scholarly journals Assoсiation analysis of gene polymorphisms col1a, mct1, col12a1 with sports hernia in football players

2020 ◽  
Vol 66 (6) ◽  
pp. 33-40
Author(s):  
O.Y. Ioffe ◽  
◽  
A.V. Omelchenko ◽  
S.V. Goncharov ◽  
D.O. Strоy ◽  
...  
Keyword(s):  
Random Forest ◽  
Genetic Research ◽  
Chronic Groin Pain ◽  
Football Players ◽  
Nucleotide Polymorphisms ◽  
Sports Hernia ◽  
Single Nucleotide ◽  
Preventive Actions ◽  
Testing Accuracy ◽  
Reduced Mobility

Sports hernias are diagnosed in over 80% of athletes presenting with chronic groin pain. The genotype distributions of the examined polymorphisms were studied in 95 football players, all males, using the Copenhagen Hip and Groin Outcome Score (HAGOS) questionnaire. DNA extracted from buccal epithelium. Statistical calculations were performed in the R statistical environment (r-project.org) and Odds ratios (OR) were used to estimate genotype associations. Multifactor dimensionality reduction was used to identify multiple sports hernia susceptibility loci.Two single nucleotide polymorphisms MCT1 rs1049434 and COL1A1 rs1800012 are associated with sports hernias (63% testing accuracy shown by random forest). According to the HAGOS questionnaire outcomes, exercise-related pain, reduced mobility, and range of motion in the groin and thigh are typically associated with sports hernia diagnosis (75% testing accuracy shown by random forest).The combination of genetic research and HAGOS questionnaire helped obtain a sensitivity of 93% for the detection of sports hernia. Active engagement in sport is the most important risk factor for sports hernia, so the identification genes SNP in footballers may contribute to taking timely preventive actions. This study is the first demonstration of an association between sports hernia and COL1A1 rs1800012 genotype. The study discovered a synergistic interaction between the indicated polymorphism and the gene polymorphism MCT1 rs1049434. Further investigations are required to study the association between COL12A1 rs240736 gene SNP and sports hernia.

scholarly journals IL-1R2 Polymorphisms and its Interaction Associates With Osteoporosis Susceptibility in Chinese Han Population

2020 ◽  
Author(s):  
Kai Rong ◽  
Zhiquan Liang ◽  
Wenyuan Xiang ◽  
Zhan Wang ◽  
Fengli Wen ◽  
...  
Keyword(s):  
Negative Regulator ◽  
Chinese Han Population ◽  
Nucleotide Polymorphisms ◽  
Chinese Han ◽  
Single Nucleotide ◽  
Han Population ◽  
Testing Accuracy ◽  
Relationship Of ◽  
The Relationship ◽  
Osteoporosis Risk

Abstract Background: IL-1R2, serves as a negative regulator of IL-1 signaling, is involved in the pathogenesis of osteoporosis. This study aimed to determine the correlation between IL-1R2 polymorphism and osteoporosis susceptibility among the Chinese Han population.Methods: We recruited 594 osteoporosis patients and 599 healthy controls. Six single nucleotide polymorphisms (SNPs) in IL-1R2 were selected for genotyping using Agena MassARRAY platform. Odds ratio (OR) and 95% confidence interval (CI) was calculated through logistic regression analysis with adjustment for age and sex. Linkage disequilibrium analysis was plotted by Haploview v4.2. Multifactor dimension reduction (MDR) was performed to estimate the SNP-SNP interaction of IL-1R2 variants.Results: Our result revealed that rs11674595 (OR = 1.86, p = 0.020), rs2072472 (OR = 1.26, p = 0.019) and rs4851527 (OR = 0.78, p = 0.007) were related to the risk of osteoporosis. Moreover, the contribution of IL-1R2 polymorphisms to osteoporosis risk presented age, sex and BMI difference. We found the relationship of Trs11674595Ars4851527 (OR = 0.80, p = 0.015), Crs11674595Grs4851527 (OR = 1.22, p = 0.043) and Ars3218977Grs2072472 (OR = 1.25, p = 0.022) haplotypes to osteoporosis occurrence, and a potential accumulated effect of IL-1R2 SNPs (testing accuracy = 0.5783 and CVC = 10/10) on osteoporosis susceptibility.Conclusion: IL-1R2 polymorphisms (rs11674595, rs4851527, rs2072472 and rs3218977) might contribute to osteoporosis risk among the Chinese Han population. Our finding may increase our understanding of the effects of IL-1R2 polymorphisms on the predisposition of osteoporosis.

