• Title/Summary/Keyword: Allelic frequency

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Association of CAPN10 gene (rs3842570) polymorphism with the type 2 diabetes mellitus among the population of Noakhali region in Bangladesh: a case-control study

  • Munia Sultana;Md. Mafizul Islam;Md. Murad Hossain;Md. Anisur Rahman;Shuvo Chandra Das;Dhirendra Nath Barman;Farhana Siddiqi Mitu;Shipan Das Gupta
    • Genomics & Informatics
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    • v.21 no.3
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    • pp.33.1-33.11
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    • 2023
  • Type 2 diabetes mellitus (T2DM) is a multifactorial, polygenic, and metabolically complicated disease. A large number of genes are responsible for the biogenesis of T2DM and calpain10 (CAPN10) is one of them. The association of numerous CAPN10 genetic polymorphisms in the development of T2DM has been widely studied in different populations and noticed inconclusive results. The present study is an attempt to evaluate the plausible association of CAPN10 polymorphism SNP-19 (rs3842570) with T2DM and T2DM-related anthropometric and metabolic traits in the Noakhali region of Bangladesh. This case-control study included 202 T2DM patients and 75 healthy individuals from different places in Noakhali. A significant association (p < 0.05) of SNP-19 with T2DM in co-dominant 2R/3R vs. 3R/3R (odds ratio [OR], 2.7; p=0.0014) and dominant (2R/3R) + (2R/2R) vs. 3R/3R (OR, 2.47; p=0.0011) genetic models was observed. High-risk allele 2R also showed a significant association with T2DM in the allelic model (OR, 1.67; p=0.0109). The genotypic frequency of SNP-19 variants showed consistency with Hardy-Weinberg equilibrium (p > 0.05). Additionally, SNP-19 genetic variants showed potential associations with the anthropometric and metabolic traits of T2DM patients in terms of body mass index, systolic blood pressure, diastolic blood pressure, total cholesterol, and triglycerides. Our approach identifies the 2R/3R genotype of SNP-19 as a significant risk factor for biogenesis of T2DM in the Noakhali population. Furthermore, a large-scale study could be instrumental to correlate this finding in overall Bangladeshi population.

Studies on Combining Ability and Inheritance of Major Agronomic Characters in Naked Barley (과맥의 주요형질에 대한 조합능력 및 유전에 관한 연구)

