• Asian-Australasian Journal of Animal Sciences
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• v.20 no.3
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• pp.328-333
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• 2007

Carboxypeptidase E (CPE) plays an important role in the regulation of the body fat content. Therefore, it has been suggested as candidate gene for traits related to meat quality in beef cattle. This study was conducted to identify single nucleotide polymorphisms (SNPs) in the CPE gene and to investigate association of SNP marker with carcass and meat quality traits in Korean cattle. Three SNPs were identified in the intron 4 (A309G SNP and C445T SNP) and exon 5 (C601T SNP) of the CPE gene by sequence analyses of CPE cDNA and genomic DNA samples. The sequences have been deposited in GenBank database with accession numbers AY970664 and AY970663. Genotyping of the gene-specific SNP marker was carried out using the PCR-RFLP with restriction enzymes DdeI for C445T SNP and NlaIII for C601T SNP. The frequencies of C and T alleles were 0.43 and 0.57 for C445T SNP and 0.42 and 0.58 for C601T SNP, respectively. Statistical analysis indicated that the C445T SNP showed a significant effect (p<0.05) on marbling score (MS) and breeding value of backfat thickness (BF-EBV), respectively. Animals with the CT genotype showed higher marbling score and backfat thickness than those with the TT genotype. This marker also showed a significant dominance effect for the MS and BF-EBV (p<0.05). However, no significant associations were observed between C601T SNP genotypes and all traits examined. The results suggest that the CPE gene may be used as a marker for carcass traits in Korean cattle.

• Animal cells and systems
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• v.1 no.1
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• pp.129-134
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• 1997

HLA-A2 is one of the most diversified HLA-class I antigen with 17 subtypes so far identified at the molecular level. HLA-A*02 subtyping has significant implications on the tissue typing for organ and bone marrow transplantations. Recently, DNA-based typing methods have been successfully applied to the elucidation of HLA gene polymorphisms. In the present study, HLA-A*O2 genotyping was established by using nested polymerase chain reaction-sequence specific primers (PCR-SSP) and distribution of A*O2 alleles were determined in Korean individuals. Genomic DNA prepared from four B-lymphoblastoid cell lines and lymphocytes from serologically defined 48 HLA-A2 Korean individuals by phenol/chloroform extractions was typed. The results of the four B-lymphoblastoid cells were consistent with the previous data typed by PCR analysis. Five A*O2 alleles-A*0201, A*0203, A*0206, A*0207 and A*0210-were commonly observed in a total of 17 A*02 alleles. Of these, A*0207 (f=49.0%) was the most frequent allele in Korean population. A*0206 (f=28.3%) and A*0201 (f=17.0%) were also found frequently while A*0203 and A*0210 types were observed in less than 5%. In conclusion, the high level of discrimination for HLA-A*O2 alleles will prove useful and informative in the study of transplant survival, and may identify the importance of allelic differences not readily detectable by serology on host and donor compatibility.

• Journal of Digital Convergence
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• v.14 no.1
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• pp.321-326
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• 2016

The aim of this study was to evaluate the association between TNF polymorphism and generalized aggressive periodontitis (GAP) in Korean subjects. The study population consisted of 60 subjects with GAP and 81 reference group. Genomic DNA was extracted from the buccal swabs and the polymorphisms of $TNF-{\alpha}-308$, -238 promoter genes, $TNF-{\beta}+252$ and TNFR 2+587 were determined by PCR-RFLP using restriction enzymes. The genotype distribution in the GAP were 3.2%, 38.7%, and 82.35% for A/A, A/G and G/G genotypes of $TNF-{\alpha}-308$. At the position of $TNF-{\alpha}-238$, the genotype distribution in the GAP were 25.5% and 74.5% for A/G and G/G genotypes. Allele A frequency of $TNF-{\alpha}-238$ were 67.6% in GAP and 72.2% in reference group. According to these findings, the polymorphism at $TNF-{\alpha}-308$ and -238 may be associated with GAP in Korean.

