• 제목/요약/키워드: single-nucleotide polymorphisms

검색결과 753건 처리시간 0.025초

Bioinformatic Prediction of SNPs within miRNA Binding Sites of Inflammatory Genes Associated with Gastric Cancer

  • Song, Chuan-Qing;Zhang, Jun-Hui;Shi, Jia-Chen;Cao, Xiao-Qin;Song, Chun-Hua;Hassan, Adil;Wang, Peng;Dai, Li-Ping;Zhang, Jian-Ying;Wang, Kai-Juan
    • Asian Pacific Journal of Cancer Prevention
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    • 제15권2호
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    • pp.937-943
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    • 2014
  • Polymorphisms in miRNA binding sites have been shown to affect miRNA binding to target genes, resulting in differential mRNA and protein expression and susceptibility to common diseases. Our purpose was to predict SNPs (single nucleotide polymorphisms) within miRNA binding sites of inflammatory genes in relation to gastric cancer. A complete list of SNPs in the 3'UTR regions of all inflammatory genes associated with gastric cancer was obtained from Pubmed. miRNA target prediction databases (MirSNP, Targetscan Human 6.2, PolymiRTS 3.0, miRNASNP 2.0, and Patrocles) were used to predict miRNA target sites. There were 99 SNPs with MAF>0.05 within the miRNA binding sites of 41 genes among 72 inflammation-related genes associated with gastric cancer. NF-${\kappa}B$ and JAK-STAT are the two most important signaling pathways. 47 SNPs of 25 genes with 95 miRNAs were predicted. CCL2 and IL1F5 were found to be the shared target genes of hsa-miRNA-624-3p. Bioinformatic methods could identify a set of SNPs within miRNA binding sites of inflammatory genes, and provide data and direction for subsequent functional verification research.

Characterization of porcine cytokine inducible SH2-containing protein gene and its association with piglet diarrhea traits

  • Niu, Buyue;Guo, Dongchun;Liu, Zhiran;Han, Xiaofei;Wang, Xibiao
    • Asian-Australasian Journal of Animal Sciences
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    • 제30권12호
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    • pp.1689-1695
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    • 2017
  • Objective: The cytokine inducible SH2-containing protein (CISH), which might play a role in porcine intestine immune responses, was one of the promising candidate genes for piglet anti-disease traits. An experiment was conducted to characterize the porcine CISH (pCISH) gene and to evaluate its genetic effects on pig anti-disease breeding. Methods: Both reverse transcription polymerase chain reaction (RT-PCR) and PCR were performed to obtain the sequence of pCISH gene. A pEGFP-C1-CISH vector was constructed and transfected into PK-15 cells to analysis the distribution of pCISH. The sequences of individuals were compared with each other to find the polymorphisms in pCISH gene. The association analysis was performed in Min pigs and Landrace pigs to evaluate the genetic effects on piglet diarrhea traits. Results: In the present research, the coding sequence and genomic sequence of pCISH gene was obtained. Porcine CISH was mainly localized in cytoplasm. TaqI and HaeIII PCR restriction fragment length polymorphism (RFLP) assays were established to detect single nucleotide polymorphisms (SNPs); A-1575G in promoter region and A2497C in Intron1, respectively. Association studies indicated that SNP A-1575G was significantly associated with diarrhea index of Min piglets (p<0.05) and SNP A2497C was significantly associated with the diarrhea trait of both Min pig and Landrace piglets (p<0.05). Conclusion: This study suggested that the pCISH gene might be a novel candidate gene for pig anti-disease traits, and further studies are needed to confirm the results of this preliminary research.

한국인 류마티스 관절염의 감수성과 TSLPR 유전자 다형성의 연관성 (Association of Thymic Stromal Lymphopoietin Receptor (TSLPR) Polymorphisms with the Susceptibility of Rheumatoid Arthritis in a Korean Population)

  • 유지인;모지수;채수천
    • 생명과학회지
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    • 제23권7호
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    • pp.919-925
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    • 2013
  • 사람의 TSLPR는 염증 유발 및 알러지 반응에 중요한 역할을 한다. 우리는 TSLPR 유전자에서 11개의 유전자 다형성과 2개의 유전적 변이 부위를 발굴하였고, 이들 TSLPR 유전자 다형성이 아토피 천식의 민감성과 연관성이 있음을 확인 하였다. 이에 우리는 TSLPR 유전자 다형성과 류마티스 관절염과의 연관성에 대해서도 알아 보고자 하였다. 457명의 류마티스 관절염 환자군과 570명의 정상 대조군으로 TSLPR 유전자 다형성의 genotype과 allele frequencies를 비교 분석 해본 결과 두 그룹 간에 유의성이 없었고, 류마티스 관절염 여성 그룹에서의 비교 분석에서도 두 그룹 간에 유의성이 없었다. 또한, 류마티스 관절염 환자에서 TSLPR 유전자 다형성이 RF나 CCP levels에 영향을 미치지 않는 것으로 분석 되었다. 따라서, TSLPR 유전자 다형성이 한국인에서의 류마티스 관절염에 대한 민감성과 연관성이 없는 것으로 생각된다.

