Association between hypertension and coffee drinking based on CYP1A2 rs762551 single nucleotide polymorphism in Taiwanese

Abstract Background Hypertension increases the likelihood of cardiovascular diseases (CVDs). Cytochrome P450 1A2 (CYP1A2) single nucleotide polymorphism (SNP) is related to caffeine metabolism and the risk of CVD among coffee drinkers. CYP1A2 rs762551 influenced the risk of stroke among hypertensive patients. We examined the relationship between hypertension and coffee drinking based on CYP1A2 rs762551 SNP in Taiwanese adults. Methods We used data contained in the Taiwan Biobank database (2011–2018) and included 19,133 participants having complete information on hypertension, rs762551 polymorphism, coffee intake, etc. The risk of hypertension was determined using multiple logistic regression. Results Coffee intake was significantly associated with a lower risk of hypertension. The odds ratio (OR), 95% confidence interval (CI), and p-value were 0.877, 0.807–0.954, and 0.0032, respectively. CYP1A2 rs762551 was not significantly associated with the risk of hypertension, but it had a significant interactive association with coffee drinking (p value = 0.0303). After stratification by rs762551 genotypes, the inverse coffee drinking-hypertension association was retained, but significant results were observed only in those with the AC + CC genotype (OR 0.678, 95% CI 0.722–900, p value = 0.0001). According to the combination of coffee drinking and rs762551 genotypes (reference group: no coffee drinking and rs762551 AA), the coffee drinking-AC + CC group had a lower risk of hypertension (OR 0.888, 95% CI 0.789–0.999, p value = 0.0483). Conclusion Coffee drinking, particularly among individuals with the CYP1A2 rs762551 AC + CC genotype was associated with lower odds of hypertension.

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Gas Chromatography-Mass Spectrometry and Single Nucleotide Polymorphism-Genotype-By-Sequencing Analyses Reveal the Bean Chemical Profiles and Relatedness of Coffea canephora Genotypes in Nigeria

Plants ◽

10.3390/plants8100425 ◽

2019 ◽

Vol 8 (10) ◽

pp. 425

Author(s):

Chinyere F. Anagbogu ◽

Christopher O. Ilori ◽

Ranjana Bhattacharjee ◽

Olufemi O. Olaniyi ◽

Diane M. Beckles

Keyword(s):

Gas Chromatography ◽

Single Nucleotide Polymorphism ◽

Coffea Canephora ◽

Gas Chromatography Mass Spectrometry ◽

P Value ◽

Polymorphism Analysis ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Chemical Profiles ◽

Genotype By Sequencing

The flavor and health benefits of coffee (Coffea spp.) are derived from the metabolites that accumulate in the mature bean. However, the chemical profiles of many C. canephora genotypes remain unknown, even as the production of these coffee types increases globally. Therefore, we used Gas Chromatography-Mass Spectrophotometry to determine the chemical composition of C. canephora genotypes in Nigeria—those conserved in germplasm repositories and those cultivated by farmers. GC-MS revealed 340 metabolites in the ripe beans, with 66 metabolites differing (p-value < 0.05) across the represented group. Univariate and multivariate approaches showed that the ‘Niaouli’ genotypes could be clearly distinguished from ‘Kouillou’ and ‘Java’ genotypes, while there was almost no distinction between ‘Kouillou’ and ‘Java,’. Varietal genotyping based on bean metabolite profiling was synchronous with that based on genome-wide Single Nucleotide Polymorphism analysis. Across genotypes, the sucrose-to-caffeine ratio was low, a characteristic indicative of low cup quality. The sucrose-to-caffeine ratio was also highly correlated, indicative of common mechanisms regulating the accumulation of these compounds. Nevertheless, this strong correlative link was broken within the ‘Niaouli’ group, as caffeine and sucrose content were highly variable among these genotypes. These ‘Niaouli’ genotypes could therefore serve as useful germplasm for starting a Nigerian C. canephora quality improvement breeding program.

