• Korean Journal of Agricultural Science
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• v.37 no.3
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• pp.399-404
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• 2010

Single nucleotide polymorphisms (SNPs) in chicken lysozyme (LYZ) gene were investigated in this study. The identification of SNPs in both exon and intron in LYZ gene has led to understanding of evolution for the domestic chicken populations. A total of 24 samples from two Korean native commercial chicken populations (CCPs) were used for the initial identification of SNPs by mixing three DNA samples for sequencing experiments. By comparing with red jungle fowl (RJF), two commercial chicken populations have 18 common polymorphisms. Between two commercial chicken populations, 15 polymorphisms were identified. Of the 33 polymorphisms identified, two indels (21 and 4 bp) were found. Whereas, only one polymorphism in exon 2 at the bp position 1426 was a non-synonymous substitution (p.Ala49Val), indicating the amino acid changes. The identified non-synonymous substitution (p.Ala49Val) is located close to the catalytic sites of the enzyme, which might affect its activity. In our investigation, the polymorphisms in LYZ gene can provide broad ideas for the variation of Korean native chicken populations from the ancestor of chicken breeds as well as the some biological functions of the LYZ gene.

• Journal of Genetic Medicine
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• v.21 no.1
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• pp.22-30
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• 2024

Purpose: Neurofibromatosis 1 (NF1) is one of the most common autosomal dominant diseases caused by heterozygous mutation in the NF1 gene. Mutation detection is complex owing to the large size of the NF1 gene, the presence of a high number of partial pseudogenes, and the great variety of mutations. We aimed to study the mutation spectrum of NF1 gene in Korean patients with NF1. Materials and Methods: We have analyzed total 69 unrelated patients who were clinically diagnosed with NF1. PCR and sequencing of the NF1 gene was performed in all unrelated index patients. Additionally, multiplex ligation-dependent probe amplification (MLPA) test of the NF1 and SPRED1 gene analysis (sequencing and MLPA test) were performed in patients with negative results from NF1 gene sequencing analysis. Results: Fifty-five different variants were identified in 60 individuals, including six novel variants. The mutations included 36 single base substitutions (15 missense and 21 nonsense), eight splicing mutations, 13 small insertion or deletions, and three gross deletions. Most pathogenic variants were unique. The mutations were evenly distributed across exon one through 58 of NF1, and no mutational hot spots were found. When fulfilling the National Institutes of Health criterion for the clinical diagnosis of NF1, the detection rate was 84.1%. Cafe-au-lait macules were observed in all patients with NF1 mutations. There is no clear relationship between specific mutations and clinical features. Conclusion: This study revealed a wide spectrum and genetic basis of patients with NF1 in Korea. Our results aim to contribute genetic management and counseling.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.7
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• pp.941-946
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• 2008

Single-minded 1 gene (SIM1) is a homolog of Drosophila SIM1 gene which plays a key role in the midline cell lineage of the central nervous system and is implicated in the regulation of feeding behavior and obesity in the human and mouse. In this study, porcine SIM1 gene was firstly mapped to chromosome 1p13 using radiation hybrid (RH) mapping and two polymorphisms were detected at position 607 (A/G) in SIM1 intron7 and position 780 (C/T) in SIM1 exon8. The last substitution was genotyped in a 364 F2 animal-population and an association analysis of these genotypes was performed with growth, carcass and meat quality traits by the statistical animal model. The results showed the significant influence of the SIM1 genotype on growth (p<0.05): live weight at birth, later period of growth and average daily gain; and effects on carcass composition (p<0.05): weight of head and buck kneed foreleg, backfat depth, loin eye area, carcass leaf fat and ham fat weights; and traits related to intramuscular fat content (p<0.05).

• Journal of The Korean Society of Inherited Metabolic disease
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• v.15 no.3
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• pp.160-164
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• 2015

Hunter syndrome(Mucopolysaccharidosis type II, MPS type II) is an X-linked disorder of glycosaminoglycans (GAGs) metabolism caused by an iduronate-2-sulfatase (IDS2) deficiency. A 24-month-old boy visited the department of pediatrics with the chief compliant of chronic purulent rhinorrhea beginning at age one. He had a history of repeated acute otitis media and chronic rhinitis. On physical examination he had a coarse face, enlarged tongue, distended abdomen, joint stiffness, and Mongolian spots at his first visit. The urine GAGs level was elevated at 66.10 mg/mmolCr (reference range, <11.1) and iduronate-2-sulfatase activity in leukocyte was decreased at 0.21 nmol/mg protein/hr (reference range, 18.7-57). Finally with an IDS gene mutational analysis, recombinant known mutation between intron 7 and distal of exon 3 in IDS2 was detected. Recombinant iduronate-2-sulfatase therapy was started without any infusion related reactions. The author highlights the importance of suspecting Hunter syndrome when pediatric patients visit with chronic purulent rhinorrhea which is a common cause of hospital visits for infants and children.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.9
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• pp.1183-1187
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• 2004

