Linkage disequilibrium and haplotype analysis of Src and Yes1 genes in thyroid cancer

2020 ◽  
Vol 16 (12) ◽  
pp. 779-792
Author(s):  
Asif Nisar ◽  
Ishrat Mahjabeen ◽  
Azhar Mehmood ◽  
Malik Waqar Ahmed ◽  
Khalida Khurshid ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Thyroid Cancer ◽  
Linkage Disequilibrium ◽  
Haplotype Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Allele Distribution ◽  
Increased Risk ◽  
Src Gene ◽  
Thyroid Cancer Risk

Purpose: This study was planned to examine the effects of Src and Yes1 single nucleotide polymorphism (SNPs) on the risk of thyroid cancer in 499 patients and 500 controls. Materials & methods: Three SNPs of Src gene and three SNPs of Yes1 gene were analyzed using Tetra-primer ARMS-PCR followed by sequencing. Results: rs121913314 of Src gene genotype TT showed 32-fold increased risk of thyroid cancer and rs2305994 of Yes1 genotypes TT and CT showed 2.7-fold and 16-fold increased risk in thyroid cancer (p < 0.0001). Haplotype analysis revealed that CATGCC, CATGCT, CATGTC, CATGTT, TATGCC and TATGTTA haplotypes are associated with thyroid cancer risk. Conclusion: Results showed that genotypes and allele distribution of Src and Yes1 genes are significantly linked with increased risk of thyroid cancer.

scholarly journals Analysis Of MYO1H Single Nucleotide Polymorphism In Class III Malocclusion With Mandibular Prognathism: A Preliminary Study

2017 ◽  
Vol 16 (2) ◽  
Author(s):  
Siti Nazirah Yahya ◽  
Nurul Syafiqah Abdul Razak ◽  
Noraini Abu Bakar ◽  
Khairani Idah Mokhtar ◽  
Azrul Fazwan Kharuddin
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Local Population ◽  
Class I ◽  
Class Iii ◽  
Class Iii Malocclusion ◽  
Nucleotide Polymorphism ◽  
Marker Allele ◽  
Single Nucleotide ◽  
Allele Distribution ◽  
Mandibular Prognathism

Introduction: Evidence suggests that several genes; including MYO1H, play an important role in the etiology of Class III malocclusion. Single nucleotide polymorphism (SNP) in marker rs10850110 (locus 12q24.11) within MYO1H gene has been associated with the incidence of mandibular prognathism (MP). MYO is a class 1 myosin that is responsible for the synthesis of Matrilin-1; an important protein involved in the formation of cartilage's extracellular matrix, hence is implicated in the formation of mandibular condyle cartilage. This study aimed to detect the presence of MYO1H (rs10850110) SNP and to determine its genotype and allele distribution in MP patient in the local population. Materials and Methods: The sample comprises of 31 patients; 14 patients from class I malocclusion (control samples) and 17 patients from class III malocclusion (MP). Cephalometric measurements were performed prior to saliva samples collection. The DNA was amplified using the specific primers for the marker rs10850110 and the genotyping was done by sequencing. Chi-square test was used to determine the over-representation of marker allele (p<0.05). Results:  Presence of MYO1H SNP (rs10850110) was detected in local population analysed and the distribution of its genotype and allele could be observed. There were significant differences between allele (p=0.000) and genotype (p=0.000) frequency within control (Class I) and Class III malocclusion. Conclusion(s):  Our findings are in agreement with previous studies suggesting positive influence of MYO1H (rs10850110) SNP in the incidence of MP. Further studies should be developed in order to understand the exact role and mechanism of MYO1H in different classes of malocclusions.

