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1.
Braz. j. med. biol. res ; 54(6): e10317, 2021. graf
Article in English | LILACS | ID: biblio-1249305

ABSTRACT

Physical performance is a multifactorial and complex trait influenced by environmental and hereditary factors. Environmental factors alone have been insufficient to characterize all outstanding phenotypes. Recent advances in genomic technologies have enabled the investigation of whole nuclear and mitochondrial genome sequences, increasing our ability to understand interindividual variability in physical performance. Our objective was to evaluate the association of mitochondrial polymorphic loci with physical performance in Brazilian elite military personnel. Eighty-eight male military personnel who participated in the Command Actions Course of the Army were selected. Total DNA was obtained from blood samples and a complete mitochondrial genome (mtDNA) was sequenced using Illumina MiSeq platform. Twenty-nine subjects completed the training program (FINISHED, 'F'), and fifty-nine failed to complete (NOT_FINISHED, 'NF'). The mtDNA from NF was slightly more similar to genomes from African countries frequently related to endurance level. Twenty-two distinct mtDNA haplogroups were identified corroborating the intense genetic admixture of the Brazilian population, but their distribution was similar between the two groups (FST=0.0009). Of 745 polymorphisms detected in the mtDNA, the position G11914A within the NADPH gene component of the electron transport chain, was statistically different between F and NF groups (P=0.011; OR: 4.286; 95%CI: 1.198-16.719), with a higher frequency of the G allele in group F individuals). The high performance of military personnel may be mediated by performance-related genomic traits. Thus, mitochondrial genetic markers such as the ND4 gene may play an important role on physical performance variability.


Subject(s)
Humans , Male , DNA, Mitochondrial/genetics , Military Personnel , Haplotypes/genetics , Brazil , Physical Functional Performance , NADP
2.
Braz. dent. j ; 31(1): 19-24, Jan.-Feb. 2020. tab
Article in English | LILACS | ID: biblio-1089269

ABSTRACT

Abstract This study evaluated the association between polymorphisms in genes encoding estrogen receptors 1 (ESR1) and 2 (ESR2), vitamin D receptor (VDR) and in microRNA17 (which binds to ESR1 and VDR) with persistent apical periodontitis (PAP) after the endodontic treatment. We included 162 patients who completed endodontic treatment at least one year ago and presented apical periodontitis at the beginning of the root canal therapy. Clinical and radiographic exams were performed to evaluate the presence of PAP or healthy periradicular tissues (healed). Saliva samples were collected as a genomic DNA. The genotyping of ESR1 (rs2234693 and rs9340799), ESR2 (rs1256049 and rs4986938), VDR (rs739837 and rs2228570) and miRNA17 (rs4284505) were performed by real-time PCR. Chi-square test was used to the distribution of genotype and allele frequencies. Haplotype analysis was also performed. Eighty-nine patients were included in the "healed" group and 73 in the "PAP" group. No association was found between the allelic and genotypic polymorphisms studied and PAP (p>0.05). Haplotype analysis also did not demonstrated an association (p>0.05). In conclusion, the genetic polymorphisms in ESR1, ESR2, VDR and miRNA17 are not associated with PAP.


Resumo Este estudo avaliou a associação entre polimorfismos em genes que codificam os receptores de estrogênio 1 (ESR1) e 2 (ESR2), receptor de vitamina D (VDR) e no microRNA17 (que se liga à ESR1 e VDR) e a periodontite apical persistente (PAP) após o tratamento endodôntico. Foram incluídos 162 pacientes com tratamento endodôntico concluído há pelo menos um ano e que apresentavam periodontite apical no início da terapia endodôntica. Exames clínicos e radiográficos foram realizados para avaliar a presença de PAP ou tecidos perirradiculares saudáveis (cicatrizados). As amostras de saliva foram coletadas como fonte de DNA genômico. A genotipagem de ESR1 (rs2234693 e rs9340799), ESR2 (rs1256049 e rs4986938), VDR (rs739837 e rs2228570) e miRNA17 (rs4284505) foram realizadas por PCR em tempo real. O teste do qui-quadrado foi utilizado para a distribuição das frequências genotípicas e alélicas. A análise de haplótipos também foi realizada. Oitenta e nove pacientes foram incluídos no grupo "curado" e 73 no grupo "PAP". Não foi encontrada associação entre os polimorfismos alélicos e genotípicos estudados e a PAP (p>0,05). Concluí-se que os polimorfismos genéticos em ESR1, ESR2, VDR e miRNA17 não estão associados à PAP.


