• Genomics & Informatics
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• v.13 no.4
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• pp.146-151
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• 2015

Previous studies in Holstein have shown 35% to 51.8% heritability in milk production traits, such as milk yield, fat, and protein, using pedigree data. Other studies in complex human traits could be captured by common single-nucleotide polymorphisms (SNPs), and their genetic variations, attributed to chromosomes, are in proportion to their length. Using genome-wide estimation and partitioning approaches, we analyzed three quantitative Holstein traits relevant to milk production in Korean Holstein data harvested from 462 individuals genotyped for 54,609 SNPs. For all three traits (milk yield, fat, and protein), we estimated a nominally significant (p = 0.1) proportion of variance explained by all SNPs on the Illumina BovineSNP50 Beadchip ($h^2_G$). These common SNPs explained approximately most of the narrow-sense heritability. Longer genomic regions tended to provide more phenotypic variation information, with a correlation of 0.46~0.53 between the estimate of variance explained by individual chromosomes and their physical length. These results suggested that polygenicity was ubiquitous for Holstein milk production traits. These results will expand our knowledge on recent animal breeding, such as genomic selection in Holstein.

• Genomics & Informatics
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• v.7 no.2
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• pp.53-56
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• 2009

Recent evidence has strongly suggested that the CAP/TC10 pathway is involved in the trafficking, docking, and fusion of vesicles containing the insulin-responsive glucose transporter Glut4 to the plasma membrane. However, little is known about how the genes employed in the CAP/TC10 pathway are associated with the development of type 2 diabetes mellitus. In this study, we sequenced 4 genes of the CAP/TC10 pathway [SORBS1, CBL, CRK, and RHOQ] in 24 individuals to identify genetic variations in these loci. A total of 48 sequence variants were identified, including 23 novel variations. To investigate the possible association with type 2 diabetes mellitus, 3 single nucleotide polymorphisms from SORBS1, 3 from CBL, and 4 from RHOQ were genotyped in 1122 Korean type 2 diabetic patients and 1138 nondiabetic controls. Using logistic regression analysis, 1 significant association between SNP rs1376405 in RHOQ and type 2 diabetes mellitus [OR = 8.714 (C.I. 1.714-44.29), p = 0.009] was found in the recessive model. Our data demonstrate a positive association of the RHOQ gene in the CAP/TC10 pathway with T2DM in the Korean population.

• Environmental Mutagens and Carcinogens
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• v.22 no.1
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• pp.47-53
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• 2002

Essential hypertension is complex disorder influenced by multiple genetic and environmental factors. Alterations of lipid metabolism in plasma have been reported to be related to an increased risk of essential hypertension. The aim of this study was to investigate the relationship between two SNPs of the human LDL receptor and CETP gene and hypertension in Korean population. There were no significant differences in allele and genotype frequencies of two SNPs in normotensives and hypertensives. With respect to Hinc II RFLP in the LDL receptor gene, pooled odds ratio value indicated the significant heterogeneity among populations studied by meta-analysis (Breslow-Day test df = 2, P<0.05). In the case of Bam HI RFLP in the CETP gene,. our study is the first report of an association between the SNP of the CETP gene and hypertension, although our result failed to demonstrate the significant association between the Bam HI RFLP of the CETP gene and hypertension in Korean population. Further work, using larger sample sizes and various ethnic groups, is required to establish the precise role of these two candidate gene polymorphisms on hypertension.

• Animal Bioscience
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• v.36 no.1
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• pp.19-28
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• 2023

Objective: The objective of this study was to perform genome (genome wide association studies [GWAS]) and chromosome (CWAS) wide association analyses to identify single nucleotide polymorphisms (SNPs) associated with growth traits in registered Simmental and Simbrah cattle. Methods: The phenotypes were deregressed BLUP EBVs for birth weight, weaning weight direct, weaning weight maternal, and yearling weight. The genotyping was performed with the GGP Bovine 150k chip. After the quality control analysis, 105,129 autosomal SNP from 967 animals (473 Simmental and 494 Simbrah) were used to carry out genotype association tests. The two association analyses were performed per breed and using combined information of the two breeds. The SNP associated with growth traits were mapped to their corresponding genes at 100 kb on either side. Results: A difference in magnitude of posterior probabilities was found across breeds between genome and chromosome wide association analyses. A total of 110, 143, and 302 SNP were associated with GWAS and CWAS for growth traits in the Simmental-, Simbrah- and joint -data analyses, respectively. It stands out from the enrichment analysis of the pathways for RNA polymerase (POLR2G, POLR3E) and GABAergic synapse (GABRR1, GABRR3) for Simmental cattle and p53 signaling pathway (BID, SERPINB5) for Simbrah cattle. Conclusion: Only 6,265% of the markers associated with growth traits were found using CWAS and GWAS. The associated markers using the CWAS analysis, which were not associated using the GWAS, represents information that due to the model and priors was not associated with the traits.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.14
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• pp.5895-5900
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• 2014