Single nucleotide polymorphism rs1128446 ТXNRD1 is a novel genetic marker of cerebral stroke

2021 ◽  
pp. 37-43
Author(s):  
О.Ю. Бушуева ◽  
А.В. Полоников ◽  
В.П. Иванов
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Ischemia Reperfusion ◽  
Basic Mechanism ◽  
Bioinformatic Analysis ◽  
Redox Status ◽  
Cerebral Stroke ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Increased Risk ◽  
Thioredoxin System

Мозговой инсульт (МИ) занимает третье место в структуре смертности во всем мире и является ведущим фактором снижения когнитивных функций и деменции. Окислительный стресс является ведущим механизмом повреждения головного мозга при ишемии и последующей реперфузии. Тиоредоксиновая система является наиболее важным антиоксидантным барьером клетки, способным регулировать ее окислительно-восстановительный статус. Целью исследования было изучение ассоциации однонуклеотидного полиморфизма rs1128446 гена эндогенного регулятора тиоредоксина ТXNRD1 с риском развития МИ. Материалом для исследования послужила выборка неродственных жителей Центральной России общей численностью 825 человек. В исследование были включены 375 пациентов с МИ (216 мужчин, 159 женщин; средний возраст 59,44±0,51 лет). Контрольную группу составили 450 относительно здоровых индивидуумов (249 мужчин, 201 женщина, средний возраст 61,69±0,38 лет) без кардио- и цереброваскулярных заболеваний в анамнезе и имеющих нормальный уровень артериального давления. Генотипирование SNP проводили методом ПЦР в режиме реального времени путем дискриминации аллелей с помощью TaqMan-зондов. Для анализа ассоциаций генотипов с развитием заболевания пользовались лог-аддитивной регрессионной моделью. Все расчеты выполнены относительно минорного аллеля; введены поправки на пол и возраст. SNP rs1128446 ТXNRD1 был связан с повышенным риском развития МИ (OR=1,89; 95% CI=1,48-2,43; p<0,0001). Проведенный биоинформатический анализ выявил высокий регуляторный потенциал данного SNP в тканях сердечно-сосудистой системы. Таким образом, впервые установлена ассоциация rs1128446 ТXNRD1 с развитием МИ. Cerebral stroke (CS) is the leading factor in cognitive decline and dementia and ranks third in the structure of mortality worldwide. Oxidative stress is the basic mechanism of brain damage after cerebral ischemia-reperfusion. The thioredoxin system is the most important antioxidant barrier of the cell, capable of regulating its redox status. The aim of this study was to investigate the association of the common single nucleotide polymorphism rs1128446 in gene encoding the endogenous thioredoxin regulator TXNRD1 with the risk of CS. A total of 825 unrelated individuals from Central Russia were included for this study: 375 patients with CS (216 males, 159 females; 59.44±0.51 years old) and 450 healthy controls (249 males, 201 females, 61.69±0.38 years old). Genotyping was performed using TaqMan-based PCR. To analyze the associations of genotypes with the risk of diseases, a log-additive regression model was used. All calculations were performed relative to the minor allele; corrections for gender and age have been introduced. SNP rs1128446 TXNRD1 was associated with an increased risk of CS (OR=1.89; 95% CI=1.48-2.43; P<0.0001). Bioinformatic analysis revealed a high regulatory potential of this SNP in tissues of the cardiovascular system. Thus, for the first time, the association of rs1128446 TXNRD1 with the development of CS was revealed.

scholarly journals Linkage Disequilibrium and Inference of Ancestral Recombination in 538 Single-Nucleotide Polymorphism Clusters across the Human Genome

2003 ◽  
Vol 73 (2) ◽  
pp. 285-300 ◽  
Author(s):  
Andrew G. Clark ◽  
Rasmus Nielsen ◽  
James Signorovitch ◽  
Tara C. Matise ◽  
Stephen Glanowski ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Linkage Disequilibrium ◽  
Human Genome ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

scholarly journals Reduced Anti-Histone Antibodies and Increased Risk of Rheumatoid Arthritis Associated with a Single Nucleotide Polymorphism in PADI4 in North Americans