scholarly journals Single nucleotide polymorphisms in the ANGPTL4 gene and the SNP-SNP interactions on the risk of atherosclerotic Ischaemic stroke

BMC Neurology ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Chaoxiong Shen ◽  
Daofeng Fan ◽  
Huajun Fu ◽  
Chong Zheng ◽  
Yinjuan Chen ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Single Nucleotide Polymorphisms ◽  
Gene Interaction ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Testing Accuracy ◽  
Medical University ◽  
The Impact ◽  
Snp Interaction ◽  
Control Study

Abstract Objectives The purpose of this study was to investigate the impact of single nucleotide polymorphisms (SNPs) in the ANGPTL4 gene and the SNP–SNP interactions on atherosclerotic ischemic stroke (IS) risk. Patients and methods A case-control study was conducted. A total of 360 patients with atherosclerotic IS and 342 controls between December 2018 and December 2019 from Longyan First Hospital affiliated to Fujian Medical University were included. A logistic regression model was used to examine the association between SNPs and atherosclerotic IS risk. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were calculated. Generalized multifactor dimensionality reduction was employed to analyze the SNP-SNP interaction. Results Logistic regression analysis showed that atherosclerotic IS risk was significantly lower in carriers with the rs11672433-T allele than those with the CC genotype (CT+ TT vs. CC); adjusted OR, 0.005; 95% CI, 0.02–0.11. We found a significant 2-locus model (P = 0.0010) involving rs11672433 and rs4076317; the cross-validation consistency of this model was 10 of 10, and the testing accuracy was 57.96%. Participants with the CT or TT of rs11672433 and CC of rs4076317 genotype have the lowest atherosclerotic IS risk, compared to subjects with CC of rs11672433 and the CC of rs4076317 genotype, OR (95%CI) was 0.06(0.02–0.22), after covariates adjustment for gender, age, smoking and alcohol status, hypertension, Diabetes mellitus, TG, TC, HDL-C, LDL-C, Uric acid. Conclusions We found that rs11672433 was associated with decreased atherosclerotic IS risk; we also found that gene–gene interaction between rs11672433 and rs4076317 was associated with decreased atherosclerotic IS risk.

scholarly journals A Machine Learning-Based Identification of Genes Affecting the Pharmacokinetics of Tacrolimus Using the DMETTM Plus Platform

2020 ◽  
Vol 21 (7) ◽  
pp. 2517
Author(s):  
Jeong-An Gim ◽  
Yonghan Kwon ◽  
Hyun A Lee ◽  
Kyeong-Ryoon Lee ◽  
Soohyun Kim ◽  
...  
Keyword(s):  
Machine Learning ◽  
Random Forest ◽  
Decision Tree ◽  
Therapeutic Index ◽  
Immunosuppressive Drug ◽  
Machine Learning Algorithms ◽  
Nucleotide Polymorphisms ◽  
Lasso Regression ◽  
Single Nucleotide ◽  
Selection Operator

Tacrolimus is an immunosuppressive drug with a narrow therapeutic index and larger interindividual variability. We identified genetic variants to predict tacrolimus exposure in healthy Korean males using machine learning algorithms such as decision tree, random forest, and least absolute shrinkage and selection operator (LASSO) regression. rs776746 (CYP3A5) and rs1137115 (CYP2A6) are single nucleotide polymorphisms (SNPs) that can affect exposure to tacrolimus. A decision tree, when coupled with random forest analysis, is an efficient tool for predicting the exposure to tacrolimus based on genotype. These tools are helpful to determine an individualized dose of tacrolimus.