Subject(s)
Humans , Polymorphism, Genetic , Vitamin D , Receptors, Calcitriol/genetics , MicroRNAs/genetics , Estrogen Receptor alpha/genetics , Estrogen Receptor beta/genetics , Haplotypes , Genetic Predisposition to Disease , Polymorphism, Single Nucleotide , Estrogens , Gene Frequency
3.
Rev. Soc. Bras. Med. Trop ; 53: e20190566, 2020. tab
Article in English | LILACS, ColecionaSUS, SES-SP | ID: biblio-1136804

ABSTRACT

Abstract INTRODUCTION: Among patients with Chagas disease, men have a higher risk of worse pathological symptoms than women. We aimed to explore the role of the Y chromosome in men diagnosed with Chagas disease and assess the relationship between their ancestry and disease status. METHODS In this comparative study, we analyzed 150 men with unrelated non-chagasic disease (nCD) and 150 men with unrelated chagasic disease (CD). We assessed the serological diagnosis of Chagas disease, biochemical parameters, thoracic X-rays, electrocardiogram, and transthoracic echocardiography and determined the haplogroup by analyzing a set of 17 microsatellites from the Y chromosome. We examined the associations between common Y chromosome haplogroups and the clinical parameters of risk by logistic regression. RESULTS For all patients, the most common haplogroups were R1b (43%), G2a (9%), and E1b1b (9%). The R1b and G2a haplogroup was more frequent in men with nCD and CD, respectively. As expected, we observed a high proportion of symptomatic patients in the CD group independent of the haplogroups. Men from both groups classified as having the R1b haplogroup showed less clinical evidence of disease. Multivariate analysis showed that CD patients without R1b were about five times more likely to have a cardio-thorax index >0.5% (OR [odds ratio] = 5.1, 95% CI [confidence interval] = 3.31-8.17). Men without the R1b haplogroup were 2.5 times more likely to show EcoCG alterations (OR = 2.50, 95% CI = 0.16-3.94). CONCLUSIONS: Our results provided evidence that the R1b haplogroup may have a potential protective cardiovascular effect for its carriers.


Subject(s)
Humans , Male , Female , Chagas Disease/complications , Chagas Disease/genetics , Cardiomyopathies , Haplotypes , Odds Ratio , Chromosomes, Human, Y/genetics
4.
Article in Chinese | WPRIM | ID: wpr-880775

ABSTRACT

OBJECTIVE@#Haplotype amplification on germline variants is suggested to imply potential selective advantages and clonal expansion susceptibility and has become an important signature for seeking cancer susceptibility gene.Here we propose an improved association method that fully considers the haplotype amplification status.@*METHODS@#The haplotype amplification status was estimated by the variant allelic frequencies.We adopted a permutation test on variant allelic frequencies to divide the candidate variants into multiple groups.A likelihood clustering method was then applied to establish the neighborhood system of the hidden Markov random field framework.A filtering pipeline was introduced into the proposed method to further refine the candidate variants, including a Wilson's interval filter and a false discovery rate controller.The final candidate set along with the haplotype amplification status was collapsed into the weighted virtual sites for association tests.@*RESULTS@#Through simulated tests on a series of datasets, we compared the type Ⅰ error rates of different minor allele frequencies, which stably fell within 2%, suggesting good robustness of the algorithm.In addition, we compared another 5 published association approaches for Type-Ⅰ and Type-Ⅱ error rates with the proposed method, which resulted in the error rates all within 2%, demonstrating significant advantages and a good statistical ability of the proposed method.@*CONCLUSIONS@#The proposed method can accurately identify tumor susceptibility variants in haplotype amplification area with good robustness and stability.


Subject(s)
Algorithms , Cluster Analysis , Gene Amplification , Gene Frequency , Haplotypes , Humans , Neoplasms/genetics , Polymorphism, Single Nucleotide
5.
Journal of Experimental Hematology ; (6): 1397-1405, 2020.
Article in Chinese | WPRIM | ID: wpr-827105