2019 ◽  
Vol 20 (12) ◽  
pp. 3093 ◽  
Author(s):  
Aisha M. Mergaert ◽  
Mandar Bawadekar ◽  
Thai Q. Nguyen ◽  
Laura Massarenti ◽  
Caitlyn L. Holmes ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Single Nucleotide Polymorphism ◽  
Enzyme Linked Immunosorbent Assay ◽  
Human Rheumatoid Arthritis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Rheumatoid Arthritis Diagnosis ◽  
North Americans ◽  
Increased Risk ◽  
Citrullinated Proteins

Autoantibodies against citrullinated proteins are a hallmark of rheumatoid arthritis, a destructive inflammatory arthritis. Peptidylarginine deiminase 4 (PAD4) has been hypothesized to contribute to rheumatoid arthritis by citrullinating histones to induce neutrophil extracellular traps (NETs), which display citrullinated proteins that are targeted by autoantibodies to drive inflammation and arthritis. Consistent with this theory, PAD4-deficient mice have reduced NETs, autoantibodies, and arthritis. However, PAD4′s role in human rheumatoid arthritis is less clear. Here, we determine if single nucleotide polymorphism rs2240335 in PADI4, whose G allele is associated with reduced PAD4 in neutrophils, correlates with NETs, anti-histone antibodies, and rheumatoid arthritis susceptibility in North Americans. Control and rheumatoid arthritis subjects, divided into anti-cyclic citrullinated peptide (CCP) antibody positive and negative groups, were genotyped at rs2240335. In homozygotes, in vitro NETosis was quantified in immunofluorescent images and circulating NET and anti-histone antibody levels by enzyme linked immunosorbent assay (ELISA). Results were compared by t-test and correlation of rheumatoid arthritis diagnosis with rs2240335 by Armitage trend test. NET levels did not significantly correlate with genotype. G allele homozygotes in the CCP− rheumatoid arthritis group had reduced anti-native and anti-citrullinated histone antibodies. However, the G allele conferred increased risk for rheumatoid arthritis diagnosis, suggesting a complex role for PAD4 in human rheumatoid arthritis.

scholarly journals The correlation between methylenetetrahydrofolate reductase gene 677C > T polymorphism and fetal congenital defects: A meta-analysis

Pteridines ◽  
2020 ◽  
Vol 31 (1) ◽  
pp. 9-17
Author(s):  
Dexia Li ◽  
Enxia Wang ◽  
Xia Gao ◽  
Ping Li
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Publication Bias ◽  
Methylenetetrahydrofolate Reductase ◽  
Meta Analysis ◽  
Random Effect ◽  
Congenital Defects ◽  
Nucleotide Polymorphism ◽  
Case Control Studies ◽  
Single Nucleotide ◽  
Increased Risk

AbstractObjective To investigate the correlation between the methylenetetrahydrofolate reductase (MTHFR) gene 677C> T polymorphism and fetal congenital defects.Method Original studies relevant to the MTHFR gene 677C>T single nucleotide polymorphism and fetal congenital defects were systematically searched in the electronic databases of Medline, EMBSE and China National Knowledge Infrastructure (CNKI). All relevant publications were screened for inclusion in the present work. The correlation between the MTHFR gene 677C > T single nucleotide polymorphism and the occurrence of fetal congenital defects was expressed as an odds ratio (OR) and its 95% confidence interval (95% CI). Publication bias was assessed by Begg’s funnel plot and Egger’s line regression test.Results Nineteen case-control studies were ultimately included in the present meta-analysis. The pooled results indicated that the general risk of fetal congenital defects was significantly elevated in subjects with the 677T allele of the MTHFR gene in dominant (OR=1.07,95%CI:1.03-1.12, P<0.05), homozygous (OR=1.17,95%CI:1.06-1.30, P<0.05) and recessive genetic models (OR=1.16,95%CI:1.03-1.31, P<0.05) through the random effect method. However, significant publication bias was identified upon pooling the individual data and evaluating the correlation.Conclusion According to the present evidence, the MTHFR gene 677C>T single nucleotide polymorphism is correlated with poor pregnancy outcomes, and subjects with the T allele have an increased risk of developing general fetal congenital defects.

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