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A Common Single Nucleotide Polymorphism in the Chromosome 7q22.3 Region, Which Is Frequently Deleted in Myeloid Malignancies, Is Associated with Mean Platelet Volume and Platelet Function in Healthy Individuals

Blood ◽

10.1182/blood.v112.11.86.86 ◽

2008 ◽

Vol 112 (11) ◽

pp. 86-86

Author(s):

Nicole Soranzo ◽

Marloes R. Tijssen ◽

Augusto Rendon ◽

Christine Meisinger ◽

Chris I. Jones ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Blood Cell ◽

Mean Platelet Volume ◽

P Value ◽

Healthy Individuals ◽

Nucleotide Polymorphism ◽

Platelet Volume ◽

Single Nucleotide ◽

Myeloid Malignancies ◽

Allele Effect

Abstract The variation in blood cell indices between individuals is to a large extent genetically controlled. In the normal population mean platelet volume (MPV) is inversely correlated with platelet count. We undertook a genome-wide association analysis of MPV on 2.5 million imputed genotypes in 1,475 individuals from the UK Blood Services Common Controls, followed by replication in an additional 7,098 samples from four independent collections. We identified a novel locus on chromosome 7q22.3, in a region frequently deleted in myeloid malignancies, where the lead single nucleotide polymorphism (SNP) had a highly significant association with MPV (average G allele effect size 0.15 log fl, 95% CI 0.0118–0.0174, P-value = 9.5×10−24) and an opposite effect on platelet counts (G allele effect −4.51 109/l, 95% CI −6.112 - −2.900, P-value = 1.46×10−7), but the SNP did not exert an effect on red cell indices. The lead SNP with a minor allele frequency of 0.46 is intergenic between the hypothetical gene FLJ36031 and the PIK3CG gene. There are 6 genes in the 1-Mb window centred around the lead SNP and all but HBP1 are transcribed in megakaryocytes (MKs) and to a variable degree in the other seven blood cell lineages. The formation and regulation of volume of platelets is critically dependent on the interaction of MK-expressed integrins with extracellular matrix proteins like fibrinogen and collagen. This prompted us to analyze, in our platelet function cohort of 500 healthy individuals, the association between the lead SNP and binding of both fibrinogen and annexin V to platelets following activation with the collagen mimetic CRP-XL, both associations were significant, with P-values of 0.05 and 0.003, respectively. In summary, we describe a common SNP associated with differences in volume, count and function of platelets from healthy individuals. Intriguingly, our results indicate that the same 7q22.3 region which is frequently deleted in myeloid malignancies harbours important regulatory elements of several platelet phenotypic traits.

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TNF-α -308G/A polymorphism and susceptibility to tuberculosis in Azeri population of Iran

Genetika ◽

10.2298/gensr1603819g ◽

2016 ◽

Vol 48 (3) ◽

pp. 819-826 ◽

Cited By ~ 1

Author(s):

Sajjad Ghorghanlu ◽

Mohammad Asgharzadeh ◽

Hossein Samadi-Kafil ◽

Fatemeh Khaki-Khatibi ◽

Jalil Rashedi ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Tuberculosis Patient ◽

P Value ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Tuberculosis Patients ◽

Specific Pcr ◽

Allele Specific ◽

And Function

Single nucleotide polymorphisms (SNPs) in cytokine genes may alter the level and function of secreted cytokine; therefore, SNPs can influence the immune response. The aim of the present study was to determine the association of TNF-? -308G/A single nucleotide polymorphism in tuberculosis patients in the Azeri population of Iran. The TNF-308G/A single nucleotide polymorphism in the promoter region was genotyped by using the allele-specific PCR method in 200 healthy controls and 124 tuberculosis patients. The distribution of allele frequencies for TNF-? -308G/A polymorphism between control and tuberculosis patient groups was not significant (P-value = 0.058, OR = 1.5). Furthermore, no statistically significant association was found between TNF-? -308G/A genotype and resistance/susceptibility to TB (P-value = 0.102). Our results suggest that TNF-? -308G/A polymorphism has no measurable effect on the development of tuberculosis in Azeri population of Iran.

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Single Nucleotide Polymorphism (SNP) Analysis of JAK2 and Relevant Cytokine Receptor Genes in Myeloproliferative Disorders.

Blood ◽

10.1182/blood.v108.11.661.661 ◽

2006 ◽

Vol 108 (11) ◽

pp. 661-661

Author(s):