ABSTRACT

OBJECTIVE@#To analyze the characteristics of allelic and haplotypic polymorphisms of human leukocyte antigens at HLA-A, -B, -C, DRB1 and DQB1 loci in Guangxi Zhuang population.@*METHODS@#Polymerase chain reaction-sequence based typing (PCR-SBT) was used to detect. The five loci (HLA-A, -B, -C, -DRB1, -DQB1) in 350 unrelated Zhuang ethnic individual from Guangxi region. Allelic and haplotypic frequencies were calculated by using Arlequin software 3.5.2.2. Phylogeny tree were constructed by using MEGA software 6.0, and SPSS software was used for principal component analysis.@*RESULTS@#Among the five loci in the population, only HLA-A and DRB1 loci were observed as departures from Hardy-Weinberg expectations. A total of 19 HLA-A, 42 HLA-B, 22 HLA-C, 25 HLA-DRB1 and 15 HLA-DQB1 alleles were found in 350 samples. The most highest frequent alleles were A*11: 01(28.57%), B*46: 01(14.00%), C*01: 02(18.43%), DRB1*16: 02 (15.71%)and DQB1*05: 02 (35.00%) . The most common five loci haplotype was A*33: 03-C*03: 02-B*58: 01-DRB1*03: 01-DQB1*02: 01(6.86%). The phylogenetic tree analysis showed that Guangxi Zhuang population had a relative close genetic relationship with southern Han Chinese populations.@*CONCLUSION@#This reaserch found that the HLA-A, B, C, DRB1 and DQB1 loci are highly polymorphic in Guangxi Zhuang population.


Subject(s)
Alleles , China , Gene Frequency , HLA-A Antigens , Genetics , HLA-B Antigens , Genetics , HLA-DRB1 Chains , Genetics , Haplotypes , Humans , Phylogeny
6.
Electron. j. biotechnol ; 40: 17-21, July. 2019. tab, ilus
Article in English | LILACS | ID: biblio-1053211

ABSTRACT

Background: Mastitis is one of the most serious diseases of dairy cattle, causing substantial financial losses. While predisposition to reduced somatic cell count in milk has been considered for in cattle breeding programs as the key indicator of udder health status, scientists are seeking genetic markers of innate immune response, which could be helpful in selecting cows with improved immunity to mastitis. Lipocalin-2 (LCN2) is a protein involved in the response of the immune system by eliminating iron ions which are necessary for the growth of pathogenic bacteria, so LCN2 may be considered as a natural bacteriostatic agent and could become a marker of infection. Results: A total of five SNPs were identified in LCN2 gene (one in the promoter, three in exon 1, and one in intron 1). A single haplotype block was identified. The locus g.98793763GNC was found to have a significant impact on protein levels in milk, and alleles of this locus were identified to have a significant positive dominance effect on this trait. None of the four analysed loci had a statistically significant impact on the milk yield, fat levels in milk or the somatic cell score. LCN-2 gene had no significant impact on the incidence of mastitis in the cows. Conclusions: Although the identified SNPs were not found to have any impact on the somatic cell count or the incidence of mastitis in cows, it seems that further research is necessary, covering a larger population of cattle, to confirm the association between lipocalin-2 and milk production traits and mastitis.


Subject(s)
Animals , Cattle , Polymorphism, Genetic , Milk/immunology , Lipocalin-2/genetics , Mastitis, Bovine/genetics , Haplotypes , Breeding , Polymorphism, Single Nucleotide , Alleles , Lipocalin-2/chemistry , Mammary Glands, Animal , Mastitis, Bovine/immunology
7.
Arch. endocrinol. metab. (Online) ; 63(3): 280-287, May-June 2019. tab, graf
Article in English | LILACS | ID: biblio-1011172

ABSTRACT

ABSTRACT Objective Methylenetetrahydrofolate reductase (MTHFR) is involved in DNA methylation that is associated with autoimmune pathology. We investigated the association between MTHFR genetic polymorphisms at g.677C>T and g.1298A>C and their haplotypes, and the risk of thyroid dysfunction among Jordanian females. Subjects and methods A case-control study involving 98 hypothyroidism cases, 66 hyperthyroidism cases and 100 controls was conducted. Polymerase chain reaction/restriction fragment length polymorphism technique was performed to determine genotypes. Statistical analysis using SPSS software was performed. Results Genetic analysis showed a significant difference in genotype frequency of g.1298A>C between cases, and controls [hypothyroidism: AA (45.9%), AC (37.8%), CC (16.3%); hyperthyroidism: AA (9.1%), AC (69.7%), CC (21.2%); controls: AA (37.8%), AC (29.6%), CC (32.7%); CChypo vs. AAhypo: 2.55, 95% CI: (1.18-5.52); OR at least on Chypo: 1.79, 95% CI: (1.07-2.99)]; CChyper vs. AAhyper: 4.01, 95% CI: (1.79-9.01); OR at least on Chyper: 0.18, 95% CI: (0.07-0.48)]. There was no significant difference in genotype frequency of g.677C>T between cases and controls [hypothyroidism: CC (50.0%), CT (32.7%), TT (17.3%); hyperthyroidism: CC (77.3%), CT (15.2%), TT (7.6%); controls: CC (55.6%), CT (32.3%), TT (12.1%)]. There was a significant difference of MTHFR haplotypes among hypothyroidism cases and controls. TA and CC had a lower hypothyroidism risk whereas; TC showed a higher risk. Conclusions g.1298A>C genetic polymorphism of MTHFR may modulate the risk of thyroid disease. CC, TA, and TC haplotypes affect the risk of hypothyroidism. Larger samples should be included in the future to verify the role of MTHFR polymorphisms in thyroid diseases.