Background: Metabolic syndrome (MS) is a cluster of complicated disorders caused by the interactive influencing factors of heredity and environment, which predisposes to many cnacers. Results from epidemic research indicate that stress is tightly related to the pathogenesis of MS and neoplasia. This paper aims to investigate the association between psychological stress and MS with respect to the tumor necrosis factor alpha (TNF${\alpha}$) and neuropeptide Y (NPY) genes in the Han and Hui ethnic groups. Methods: All subjects for this case-control study matched strict enrollment criteria (nationality, gender and age) and lived in the city of Wu Zhong of Ningxia Province in China. The enrolled group contained 102 matched pairs of Hui ethnic individuals and 98 matched pairs of Han ethnic individuals. Enrolled subjects completed the general Symptom Checklist-90 (SCL-90). The TNF${\alpha}$-308G/A variant and NPYrs16147 polymorphism were detected in case (81 males, 119 females) and control (81 males, 119 females) groups by polymerase chain reaction (PCR) amplification. Results: Nine factors of the SCL-90 were found to be statistically different (p<0.05) between case and control groups. The homozygous mutant genotype (AA) and the mutant allele (A) of the TNF${\alpha}$-308G/A gene were less frequently observed in the control population compared to the case group. The odds ratio (95% confidence interval) in "Allele" for MS was 2.28 (1.47-3.53), p=0.0001, while "OR" was 1.11 (0.83-1.47), p=0.15, for the NPYrs16147 gene polymorphism. Conclusions: Psychological stress has been positively associated with MS. A previous study from our group suggested there were differences in the level of psychological stress between Hui and Han ethnic groups. Furthermore, we found that the stress-related TNF${\alpha}$ gene was associated with MS for both Han and Hui ethnic groups. In contrast, NPY may be a possible contributor to MS and associated cancer for the Han ethnic group.

• Journal of Animal Science and Technology
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• v.53 no.5
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• pp.389-395
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• 2011

This study was conducted to investigate the combined effect of fatty acid synthase (FASN) and Acetyl CoA Carboxylase-${\alpha}$ (ACACA) genes on carcass traits of Korean cattle (Hanwoo). A total of 1,057 commercial Hanwoo cattle provided by the NongHyup Livestock Research Center (NLRC) and Hanwoo Performance Competition (HPC) were used to analyze the effect of four single nucleotide polymorphisms (SNPs) within FASN (g.11280A>G, g.16024A>G, g.16039T>C, and g.17924A>G) and one SNP within ACACA (g.2274G>A) genes. In addition, the effect of genotypic combinations between FASN (g.17924A>G) and ACACA (g.2274G>A) SNPs has been studied with carcass traits. Significant associations were identified between g.17924A>G of FASN and carcass weight and back fat, and between the ACACA gene SNP g.2274G>A and longissimus muscle area with HPC samples. It was also found that both effects of FASN g.17924A>G and ACACA g.2274G>A polymorphisms were consistent in NLRC samples. Combined analyses of both NLRC and HPC samples also revealed the significant associations between the FASN g.17924A>G and carcass weight and back fat and between the ACACA g.2274G>A and back fat, respectively. The effect of the genotypic combination of g.17924A>G within FASN and g.2274G>A within ACACA genes showed that the combination of both GG genotypes of FASN and ACACA SNPs causes higher carcass weight and marbling score. The results of this study indicate that the two SNP markers within the FASN and ACACA genes can be utilized to select superior Hanwoo cows and calves in commercial Hanwoo farms.

• Clinical and Experimental Pediatrics
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• v.53 no.4
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• pp.548-553
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• 2010

Purpose : IgA nephropathy (IgAN) is the most commonly occurring form of chronic glomerulonephritis in pediatric cases. Human leukocyte antigen (HLA) genes have been implicated in various inflammatory and autoimmune diseases. The present study was conducted to investigate the association between 2 single nucleotide polymorphisms (SNPs) of the HLA-G gene and childhood IgAN. Methods : The authors analyzed and compared $HLA-G$ gene SNPs (rs1736936 and rs2735022) in 174 patients with childhood IgAN and in 438 healthy controls. In addition, IgAN patients were dichotomized and compared with respect to proteinuria (< and >$4mg/m^2/hour$), the presence or absence of podocyte foot process effacement, and the presence of pathologically early and advanced disease markers such as interstitial fibrosis, tubular atrophy, or global sclerosis. Results : No significant SNP frequency differences were observed for the $HLA-G$ gene between IgAN patients and the control group. Moreover, no significantly associated SNP was observed with the presence of proteinuria, podocyte foot process effacement, or pathologically advanced markers. However, the haplotype, composed of rs1736936 and rs2735022, showed a significant association with the susceptibility to develop childhood IgAN (haplotype T/C: dominant model, $P$=0.049; haplotype C/T: recessive model, $P$=0.030). Conclusion : Our results indicate that rs1736936 and rs2735022 as the $HLA-G$ gene promoter haplotype might be associated with the susceptibility to develop childhood IgAN in the Korean population.