Animesh Pardanani ◽

Brooke Fridley ◽

Terra Lasho ◽

Sara Achenbach ◽

D. Gary Gilliland ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Genetic Variation ◽

Odds Ratio ◽

Myeloproliferative Disorders ◽

Cytokine Receptor ◽

Jak2v617f Mutation ◽

P Value ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

P Values

Abstract Background: Constitutive activation of the JAK-STAT signaling pathway through acquisition of the JAK2V617F mutation plays a key role in the pathogenesis of related myeloproliferative disorders (MPD) including polycythemia vera (PV), agnogenic myeloid metaplasia (AMM), and essential thrombocythemia (ET). Hypothesis: Genetic variation in JAK2 and/or the cytokine receptor genes for erythropoietin (EPOR), thrombopoietin (MPL), and granulocyte colony stimulating factor (GCSFR), influences the expression of a specific disease phenotype (PV, AMM, or ET). Methods: We studied 179 Caucasian MPD patients (PV=84, AMM=58, ET=37) for genetic variation in 4 candidate genes (i.e. JAK2, EPOR, MPL, GCSFR) through single nucleotide polymorphism (SNP) and haplotype analyses. A total of 32 LD (linkage disequilibrium) tag-SNPs with a minimum allele frequency of at least 5% were selected from the HapMap CEU database (JAK2=13, EPOR=4, MPL=5, GCSFR=10). Genotyping was performed using archived DNA from enriched neutrophils. Results: Seventy six (94%), 26 (45%), and 14 (38%) patients with PV, AMM, and ET, respectively, carried the JAK2V617F mutation. Significant differences in allele frequencies was observed at 6 SNP loci (rs10758669, rs3808850, rs7849191, rs7046736, rs10815148, and rs12342421, p-values < 0.0005), all within the JAK2 gene, in comparing our overall study population with the founder Caucasian population in the HapMap database. In the additive genotype-phenotype association analysis adjusted for gender and age at diagnosis, 3 SNP loci in JAK2 (rs7046736, rs10815148, and rs12342421) were found to be significantly, but reciprocally associated with PV (p-values < 0.00006, odds ratio=0.37, 2.82, and 2.39, respectively) and ET (p-values < 0.002, odds ratio=2.50, 0.36, and 0.41, respectively), but not AMM, in terms of the minor allele being ’protective’. These three SNPs were all in high LD, with the ’r2’ measures of LD between 0.59 and 0.71. Furthermore, 2 additional JAK2 SNP loci (rs10758669, p-value = 0.0024 and rs10974947, p-value = 0.0046) were significantly associated with PV (odds ratio=1.88 and 0.47, respectively), but not ET or AMM. Similarly, presence of the minor allele at a single SNP locus in EPOR (rs318699, p-value = 0.0012) was significantly associated with PV only (odds ratio=2.16). For the phenotype-genotype intragene haplotype analyses, the EPOR intragene haplotypes GAAA and GGAA were significantly associated with PV (simulated global p-value = 0.058, simulated individual p-values 0.0013 and 0.0068, haplotype frequency of 35% and 56%, respectively). In addition to EPOR, 6 intragene haplotypes within JAK2 where significantly associated with PV (simulated global p-value < 0.0001, individual simulated p-values < 0.03). Conclusion: The current study demonstrates a genotype-phenotype association that involves JAK2 and EPOR in the setting of PV, but not that of AMM. Some JAK2 SNPs were found to be associated with both PV and ET but in opposite direction. Therefore, genetic variation among MPDs might contribute to phenotypic diversity in the presence of specific mutations.

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Development of a 38K Single Nucleotide Polymorphism Array and Application in Henomic Selection for Resistance Against Vibrio harveyi in Chinese Tongue sole, Cynoglossus Semilaevis

10.21203/rs.3.rs-48867/v1 ◽

2020 ◽

Author(s):

Sheng Lu ◽

Qian Zhou ◽

Yadong Chen ◽

Yang Liu ◽

Yangzhen Li ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Vibrio Harveyi ◽