Genetic Variants of IL-13 and IL-4 in the Korean Population: Polymorphisms, Haplotypes and Linkage Disequilibrium

  • Ryu, Ha-Jung;Jung, Ho-Youl;Park, Jung-Sun;Kim, Jun-Woo;Kim, Hyung-Tae;Park, Choon-Sik;Han, Bok-Ghee;Koh, In-Song;Park, Chan;Kimm, Ku-Chan;Oh, Berm-Seok;Lee, Jong-Keuk
    • Genomics & Informatics
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    • 제3권4호
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    • pp.149-153
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    • 2005
  • Asthma is an inflammatory airways disease characterized by bronchial hyperresponsiveness and airways obstruction, which results from a complex interaction of genetic and environmental factors. Interleukin (IL)-13 and IL-4 are important in IgE synthesis and allergic inflammation, therefore genes encoding IL-13 and IL-4 are candidates for predisposition to asthma. In the present study, we screened single-nucleotide polymorphisms (SNPs) in IL-13 and IL-4 and examined whether they are risk factors for asthma. We resequenced all exons and the promoter region in 12 asthma patients and 12 normal controls, and identified 18 SNPs including 2 novel SNPs. The linkage disequilibrium(LD) pattern was evaluated with 16 common SNPs, and haplotypes were also estimated within the block. Although IL-13 and IL-4 are localized within 27 kb on chromosome 5q31 and share many biological profiles, this region was partitioned into 2 blocks. One SNP and three SNPs were determined as haplotype-taggingSNPs (htSNPs) within IL-13 and IL-4 haplotype-block, respectively. No significant associations were observed between any of the SNPs or haplotypes and development of asthma in small number of Korean subjects. However, the genetic variants of IL-13 and IL-4 would provide valuable strategies for the genotyping studies in large population.

Identification of Genomic Differences between Hanwoo and Holstein Breeds Using the Illumina Bovine SNP50 BeadChip

  • Melka, Hailu Dadi;Jeon, Eun-Kyeong;Kim, Sang-Wook;Han, James-Bond;Yoon, Du-Hak;Kim, Kwan-Suk
    • Genomics & Informatics
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    • 제9권2호
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    • pp.69-73
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    • 2011
  • The use of genomic information in genomic selection programs for dairy and beef cattle breeds has become a reality in recent years. In this investigation, we analyzed single-nucleotide polymorphisms (SNPs) for Hanwoo (n=50) and Holstein (n=50) breeds using the Illumina Bovine SNP50 BeadChip to facilitate genomic selection and utilization of the Hanwoo breed in Korea. Analysis of the entire genomes showed different spectra of SNP frequencies for Hanwoo and Holstein cattle. The study revealed a highly significant (p<0.001) difference between Hanwoo and Holstein cattle in minor allele frequency (MAF). The average MAFs were $0.19{\pm}0.16$ and $0.22{\pm}0.16$ for Hanwoo and Holstein, respectively. From the total of 52,337 SNPs that were successfully identified, about 72% and 79% were polymorphic in Hanwoos and Holsteins, respectively. Polymorphic and fixed SNPs were not distributed uniformly across the chromosomes within breeds or between the two breeds. The number of fixed SNPs on all chromosomes was higher in Hanwoo cattle, reflecting the genetic uniqueness of the Hanwoo breed. In general, the rate of polymorphisms detected in these two breeds suggests that the SNPs can be used for different applications, such as whole-genome association and comparative genetic studies, and are a helpful tool in developing breed identification genetic markers.

소금민감성유전자와 비만 (Salt-sensitive genes and their relation to obesity)