The natural resistance-associated macrophage protein 1 (NRAMP1) gene was identified as a candidate gene controlling the resistance and susceptibility to a number of intracellular parasites in pigs. The genetic variations in a 1.6 kb region spanning exon 1 and exon 3 of the porcine NRAMP1 gene were investigated by PCR-HinfI-RFLP in samples of 1347 individuals from 21 Chinese indigenous pig populations and 3 western pig breeds. Three alleles (A, B, C) and four genotypes (AA, BB, AB, BC) were detected. Significant differences in genotype and allele frequencies were observed between Chinese indigenous pig populations and exotic pig breeds, while in general the differences in genotype and allele frequencies among Chinese indigenous pig populations were not significant. The allele C was detected only in Duroc, Leping Spotted and Dongxiang Spotted pig, and the two Chinese pig populations showed similar genotype and allele frequencies. Four Chinese Tibetan pig populations displayed genetic differentiation at the NRAMP1 gene locus. In addition, intron 5 of the NRAMP1 gene was isolated and characterized by directly sequencing the PCR products encompassing intron 5. The alignment of intron 5 of the porcine, human, equine and ovine NRAMP1 gene showed a similarity of 45.38% between pig and human, 52.55% between pig and horse, 63.47% between pig and sheep, respectively.

• Molecules and Cells
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• v.25 no.2
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• pp.265-271
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• 2008

Single nucleotide polymorphisms (SNPs) are the most common form of human genetic variation. Non-synonymous SNPs (nsSNPs) change an amino acid. Organic anion transporters (OATs) play an important role in eliminating or reabsorbing endogenous and exogenous organic anionic compounds. Among OATs, hOAT4 mediates high affinity transport of estrone sulfate and dehydroepiandrosterone sulfate. The rapid bone loss that occurs in post-menopausal women is mainly due to a net decrease of estrogen. In the present study we searched for SNPs within the exon regions of hOAT4 in Korean women osteoporosis patients. Fifty healthy subjects and 50 subjects with osteoporosis were screened for genetic polymorphism in the coding region of SLC22A11 (hOAT4) using GC-clamp PCR and denaturing gradient gel electrophoresis (DGGE). We found three SNPs in the hOAT4 gene. Two were in the osteoporosis group (C483A and G832A) and one in the normal group (C847T). One of the SNPs, G832A, is an nsSNP that changes the $278^{th}$ amino acid from glutamic acid to lysine (E278K). Uptake of [$3^H$] estrone sulfate by oocytes injected with the hOAT4 E278K mutant was reduced compared with wild-type hOAT4. Km values for wild type and E278K were $0.7{\mu}M$ and $1.2{\mu}M$, and Vmax values were 1.8 and 0.47 pmol/oocyte/h, respectively. The present study demonstrates that hOAT4 variants can causing inter-individual variation in anionic drug uptake and, therefore, could be used as markers for certain diseases including osteoporosis.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3667-3673
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• 2014

Background: colorectal cancer (CRC) is the third most common type of cancers and the fourth leading cause of death worldwide. In Saudi Arabia, CRC accounts for 8.5% of all tumors; it ranks first among all cancers in males and third among females. The aim of this study was to link between different PARP-1 mutations and risk of CRC in Saudi population and to determine common variants of PARP-1 in Saudi CRC patients and normal individuals. Materials and Methods: DNA samples were isolated from fifty CRC patients and from a comparable number of control subjects then sequenced to detect different variations present in exons 3, 17, and 21 of the PARP-1 gene. Results and Conclusions: When comparing the genotype and allele frequencies of all detected SNPs in CRC patients with those in controls, we found none were significantly different for all variants even the most common SNP in PARP-1 gene (Val762Ala). However, two novel alterations in exon 21 were found to be associated with increased risk of CRC. The variants identified as (1) Lys933Asn [p-value 0.0318] and (2) Lys945Asn [p-value 0.0257]. Our results suggest that PARP-1 Lys933Asn and Lys945Asn alterations could be associated with increased risk of CRC in the Saudi population.