Subject(s)
Humans , Female , Adult , Middle Aged , Young Adult , Polymorphism, Restriction Fragment Length/genetics , Polymorphism, Single Nucleotide/genetics , Methylenetetrahydrofolate Reductase (NADPH2)/genetics , Hyperthyroidism/genetics , Hypothyroidism/genetics , Haplotypes , Case-Control Studies , Polymerase Chain Reaction , Risk Factors , DNA Methylation , Genetic Predisposition to Disease , Alleles , Genotype , Jordan
8.
Article in Chinese | WPRIM | ID: wpr-772002

ABSTRACT

OBJECTIVE@#To assess the association of Eph-receptor tyrosinekinase-type A2 (EphA2) gene polymorphisms with susceptibility to age-related cataract (ARC) among ethnic Han Chinese from Hubei Province.@*METHODS@#280 patients with cortical ARC and 200 healthy controls were recruited. Polymorphisms at four loci (rs3768293, rs3754334, rs477558 and rs7548209) of the EphA2 gene were detected by PCR-restriction fragment length polymorphism (PCR-RELP) assay. Allelic and genotypic frequencies of the two groups were compared.@*RESULTS@#Compared with the control group, the AA genotype of rs3768293 locus was more common, while the AC genotype was much rarer (P 0.05). The AA genotype of the rs477558 locus was more common in the patient group, while the AG genotype was much rarer (P 0.05).@*CONCLUSION@#Polymorphisms of rs477558, rs7548209 and rs3768293 loci of the EphA2 gene are associated with susceptibility to ARC among ethnic Han Chinese from Hubei province.


Subject(s)
Asian Continental Ancestry Group , Cataract , Genetics , China , Gene Frequency , Genetic Predisposition to Disease , Genotype , Haplotypes , Humans , Polymorphism, Genetic
9.
Article in Chinese | WPRIM | ID: wpr-776744

ABSTRACT

OBJECTIVE@#To assess the association of single nucleotide polymorphisms of multidrug resistance gene 1 (MDR1) with refractory epilepsy in children.@*METHODS@#Peripheral blood samples were collected from 200 children with epilepsy and 100 healthy controls. Genomic DNA was extracted and subjected to PCR amplification, agarose gel electrophoresis and target site sequencing. Genotypes of rs1922242, rs2235048, rs10808072, rs868755 and rs1202184 loci of the MDR1 gene were analyzed.@*RESULTS@#No significant difference was found in genotypic distribution and allelic frequencies of the rs1922242, rs2235048, rs10808072 and rs868755 loci between the drug-resistant and drug-sensitive groups. For the rs1202184 locus, a significant difference in genotypic distribution was found (P=0.008). No significant difference was found in the frequencies of various haplotypes between the two groups.@*CONCLUSION@#Genotypes of the rs1202184 locus of the MDR1 gene are associated with refractory epilepsy in children, for which the AA genotype plays a dominant role.


Subject(s)
ATP Binding Cassette Transporter, Subfamily B , Genetics , Case-Control Studies , Child , Drug Resistant Epilepsy , Genetics , Gene Frequency , Genotype , Haplotypes , Humans , Polymorphism, Single Nucleotide
10.
Article in Chinese | WPRIM | ID: wpr-776740

ABSTRACT

OBJECTIVE@#To assess the value of next-generation sequencing (NGS)-based single nucleotide polymorphism (SNP) haplotyping for preimplantation genetic diagnosis (PGD) for beta-thalassemia coupled with human leukocyte antigen (HLA) matching.@*METHODS@#Three couples were recruited. Couple 1 both carried a β (IVS-2-654) variation and had previously given birth to a son with β thalassemia major. Couple 2 respectively carried (cd41-42) and β (IVS-2-654) but had no history of pregnancy. Couple 3 respectively carried β (CD17) and β (IVS-2-654), and had a daughter carrying β (CD17).@*RESULTS@#For couple 1, NGS-SNP typing identified two embryos not only unaffected with thalassemia but also with matched HLA. One blastocyst was transferred and resulted in successful pregnancy. A healthy baby was born at 39th week of gestation. Its umbilical blood was used to treat the sick brother through hemopoietic stem cell transplantation. For couple 2, seven blastocysts were obtained. Second transplantation has resulted in successful pregnancy. Prenatal diagnosis was consistent with PGD. For couple 3, two blastocysts not only unaffected with thalassemia but also with no pathogenic copy number variations were obtained. Transfer of one blastocyte resulted in successful pregnancy, and prenatal diagnosis was consistent with PGD.@*CONCLUSION@#NGS-based SNP typing is an useful tool for selecting embryos unaffected with beta-thalassemia and matched HLA through PGD.