  • Kyung-Soo Min
    • KOREAN JOURNAL OF CROP SCIENCE
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    • v.23 no.2
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    • pp.1-24
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    • 1978
  • To obtain basic information on the breeding of early maturing, short culm naked-barley varieties, the following 10 varieties, Ehime # 1, Shikoku #42, Yamate hadaka, Eijo hadaka, Kagawa # 1, Jangjubaeggwa, Baegdong, Cheongmaeg, Seto-hadaka and Mokpo #42 were used in diallel crosses in 1974. Heading date, culm length and grain yield per plant for the parents, $F_1's$ and $F_2's$ of the 10X10 partial diallel crosses were measured in 1976 for analysis of their combining ability, heritability and inheritance. The results obtained are summarized below; 1. Heritabilities in broad sense for heading date, culm length and grain yield per plant were 0.7831, 0.7599 and 0.6161, respectively. Narrow sense heritabilities for heading date were 0.3972 in $F_1$ and 0.7789 in $F_2$ and for culm length 0.6567 in $F_1$ and 0.6414 in $F_2.$ These values suggest that earliness and culm length could be successfully selected for in the early generations. Narrow sense heritability for grain yield was 0.3775 in $F_1$ and 0.4170 in $F_2.$ 2. GCA effects of the $F_1$ and $F_2$ generations for days to heading were high in the early direction for early-heading varieties, while for late-heading varieties the GCA effects were high in the late direction. Absolute values for GCA effects in $F_1$ were higher than in $F_2.$ SCA effects of the $F_1$ and $F_2$ generations were high in the early-heading direction for Shikoku # 42 x Mokpo # 42, Ehime # 1 x Yamate hadaka, Shikoku # 42 x Yamate hadaka and Shikoku #42 x Eijo hadaka. 3. The GCA effects for culm length in the $F_1$ and $F_2$ generations for tall varieties were high in the tall direction while short varieties were high in the short direction. Absolute values for the GCA effects in $F_1$ were higher than in $F_2.$ SCA effects were high in the short direction for the combinations of Mokpo # 42 with Ehime # 1, Yamate had aka and Eijo hadaka. 4. The GCA effects for grain yields per plant in the $F_1$ and $F_2$ generations for varieties with high yields per plant were high in the high yielding direction, while varieties with low yields per plant were high in the low yielding direction. Absolute values of the $F_1$ GCA effects were higher than the $F_2$ effects. The combinations with high SCA effects were Mokpo # 42 x Shikoku # 42, Mokpo # 42 x Seto hadaka and Mokpo # 42 x Cheongmaeg. 5. Mean heading dates of the $F_1$ and $F_2$ generations were earlier than those of mean mid-parent. Mean heading date of the $F_1$ generation was earlier than the $F_2$ generation. Crosses involving early-heading varieties showed a greater $F_1, $ mid-parent difference than crosses involving late-heading varieties. 6. Heading date was controlled by a partial dominance effect. Nine varieties excluding Mokpo # 42 showed allelic gene action. Ehime # 1, Shikoku # 42, Kagawa # 1 and Mokpo # 42 were recessive to the other tested varieties. 7. The $F_2$ segregations of the 45 crosses for days to heading showed that 33 cosses were of such complexity that they could not be explained by simple genetic inheritance. One cross showed a 3 : 1 ratio where earliness was dominant. Another cross showed a 3 : 1 ratio where lateness was dominant. Four other crosses showed a 9 : 7 ratio for earliness while six crosses showed a 9 : 7 ratio for lateness. 8. Many transgressive segregants for earliness were found in the following crosses; Eijo hadaka x Baegdong, Ehime # 1 x Seto hadaka, Yamate had aka x Kagawa # 1, Kagawa # 1 x Sato hadaka, Shikoku # 42 x Kagawa # 1, Ehime # 1 x Kagawa # 1, Ehime # 1 x Shikoku # 42, Ehime # 1 x Eijo hadaka. 9. Mean culm length of the F, and F. generations were usually taller than the mid-parent where tall parent were used. These trends were high in the short varieties, but low in the tall varieties. 10. Culm length was controlled by partial dominace which was gonverned by allelic gene(s). Culm length showed a high degree of control by additive genes. Mokpo # 42 was recessive while Baegdong was dominant. 11. The F_2 frequency for culm length was in large part normally distributed around the midparent value. However, some combinations showed transgressive segregation for either tall or short culm length. From combinations between medium tall varieties, Ehime # 1, Shikoku # 42, Eijo hadaka and Seto hadaka, many short segregants could be found. 12. Mean grain yields per plant of the F_1 and F_2 generations were 6% and 5% higher than those of mid-parents, respectively. The varieties with high yields per plant showed a low rate of yield increase in their F_1's and F_2's while the varieties with low yields per plant showed a high rate of yield increase in their F_1's and F_1's. 13. Grain yields per plant showed over-dominnee effects, governed by non-allelic genes. Mokpo # 42 showed recessive genetic control of grain yield per plant. It remains difficult to clarify the inheritance of grain yields per plant from these data.

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Analysis of the Tumor Necrosis Factor-${\alpha}$ Promoter Polymorphism in Children with Henoch-Sch$\"{o}$nlein Purpura (Henoch-Sch$\"{o}$nlein 자반증에서 Tumor Necrosis Factor-${\alpha}$ 유전자 다형성 분석)

