• Asian-Australasian Journal of Animal Sciences
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• v.18 no.1
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• pp.3-7
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• 2005

The insulin-like growth factors (IGFs), their receptors, and their binding proteins play key roles in regulating cell proliferation and apoptosis. Insulin-like growth factor binding protein-3 (IGFBP3, OMIM #146732) is one of the proteins that bind to the IGFs. IGFBP3 is a modulator of IGF bioactivity, and direct growth inhibitor in the extravascular tissue compartment. We identified twenty-two novel single nucleotide polymorphisms (SNPs) in IGFBP3 gene in Korean cattle (Hanwoo, Bos taurus coreanae) by direct sequencing of full gene including -1,500 bp promoter region. Among the identified SNPs, five common SNPs were screened in 650 Korean cattle; one SNP in promoter (IGFBP3 G-854C), one in 5'UTR region (IGFBP3 G-100A), two in intron 1 (IGFBP3 G+421T, IGFBP3 T+1636A), and one in intron 2 (IGFBP3 C+3863A). The frequencies of each SNP were 0.357 (IGFBP3 G-854C), 0.472 (IGFBP3 G-100A), 0.418 (IGFBP3 G+421T), 0.363 (IGFBP3 T+1636A) and 0.226 (IGFBP3 C+3863A), respectively. Haplotypes and their frequencies were estimated by EM algorithm. Six haplotypes were constructed with five SNPs and linkage disequilibrium coefficients (|D'|) between SNP pairs were also calculated. The information on SNPs and haplotypes in IGFBP3 gene could be useful for genetic studies of this gene.

• Journal of KIISE:Software and Applications
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• v.32 no.2
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• pp.99-107
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• 2005

In this paper, wc propose a now missing imputation method for minimizing loss of information linkage disequilibrium-based and haplotype-based imputation method, which estimate missing values of the data based on the specificity of Single Nucleotide Polymorphism(SNP) genotype data. Method for imputing data is needed to minimize the loss of information caused by experimental missing data. In general, missing imputation of biological data has used major allele imputation method. but this approach is not optima]. 1'his method has high error rates of missing values estimation since the characteristics of the genotype data are not considered not take into consideration the specific structure of the data. In this paper, we show the results of the comparative evaluation of our model methods and major imputation method for the estimation of missing values.

• Journal of Animal Science and Technology
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• v.51 no.6
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• pp.453-458
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• 2009

Prion protein (PRNP) is known to be a causative protein for transmissible spongiform encephalopathy (TSE), a disease occurring in human and animals. Previous results indicate that the genetic variability can affect the resistance and susceptibility of goat scrapie and can give the guideline for reducing the risk of this disease. Until now, 35 single nucleotide polymorphisms (SNPs) were identified in goat PRNP gene from many countries such as Great Britain, Italy, United States of America and Asian countries etc. In this study, SNPs in PRNP gene have been investigated to research the PRNP variations and their possible TSE risks in 60 Korean native goats. Based on the sequencing results, we identified four SNPs and three of those polymorphisms (G126A, C414T and C718T) were synonymous and the A428G polymorphism was non-synonymous which changes the amino acid histidine to arginine. Previously, all of these four SNPs were identified in Asian native goats. Specifically, five polymorphisms were identified in Asian native goats and two of them (G126A and C414T) were silent mutations, and the other SNPs (T304G, A428G and T718C) caused amino acid changes (W102G, H143R and S240P). Comparing with SNP results from other breeds, this study is an initial step to understand resistance and susceptibility of this disease in Korean native goats.

• Bulletin of the Korean Chemical Society
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• v.31 no.7
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• pp.2077-2080
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• 2010

• Genomics & Informatics
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• v.11 no.1
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• pp.34-37
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• 2013

This study evaluated the effects of somatic mutations and single nucleotide polymorphisms (SNPs) on disease progression and tried to verify the two-hit theory in cancer pathogenesis. To address this issue, SNP analysis was performed using the UCSC hg19 program in 10 acute myeloid leukemia patients (samples, G1 to G10), and somatic mutations were identified in the same tumor sample using SomaticSniper and VarScan2. SNPs in KRAS were detected in 4 out of 10 different individuals, and those of DNMT3A were detected in 5 of the same patient cohort. In 2 patients, both KRAS and DNMT3A were detected simultaneously. A somatic mutation in IDH2 was detected in these 2 patients. One of the patients had an additional mutation in FLT3, while the other patient had an NPM1 mutation. The patient with an FLT3 mutation relapsed shortly after attaining remission, while the other patient with the NPM1 mutation did not suffer a relapse. Our results indicate that SNPs with additional somatic mutations affect the prognosis of AML.