• Genes and Genomics
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• v.40 no.12
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• pp.1279-1285
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• 2018

Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.2
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• pp.163-169
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• 2012

Interferon regulatory factor 6 (IRF6) gene is a member of the IRF-family, and plays functionally diverse roles in the regulation of the immune system. In this report, the 13,720 bp porcine IRF6 genomic DNA structure was firstly identified with a putative IRF6 protein of 467 amino acids. Alignment and phylogenetic analysis of the porcine IRF6 amino acid sequences with their homologies to other species showed high identity (over 96%). Tissues expression of IRF6 mRNA was observed by RT-PCR, the results revealed IRF6 expressed widely in eight tissues. One SNP (HQ026023:1383 G>C) in exon7 and two SNPs (HQ026023:130 G>A; 232 C>T) in the 5′ promoter region of porcine IRF6 gene were demonstrated by DNA sequencing analysis. A further analysis of SNP genotypes associated with immune traits including IFN-${\gamma}$ and IL10 concentrations in serum was carried out in three pig populations including Large White, Landraces and Songliao Black pig (a Chinese indigenous breed). The results showed that the SNP (HQ026023:1383 G>C) was significantly associated with the level of IFN-${\gamma}$ (d 20) in serum (p = 0.038) and the ratio of IFN-${\gamma}$ to IL10 (d 20) in serum (p = 0.041); The other two SNPs (HQ026023:130 G>A; 232 C>T) were highly significantly associated with IL10 level in serum both at the day 20 (p = 0.005; p = 0.001) and the day 35 (p = 0.004; p = 0.006). Identification of the porcine IRF6 gene will help our further understanding of the molecular basis of the IFN regulation pathway in the porcine immune response. All these results should indicate that the IRF6 gene can be regarded as a molecular marker associated with the IL10 level in serum and used for genetic selection in the pig breeding.

• Asian-Australasian Journal of Animal Sciences
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• v.25 no.8
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• pp.1089-1095
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• 2012

Neonatal Fc receptor (FcRn) gene encodes a receptor that binds the Fc region of monomeric immunoglobulin G (IgG) and is responsible for IgG transport and stabilization. In this report, the 8,900 bp porcine FcRn genomic DNA structure was identified and putative FcRn protein included 356 amino acids. Alignment and phylogenetic analysis of the porcine FcRn amino acid sequences with their homologies of other species showed high identity. Tissues expression of FcRn mRNA was detected by real time quantitative polymerase chain reaction (Q-PCR), the results revealed FcRn expressed widely in ten analyzed tissues. One single nucleotide polymorphism (SNP) (HQ026019:g.8526 C>T) in exon6 region of porcine FcRn gene was demonstrated by DNA sequencing analysis. A further analysis of SNP genotypes associated with serum Classical Swine Fever Virus antibody (anti-CSFV) concentration was performed in three pig populations including Large White, Landrace and Songliao Black pig (a Chinese indigenous breed). Our results of statistical analysis showed that the SNP had a highly significant association with the level of anti-CSFV antibody (At d 20; At d 35) in serum (p = 0.008; p = 0.0001). Investigation of expression and polymorphisms of the porcine FcRn gene will help us in further understanding the molecular basis of the antibody regulation pathway in the porcine immune response. All these results indicate that FcRn gene might be regarded as a molecular marker for genetic selection of anti-CSFV antibody level in pig disease resistance breeding programmes.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.8
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• pp.4559-4565
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• 2013

Background: Methylenetetrahydrofolate reductase (MTHFR) is involved in DNA synthesis and repair. We here aimed to investigate two common polymorphisms, C677T and A1298C, with genotype and haplotype frequencies in colorectal cancer (CRC) cases among Jordanian. Materials and Methods: 131 CRC cases were studied for MTHFR C677T and A1298C polymorphisms, compared to 117 controls taken from the general population, employing the PCR-RFLP technique. Results: We found the frequency of the three different genotypes of MTHFR C677T among Jordanians to be CC: 61.7%, CT: 35.2%, and TT 3.1% among CRC cases and 50.9%, 38.8% and 10.3% among controls. Carriers of the TT genotype were less likely to have CRC (OR=0.25; 95%CI: 0.076-0.811; p=0.021) as compared to those with the CC genotype. Genotype analysis of MTHFR A12987C revealed AA: 38.9%, AC: 45%, and CC 16% among CRC cases and 37.4%, 50.4% and 12.2% among controls. There was no significant association between genetic polymorphism at this site and CRC. Haplotype analysis of MTHFR polymorphism at the two loci showed differential distribution of the TA haplotype (677T-1298A) between cases and controls. The TA haplotype was associated with a decreased risk for colorectal cancer (OR=0.6; 95% CI: 0.4-0.9, p=0.03). Conclusions: The genetic polymorphism of MTHFR at 677 and the TA haplotype may modulate the risk for CRC development among the Jordanian population. Our findings may reflect an importance of genes involved in folate metabolism in cancer risk.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.1
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• pp.369-374
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• 2014