• Genomics & Informatics
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• v.3 no.4
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• pp.142-148
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• 2005

The immune response-related genes have been suggested to be the most favorable genes for positive selection during evolution. Comparing the entire DNA sequence of chimpanzee chromosome 22 (PTR22) with human chromosome 21 (HSA21), we have identified 15 orthologs having indel in their coding sequences. Among them, interferon-${\alpha}$ receptor-1 gene (IFNAR1), an immuneresponse-related gene, is subjected to comparative genomic analysis. Chimpanzee IFNAR1 showed the same genomic structure as human IFNAR1 (11 exons and 10 introns) except the 3 bp insertion in exon 4. The sequence alignment of IFNAR1 coding sequence indicated that 'ISPP' amino acid sequence motif is highly conserved in chimpanzee and other animals including mouse and chicken. However, the human IFNAR1 shows that one proline residue is missing in the sequence motif. The homology modeling of the IFNAR1 structures suggests that the proline deletion in human IFNAR1 leads to the formation of the following ${\alpha}$-helix, whereas two sequential prolines in chimpanzee IFNAR1 inhibit it. As a result, human IFNAR1 may adopt a characteristic structure distinct from chimpanzee IFNAR1. This human specific trait could contribute to specific immune response in the most optimized manner for humans. Further molecular biological studies on the IFNAR1 will help us to gain insights into the molecular implication of species-specific host-pathogen interaction in primate evolution.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.6
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• pp.2787-2793
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• 2016

Background: Urinary bladder cancer is a common malignancy in the West and ranks as the $7^{th}$ most common cancer in our region of Kashmir, India. FGFR3 mutations are frequent in superficial urothelial carcinoma (UC) differing from the RAS gene mutational pattern. The aim of this study was to analyze the frequency and association of FGFR3 and RAS gene mutations in UC cases. Materials and Methods: Paired tumor and adjacent normal tissue specimens of 65 consecutive UC patients were examined. DNA preparations were evaluated for the occurrence of FGFR3 and RAS gene mutations by PCR-SCCP and DNA sequencing. Results: Somatic point mutations of FGFR3 were identified in 32.3% (21 of 65). The pattern and distribution were significantly associated with low grade/stage (p<0.05). The overall mutations in exon 1 and 2 in all the forms of RAS genes aggregated to 21.5% and showed no association with any clinic-pathological parameters. In total, 53.8% (35 of 65) of the tumors studied had mutations in either a RAS or FGFR3 gene, but these were totally mutually exclusive in and none of the samples showed both the mutational events in mutually exclusive RAS and FGFR3. Conclusions: We conclude that RAS and FGFR3 mutations in UC are mutually exclusive and non-overlapping events which reflect activation of oncogenic pathways through different elements.

• Dementia and Neurocognitive Disorders
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• v.21 no.2
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• pp.71-78
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• 2022

Background and Purpose: The expression of the 18-kDA mitochondrial translocator protein (TSPO) in the brain is an attractive target to study neuroinflammation. However, the binding properties of TSPO ligands are reportedly dependent on genetic polymorphism of the TSPO gene (rs6971). The objective of this study is to investigate the rs6971 gene polymorphism in the Korean population. Methods: We performed genetic testing on 109 subjects including patients with mild cognitive impairment, Alzheimer's disease (AD) dementia, non-AD dementia, and cognitively unimpaired participants. Magnetic resonance imaging scans and detailed neuropsychological tests were also performed, and 29 participants underwent ¹⁸F-DPA714 PET scans. Exon 4 of the TSPO gene containing the polymorphism rs6971 (Ala or Thr at position 147) was polymerase chain reaction amplified and sequenced using the Sanger method. The identified rs6971 genotype codes (C/C, C/T, or T/T) of the TSPO protein generated high-, mixed-, or low-affinity binding phenotypes (HABs, MABs, and LABs), respectively. Results: We found that 96.3% of the study subjects were HAB (105 out of 109 subjects), and 3.7% of the subjects were MAB (4 out of 109 subjects). ¹⁸F-DPA-714 PET scans showed nonspecific binding to the thalamus and brainstem, and increased tracer uptake throughout the cortex in cognitively impaired patients. The participant with the MAB polymorphism had a higher DPA714 signal throughout the cortex. Conclusions: The majority of Koreans are HAB (aprox. 96%). Therefore, the polymorphism of the rs6971 gene would have a smaller impact on the availability of second-generation TSPO PET tracers.