• Title/Summary/Keyword: gene polymorphisms

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p53 Polymorphisms and Haplotypes as a Possible Predictor of a High-risk Group for Hepatocellular Carcinoma

  • Sato Shigeaki;Shiraki Takashi;Inoue Yoshiki;Takeshita Tatsuya;Morimoto Kanehisa
    • 대한예방의학회:학술대회논문집
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    • 1999.10a
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    • pp.1-15
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    • 1999
  • In a case-control study to evaluate the factors involved in the development of hepatocellular carcinoma, polymorphisms of the p53 gene were compared in 68 cases mostly infected with hepatitis C virus (HCV) and 68 controls matched for sex and age: DNA from peripheral blood leukocytes was analyzed by the polymerase chain reaction-single strand conformation polymorphism method and direct sequencing. Polymorphisms analyzed were those in exon 4 (CCC vs. CGC, Pro vs. Arg at codon 72, Al allele vs. A2 allele), intron 2 (C vs. G at nucleotide 38, Al vs. A2), intron 3 (C vs. A at nucleotide 65, Al vs. A2; absence and presence of 16 base pair repeat at nucleotides 24 to 39, Al vs. A2), intron 6 (A vs. G at nucleotide 62, Al vs. A2) and intron 7 (C and T vs. T and G at nucleotides 72 and 92, Al vs. A2). A significantly higher frequency of the allele for CCC (Pro, Al) at codon 72 of exon 4 was found in cases (39%) than in controls (26%) (p<0.05). Highly significant linkage of the polymorphisms in exon 4, intron 2, intron 3 and intron 7, and between the intron 3-16 bp duplication and polymorphism in intron 6 also was found. Matched Fair analysis showed significantly higher frequencies of certain haplotypes (1-1-1-1-2-2 or 1-1-2-1-2-1 for exon 4, intron 2, intron 3, the intron 3-16 bp duplication, intron 6 and intron 7) in cases than in controls (p=0.014, OR=2.27, 95% CI= 1.08-5.12). No preference of specific p53 polymorphisms for specific HCV genotype was detected. These findings suggest that in hepatocarcinogenesis mainly due to HCV infection, genetic factors may be involved and that genetic markers can serve as predictors of a high-risk group for hepatocarcinogenesis.

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NR3C1 Polymorphisms for Genetic Susceptibility to Schizophrenia

  • Park, Joo Seok;Lee, Sang Min;Kim, Jong Woo;Kang, Won Sub
    • Korean Journal of Biological Psychiatry
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    • v.26 no.2
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    • pp.88-93
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    • 2019
  • Objectives Psychological stress has been known to increase the risk of schizophrenia. Because stress responses are mainly mediated by cortisol, the action of the glucocorticoid receptors (Nuclear Receptor Subfamily 3 Group C Member 1, NR3C1) is possibly related to the pathogenesis of schizophrenia. In this study, we investigated the associations between polymorphisms of NR3C1 and schizophrenia. Methods Four single nucleotide polymorphisms (SNPs) (rs17100236, rs2963155, rs9324924, and rs7701443) of NR3C1 were genotyped in 208 patients with schizophrenia and 339 healthy individuals. A chi-square test was performed to test differences in allele distributions among groups. A multiple logistic regression model was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs), and multiple inheritance models to analyze the associations between schizophrenia and SNPs (the dominant, recessive and additive models). Results The minor allele frequencies of two SNPs were significantly higher in the schizophrenia group than in those of the control group (rs2963155 G > A : 0.25 vs. 0.18, p = 0.0066 ; rs7701443 A > G : 0.40 vs. 0.33, p = 0.012). The genotype frequencies of two SNPs were found to be significantly different between patients with schizophrenia and controls in the dominant model (rs2963155 : AG/GG vs. AA, OR = 1.66, 95% CI = 1.16-2.38, p = 0.0055, rs7701443 : AG/AA vs. GG, OR = 1.61, 95% CI = 1.11-2.34, p = 0.01) and the log-additive model (rs2963155 : AG vs. GG vs. AA, OR = 1.54, 95% CI = 1.13-2.10, p = 0.0067). Conclusions This study showed significant associations between NR3C1 polymorphisms and schizophrenia. It suggests that NR3C1 may play a role in the pathogenesis of schizophrenia.