  • Yang, Hye-Ran;Ko, Jae-Sung;Seo, Jeong-Kee
    • Pediatric Gastroenterology, Hepatology & Nutrition
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    • v.10 no.1
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    • pp.11-19
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    • 2007
  • Purpose: Henoch-Sch$\"{o}$nlein purpura (HSP) is a systemic vasculitis involving the skin, joints, gastrointestinal tract, and kidney. Although the pathogenesis of HSP is still unclear, tumor necrosis factor (TNF-${\alpha}$) is regarded as an important cytokine contributing to the disease. The goal of this study was to determine the role of TNF-${\alpha}$ in the pathogenesis of HSP, and to evaluate the TNF-${\alpha}$ polymorphism for genetic susceptibility to HSP. Methods: From March 2004 to November 2005, 40 children with HSP and 32 healthy controls were included. Serum TNF-${\alpha}$ levels were measured using the ELISA method during the acute and convalescent phase of HSP. The genotypic and allelic frequencies of the TNF-${\alpha}$ gene polymorphisms at positions -308 and -238 were evaluated in patients and controls. Results: Serum TNF-${\alpha}$ levels were $23.17{\pm}11.31$ pg/mL in the acute phase of children with HSP and $10.56{\pm}5.59$ pg/mL in the convalescent phase (p=0.000). There was no significant correlation between the serum TNF-${\alpha}$ levels and the clinical scores of HSP (r=0.310, p=0.070). The genotypic frequency of the TNF-${\alpha}$ -308 polymorphism in children with HSP was not significantly different compared to healthy controls (GG 80%, GA 20% vs. GG 93.8%, GA 6.2%; p=0.094). The genotypic frequency of the TNF-${\alpha}$ -238 polymorphism in children with HSP was not significantly different (GG 97.5%, GA 2.5% vs. GG 93.8%, GA 6.3%; p=0.429). Conclusion: TNF-${\alpha}$ is assumed to be the main cytokine associated with the pathogenesis of HSP during the acute phase. However, the presence of TNF-${\alpha}$ gene polymorphisms at positions -308 and -238 did not distinguish children with HSP from normal controls.

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The relationship between catechol-O-methyltransferase gene polymorphism and coronary artery abnormality in Kawasaki disease (가와사키병의 관상동맥 이상과 catechol-O-methyltransferase 유전자의 단일염기다형성)

  • Lee, Hyo Jin;Lee, Myung Sook;Kim, Ji Sook;Kim, Eun Ryoung;Kang, Sung Wook;Kim, Soo Kang;Chung, Joo Ho;Yoon, Kyung Lim;Han, Mi Young;Cha, Seong Ho
    • Clinical and Experimental Pediatrics
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    • v.52 no.1
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    • pp.87-92
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    • 2009
  • Purpose : Many gene polymorphisms are associated with coronary artery abnormalities in Kawasaki disease. Catechol-O- methyltransferase (COMT) plays an important role in the metabolism of catecholamines, catechol estrogen, and catechol drugs. Polymorphisms of the COMT gene are reported to be associated with myocardial infarction and coronary artery abnormalities. The aim of this study was to evaluate the relationship between COMT gene polymorphisms and coronary artery abnormalities in Kawasaki disease patients. Methods : One hundred and one Korean children with Kawasaki disease and 306 healthy Korean control subjects were enrolled in this study. The polymorphisms of the COMT gene were analyzed by direct sequencing. Results : There were no differences in the genotype and allelic frequency of the rs4680 and rs769224 polymorphic sites between Kawasaki disease and control subjects. Further, no significant difference was found in the rs4680 polymorphism between patients with coronary artery abnormalities and patients without coronary artery abnormalities (codominant P=0.32, dominant P=0.74, recessive P=0.13). However, the distribution of the rs769224 polymorphism was significantly different between patients with coronary artery abnormalities and patients without coronary artery abnormalities (codominant P= 0.0077, dominant P=0.0021, recessive P=0.16). Conclusion : Our results indicate that the polymorphisms of the rs769224 gene might be related to the development of coronary artery abnormalities in Kawasaki disease.

