• 대한예방한의학회지
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• 제14권1호
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• pp.111-123
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• 2010

Backgrounds : Stroke is characterized by loss of brain functions due to a disturbance in the blood vessels supplying blood to the brain, and classified into hemorrhage and ischemia. Stroke is known to be affected by genetic factors and other diseases such as hypertension and cardiovascular diseases. However, the distinctive association between stroke and genetic variations has not discovered yet. Objectives : This study investigated the effects of fibrinogen level and genetic variations in FGA (Fibrinogen alpha chain) gene on stroke in Korean stroke patients and controls. Methods : DNA samples from 674 stroke patients diagnosed by Oriental medical hospitals and 267 controls were used in this study. Two common single nucleotide polymorphism(SNP) with high minor allele frequency(MAF), rs2070011G/A of promoter region and nonsynonymous rs6050A/G of exon 5 in FGA gene, were targeted for Taqman genotyping. Because the TOAST classification is important to the factors and symptoms of stroke, ischemic patients were further classified into five subtypes using diagnosis and clinical data. One-way ANOVA and chi-square test were used for clinical data and genetic association, respectively. Haploview v4.1 program was used for linkage disequilibrium(LD), haplotype and haplotype block analysis. Results : The levels of red blood cells and fibrinogen from clinical data were shown to be significant factors for the sub-groups of TOAST classification. No significant associations of stroke, hemorrhage, ischemic and subtypes of TOAST with rs2070011 and rs6050 of FGA gene were found(P > 0.05). However, rs2070011 in promoter region and nonsynonymous rs6050 in exon 5 which produce the amino acid change from threonine to alanine showed a haplotype block and three haplotypes of A-G, G-A, A-A, suggesting that rs2070011 and rs6050 might be co-segregated in generic recombination. Although A-A haplotype of stroke patients showed 64-69% low frequency compared to controls, there was no significant association between stroke and haplotype(P > 0.05). Conclusion : This study showed that there was no significant association between stroke and two SNP of rs2070011G/A and nonsynonymous rs6050A/G in FGA gene. However, these two SNP compose a haplotype block and three haplotypes of A-G, G-A, A-A. This finding suggests that rs2070011 and rs6050 are so close as to be positioned as linkage disequilibrium. Nevertheless, no significant association between haplotypes and stroke was found.

• Clinical and Experimental Reproductive Medicine
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• 제41권3호
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• pp.120-124
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• 2014

Objective: The aim of the present study was to examine whether interactions between polymorphisms in the thyroglobulin and ADAM metallopeptidase with thrombospondin type 1 motif, 16 (ADAMTS16) genes are associated with the development of premature ovarian failure (POF). Methods: A total of 75 patients with POF and 196 controls were involved in this study. We used a GoldenGate assay to genotype single nucleotide polymorphisms (SNPs). Logistic regression analysis was performed to identify POF-associated polymorphisms and synergistic interactions between polymorphisms in the thyroglobulin and ADAMTS16 genes. Results: Single gene analyses using logistic regression analysis showed no significant association between polymorphisms in the two genes and POF. In the results from interaction analyses, we found seven synergistic interactions between the polymorphisms in thyroglobulin and ADAMTS16, although there was no combination showing p-values lower than the significant threshold using the Bonferroni correction. When the AG genotype was present at the rs853326 missense SNP, the A and G alleles at the tagging SNPs rs16875268 and rs13168665 showed significant interactions (odds ratios=5.318 and 16.2 respectively; 95% confidence intervals, 1.64-17.28 and 2.08-126.4; p=0.0054 and 0.0079). Conclusion: Synergistic interactions between polymorphisms in the thyroglobulin and ADAMTS16 genes were associated with an increased risk of POF development in Korean women.

• The Korean Journal of Physiology and Pharmacology
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• 제12권3호
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• pp.125-129
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• 2008

The aim of this study was to determine whether single nucleotide polymorphisms (SNPs) of matrix metallopeptidase 2 (MMP2) are associated with obesity. MMP2 is an enzyme with proteolytic activity against matrix and nonmatrix proteins, particularly basement membrane constituents. To identify the relationship between polymorphisms of MMP2 and overweight/obese, we genotyped 5 SNPs (rs17242319, rs1053605, rs243849, rs2287074, and rs10775332) of the coding region of MMP2 using the Golden Gate assay on an Illumina BeadStation 500 GX. One hundred and forty two overweight/obese ($BMI\;{\ge}\;23$) and 145 normal (BMI 18 to < 23) subjects were analyzed. SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs were used for the analysis of genetic data. A linkage disequilibrium (LD) block was discovered among the 5 SNPs selected, including rs17242319, rs1053605, rs243849, and rs2287074. Of the 5 polymorphisms, 2 synonymous SNPs [rs17242319 (Gly226Gly) and rs10775332 (Phe602Phe)] were found significant associations with overweight/obese. Recently, rs1132896 replaced rs17242319 as a new number (SNP database, BUILD 129). In haplotype analysis using Haploview, a haplotype (haplotype: CCCA) containing a meaningful polymorphism (rs17242319) was found to be significantly different. The results suggest that MMP2 may be associated with overweight/obese in Korean population.

