• Proceedings of the Korean Society of Sericultural Science Conference
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• 2003.10a
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• pp.23-23
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• 2003

We made use of 81, 635 expressed sequence tags (ESTs) derived from 12 different cDNA libraries of Bombyx mori to identify high-quality candidate single nucleotide polymorphisms (SNPs). By PHRAP assembling, we obtained 12, 980 contigs containing 11, 531 contigs assembled by more than one reads. From 117 contig sequences, which were assembled by 1, 576 high-quality reads base-called with PHRED, we identified 101 candidate SNPs and 27 single base insertions/deletions based on a neighborhood quality standard(NQS) of SNP. (omitted)

• Genomics & Informatics
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• v.14 no.3
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• pp.85-89
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• 2016

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease that affects multiple organ systems. Although the etiology of SLE remains unclear, it is widely accepted that genetic factors could be involved in its pathogenesis. A number of genome-wide association studies (GWASs) have identified novel single-nucleotide polymorphisms (SNPs) associated with the risk of SLE in diverse populations. However, not all the SNP candidates identified from non-Asian populations have been validated in Koreans. In this study, we aimed to replicate the SNPs that were recently discovered in the GWAS; these SNPs have not been validated in Koreans or have only been replicated in Koreans with an insufficient sample size to conclude any association. For this, we selected five SNPs (rs1801274 in FCGR2A and rs2286672 in PLD2, rs887369 in CXorf21, rs9782955 in LYST, and rs3794060 in NADSYN1). Through the replication study with 656 cases and 622 controls, rs1801274 in FCGR2A was found to be significantly associated with SLE in Koreans (odds ratio, 1.26, 95% confidence interval, 1.06 to 1.50; p = 0.01 in allelic model). This association was also significant in two other models (dominant and recessive). The other four SNPs did not show a significant association. Our data support that FCGR polymorphisms play important roles in the susceptibility to SLE in diverse populations, including Koreans.

• Journal of Korean Medicine for Obesity Research
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• v.4 no.1
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• pp.139-160
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• 2004

The obesity is detrimental to the health of people living in affluent societies. Individual differences in energy metabolism are caused primarily by single nucleotide polymorphisms(SNPs), some of which promote the development of obesity-related type 2 diabetes mellitus. Type 2 diabetes mellitus is a common multifactorial genetic syndrome, which is determined by several different genes and environmental factors. In this review, five major conclusions are reached: (1)To be clinically significant, SNPs must be relevant, prevalent, modifiable, and measurable. (2)Differences in SNPs may have been caused by famine, ultraviolet light, alcohol, climate, agricultural revolution. livestock, lactase persistence, and westernized lifestyle. (3)Candidate obesity genes of calorie intake restriction are SIM 1, MC3R, MC4R, AGRP, CART, CCK, CNTFR, DRD2, Ghrelin, 5-HT receptor, NPY, PON and those of energy metabolism are LEP, LEPR, UCP1, UCP2, UCP3, B2AR, B3AR, PGC-1, Androgen receptor and those of fat mobilization are AGT, ACE, ADA, APM1, Apolipoproteins, PPAR, FABP, FOXC2, GCGR, $11-{\beta}HSDI$, LDLR, Hormonal sensitive lipase, Perilipin, $TNF-{\alpha}$, $TNF-{\beta}$ (4)Candidate obesity genes in the eastern are NPY, LEP, LEPR, UCP1, UCP2, UCP3, B2AR, B3AR, ACE, APM1, PPAR, and FABP. (5)Candidate obesity genes in type 2 diabetes mellitus are MC3R, MC4R, B2AR, B3AR, ADA, APM1, PPAR, FABP, FOXC2, PC1, PC2, ABCC8, CAPN10, CYP19, CYP7, ENPP1, GCK, GYS1, IGF, IL-6, Insulin receptor, IRS, and LPL. The discovery of SNPs will lead to a greater understanding of the pathogenesis of obesity and to better diagnostics, treatment, and eventually prevention.

• Journal of Periodontal and Implant Science
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• v.42 no.5
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• pp.151-157
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• 2012