Subject(s)
DNA Copy Number Variations , Female , Fertilization in Vitro , HLA Antigens , Genetics , Haplotypes , High-Throughput Nucleotide Sequencing , Humans , Male , Polymorphism, Single Nucleotide , Pregnancy , Preimplantation Diagnosis , beta-Thalassemia , Diagnosis , Genetics
11.
Article in Chinese | WPRIM | ID: wpr-772121

ABSTRACT

OBJECTIVE@#To investigate the association of genetic polymorphisms of norepinephrine metabolizing enzymes with postpartum depression and analyze the risk factors for postpartum depression in women following cesarean section.@*METHODS@#A total of 591 Chinese woman of Han Nationality undergoing caesarean section were enrolled in this study. The diagnosis of postpartum depression was established for an Edinburgh Postnatal Depression Scale (EPDS) score ≥9. For all the women without antepartum depression, the genotypes of catechol-O-methyltransferase (COMT; at 5 sites including rs2020917 and rs737865) and monoamine oxidase A (rs6323) were determined using Sequenom Mass Array single nucleotide polymorphism (SNP) analysis. We analyzed the contribution of the genetic factors (SNPs, linkage disequilibrium and haplotype) to postpartum depression and performed logistic regression analysis to identify all the potential risk factors for postpartum depression and define the interactions between the genetic and environmental factors.@*RESULTS@#The incidence of postpartum depression was 18.1% in this cohort. Univariate analysis suggested that COMT polymorphism at rs2020917 (TT genotype) and rs737865 (GG genotype) were significantly correlated with the occurrence of postpartum depression ( < 0.05). Logistic regression analysis showed that COMT polymorphism at rs2020917 (TT genotype) and rs737865 (GG genotype), severe stress during pregnancy, and domestic violence were the risk factors for postpartum depression ( < 0.05); no obvious interaction was found between the genetic polymorphisms and the environmental factors in the occurrence of postpartum depression.@*CONCLUSIONS@#The rs2020917TT and rs737865GG genotypes of COMT, stress in pregnancy, and domestic violence are the risk factors for postpartum depression.


Subject(s)
Catechol O-Methyltransferase , Genetics , Cesarean Section , Depression, Postpartum , Diagnosis , Genetics , Domestic Violence , Psychology , Female , Gene-Environment Interaction , Genotype , Haplotypes , Humans , Linkage Disequilibrium , Monoamine Oxidase , Genetics , Norepinephrine , Metabolism , Polymorphism, Single Nucleotide , Postoperative Complications , Diagnosis , Genetics , Pregnancy , Pregnancy Complications , Psychology , Risk Factors , Stress, Psychological
12.
Article in Chinese | WPRIM | ID: wpr-776536

ABSTRACT

OBJECTIVE@#To study whether polymorphisms in the iodothyronine deiodinase (DIO) gene region contribute to endurance exercise capacity and to validate whether TSHR gene can be used as genetic marks associated with aerobic endurance performance.@*METHODS@#Three SNPs (C785T in DIO1 gene regions, Thr92Ala and Gly3Asp in DIO2 gene regions) were selected. The genotypes of the 123 elite long running athletes(EEA) and 127 college students from northern China(CG) were analyzed using the matrix assisted laser desorption ionisation-time of flight mass spectrometry method(MALDI-TOF). The athletes were divided into different groups according to the sports level and the items, which are international masters and masters (43 vs 80), 5/10 km and marathon (92 vs 31).@*RESULTS@#There was no significant difference of the C785T loci in DIO1 gene and the Thr92Ala loci in DIO2 gene between the EEA and the CG(P>0.05), while at Gly3Asp loci, the frequency distributions of the 3 genotypes were remarkably different in the groups of control and international masters of sports, as well as in the groups of control and marathon athletes(P<0.05). The genotype TT only existed in EEA not in CG, however, the frequency distribution was very low. The Thr92Ala and Gly3Asp loci of DIO2 gene were in strong linkage disequilibrium. The frequency distributions of the haplotype CT were significantly different in the male CG and the female CG, the male CG and the male EEA(P<0.05), the male CG and the male masters of sports, as well as in the male CG and the male marathon athletes(P<0.05). The frequency distributions of the haplotype TC were remarkably higher in the groups of female international masters of sports and female 5 000 m/10 000 m than those in the female CG(P<0.05).@*CONCLUSION@#The frequency distributions of the haplotype CT were different in male and female CG, and haplotype CT could be used as a genetic mark associated with aerobic endurance performance of the male EEA, especially for the long running athletes of masters of sports and marathon, while the haplotype CT was associated with the aerobic endurance performance of the female long running athletes of international masters of sports and 5 000 m/10 000 m.