Lack of Association of BIRC5 Polymorphisms with Clearance of HBV Infection and HCC Occurrence in a Korean Population

  • Lee, Jin-Sol;Kim, Jeong-Hyun;Park, Byung-Lae;Cheong, Hyun-Sub;Kim, Jason-Y.;Park, Tae-Joon;Chun, Ji-Yong;Bae, Joon-Seol;Lee, Hyo-Suk;Kim, Yoon-Jun;Shin, Hyoung-Doo
    • Genomics & Informatics
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    • v.7 no.4
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    • pp.195-202
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    • 2009
  • BIRC5 (Survivin) belongs to the inhibitor of apoptosis gene family. The BIRC5 protein inhibits caspases and consequently blocks apoptosis. Thus, BIRC5 contributes to the progression of cancer allowing for continued cell proliferation and survival. In this study, we identified eight sequence variants of BIRC5 through direct DNA sequencing. Among the eight single nucleotide polymorphisms (SNPs), six common variants with frequencies higher than 0.05 were selected for larger-scale genotyping (n=1,066). Results of the study did not show any association between the promoter region polymorphisms and the clearance of hepatitis B virus (HBV) infection and hepatocellular carcinoma (HCC) occurrence. This is in line with a previous study in which polymorphisms in the promoter region does not influence the function of BIRC5. Initially, we were able to detect a signal with the +9194A>G, which disappeared after multiple corrections but led to a change in amino acid. Similarly, we were also able to detect an association signal between two haplotypes (haplotype-2 and haplotype-5) on the onset age of HCC and/or HCC occurrence, but the signals also disappeared after multiple corrections. As a result, we concluded that there was no association between BIRC5 polymorphisms and the clearance HBV infection and/or HCC occurrence. However, our results might useful to future studies.

The Effects of UCP-2, 3 Polymorphisms on Weight Loss among Korean Overweight Women (UCP-2, 3 단일염기다형성이 한국인 여성의 체중감량에 미치는 영향)

  • Shim, Woo-Jin;Moon, Jin-Seok;Choi, Sun-Mi;Shin, Seung-Uoo;Kim, Kil-Soo
    • Journal of Korean Medicine for Obesity Research
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    • v.6 no.2
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    • pp.59-73
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    • 2006
  • Objectives: This study was conducted to investigate the effects of Uncoupling protein (UCP) polymorphisms on weight loss. We analyzed associations between polymorphisms of UCP-2, 3 and changes in percentage of obesity phenotypes (Body mass index and percent body fat) after treatment. Materials and Methods: A total of 207 Korean women (BMI over 25) were recruited from the obesity clinic in Kirin Oriental Medical Hospital (Seoul, Korea). All patients were treated with a very low calorie diet and oriental medical therapy for one month. The effect of UCP polymorphisms on changes in obesity-phenotypes were analyzed. For the genotyping of a single nucleotide polymorphism (SNPs), genomic DNA from each subject was extracted from whole blood and genotyped using the TaqMan Method. Associations between changes in percentage of obesity phenotypes (BMI and percent body fat) and UCP polymorphisms were analyzed using age-adjusted general linear model. Results and Conclusions: In this study, AG, GG type of UCP-2 -866A>G, CC, CT type of UCP-2 +4787C>T, CG, GG type of UCP-3 +2564C>G, AG, GG type of UCP-3 +3106A>G, and TC, CC type of UCP-3 +4589T>C played a role as a resistance gene to weight loss.