Reference Group ◽

Single Nucleotide Polymorphism Array ◽

Snp Array ◽

Cynoglossus Semilaevis ◽

Breeding Value ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Tongue Sole

Abstract Background: In recent years, the disease outbreak caused by Vibrio harveyi upset the booming development of the Chinese tongue sole (Cynoglossus semilaevis) farming industry. Genomic selection (GS) is a powerful method to improve the traits of interest, which has been proved in livestock and some fishes. Besides, the single nucleotide polymorphism (SNP) array is an efficient genotyping platform that can be used for genetic studies. To improve V. harveyi resistance in C. semilaevis, we firstly constructed a reference group of 1,572 individuals and investigated accuracies of four genomic methods (genomic best linear unbiased prediction (GBLUP), weighted GBLUP, BayesB, and BayesC) at predicting the genomic estimated breeding value (GEBV) using five-fold cross-validation and SNPs varying from 0.5 k to 500 k. Then, an SNP array was developed using the Affymetrix Axiom technology, and its accuracy in genotyping was evaluated by comparing SNPs generated by the array and by the re-sequencing technology. Finally, we selected 44 candidates as the parents of 23 families of C. semilaevis to evaluate the feasibility of the SNP array for GS.Results: all genomic methods outperformed the pedigree-based BLUP (ABLUP) when at least 50 k SNPs used for prediction, of which GBLUP resulted in better estimation than ABLUP when more than 1 k SNPs used. A 38 k SNP array, “Solechip No.1”, was developed with an average of 10.5 kb inter-spacing between two adjacent SNPs. The SNPs generated by the array and by the re-sequencing reached an average consistency of 94.8 %, of which 79.3 % of loci had a more than 90 % of the consistency. The survival rates of these 23 offspring families had a correlation of 0.706 with the family GEBVs (mid-parental GEBVs), and the average survival rate of the top five families in GEBVs (79.1 %) is higher than the bottom five families (58.1 %).Conclusion: GS is an efficient method to improve the V. harveyi resistance in C. semilaevis, and the SNP array “Solechip No.1” is a convenient and reliable tool for the Chinses tongue sole selective breeding practice.

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Impact of IL-10 (-1082) Promoter–Single Nucleotide Polymorphism on the Outcome of Hepatitis C Virus Genotype 4 Infection

Clinical Medicine Insights Gastroenterology ◽

10.4137/cgast.s13658 ◽

2014 ◽

Vol 7 ◽

pp. CGast.S13658 ◽

Cited By ~ 6

Author(s):

Soheir F. Helal ◽

Howayda E. Gomaa ◽

Eman H. Thabet ◽

Mariam A. Younan ◽

Neveen A. Helmy

Keyword(s):

Single Nucleotide Polymorphism ◽

Hepatitis C Virus ◽

Hepatitis C ◽

P Value ◽

Nucleotide Polymorphism ◽

Virus Genotype ◽

Genotype 4 ◽

Single Nucleotide ◽

Significant Difference ◽

Chronic Hcv

Immuneregulatory cytokines may influence the hepatitis C virus (HCV) infection outcome. This study aimed to determine the genotypic and allelic frequencies of the interleukin (IL)-10 (-1082) G/A polymorphism, and its association with chronicity or resolution of HCV genotype 4 infection in Egypt. The frequencies of different dimorphic polymorphisms based on single nucleotide substitution in chronic HCV patients (50) and resolved HCV patients (50) were: IL-10 (-1082) G/G 22 (44%) and 18 (36%), G/A 19 (38%) and 24 (48%), and A/A 9 (18%), and 8 (16%), respectively. In the sustained virologic response (SVR) (36) and spontaneously resolved subjects (14) groups, the frequencies were: IL-10 (-1082) G/G 11 (30.6%) and 7 (50%) G/A 18 (50%) and 6 (42.9%), A/A 7 (19.4%) and 1 (7.1%), respectively. An association between male gender and chronic hepatitis C outcome ( P value 0.041) was found. However, no significant gender difference was found when we compared females versus males with elevated alanine transaminase (ALT) levels in the chronic HCV patient group ( P value = 1). Conclusion No significant difference in the frequency of IL-10 single nucleotide polymorphism (SNP) at position 1082 was found between chronic and resolved HCV subjects.

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A mutant single nucleotide polymorphism of follicle-stimulating hormone receptor is associated with a lower risk of endometriosis

Fertility and Sterility ◽

10.1016/j.fertnstert.2010.07.1092 ◽

2011 ◽

Vol 95 (1) ◽

pp. 455-457 ◽

Cited By ~ 15

Author(s):

Hsin-Shih Wang ◽

Bi-Hwa Cheng ◽

Hsien-Ming Wu ◽

Chih-Feng Yen ◽

Chun-Ting Liu ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Hormone Receptor ◽

Lower Risk ◽

Follicle Stimulating Hormone ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Stimulating Hormone

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Frequencies of CYP1A2 Single Nucleotide Polymorphism in Indonesian and Its Effect on Blood Pressure

The Indonesian Biomedical Journal ◽

10.18585/inabj.v10i3.374 ◽

2018 ◽

Vol 10 (3) ◽

pp. 297-302

Author(s):

Erizal Sugiono ◽

Andi Wijaya ◽

Anwar Santoso ◽

Ferry Sandra ◽

Ilham Jaya Patellongi ◽

...