Subject(s)
Athletes , China , Female , Genotype , Haplotypes , Humans , Iodide Peroxidase , Genetics , Male , Physical Endurance , Genetics , Polymorphism, Single Nucleotide , Running
13.
Article in Chinese | WPRIM | ID: wpr-775105

ABSTRACT

OBJECTIVE@#To study the association of interleukin-10 (IL-10) -1082A/G, -819C/T, and -592C/A polymorphisms with IL-10 level and the severity of enterovirus 71 (EV71) infection in children.@*METHODS@#A total of 137 children with hand-foot-mouth disease due to EV71 infection were enrolled as EV71 infection group, which was further divided into mild group with 91 children and severe group with 46 children, and 122 healthy children who underwent physical examination were enrolled as healthy control group. Related clinical data were collected. ELISA was used to measure the serum level of IL-10, and polymerase chain reaction-restriction fragment length polymorphism was used to analyze IL-10 -1082A/G, -819C/T and -592C/A polymorphisms.@*RESULTS@#Compared with the healthy control group, the children with EV71 infection had significantly higher frequency of -1082 AA genotype and A allele (P0.05). The severe group had a significantly higher serum level of IL-10 than the mild group and the healthy control group. IL-10 -1082 AA genotype, -819 TT genotype, and -592 AA genotype were associated with the low expression of IL-10 (P0.05).@*CONCLUSIONS@#IL-10 gene polymorphisms are associated with IL-10 expression and the severity of EV71 infection in children.


Subject(s)
Child , Enterovirus A, Human , Enterovirus Infections , Gene Frequency , Genetic Predisposition to Disease , Genotype , Haplotypes , Humans , Interleukin-10 , Genetics , Polymorphism, Single Nucleotide
14.
Article in English | WPRIM | ID: wpr-739011

ABSTRACT

BACKGROUND: Genetic variants and haplotypes of the interleukin-10 (IL10) gene have been shown to affect clinical outcomes, including the incidence of opportunistic infections (OIs), in HIV-infected patients. This study investigated the effect of IL10 gene variants on susceptibility to OIs in HIV-infected Korean patients in the era of highly active antiretroviral therapy (HAART). METHODS: Eighty-five HIV-infected patients receiving HAART were enrolled in the study. OIs were diagnosed based on the published criteria of the Korean Society for AIDS. Three promoter SNPs and four haplotype-tagging SNPs (htSNPs) of IL10 were selected and genotyped. The haplotypes were reconstructed according to the genotyping data and linkage disequilibrium (LD) status of these SNPs. RESULTS: During the study, 38 OIs developed in 23 of the 85 patients (27.1%), at a rate of 1.7 episodes/patient. Carrying the minor alleles at the rs1518111, rs3024490, and rs1800871 SNPs had a protective effect against OIs (adjusted P=0.035). Among the seven assessed variants, only three possible haplotypes were observed. The second most common haplotype, which was composed of the rs1518111 minor allele and the rs3021094 major allele showed a protective effect against OIs (P=0.0153). CONCLUSION: This study demonstrated that some IL10 genetic variants and haplotypes are associated with protective effects against OIs in the era of HAART. These data suggest the potential of two htSNPs, rs1518111 and rs3021094, as markers revealing the genetic association of IL10 in Koreans. This is the first report on the association of IL10 with OIs in HIV-infected Korean patients in the era of HAART.


Subject(s)
Alleles , Antiretroviral Therapy, Highly Active , Haplotypes , HIV , Humans , Incidence , Interleukin-10 , Korea , Linkage Disequilibrium , Opportunistic Infections , Polymorphism, Single Nucleotide
15.
Article | WPRIM | ID: wpr-763557

