ten articles, including eleven studies reporting rs13041247 polymorphism, included 3082 NSCL/P patients and 4104 controls. Three studies that reported rs11696257 polymorphism involved 845 NSCL/P patients and 927 controls. The rs11696257 polymorphism was not associated with the risk of NSCL/P, but the CC and TC genotypes of rs13041247 polymorphism were associated with the risk of NSCL/P. Nevertheless, the C allele and CC and TC genotypes were associated with a significant decline in the risk of NSCL/P in population-based studies. The results of this meta-analysis demonstrated that the risk of NSCL/P was related to rs13041247 polymorphism, not rs11696257 polymorphism. Well-designed studies are required to assess the interaction of and other genes with environmental factors in different ethnic groups.
Topics: Cleft Lip; Cleft Palate; Genetic Predisposition to Disease; Genetic Variation; Genotype; Humans; MafB Transcription Factor
PubMed: 31387249
DOI: 10.3390/ijerph16152792 -
PloS One 2016Warfarin is the most commonly used oral anticoagulant for the treatment and prevention of thromboembolic disorders. Pharmacogenomics studies have shown that variants in... (Review)
Review
BACKGROUND
Warfarin is the most commonly used oral anticoagulant for the treatment and prevention of thromboembolic disorders. Pharmacogenomics studies have shown that variants in CYP2C9 and VKORC1 genes are strongly and consistently associated with warfarin dose variability. Although different populations from the Middle East and North Africa (MENA) region may share the same ancestry, it is still unclear how they compare in the genetic and non-genetic factors affecting their warfarin dosing.
OBJECTIVE
To explore the prevalence of CYP2C9 and VKORC1 variants in MENA, and the effect of these variants along with other non-genetic factors in predicting warfarin dose.
METHODS
In this systematic review, we included observational cross sectional and cohort studies that enrolled patients on stable warfarin dose and had the genetics and non-genetics factors associated with mean warfarin dose as the primary outcome. We searched PubMed, Medline, Scopus, PharmGKB, PHGKB, Google scholar and reference lists of relevant reviews.
RESULTS
We identified 17 studies in eight different populations: Iranian, Israeli, Egyptian, Lebanese, Omani, Kuwaiti, Sudanese and Turkish. Most common genetic variant in all populations was the VKORC1 (-1639G>A), with a minor allele frequency ranging from 30% in Egyptians and up to 52% and 56% in Lebanese and Iranian, respectively. Variants in the CYP2C9 were less common, with the highest MAF for CYP2C9*2 among Iranians (27%). Variants in the VKORC1 and CYP2C9 were the most significant predictors of warfarin dose in all populations. Along with other genetic and non-genetic factors, they explained up to 63% of the dose variability in Omani and Israeli patients.
CONCLUSION
Variants of VKORC1 and CYP2C9 are the strongest predictors of warfarin dose variability among the different populations from MENA. Although many of those populations share the same ancestry and are similar in their warfarin dose predictors, a population specific dosing algorithm is needed for the prospective estimation of warfarin dose.
Topics: Africa, Northern; Cytochrome P-450 CYP2C9; Female; Genetic Variation; Humans; Male; Middle East; Pharmacogenomic Testing; Vitamin K Epoxide Reductases; Warfarin
PubMed: 27992547
DOI: 10.1371/journal.pone.0168732 -
Journal of Diabetes Dec 2009We previously reported that the fasting serum insulin level was significantly lower in Japanese patients than in Korean and Chinese patients, and showed evidence that a... (Meta-Analysis)
Meta-Analysis
BACKGROUND
We previously reported that the fasting serum insulin level was significantly lower in Japanese patients than in Korean and Chinese patients, and showed evidence that a difference in the dietary component would be one of the most influential factors for the ethnic difference. However, it is well known that type 2 diabetes mellitus (T2DM) results from the interaction between genetic predispositions and environmental risk factors. Therefore, we investigated ethnic differences by focusing on gene polymorphism, possibly related to T2DM in Japanese, Korean, and Chinese subjects.
METHODS
Data sources included MEDLINE and EMBASE between January 2001 and October 2008. We conducted a search for articles containing minor allele frequency (MAF) in the gene polymorphisms of peroxisome proliferator-activated receptor-γ (PPARG), inward-rectifying potassium channel Kir6.2 (KCNJ11), Calpain 10 (CAPN10), and transcription factor 7-like 2 (TCF7L2). The pooled odds ratio was calculated by using a fixed-effects model with the Mantel-Haenszel method after confirming statistical evidence of homogeneity across the ethnicities using the Breslow-Day test.
RESULTS
The Breslow-Day test revealed that there were no statistically significant differences between ethnicities in pooled odds ratios for the gene polymorphisms in PPARG (P = 0.828), KCNJ11 (P = 0.194), CAPN10 (P = 0.090), and TCF7L2 (P = 0.376). Also, pooled odds ratios of each gene polymorphism in East Asians were 0.645 for PPARG (P = 0.000), 1.168 for KCNJ11 (P = 0.000), 0.967 for CAPN10 (P = 0.759), and 1.386 for TCF7L2 (P = 0.000).
CONCLUSION
The results of this study and our previous studies suggest that behavioral and environmental risk factors have a more significant impact on ethnic difference in East Asian patients with T2DM compared with genetic predispositions.
Topics: Alleles; Asian People; China; Diabetes Mellitus, Type 2; Ethnicity; Asia, Eastern; Gene Frequency; Humans; Japan; Korea; Odds Ratio; Polymorphism, Genetic; Polymorphism, Single Nucleotide; Sample Size
PubMed: 20923526
DOI: 10.1111/j.1753-0407.2009.00040.x