• 대한의생명과학회지
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• 제24권1호
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• pp.23-29
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• 2018

Abdominal obesity is considered as one of the most risky factors governing the development of metabolic diseases. Here we identify that human chitinase 3-like 1 (CHI3L1, also called YKL-40 in human) single nucleotide polymorphism (SNP), rs883125, is associated with abdominal obesity in Korean women. Korean women subjects with the rs883125 G/G or C/G genotype present higher waist-hip ratio than subjects with C/C genotype suggesting that human subjects who G nucleotide substitution at the rs883125 tended to more accumulate intra-abdominal fat at the abdominal cavity. In addition, Chi3l1 gene expression is increased in adipose tissue from obese mice and pro-inflammatory cytokine enhances Chi3l1 expression in adipocytes, indicating that Chi3l1 is greatly related with obesity and obesity-induced pro-inflammatory responses. Taken together, the minor allele of rs883125 is associated with a higher prevalence of abdominal obesity in Korean women. These findings suggest that genotype of rs883125 can be a biomarker of incident abdominal obesity and abdominal obesity-related metabolic diseases.

• 한국균학회지
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• 제49권1호
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• pp.33-44
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• 2021

본 연구에서는 국내에 유통되고 있는 40개 표고 품종들로부터 산백향과 설백향의 구분이 가능한 CAPS 마커를 개발하였다. 제한효소 Hha I 과 HpyCH4IV를 이용한 밴드 패턴 분석을 통해 각각 산백향과 설백향을 다른 균주들과 구분하여 구별성을 확보할 수 있었다. 본 연구에서 개발된 CAPS 마커는 표고의 품종들 간에 유전적 다양성을 부여함으로써, 품종을 보호할 수 있는 분자생물학적 근거가 될 수 있다. 이로써 향후 유전자원에 대한 국가간 분쟁을 미연에 방지할 수 있을 것이다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권18호
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• pp.8377-8382
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• 2016

Background: The aim of this study was to evaluate any association between a single nucleotide polymorphism (SNP) in the patatin-like phospholipase domain containing 3 (PNPLA3) (rs738409, C>G) and the development and prognosis in patients with hepatocellular carcinoma (HCC). Materials and Methods: Two hundred heathy controls and 388 HCC cases were included: 211 with HBV, 98 patients with HCV, 29 with alcoholic steatohepatitis (ASH) and 52 with non-alcoholic steatohepatitis (NASH). The SNP was determined by real-time PCR based on TaqMan assays. Results: The prevalence of rs738409 genotypes CC, CG and GG in controls was 91 (45.5%), 88 (44.0%), and 21 (10.5%), respectively, while the corresponding genotypes in all patients with HCC was 158 (40.7%), 178 (45.9%), and 52 (13.4%). The GG genotype had significantly higher distribution in patients with ASH/NASH-related HCC compared with controls (OR=2.34, 95% CI=1.16-4.71, P=0.018), and viral-related HCC cases (OR=2.15, 95% CI=1.13-4.08, P=0.020). However, the frequency of the GG genotype was similar between controls and patients with viral-related HCC. At initial diagnosis, HBV-related HCC were larger and at more advanced BCLC stage than the other HCC groups. There were no significant differences between the GG and non-GG groups regarding clinical characteristics, tumor stage and overall survival. Conclusions: These data suggest an influence of the PNPLA3 polymorphism on the occurrence of HCC in patients with ASH/NASH but not among those with chronic viral hepatitis. However, the polymorphism was not associated with the prognosis of HCC.