ABSTRACT

OBJECTIVE: Genetics factors are likely to play a role in the risk, clinical presentation and treatment outcome in major depressive disorder (MDD). In this study, we investigated the role of three candidate genes for MDD; calcium voltage-gated channel subunit alpha1 C (CACNA1C), cholinergic receptor nicotinic alpha 7 subunit (CHRNA7), and mitogen-activated protein kinase 1 (MAPK1). METHODS: Two-hundred forty-two MDD patients and 326 healthy controls of Korean ancestry served as samples for the analyses. Thirty-nine single nucleotide polymorphisms (SNPs) within CACNA1C, CHRNA7, and MAPK1 genes were genotyped and subsequently tested for association with MDD (primary analysis) and other clinical features (symptoms’ severity, age of onset, history of suicide attempt, treatment outcome) (secondary analyses). Single SNPs, haplotypes and epistatic analyses were performed. RESULTS: Single SNPs were not associated with disease risk and clinical features. However, a combination of alleles (haplotype) within MAPK1 was found associated with MDD-status. Secondary analyses detected a possible involvement of CACNA1C haplotype in resistance to antidepressant treatment. CONCLUSION: These data suggest a role for MAPK1 and CACNA1C in MDD risk and treatment resistance, respectively. However, since many limitations characterize the analysis, the results must be considered with great caution and verified.


Subject(s)
Age of Onset , Alleles , Calcium , Depression , Depressive Disorder, Major , Genetics , Haplotypes , Humans , Mitogen-Activated Protein Kinase 1 , Neuronal Plasticity , Polymorphism, Single Nucleotide , Suicide , Treatment Outcome
16.
Journal of Liver Cancer ; : 46-54, 2019.
Article in English | WPRIM | ID: wpr-765705

ABSTRACT

BACKGROUND/AIMS: Phosphatase and tensin homolog (PTEN) is a known tumor suppressor gene that is downregulated in hepatocellular carcinoma (HCC). Here, we investigated the association between single nucleotide polymorphisms (SNPs) of PTEN and HCC development in patients with hepatitis B virus (HBV) infection. METHODS: Six SNPs of PTEN at positions rs1234221, rs1903860, rs1234220, rs1903858, rs2299941, and rs17431184 were analyzed in a development population (417 chronic HBV carriers without HCC and 281 chronic HBV carriers with HCC). PTEN rs1903858, rs1903860, and rs2299941 SNPs were further assessed for the development of HCC in a validation population of 200 patients with HBV-related liver cirrhosis. RESULTS: In the development population, PTEN rs1903860 C allele, rs1903858 G allele, and rs2299941 G allele were associated with a low risk of HCC. The haplotype A-T-A-A-A was associated with an increased risk of HCC (recessive model; odds ratio=2.277, 95% confidence interval [CI] =1.144-4.532, P=0.019). In the validation population, PTEN rs2299941 G allele was the only significant protective genetic polymorphism related to HCC development after adjustment for age and sex (hazard ratio=0.582, 95% CI =0.353–0.962, P=0.035). CONCLUSIONS: These findings suggest that genetic polymorphisms in PTEN may affect HCC development in patients with chronic HBV infection.


Subject(s)
Alleles , Carcinoma, Hepatocellular , Genes, Tumor Suppressor , Haplotypes , Hepatitis B virus , Hepatitis B , Hepatitis , Humans , Liver Cirrhosis , Polymorphism, Genetic , Polymorphism, Single Nucleotide
17.
Yonsei Medical Journal ; : 659-666, 2019.
Article in English | WPRIM | ID: wpr-762094

ABSTRACT

PURPOSE: To investigate associations for polymorphisms in β-carotene 9′,10′-oxygenase (BCO2, rs10431036 and rs11214109), proprotein convertase subtilisin kexin type 9 (PCSK9, rs11583680), and tribbles pseudokinase 1 (TRIB1, rs17321515 and rs2954029), as well as lifestyle factors, with ischemic stroke (IS). MATERIALS AND METHODS: This nested case-control study included 161 patients with IS and 483 matched control individuals. We collected medical reports, lifestyle details, and blood samples from individuals and used the PCR-ligase detection reaction method to genotype single nucleotide polymorphisms (SNPs). RESULTS: The GA+AA genotype of rs10431036 (p<0.001) and rs17321515 (p=0.003), the CT+TT genotype of rs11214109 (p=0.005), and the TA+AA genotype of rs2954029 (p=0.006) in dominant models increased the risk of IS. In additive models, the GG genotype of rs17321515 (p=0.005) and the TT genotype of rs2954029 (p=0.008) increased the risk of IS. Adequate intake of fruits/vegetables reduced the risk of IS (p=0.005). Although there was no interaction between genes and fruits/vegetables, people with inadequate intake of fruits/vegetables who carried a risk genotype had a higher risk of IS than those only having inadequate fruits/vegetables intake or those only carrying a risk genotype. Also, the haplotypes AC, AT, and GT (comprising rs10431036 and rs11214109) and GT (comprising rs2954029 and rs17321515) were found to be associated with an increased risk of IS (p<0.05). CONCLUSION: Polymorphisms in BCO2 and TRIB1 and fruits/vegetables intake were associated with IS. These results provide the theoretical basis for gene screening to prevent chronic cerebrovascular diseases.