• Journal of Animal Science and Technology
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• v.45 no.5
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• pp.703-710
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• 2003

The purpose of this study was to detect association between genetic variation and economic trait in the porcine heart type fatty acid-binding protein gene as a candidate gene for the traits related with growth and meat quality in pigs. The H-FABP is a 15-kDa protein expressed in several tissues with high demand for fat metabolism such as cardiac and skeletal muscle and lactating mammary gland. H-FABP is small intracellular protein involved in fatty acid transport from the plasma membrane to the site of $\beta$-oxidation and/or triacylglycerol or phospholipid synthesis. In this study, H-FABP PCR-RFLP was performed in F$_2$ population composed of 214 individuals from an intercross between Korean Native Boars and Landrace sows. PCR products from two primer sets within H-FABP gene were amplified in 850bp and 700bp. Digestion of PCR products with the restriction digestion enzymes HaeⅢ and HinfⅠ, revealed fragment length polymorphisms(RFLPs). The genotype frequencies from H-FABP/HaeⅢ was .29 for genotype DD, .53 for genotype Dd, and .15 for genotype dd, respectively. The genotype frequencies of HH, Hh, and hh from H-FABP/HinfⅠ was .38, .41 and .20, respectively, in the population. Relationships between their genotypes and economic traits were estimated. In H-FABP/HaeⅢ locus, there were specific genotypes(Dd and dd) associated with economic traits such as body weights at 3, 5, 12, and 30 week of age (p〈.05 to .001). The ‘d’ allele was associated with gaining of body weight. In H-FABP/HinfⅠ locus, Genotypes of HH and Hh associated with growth traits such as body weights at 5, 12, and 30 week of age (p〈.05 or p〈.001) and back fat thickness, body fat including abdominal and trimmed fat (p〈.001) and intramuscular fat(p〈.05) The ‘H’ allele was positively associated with gaining of body weight and fatness deposition. In conclusion, a significant association of the H-FABP gene from its genetic variation was found on body weight, intramuscular fat and backfat thickness.

• Tuberculosis and Respiratory Diseases
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• v.50 no.4
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• pp.473-483
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• 2001

Background : There are only a few studies regarding the causes of treatment failure for tuberculosis. Therefore, this study aimed to determine the causes of intractable tuberculosis. Methods : M. tuberculosis, differentiated MOTT (Mycobacterium Other Than Tuberculosis) were isolated, and the RFLP (Restriction fragments length polymorphisms) pattern was analyzed from 204 patients with pulmonary tuberculosis and 53 suffering from neck tuberculosis. The IL-$1{\beta}$, IL-12, $^*1\;IFN{\gamma}$ and $^*2\;TNF{\alpha}$ blood levels were measured. All patients were regularly followed for 18 months after treatment. Results : There was no correlation between the RFLP patterns of M. tuberculosis treatment failure. From the 204 cases, 31.9% were intractable. The characteristics of patients with intractable tuberculosis were old age, being male and recurrent cases. The causes of treatment failure were identified as follows ; a decrease in the IL-12(59.4%) concentration, drug resistant strain(54.7%), irregular medication(15.4%), MOTT(6.2%) and a heavy infection(4.6%). The causes of all cases of intractable tuberculosis could be investigated. The IL-12 concentration in the blood was significantly lower in the intractable cases, where it disclosed a maximum sensitivity(64.7%) and specificity(75.4%) at 165.0 pg/mL. Most of the 53 cases of neck node tuberculosis were treated successfully. Therefore, we were unable to analyze the cause of treatment failure. Conclusion : A decrease in the blood IL-12 concentration and drug resistant strains were identified as the most significant causes of treatment failure for tuberculosis. In Korea, infection by clusters were prevalent, but no difference in the clinical course between clusters and non-clusters could be found.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.5
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• pp.1749-1752
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• 2012

Colorectal cancer (CRC), now the third most common cancer across the world, is known to aggregate in families. USP7 is a very important protein with an important role in regulating the p53 pathway, which is critical for genomic stability and tumor suppression. We here genotyped eight SNPs within the USP7 gene and conducted a case-control study in 312 CRC patients and 270 healthy subjects in the Chinese Han population. No significant associations were found for any single SNP and CRC risk. Our data eliminate USP7 as a potential candidate gene towards for CRC in the Han Chinese population.