scholarly journals Association of Single Nucleotide Polymorphisms on Locus 18q21.1 in the Etiology of Nonsyndromic Cleft Lip Palate (NSCLP) in Indian Multiplex Families

2021 ◽  
Vol 08 (01) ◽  
pp. 024-031
Author(s):  
Praveen Kumar Neela ◽  
Gosla Srinivas Reddy ◽  
Akhter Husain ◽  
Vasavi Mohan ◽  
Sravya Thumoju ◽  
...  
Keyword(s):  
High Risk ◽  
Single Nucleotide Polymorphisms ◽  
Cleft Lip ◽  
Genetic Research ◽  
P Value ◽  
Allelic Association ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Cleft Lip Palate ◽  
Multiplex Families

Abstract Background Cleft lip palate (CLP) is a common congenital anomaly with multifactorial etiology. Many polymorphisms at different loci on multiple chromosomes were reported to be involved in its etiology. Genetic research on a single multigenerational American family reported 18q21.1 locus as a high-risk locus for nonsyndromic CLP (NSCLP). However, its association in multiple multiplex families and Indian population is not analyzed for its association in NSCLP. Aim This study was aimed to evaluate whether high-risk single nucleotide polymorphisms (SNPs) on chromosome 18q21.1 are involved in the etiology of NSCLP in multiplex Indian families. Materials and Methods Twenty multigenerational families affected by NSCLP were selected for the study after following inclusion and exclusion criteria. Genomic DNA was isolated from the affected and unaffected members of these 20 multiplex families and sent for genetic analysis. High-risk polymorphisms, such as rs6507872 and rs8091995 of CTIF, rs17715416, rs17713847 and rs183559995 of MYO5B, rs78950893 of SMAD7, rs1450425 of LOXHD1, and rs6507992 of SKA1 candidate genes on the 18q21.1 locus, were analyzed. SNP genotyping was done using the MassARRAY method. Statistical analysis of the genomic data was done by PLINK. Results Polymorphisms followed the Hardy–Weinberg equilibrium. In the allelic association, all the polymorphisms had a p-value more than 0.05. The odds ratio was not more than 1.6 for all the SNPs. Conclusion High-risk polymorphisms, such as rs6507872 and rs8091995 of CTIF, rs17715416, rs17713847 and rs183559995 of MYO5B, rs78950893 of SMAD7, rs1450425 of LOXHD1, and rs6507992 of SKA1 in the locus 18q21.1, are not associated with NSCLP in Indian multiplex families.

scholarly journals Waste not, want not: microsatellites remain an economical and informative technology for conservation genetics

2021 ◽  
Author(s):  
Samantha Hauser ◽  
Giridhar Athrey ◽  
Paul Leberg
Keyword(s):  
Genetic Diversity ◽  
Population Genetic ◽  
Genetic Research ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Analyses ◽  
Source Populations ◽  
Landscape Genetic ◽  
Source Sink ◽  
Population Genetic Analyses

Comparisons of microsatellite and single-nucleotide polymorphisms (SNPs) have found that SNPs outperform microsatellites in population genetic analyses, calling into the question the continued utility of microsatellites in population and landscape genetics. Yet highly polymorphic markers may be of value in species that have reduced genetic variation. This study repeated analyses previously done using microsatellites with SNPs developed from ddRAD sequencing in the black-capped vireo source-sink system. SNPs provided greater resolution of genetic diversity, population differentiation, and migrant detection but could not reconstruct parentage relationships due to insufficient heterozygosities. The biological inferences made by both sets of markers were similar: asymmetrical gene flow from source populations to the remaining sink populations. With the landscape genetic analyses, we found different results between the two molecular markers, but associations of the top environmental features (riparian, open habitat, agriculture, and human development) with dispersal estimates were shared between marker types. Despite the higher precision of SNPs, we find that microsatellites effectively uncover population processes and patterns and are superior for parentage analyses in this species with reduced genetic diversity. This study illustrates the continued applicability and relevance of microsatellites in population genetic research.