Subject(s)
Case-Control Studies , Cerebrovascular Disorders , Genotype , Haplotypes , Humans , Life Style , Mass Screening , Methods , Polymorphism, Single Nucleotide , Proprotein Convertases , Stroke , Subtilisin
18.
Article in English | WPRIM | ID: wpr-761778

ABSTRACT

Mitochondrial DNA sequence variability of Spirometra erinaceieuropaei in GenBank was observed by reinvestigation of mitochondrial cox1 and cytb sequences. The DNA sequences were analyzed in this study, comprising complete DNA sequences of cox1 (n=239) and cytb (n=213) genes. The 10 complete mitochondrial DNA sequences of Spirometra species were compared with those of Korea, China and Japan. The sequences were analyzed for nucleotide composition, conserved sites, variable sites, singleton sites and parsimony-informative sites. Phylogenetic analyses was done using neighbor joining, maximum parsimony, Bayesian inference and maximum-likelihood on cox1 and cytb sequences of Spirometra species. These polymorphic sites identified 148 (cox1) and 83 (cytb) haplotypes within 239 and 213 isolates from 3 Asian countries. Phylogenetic tree topologies were presented high-level confidence values for the 2 major branches of 2 Spirometra species containing S. erinaceieuropaei and S. decipiens, and S. decipiens sub-clades including all sequences registered as S. erinaceieuropaei in cox1 and cytb genes. These results indicated that mitochondrial haplotypes of S. erinaceieuropaei and S. decipiens were found in the 3 Asian countries.


Subject(s)
Asian Continental Ancestry Group , Base Sequence , China , Databases, Nucleic Acid , DNA, Mitochondrial , Haplotypes , Humans , Japan , Korea , Mitochondria , Spirometra , Trees
19.
Article in English | WPRIM | ID: wpr-761751

ABSTRACT

Human infections due to the monkey malaria parasite Plasmodium knowlesi is increasingly being reported from most Southeast Asian countries specifically Malaysia. The parasite causes severe and fatal malaria thus there is a need for urgent measures for its control. In this study, the level of polymorphisms, haplotypes and natural selection of full-length pkmsp8 in 37 clinical samples from Malaysian Borneo along with 6 lab-adapted strains were investigated. Low levels of polymorphism were observed across the full-length gene, the double epidermal growth factor (EGF) domains were mostly conserved, and non-synonymous substitutions were absent. Evidence of strong negative selection pressure in the non-EGF regions were found indicating functional constrains acting at different domains. Phylogenetic haplotype network analysis identified shared haplotypes and indicated geographical clustering of samples originating from Peninsular Malaysia and Malaysian Borneo. This is the first study to genetically characterize the full-length msp8 gene from clinical isolates of P. knowlesi from Malaysia; however, further functional characterization would be useful for future rational vaccine design.


Subject(s)
Asian Continental Ancestry Group , Borneo , Epidermal Growth Factor , Genetic Variation , Haplorhini , Haplotypes , Humans , Malaria , Malaysia , Merozoites , Parasites , Plasmodium knowlesi , Selection, Genetic
20.
Article in English | WPRIM | ID: wpr-761726

ABSTRACT

Echinococcus granulosus is an important zoonotic parasite globally causing cystic echinococcosis (CE) in humans and animals. In this study, prevalence of CE and variation of cox1 gene sequence were analyzed with isolates E. granulosus collected from different areas in northern Xinjiang, China. The survey showed that 3.5% of sheep and 4.1% of cattle were infected with CE. Fragment of cox1 was amplified from all the positive sheep and cattle samples by PCR. In addition, 26 positive samples across the 4 areas were included. The isolates were all E. granulosus sensu stricto (s.s.) containing 15 haplotypes (Hap1-15), and clustered into 2 genotypes, G1 (90.1%, 91/101) and G3 (9.9%, 10/101). Hap1 was the most common haplotype (48.5%, 49/101). Hap9 were found in humans samples, indicating that sheep and cattle reservoir human CE. It is indicate that E. granulosus may impact on control of CE in livestock and humans in the region.


Subject(s)
Animals , Cattle , China , Cross-Sectional Studies , Echinococcosis , Echinococcus granulosus , Echinococcus , Genotype , Haplotypes , Humans , Livestock , Parasites , Polymerase Chain Reaction , Prevalence , Sheep
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