• BMB Reports
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• v.40 no.6
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• pp.1021-1027
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• 2007

We demonstrated the genetic polymorphism of aldehyde oxidase (AO) in Donryu strain rats: the ultrarapid metabolizer (UM) with nucleotide mutation of (377G, 2604C) coding for amino acid substitution of (110Gly, 852Val), extensive metabolizer (EM) with (377G/A, 2604C/T) coding for (110Gly/Ser, 852Val/Ala), and poor metabolizer (PM) with (377A, 2604T) coding for (110Ser, 852Ala), respectively. The results suggested that 377G > A and/or 2604C > T should be responsible for the genetic polymorphism. In this study, we constructed an E. coli expression system of four types of AO cDNA including Mut-1 with (377G, 2604T) and Mut-2 with (377A, 2604C) as well as naturally existing nucleotide sequences of UM and PM in order to clarify which one is responsible for the polymorphism. Mut-1 and Mut-2 showed almost the same high and low activity as that of the UM and PM groups, respectively. Thus, the expression study of mutant AO cDNA directly revealed that the nucleotide substitution of 377G > A, but not that of 2604C > T, will play a critical role in the genetic polymorphism of AO in Donryu strain rats. The reason amino acid substitution will cause genetic polymorphism in AO activity was discussed.

• Sleep Medicine and Psychophysiology
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• v.23 no.1
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• pp.25-28
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• 2016

Objectives: The retinoid-related orphan receptor A (RORA) gene has been reported to have an impact on circadian rhythm regulation. In this study, we analyzed the relationship between the RORA gene polymorphism and diurnal preference in Korean young adults. Methods: A population of 504 young adults was included in the study. All subjects were given and completed a 13-item composite scale for morningness (CSM). The RORA gene rs11071547 single-nucleotide polymorphism (SNP) was genotyped by PCR-based methods. Results: CSM score was not associated with genotype or allele carrier status of the RORA rs11071547 SNP. Conclusion: This result indicates that the RORA rs11071547 SNP does not play a role in diurnal preference.

• Asian-Australasian Journal of Animal Sciences
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• v.19 no.11
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• pp.1529-1535
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• 2006

Leptin has been investigated as a candidate gene for fat characteristics in beef cattle. Previously, we have reported 57 sequence variants discovered in Korean cattle (Bos Taurus coreanae). In this study, we examined the association between polymorphisms of leptin and carcass traits (cold carcass weight (CWT) and marbling score (Marb)) in Korean cattle. Among 57 polymorphisms, 11 common polymorphic sites were genotyped in our beef cattle (n = 437). Statistical analysis revealed that one single nucleotide polymorphism in coding exon (c.+411T>C (A137A)) showed a significant association with the yield trait, CWT. The C-bearing genotypes (CC or CT) of c.+411T>C (A137A) showed the higher CWT (p = 0.006). c.+150C>G (S50S) also showed a significant association with the quality trait, Marb (p = 0.01). Our findings suggest that polymorphisms in leptin might be one of the important genetic factors that influence carcass yield and quality in beef cattle, especially in CWT and Marb.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.10
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• pp.6025-6030
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• 2013

Background: Matrix metalloproteinase-2 (MMP-2) is an enzyme with proteolytic activity against matrix proteins, particularly basement membrane constituents. A single nucleotide polymorphism (SNP) at -1306, which disrupts a Sp1-type promoter site (CCACC box), results in strikingly lower promoter activity with the T allele. In the present study, we investigated whether this MMP-2 genetic polymorphism might be associated with susceptibility to colorectal cancer (CRC) in the Saudi population. We also analyzed MMP-2 gene expression level sin CRC patients and 4 different cancer cell lines. Materials and Methods: TaqMan allele discrimination assays and DNA sequencing techniques were used to investigate the $C^{-1306}T$ SNP in the MMP-2 gene of Saudi colorectal cancer patients and controls. The MMP-2 gene expression level was also determined in 12 colon cancer tissue samples collected from unrelated patients and histologically normal tissues distant from tumor margins. Results and Conclusions: The MMP-2 $C^{-1306}T$ SNP in the promoter region was associated with CRC in our Saudi population and the MMP-2 gene expression level was found to be 10 times higher in CRC patients. The MMP-2 $C^{-1306}T$ SNP is significantly associated with CRC in the Saudi population and this finding suggested that MMP-2 variants might help predict CRC progression risk among Saudis. We propose that analysis of this gene polymorphism could assist in identification of patient subgroups at risk of a poor disease outcome.

• Horticultural Science & Technology
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• v.31 no.2
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• pp.219-223
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• 2013

DNA markers can determine the genotype of many species. Single nucleotide polymorphism (SNP) detection is difficult without sequencing but it becomes easier with sdCAPS method. Here an experiment was performed for developing molecular markers using two SNPs, CSatpB-SNP and CSycf1-SNP, of chloroplast in cucumber plants. Properly designed primers with nucleotide sequences for restriction enzymes proved success of PCR and efficacy of digestion by the restriction enzymes. Then these markers were used to study the genotyping of cucumber breeding lines and cultivars obtained from various sources in respect of their chilling stress response. We confirmed that a U.S. cucumber line, 'NC76' known to possess a nuclear factor for the chilling tolerance showed the chloroplast genotypes related to chilling tolerance. However all Korean cucumber cultivars tested in this study showed the chloroplast genotypes related to chilling susceptibility. In conclusion, to develop chilling tolerant cucumber, both maternal and a nuclear factors related to chilling tolerance should be transferred from 'NC76' when 'NC76' is used as a female source and other elite lines as recurrent parents.