scholarly journals Genome-Wide Variation Analysis of Four Vegetable Soybean Cultivars Based on Re-Sequencing

Plants ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 28
Author(s):  
Xiaomin Yu ◽  
Xujun Fu ◽  
Qinghua Yang ◽  
Hangxia Jin ◽  
Longming Zhu ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Research ◽  
Value Added ◽  
Enrichment Analysis ◽  
Nucleotide Polymorphisms ◽  
Vegetable Soybean ◽  
Single Nucleotide ◽  
Coverage Ratio ◽  
Simple Sequence Repeat Analysis ◽  
The Difference

Vegetable soybean is a type of value-added specialty soybean, served as a fresh vegetable or snack in China. Due to the difference from other types, it is important to understand the genetic structure and diversity of vegetable soybean for further utilization in breeding programs. The four vegetable cultivars, Taiwan-75, Zhexiandou No. 8, Zhexian No. 9 and Zhexian No. 10 are popular soybean varieties planted in Zhejiang province, and have large pods and intermediate maturity. The clustering showed a close relationship of these four cultivars in simple sequence repeat analysis. To reveal the genome variation of vegetable soybean, these four improved lines were analyzed by whole-genome re-sequencing. The average sequencing depth was 7X and the coverage ratio of each cultivar was at least more than 94%. Compared with the reference genome, a large number of single-nucleotide polymorphisms, insertion/deletions and structure variations were identified with different chromosome distributions. The average heterozygosity rate of the single-nucleotide polymorphisms was 11.99% of these four cultivars. According to the enrichment analysis, there were 23,371 genes identified with putative modifications, and a total of 282 genes were related to carbohydrate metabolic processes. These results provide useful information for genetic research and future breeding, which can facilitate the selection procedures in vegetable soybean breeding.

The CLDN5 locus may be involved in the vulnerability to schizophrenia

2004 ◽  
Vol 19 (6) ◽  
pp. 354-357 ◽  
Author(s):  
Z.-Y. Sun ◽  
J. Wei ◽  
L. Xie ◽  
Y. Shen ◽  
S.-Z. Liu ◽  
...  
Keyword(s):  
Transmission Disequilibrium Test ◽  
Untranslated Region ◽  
Genetic Research ◽  
Chinese Family ◽  
Nucleotide Polymorphisms ◽  
Chi Square ◽  
Single Nucleotide ◽  
Pathological Conditions ◽  
Flanking Region ◽  
Genetic And Environmental Factors

AbstractThe present study was designed to detect three single nucleotide polymorphisms (SNPs) located on 22q11 that was thought as being of particularly importance for genetic research into schizophrenia. We recruited a total of 176 Chinese family trios of Han descent, consisting of mothers, fathers and affected offspring with schizophrenia for the genetic analysis. The transmission disequilibrium test (TDT) showed that of three SNPs, rs10314 in the 3′-untranslated region of the CLDN5 locus was associated with schizophrenia (χ2 = 4.75, P = 0.029). The other two SNPs, rs1548359 present in the CDC45L locus centromeric of rs10314 and rs739371 in the 5′-flanking region of the CLDN5 locus, did not show such an association. The global chi-square (χ2) test showed that the 3-SNP haplotype system was not associated with schizophrenia although the 1-df test for individual haplotypes showed that the rs1548359(C)-rs10314(G)-rs739371(C) haplotype was excessively non-transmitted (χ2 = 5.32, P = 0.02). Because the claudin proteins are a major component for barrier-forming tight junctions that could play a crucial role in response to changing natural, physiological and pathological conditions, the CLDN5 association with schizophrenia may be an important clue leading to look into a meeting point of genetic and environmental factors.