Keyword(s):

Blood Pressure ◽

Single Nucleotide Polymorphism ◽

High Performance ◽

Enzyme Polymorphism ◽

Interindividual Variation ◽

Nucleotide Polymorphisms ◽

Nucleotide Polymorphism ◽

Cross Sectional ◽

Single Nucleotide ◽

Coffee Drinking

BACKGROUND: The association between caffeine with blood pressure (BP) still remains controversial. Caffeine is mainly metabolized by cytochrome-P450 (CYP)1A2 enzyme. Polymorphism of CYP1A2 is known to cause interindividual variation on enzymatic activity, thus affects caffeine metabolism and its effect on cardiovascular (CV) system.METHODS: We conducted a cross-sectional study and recruited 121 Indonesian subjects aged 25-60 years with varying coffee-drinking habits. DNA was extracted from peripheral blood and genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCRRFLP) technique. Blood pressures were measured in the morning prior to the daily activity. Caffeine concentration in blood plasma was measured using high-performance liquid chromatography (HPLC). The differences between variables were analyzed using MannWhitney analysis and the correlations among variables were determined using multivariate logistic regression analysis.RESULTS: This study showed that the frequencies of single nucleotide polymorphisms (SNPs) among Indonesian were 31.8%, 18.2%, 25.2% and 24.8% respectively for CYP1A2*1A, CYP1A2*1B, CYP1A2*1C and CYP1A2*1F alleles. The genotype analysis showed that the subject number of the wild type (*1A/*1A) and the variants were 9.92% and 90.08%. There were no significant differences in term of BP levels among CYP1A2 genotypes and coffee drinking habit groups.CONCLUSIONS: The frequencies of CYP1A2 SNPs in Indonesian are different with frequencies in other populations. Since the association were not statistically significant, CYP1A2 polymorphisms as the predictor of elevated blood pressuare should be investigated further.KEYWORDS: coffee, caffeine, blood pressure, single nucleotide polymorphism, CYP1A2

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Role of Interferon-Gamma +874 A/T Single-Nucleotide Polymorphism and Tuberculosis Susceptibility of Pediatric Population in North Sumatera, Indonesia

Open Access Macedonian Journal of Medical Sciences ◽

10.3889/oamjms.2021.7441 ◽

2021 ◽

Vol 9 (A) ◽

pp. 1057-1060

Author(s):

Rini Savitri Daulay ◽

Rina Amalia C. Saragih ◽

Ridwan Muchtar Daulay ◽

Ratna Akbari Ganie ◽

Gino Tann ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Interferon Gamma ◽

Disease Susceptibility ◽

Pediatric Population ◽

Immune Defense ◽

Enzyme Linked Immunosorbent Assay ◽

P Value ◽

Nucleotide Polymorphism ◽

Single Nucleotide

BACKGROUND: Tuberculosis (TB) remains to be a leading cause of morbidity and mortality worldwide. The immune defense against Mycobacterium tuberculosis (M. tuberculosis) is complicated. Interferon gamma (IFN-g) is the main cytokine involved in the immune response of TB. To date, the role of +874 A/T single nucleotide polymorphism (SNP) and TB disease susceptibility continue to be controversial. OBJECTIVES: The aim of this study was to investigate the role of +874 A/T SNP and TB disease susceptibility of pediatric population in North Sumatera, Indonesia METHODS: A case control study was conducted in Medan and Batubara, North Sumatera, Indonesia from January to December 2016. A total of 51 children with TB and 51 healthy controls were enrolled in this study. Subjects were 2 months to 14 years old age children diagnosed with TB and written informed consent from the parents or the caregivers to participate. Subjects were withdrawn from the study when immunodeficiency condition was found or suffered from other infection disease. DNA samples were obtained from all of the subjects. +874 A/T SNP was identified by performing the amplification refractory mutational system - polymerase chain reaction (ARMS-PCR) method. IFN-g levels were measured by using human enzyme-linked immunosorbent assay/ELISA. Data analysis was performed using chi square and Mann Whitney test. p value <0.05 was considered significant. RESULTS: The result of this study reveals the presence of AA, AT and TT genotype in TB patients were 31 (60.8%), 20 (39.2%) and 0 (0%); respectively (p=0.023). Significant decreased production of IFN-g levels (p=0.042) were found in TB patients 9.41 (1.10 – 28.06) pg/ml. CONCLUSION: Our study demonstrated significant evidence of the role of +874 A/T SNP and TB disease susceptibility of pediatric population in North Sumatera, Indonesia predominantly AA genotype. Significant decreased production of IFN-g reported among pediatric TB.

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