  • 전용필;이명숙
    • Journal of Nutrition and Health
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    • 제50권3호
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    • pp.217-224
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    • 2017
  • Purpose: Although it is well known thatmortality and morbidity due to cardiovascular diseases are higher in salt-sensitive subjects than in salt-resistant subjects, their underlying mechanisms related to obesity remain unclear. Here, we focused on salt-sensitive gene variants unrelated to monogenic obesity that interacted with sodium intake in humans. Methods: This review was written based on the modified $3^rd$ step of Khans' systematic review. Instead of the literature, subject genes were based on candidate genes screened from our preliminary Genome-Wide Association Study (GWAS). Finally, literature related to five genes strongly associated with salt sensitivity were analyzed to elucidate the mechanism of obesity. Results: Salt sensitivity is a measure of how blood pressure responds to salt intake, and people are either salt-sensitive or salt-resistant. Otherwise, dietary sodium restriction may not be beneficial for everyone since salt sensitivity may be associated with inherited susceptibility. According to our previous GWAS studies, 10 candidate genes and 11 single nucleotide polymorphisms (SNPs) associated with salt sensitivity were suggested, including angiotensin converting enzyme (ACE), ${\alpha}$-adducin1 (ADD1), angiotensinogen (AGT), cytochrome P450 family 11-subfamily ${\beta}$-2 ($CYP11{\beta}$-2), epithelial sodium channel (ENaC), G-protein b3 subunit (GNB3), G protein-coupled receptor kinases type 4 (GRK4 A142V, GRK4 A486V), $11{\beta}$-hydroxysteroid dehydrogenase type-2 (HSD $11{\beta}$-2), neural precursor cell-expressed developmentally down regulated 4 like (NEDD4L),and solute carrier family 12(sodium/chloride transporters)-member 3 (SLC 12A3). We found that polymorphisms of salt-sensitive genes such as ACE, $CYP11{\beta}$-2, GRK4, SLC12A3, and GNB3 may be positively associated with human obesity. Conclusion: Despite gender, ethnic, and age differences in genetics studies, hypertensive obese children and adults who are carriers of specific salt-sensitive genes are recommended to reduce their sodium intake. We believe that our findings can contribute to the prevention of early-onset of chronic diseases in obese children by facilitating personalized diet-management of obesity from childhood to adulthood.

Novel Genome-Wide Interactions Mediated via BOLL and EDNRA Polymorphisms in Intracranial Aneurysm

  • Eun Pyo Hong;Dong Hyuk Youn;Bong Jun Kim;Jae Jun Lee;Sehyeon Nam;Hyojong Yoo;Heung Cheol Kim;Jong Kook Rhim;Jeong Jin Park;Jin Pyeong Jeon
    • Journal of Korean Neurosurgical Society
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    • 제66권4호
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    • pp.409-417
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    • 2023
  • Objective : The association between boule (BOLL) and endothelin receptor type A (EDNRA) loci and intracranial aneurysm (IA) formation has been reported via genome-wide association studies. We sought to identify genome-wide interactions involving BOLL and EDNRA loci for IA in a Korean adult cohort. Methods : Genome-wide pairwise interaction analyses of BOLL and EDNRA involving 250 patients with IA and 296 controls were performed using the additive effect model after adjusting for confounding factors. Results : Among 512575 single-nucleotide polymorphisms (SNPs), 23 and 11 common SNPs suggested a genome-wide interaction threshold (p<1.25×10-8) involving rs700651 (BOLL) and rs6841581 (EDNRA). Rather than singe SNP effect of BOLL or EDNRA on IA development, they showed a synergistic effect on IA formation via multifactorial pair-wise interactions. The rs1105980 of PTCH1 gene showed the most significant interaction with rs700651 (natural log-transformed odds ratio [lnOR], 1.53; p=6.41×10-11). The rs74585958 of RYK gene interacted strongly with rs6841581 (lnOR, -19.91; p=1.64×10-9). Although, there was no direct interaction between BOLL and EDNRA variants, two EDNRA-interacting gene variants of TNIK (rs11925024 and rs1231) and FTO (rs9302654), and one BOLL-interacting METTL4 gene variant (rs549315) exhibited marginal interaction with BOLL gene. Conclusion : BOLL or EDNRA may have a synergistic effect on IA formation via multifactorial pair-wise interactions.

Polymorphisms and expression levels of TNP2, SYCP3, and AZFa genes in patients with azoospermia

  • Mohammad Ismael Ibrahim Jebur;Narges Dastmalchi;Parisa Banamolaei;Reza Safaralizadeh
    • Clinical and Experimental Reproductive Medicine
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    • 제50권4호
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    • pp.253-261
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    • 2023
  • Objective: Azoospermia (the total absence of sperm in the ejaculate) affects approximately 10% of infertile males. Despite diagnostic advances, azoospermia remains the most challenging issue associated with infertility treatment. Our study evaluated transition nuclear protein 2 (TNP2) and synaptonemal complex protein 3 (SYCP3) polymorphisms, azoospermia factor a (AZFa) microdeletion, and gene expression levels in 100 patients with azoospermia. Methods: We investigated a TNP2 single-nucleotide polymorphism through polymerase chain reaction (PCR) restriction fragment length polymorphism analysis using a particular endonuclease. An allele-specific PCR assay for SYCP3 was performed utilizing two forward primers and a common reverse primer in two PCR reactions. Based on the European Academy of Andrology guidelines, AZFa microdeletions were evaluated by multiplex PCR. TNP2, SYCP3, and the AZFa region main gene (DEAD-box helicase 3 and Y-linked [DDX3Y]) expression levels were assessed via quantitative PCR, and receiver operating characteristic curve analysis was used to determine the diagnostic capability of these genes. Results: The TNP2 genotyping and allelic frequency in infertile males did not differ significantly from fertile volunteers. In participants with azoospermia, the allelic frequency of the SYCP3 mutant allele (C allele) was significantly altered. Deletion of sY84 and sY86 was discovered in patients with azoospermia and oligozoospermia. Moreover, SYCP3 and DDX3Y showed decreased expression levels in the azoospermia group, and they exhibited potential as biomarkers for diagnosing azoospermia (area under the curve, 0.722 and 0.720, respectively). Conclusion: These results suggest that reduced SYCP3 and DDX3Y mRNA expression profiles in testicular tissue are associated with a higher likelihood of retrieving spermatozoa in individuals with azoospermia. The homozygous genotype TT of the SYCP3 polymorphism was significantly associated with azoospermia.