scholarly journals Gene-Gene Interactions in Renin-Angiotensin-Aldosterone System Contributes to End-Stage Renal Disease Susceptibility in a Han Chinese Population

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Sui-Lung Su ◽  
Hsin-Yi Yang ◽  
Chia-Chao Wu ◽  
Herng-Sheng Lee ◽  
Yuh-Feng Lin ◽  
...  
Keyword(s):  
Gene Interaction ◽  
Han Chinese ◽  
Simultaneous Occurrence ◽  
Gene Interactions ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Testing Accuracy ◽  
Stage Renal Disease ◽  
End Stage ◽  
Control Study

Objective. In this study, we investigated whether RAAS gene single nucleotide polymorphisms (SNPs) and their interactions were associated with end-stage renal stage (ESRD).Methodology and Results. This was a case-control study for 647 ESRD cases and 644 controls. AGT (M235T (rs699) and T174M (rs4762)), AGTR1 (A1166C (rs5186) and C573T (rs5182)), ACE (I/D (rs1799752) and G2350A (rs4343)), and CYP11B2 C-344T (rs1799998) were genotyped and compared between cases and controls to identify SNPs associated with ESRD susceptibility. Multifactor dimensionality reduction (MDR) was used to identify gene-gene interactions. Several RAAS genes were associated with ESRD: AGT M235T, ACE I/D, ACE G2350A, and CYP11B2 C-344T. By MDR analysis, a three-locus model (ACE ID/ACE G2350A/CYP11B2 C-344T) of gene-gene interaction was the best for predicting ESRD risk, and its maximum testing accuracy was 56.08% and maximum cross-validation consistency was 9/10. ESRD risk was higher with the simultaneous occurrence of ACE I/D DD-ACE G2350A AA. AGT, ACE, and CYP11B2 gene polymorphisms are associated with ESRD.Conclusions. The gene-gene interaction effects of ACE I/D, ACE G2350A, and CYP11B2 C-344T polymorphisms are more important than individual factors for ESRD development among Han Chinese.

scholarly journals Plant-ImputeDB: an integrated multiple plant reference panel database for genotype imputation

2020 ◽  
Vol 49 (D1) ◽  
pp. D1480-D1488
Author(s):  
Yingjie Gao ◽  
Zhiquan Yang ◽  
Wenqian Yang ◽  
Yanbo Yang ◽  
Jing Gong ◽  
...  
Keyword(s):  
Plant Species ◽  
Genetic Research ◽  
Genotype Imputation ◽  
Reference Panel ◽  
Nucleotide Polymorphisms ◽  
High Quality ◽  
Single Nucleotide ◽  
Online Tool ◽  
Whole Genome Resequencing ◽  
Missing Genotypes

Abstract Genotype imputation is a process that estimates missing genotypes in terms of the haplotypes and genotypes in a reference panel. It can effectively increase the density of single nucleotide polymorphisms (SNPs), boost the power to identify genetic association and promote the combination of genetic studies. However, there has been a lack of high-quality reference panels for most plants, which greatly hinders the application of genotype imputation. Here, we developed Plant-ImputeDB (http://gong_lab.hzau.edu.cn/Plant_imputeDB/), a comprehensive database with reference panels of 12 plant species for online genotype imputation, SNP and block search and free download. By integrating genotype data and whole-genome resequencing data of plants from various studies and databases, the current Plant-ImputeDB provides high-quality reference panels of 12 plant species, including ∼69.9 million SNPs from 34 244 samples. It also provides an easy-to-use online tool with the option of two popular tools specifically designed for genotype imputation. In addition, Plant-ImputeDB accepts submissions of different types of genomic variations, and provides free and open access to all publicly available data in support of related research worldwide. In general, Plant-ImputeDB may serve as an important resource for plant genotype imputation and greatly facilitate the research on plant genetic research.

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