• Animal Bioscience
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• 제34권4호
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• pp.489-498
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• 2021

Objective: Milk production is one of the most desirable traits in livestock. Recently, the toll-like receptor (TLR) has been identified as a candidate gene for milk traits in cows. So far, there is no information concerning the contribution of this gene in milk traits in sheep. This study was designed to investigate the TLR 4 gene polymorphisms in Barki ewes in Egypt and then correlate that with milk traits in order to identify potential single nucleotide polymorphisms (SNPs) for these traits in sheep. Methods: A part of the ovine TLR 4 gene was amplified in Barki ewes, to identify the SNPs. Consequently; Barki ewes were genotyped using polymerase chain reaction-single strand conformation polymorphism protocol. These genotypes were correlated with milk traits, which were the daily milk yield (DMY), protein percentage (PP), fat percentage (FP), lactose percentage, and total solid percentage (TSP). Results: Age and parity of the ewe had a significant effect (p<0.05 or p<0.01) on DMY, FP, and TSP. The direct sequencing identified a missense mutation located in the coding sequence of the gene (rs592076818; c.1710C>A) and was predicted to change the amino acid sequence of the resulted protein (p.Asn570Lys). The association analyses suggested a significant effect (p<0.05) of the TLR genotype on the FP and PP, while the DMY tended to be influenced as well (p = 0.07). Interestingly, the presence of the G allele tended to increase the DMY (+40.5 g/d) and significantly (p<0.05 or p<0.01) decreased the FP (-1.11%), PP (-1.21%), and TSP (-7.98%). Conclusion: The results of this study suggested the toll-like receptor 4 (TLR4) as a candidate gene to improve milk traits in sheep worldwide, which will enhance the ability to understand the genetic architecture of genes underlying SNPs that affect such traits.

• Reproductive and Developmental Biology
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• 제38권3호
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• pp.123-127
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• 2014

This study was conducted for SNPs in the 5'-regions of estrogen receptor-${\alpha}$ (ESR-${\alpha}$), and association with calving interval (CI), service per conception (SPC) and 305 days milk yield in Hanwoo and Holstein dairy cattle. The genetic improvement was incurred low reproduction performance. The objective of this study was to investigate connections between single nucleotide polymorphisms (SNP) of Estrogen receptor-${\alpha}$ (ESR-${\alpha}$) with reproduction performance (calving interval, service per conception, and 305 d milk yield) in Hanwoo and Holstein dairy cattle. Hanwoo and Holstein blood samples were collected from 183 and 124 dam of breeding farms and DNA was extracted. Primer design was based on NCBI GenBank (Accession No. AY340579). The PCR-RFLP method with Bgl I was used to genotype the cattle. The result showed two variants of the ESR-${\alpha}$ gene. The Bgl I cut the 492 bp amplification product into 322 bp and 170 bp fragments for allele G, while allele A remained uncut, resulting in two restriction fragments for homozygote G/G and three fragments for heterozygote A/G. We found two of different genotypes in these breeds, A/G and G/G. In Hanwoo, the A/G genotype frequency was 0.13, and G/G was 0.87. The CI of A/G was $382.18{\pm}10.03$ days, and G/G was $381.69{\pm}5.22$ days. The SPC of A/G was $1.62{\pm}0.16$, and G/G was $1.32{\pm}0.04$. While CI showed no significance difference, SPC exhibited significant difference (p<0.05). In Holstein cattle, the frequency of genotype A/G was 0.02 and G/G was 0.98. The 305 days milk yield of A/G was $7,253.00{\pm}936.00kg$ and of G/G was $8,747.51{\pm}204.88kg$, showing no significant difference.

• Journal of Animal Science and Technology
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• 제53권4호
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• pp.311-317
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• 2011

본 연구는 한우에서 소 염색체 14번(BTA14)에서 근내지방도 및 도체중과 관련성이 보고된 QTL영역(48-58cM) 내의 FABP5 유전자를 대상으로 SNP를 발굴하고 도체형질과의 관련성 분석을 위하여 수행하였다. PCR 및 염기서열결정법을 통해 FABP5 유전자내 4개의 SNP (-1141A>G, 949A>G, 969A>G, 1085C>G)를 발굴하였고, 이중 promoter 영역에 위치하는 SNP의 경우 미 보고된 신규 SNP로 확인되었다. 발굴된 4개의 SNP를 대상으로 표현형 기록치를 보유한 후대검정후 583두에 대하여 유전자형 분석 및 관련성 분석을 수행하였다. 분석 결과 4개의 SNP중 SNP1(-1141A>G)은 근내지방도에 있어서 G유전자형이 A유전자형에 비해서 근내지방도가 2.2 정도 높았고, SNP2 (949A>G)는 배최장근 단면적에 있어서 G유전자형이 A유전자형보다 배장근단면적에 있어서 3 $cm^2$ 만큼 높은 효과를 보였다. 본 결과에 대해 추후 지속적인 연구가 요구되어지며, FABP5의 SNPs은 한우의 도체 및 육질 관련 형질을 위한 유전자 마커로서 활용 가능할 수 있을 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권8호
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• pp.1066-1074
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• 2015

In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five YSNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (${\pi}=5.6{\times}10^{-4}$) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (${\pi}=0.00000$) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.