한국재래닭의 ADSL 유전자 내 단일염기변이를 이용한 경제형질과의 연관성 분석 (Identification of Novel Single Nucleotide Polymorphisms on ADSL Gene Using Economic Traits in Korean Native Chicken)

  • 이진아;전세아;오재돈;박경도;최강덕;전광주;이학교;공홍식
    • 한국가금학회지
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    • 제36권3호
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    • pp.207-213
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    • 2009
  • 퓨린 합성의 반응을 촉진시키며 뇌기능장애, 성장장애 그리고 에너지대사에 핵심적인 역할을 하는 ADSL(Adenylosuccinate lyase)의 exon 영역을 중심으로 PCR을 수행하여 DNA 염기서열 분석을 통해 한국재래닭에서 단일염기다형성을 확인하였다. 염기분석 결과 총 11개(intron 5: T7724C, C7732T intron 8: G10108T intron 9: A10356T, G10375A, A10402 intron 10: A12716T, T12717A intron 12: C15491T exon 13: C15542T, C15550T)를 확인할 수 있었으며 특히 exon 13지역의 변이들은 각각 아미노산이 바뀌는 missense mutation 임이 확인되었다(Alanine$\rightarrow$Valine, Proline$\rightarrow$Serine). 또한 C15542T 변이는 NCBI의 SNP 데이터베이스에 등록된 것으로 확인되었고, C15550T는 SNP 데이터베이스에 등록되지 않은 신규 변이지역으로 확인되었다. 이는 단백질 발현이 향상되는 3'UTR 지역 근처인 exon 13 부위이며 추가적으로 ADSL 유전자의 아미노산 변이가 닭 집단의 성장 및 에너지 대사와의 연관성 검증을 통해 본 연구 결과는 중요하게 활용될 것으로 기대된다.

Interleukin-10 Gene Promoter Polymorphisms and Risk of Gastric Cancer in a Chinese Population: Single Nucleotide and Haplotype Analyses

  • Pan, Xiong-Fei;Yang, Shu-Juan;Loh, Marie;Xie, Yao;Wen, Yuan-Yuan;Tian, Zhi;Huang, He;Lan, Hui;Chen, Feng;Soong, Richie;Yang, Chun-Xia
    • Asian Pacific Journal of Cancer Prevention
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    • 제14권4호
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    • pp.2577-2582
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    • 2013
  • Objectives: Interleukin (IL) -10 is a potent cytokine with a dual ability to immunosuppress or immunostimulate. We aimed to explore the association of IL10 promoter polymorphisms with risk of gastric cancer (GC) in a Han population in Southwestern China. Methods: We enrolled 308 pairs of GC and control subjects from four hospitals and a community between October 2010 and August 2011 in a 1:1 matched case-control design. Demographic information was collected using a designed questionnaire. IL10-592 A>C and IL10-1082 A>G polymorphisms were determined by Sequenom MassARRAY analysis. Results: Patients with GC reported statistically higher proportions of family history of cancer (29.9% versus 10.7%, P<0.01) and alcohol drinking (54.6% versus 43.2%, P<0.01) than did controls. Similar results were observed in comparison between non-cardia GC patients and controls (P<0.01 and P=0.03). Variant genotypes of IL10-592 A>C and IL10-1082 A>G were not associated with overall GC risk (adjusted OR, 0.94, 95% CI, 0.66-1.33; adjusted OR, 1.00, 95% CI, 0.62-1.60). Sub-analysis showed that the IL10-592 AC/CC variant genotype was associated with decreased non-cardia GC risk (adjusted OR, 0.58; 95% CI, 0.36-0.95). No association was found between any of the IL10 haplotypes established from two polymorphisms and risk of non-cardia GC. Conclusions: In conclusion, our data do not link the two SNPs of IL10-592 and IL10-1082 with overall GC risk. We demonstrate that IL10-592 polymorphism is associated with protective effect against non-cardia GC. Our findings may offer insight into risk associated with the development of GC in this region.