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Gene Expression Analysis and Polymorphism Discovery to Investigate Drought Responsive System in Tropical Maize

  • Song, Kitae;Kim, Hyo Chul;Kim, Kyung-Hee;Moon, Jun-Cheol;Kim, Jae Yoon;Lee, Sang-Kyu;Lee, Byung-Moo
    • Plant Breeding and Biotechnology
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    • v.6 no.4
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    • pp.354-362
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    • 2018
  • Maize has high food and industrial value, whereas has difficulties in research because of their complex and huge size genome. Nested association mapping (NAM) was constructed to better understand maize genetics. However, most studies were conducted using the reference genome B73, and only a few studies were conducted on tropical maize. Ki3, one of the founder lines of the NAM population, is a tropical maize. We analyzed the genetic characteristics of Ki3 by using RNA sequencing and bioinformatics tools for various genetic studies. As results, a total of 30,526 genes were expressed, and expression profile were constructed. A total of 1,558 genes were differentially expressed in response to drought stress, and 513 contigs of them come from de novo assemblies. In addition, high-density polymorphisms including 464,930 single nucleotide polymorphisms (SNPs), 21,872 multiple nucleotide polymorphisms (MNPs) and 93,313 insertions and deletions (InDels) were found compared to reference genome. Among them, 15.0 % of polymorphisms (87,838) were passed non-synonymous test which could alter amino acid sequences. The variants have 66,550 SNPs, 5,853 MNPs, and 14,801 InDels, also proportion of homozygous type was higher than heterozygous. These variants were found in a total of 15,643 genes. Of these genes, 637 genes were found as differentially expressed genes (DEGs) under drought stress. Our results provide a genome-wide analysis of differentially expressed genes and information of variants on expressed genes of tropical maize under drought stress. Further characterization of these changes in genetic regulation and genetic traits will be of great value for improvement of maize genetics.

CAPS Marker Linked to Tomato Hypocotyl Pigmentation

  • Kim, Hyoun-Joung;Lee, Heung-Ryul;Hyun, Ji-Young;Won, Dong-Chan;Hong, Dong-Oh;Harn, Chee-Hark
    • Horticultural Science & Technology
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    • v.30 no.1
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    • pp.56-63
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    • 2012
  • Tomato hypocotyl can generally be one of two colors, purple or green. Genetically, this trait is controlled by a single dominant gene. Hypocotyl tissue specific color expression is one of many visible genetic marker sources used to select tomato progeny. However, the visible marker does not show a clear distinction between homozygous genotype and heterozygous genotype from the breeding lines. Therefore, to identify a hypocotyl pigmentation related marker, we screened DNA polymorphisms in thirteen tomato lines showing purple or green hypocotyls. The markers used for screening consisted of primer set information obtained from anthocyanin related genes, conserved ortholog set II (COS II) marker sets localized near anthocyanin related genes, and restriction fragment length polymorphism (RFLP) markers localized near COS II markers, which produce polymorphisms between purple and green tomatoes. One primer from a RFLP fragment resulted in a polymorphism on agarose gel electrophoresis. From the RFLP fragment, a cleaved amplified polymorphic sequence (CAPS) marker was developed to distinguish between purple and green hypocotyls. The genotypes of 135 $F_2$ individuals were analyzed using the CAPS marker, and among them, 132 individuals corresponded to the phenotypes of hypocotyl pigmentation.

Identification of Superior Single Nucleotide Polymorphisms (SNP) Combinations Related to Economic Traits by Genotype Matrix Mapping (GMM) in Hanwoo (Korean Cattle)

  • Lee, Yoon-Seok;Oh, Dong-Yep;Lee, Yong-Won;Yeo, Jung-Sou;Lee, Jea-Young
    • Asian-Australasian Journal of Animal Sciences
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    • v.24 no.11
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    • pp.1504-1513
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    • 2011
  • It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.