Background: Colorectal cancer (CRC) is the fourth most common cause of cancer death in the world. Genetic variants in 8q24.21 including rs10505477 and rs6983267 have been hypothesized to be involved in susceptibility to CRC. This study aims to investigate the possible association between these loci and their haplotypes with CRC risk in Iranian population. Materials and Methods: Subjects were recruited from two hospitals in Tehran. The rs10505477 and rs6983267 polymorphisms were genotyped by TaqMan real time PCR using subject genomic DNA, extracted either from formalin-fixed, paraffin-embedded tissue of patients or from blood of the controls by standard methods. Results: A total of 715 subjects (380 CRC patients and 335 matched controls) were genotyped in this study. Allele and genotype analysis of the rs10505477 and rs6983267 polymorphisms by gender, age at diagnosis, tumor location, tumor grade, and tumor node metastasis (TNM) showed no significant association with CRC risk. There was a significant relationship between GG haplotype and susceptibility to age at diagnosis for both <60 and ${\geq}60$ (p=0.0005 and p=0.000004, respectively) and between GT and CRC in the age at diagnosis ${\geq}60$ (Table 3: p=0.031). The GG haplotype was less frequent in CRC patients with the age at diagnosis <60, but was more common in subjects with the age at diagnosis ${\geq}60$. Conclusions: Results of this study suggests that the rs6983267 and rs10505477 polymorphisms alone may not be relevant to CRC risk, but their GG haplotype plays a notable role in age at diagnosis of CRC in the Iranian population.

• Journal of Animal Science and Technology
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• v.51 no.4
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• pp.289-294
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• 2009

Inositol 1,4,5-triphosphate receptor type 1 (IP3R1) is a $Ca^{2+}$ release channel that responds to the second messenger IP3 and that modulates diverse cellular functions such as contraction/excitation, secretion, gene expression and cellular growth. We discovered single nucleotide polymorphisms (SNPs) within IP3R1 gene and analyzed associations between gene polymorphisms and carcass traits in Korean cattle (Hanwoo) in order to develop novel DNA markers at genomic level. Three SNPs were detected at the position of g.1428617A>G, g.1418843C>T and g.1414377C>T with 24 unrelated Hanwoo samples by direct sequencing of the PCR products. We found that genotype of g.1414377C>T SNP was associated with live weight (P<0.05) and carcass weight (P<0.01) using the general linear model of SAS package. These results suggest that polymorphism of IP3R1 gene was associated with weight-related traits in Hanwoo.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.21 no.1
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• pp.17-22
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• 2010

Objectives ： Autism spectrum disorder (ASD) is a neurodevelopmental disorder that is characterized by abnormalities of social functioning, communication and behavior. The association of the 7q21-34 region with ASD has been reported. The DLX6 gene, which is located at the 7q22 region, is one of the positional and functional candidate genes for ASD. We found that there is no association between DLX6 polymorphisms and ASD in the Korean male population. Methods ： We selected three single nucleotide polymorphisms (SNPs) that might be implicated in the change of the DLX6 gene expression. The genomic DNA was collected from the venous blood of 147 male controls and 179 male patients with ASD. The genotypes of the selected SNPs were determined using the Illumina GoldenGate assay, and the statistical analyses were performed using HapAnalyzer software and SAS Enterprise. Results ： We found no association of the three SNPs in the DLX6 gene with ASD in the Korean male population. Conclusion ： Our study suggests that the three SNPs in the DLX6 gene are not associated with ASD, and we need to analyze the previously reported regions for their associations with ASD.