Susceptibility Loci Associations with Prostate Cancer Risk in Northern Chinese Men

  • Wang, Na-Na;Xu, Yong;Yang, Kuo;Wei, Dong;Zhang, Yao-Guang;Liu, Ming;Shi, Xiao-Hong;Liang, Si-Ying;Sun, Liang;Zhu, Xiao-Quan;Yang, Yi-Ge;Tang, Lei;Zhao, Cheng-Xiao;Wang, Xin;Chen, Xin;Hui, Juan;Zhang, Yu-Hong;Zhu, Ling;Yang, Fan;Zhang, Yu-Rong;Yang, Ze;Wang, Jian-Ye
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.5
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    • pp.3075-3078
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    • 2013
  • Background: KLK3 gene products, like human prostate-specific antigen (PSA), are important biomarkers in the clinical diagnosis of prostate cancer (PCa). G protein-coupled receptor RFX6, C2orf43 and FOXP4 signaling plays important roles in the development of PCa. However, associations of these genes with PCa in northern Chinese men remain to be detailed. This study aimed to investigate their impact on occurrence and level of malignancy. Methods: All subjects were from Beijing and Tianjin, including 266 cases with prostate cancer and 288 normal individuals as controls. We evaluated associations between clinical covariates (age at diagnosis, prostate specific antigen, Gleason score, tumor stage and aggressive) and 6 candidate PCa risk loci, genotyped by PCR- high resolution melting curve and sequencing methods. Results: Case-control analysis of allelic frequency of PCa associated with PCa showed that one of the 6 candidate risk loci, rs339331 in the RFX6 gene, was associated with reduced risk of prostate cancer (odds ratio (OR) = 0.73, 95% confidence interval (CI) =0.57-0.94, P = 0.013) in northern Chinese men. In addition, subjects with CX (CC+TC) genotypes had a decreased risk for prostrate cancer compared to those carrying the TT homozygote (OR =0.64, 95% CI = 0.45- 0.90, P = 0.008). The TT genotype of 13q22 (rs9600079, T) was associated with tumor stage (P=0.044, OR=2.34, 95% CI=0.94-5.87). Other SNPs were not significantly associated with clinical covariates in prostate cancer (P > 0.05). Conclusions. rs339331 in the RFX6 gene may be associated with prostate cancer as a susceptibility locus in northern Chinese men.

Microsatellite Instability in Non-Small Cell Lung Cancer (비소세포폐암에서 Microsatellite Instability)

  • Jeon, Hyo-Sung;Kim, Jeong-Ran;Son, Ji-Woong;Park, Sun-Ha;Park, Tae-In;Kim, Chang-Ho;Kim, In-San;Jung, Tae-Hoon;Park, Jae-Yong
    • Tuberculosis and Respiratory Diseases
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    • v.48 no.1
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    • pp.24-32
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    • 2000
  • Purpose: Microsatellite instability(MSI) is frequently used as an indicator of microsatellite mutator phenotype(MMP) tumors. MSI has been observed in a percentage of non-small cell lung cancer(NSCLC). However, its role in tumorigenesis of NSCLC remains unknown. The frequency and pattern of MSI in NSCLC were evaluated and clinical parameters of MSI-positive tumors with those of MSS(microsatellite stable) tumors were compared. Materials and Methods: Twenty surgically resected NSCLCs were analyzed for 15 microsatellite markers located at chromosomes 3p and 9p. The peripheral blood lymphocytes of patients were used as the source of the normal DNA. Results: 1) Of 20 cases, 8(40%) demonstrated MSI. 2) Instability was observed more frequently in tri- and tetra-nucleotide repeats than in dinucleotide repeats. In all cases, instability appeared as a shift of individual allelic bands. 3) LDH was observed in 10(50%) of 20 tumors analyzed. 4) Of 20 cases, MSI-H tumor(showing MSI in the majority of markers) was absent. There were 5 MSI-L tumors(showing MSI in a greater than 10% of markers). 5) No significant difference was observed between MSI-L tumors and MSI-negative tumors in terms of clinicopathologic features such as pack-year history of smoking, histologic subtype, and(delete) stage of disease. There was also no significant difference in the incidence of LDH in relation to the status of MSI. Conclusion: These data strongly suggest that MSI plays different roles in lung and colon cancer. MMP pathway appears to be far less important in the tumorigenesis of NSCLC, caused mainly by cigarette smoke, with little familial tendency.

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