Risk Effects of GST Gene Polymorphisms in Patients with Acute Myeloid Leukemia: A Prospective Study

  • Zhou, Lei;Zhu, Yan-Yun;Zhang, Xiao-Dong;Li, Yang;Liu, Zhuo-Gang
    • Asian Pacific Journal of Cancer Prevention
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    • v.14 no.6
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    • pp.3861-3864
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    • 2013
  • Glutathione S-transferase (GST) enzyme levels are associated with risk of many cancers, including hematologic tumours. We here aimed to investigate the relationships between GSTM1, GSTT1 and GSTP1 polymorphisms and the risk of AML. Genotyping of GSTs was based upon duplex polymerase-chain-reactions with the confronting-two-pair primer (PCR-CTPP) method in 163 cases and 204 controls. Individuals carrying null GSTT1 genotype had a 1.64 fold risk of acute leukemia relative to a non-null genotype (P<0.05). A heavy risk was observed in those carrying combination of null genotypes of GSTM1 and GSTT1 and GSTP1 Val allele genotypes when compared with those carrying wild genotypes, with an OR (95% CI) of 3.39 (1.26-9.26) (P<0.05). These findings indicate that genetic variants of GST and especially the GSTT1 gene have a critical function in the development of AML. Our study offers important insights into the molecular etiology of AML.

Genome-Wide Association Study of Medication Adherence in Chronic Diseases in the Korean Population

  • Seo, Incheol;Suh, Seong-Il;Suh, Min-Ho;Baek, Won-Ki
    • Genomics & Informatics
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    • v.12 no.3
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    • pp.121-126
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    • 2014
  • Medication adherence is generally defined as the extent of voluntary cooperation of a patient in taking medicine as prescribed. Adherence to long-term treatment with chronic disease is essential for reducing disease comorbidity and mortality. However, medication non-adherence in chronic disease averages 50%. This study was conducted a genome-wide association study to identify the genetic basis of medication adherence. A total of 235 medication non-adherents and 1,067 medication adherents with hypertension or diabetes were used from the Korean Association Resource project data according to the self-reported treatment status of each chronic disease, respectively. We identified four single nucleotide polymorphisms with suggestive genome-wide association. The most significant single nucleotide polymorphism was rs6978712 (chromosome 7, $p=4.87{\times}10^{-7}$), which is located proximal to the GCC1 gene, which was previously implicated in decision-making capability in drug abusers. Two suggestive single nucleotide polymorphisms were in strong linkage disequilibrium ($r^2$ > 0.8) with rs6978712. Thus, in the aspect of decision-making in adherence behavior, the association between medication adherence and three loci proximal to the GCC1 gene seems worthy of further research. However, to overcome a few limitations in this study, defining the standardized phenotype criteria for self-reported adherence should be performed before replicating association studies.

Assessment of an Apo-1/Fas Promoter Polymorphism in Korean Schizophrenia Patients

  • Kim, Soon-Ae;Kim, Youn-Jung;Choe, Bong-Keun;Lee, Hee-Jae;Kim, Jong-Woo;Park, Jong-Deuk;Kim, Chang-Ju;Park, Seung-Joon;Jung, Jee-Chang;Chung, Joo-Ho
    • The Korean Journal of Physiology and Pharmacology
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    • v.6 no.3
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    • pp.161-163
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    • 2002
  • Apoptosis has been hypothesized to be involved in the pathogenesis in schizophrenia. A large number of genes are known to mediate the apoptotic process; Apo-1/Fas (CD95) is a well-known example of such genes. In the present study, MvaI restriction fragment length polymorphism, a polymorphic marker present within the Apo-1/Fas gene, was examined in a population consisting of 226 control subjects and 110 schizophrenia patients, all of them Korean in ethnicity. No statistically significant difference in the genotypic distribution and allelic frequencies was observed between the control and the schizophrenia patient group. To find out the precise effect of Apo-1/Fas gene polymorphisms on the susceptibility to schizophrenia, further studies are warranted to investigate possible involvement of other polymorphisms with a larger sample population.