Purpose: Cyclooxygenase (COX) enzyme catalyzes the production of prostaglandins, which are important mediators of tissue destruction in periodontitis. Single nucleotide polymorphisms of $COX_2$ enzyme have been associated with increasing susceptibility to inflammatory diseases. The present study evaluates the association of two single nucleotide polymorphisms in $COX_2$ gene (-1195G>A and $8_{473}$C>T) with chronic periodontitis in North Indians. Methods: Both SNPs and their haplotypes were used to explore the associations between $COX_2$ polymorphisms and chronic periodontitis in 56 patients and 60 controls. Genotyping was done by polymerase chain reaction followed by restriction fragment length polymorphism. Chi-square test and logistic regression analysis were performed for association analysis. Results: By the individual genotype analysis, mutant genotypes (GA and AA) of $COX_2$-1195 showed more than a two fold risk (odds ratio [OR]>2) and $COX_2$ $8_{473}$ (TC and CC) showed a reduced risk for the disease, but the findings were not statistically significant. Haplotype analysis showed that the frequency of the haplotype AT was higher in the case group and a significant association was found for haplotype AT (OR, 1.79; 95% confidence interval, 1.03 to 3.11; P=0.0370) indicating an association between the AT haplotype of $COX_2$ gene SNPs and chronic periodontitis. Conclusions: Individual genotypes of both the SNPs were not associated while haplotype AT was found to be associated with chronic periodontitis in North Indians.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.8
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• pp.3601-3606
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• 2014

Single nucleotide polymorphisms located at microRNA (miRNA)-binding sites are likely to affect the expression of miRNA targets and may contribute to the susceptibility of humans to common diseases. Here 335 candidate lung cancer-related inflammatory genes were selected according to the existing literature and database. We identified putative miRNA-binding sites of 149 genes by specialised algorithms and screened SNPs in the 3'UTRs of these genes. By calculating binding free energy, we sorted 269 SNPs on the basis of the possibility of prediction. The proposed approach could help to easy the identification of functionally relevant SNPs and minimize the workflow and the costs.

• Food Science of Animal Resources
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• v.33 no.6
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• pp.715-722
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• 2013

Heugu (Korea Black Cattle) is one of the indigenous cattle breeds in Korea; however there has been severe lack of genomic studies on the breed. In this study, we report the first whole genome resequencing of Heugu at higher sequence coverage using Illumina HiSeq 2000 platform. More than 153.6 Giga base pairs sequence was obtained, of which 97% of the reads were mapped to the bovine reference sequence assembly (UMD 3.1). The number of non-redundantly mapped sequence reads corresponds to approximately 28.9-fold coverage across the genome. From these data, we identified a total of over six million single nucleotide polymorphisms (SNPs), of which 29.4% were found to be novel using the single nucleotide polymorphism database build 137. Extensive annotation was performed on all the detected SNPs, showing that most of SNPs were located in intergenic regions (70.7%), which is well corresponded with previous studies. Of the total SNPs, we identified substantial numbers of non-synonymous SNPs (13,979) in 5,999 genes, which could potentially affect meat quality traits in cattle. These results provide genome-wide SNPs that can serve as useful genetic tools and as candidates in searches for phenotype-altering DNA difference implicated with meat quality traits in cattle. The importance of this study can be further pronounced with the first whole genome sequencing of the valuable local genetic resource to be used in further genomic comparison studies with diverse cattle breeds.

• Animal cells and systems
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• v.5 no.2
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• pp.153-156
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• 2001

A key aspect of genomic research in the “post-genome era”is to associate sequence variations with heritable phenotypes. The most common variations in the human genome are single nucleotide polymorphisms (SNPs) that occur approximately once in every 500 to 1,000 bases. Although analyzing the phenotypic outcome of these SNPs is crucial to facilitate large-scale association studies of genetic diseases, detection of SNPs from an extended number of human DNA samples is often difficult, labor-intensive and time-consuming. Recent development in SNP detection methods using DNA microarrays and mass spectrophotometry has allowed automated high throughput analyses, but such equipments are not accessible to many scientists. In this study, we demonstrate that a simple PCR-based method using primers with a mismatched base at the 3'-end provides a fast and easy tool to identify known SNPs from human genomic DNA in a regular molecular biology laboratory. Results from this PCR amplification of specific alleles (PASA) analysis efficiently and accurately typed the Q576R polymorphism of human IL4 receptor from the genomic DNAs of 29 Koreans, including 9 samples whose genotype could not be discerned by the conventiona1 PCR-SSCP (single strand conformation polymorphism) method. Given the increasing attention to disease-associated polymorphisms in genomic research, this alternative technique will be very useful to identify SNPs in large-scale population studies.

• Journal of Animal Science and Technology
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• v.53 no.6
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• pp.511-516
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• 2011

Fas gene known to associate with intramuscular fat content in Korean cattle was selected for DNA marker development. Fas (APO-1, CD95), a member of the tumor necrosis factor (TNF) receptor superfamily, is a cell membrane protein that mediates apoptosis (programmed cell death). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers at genomic level. Of this gene to search for SNP, sequences of whole exon and 1kb range of both front and back of the gene using 24 cattle were determined by direct-sequencing methods. As a result, 16 SNPs in exon, 37 SNPs in intron and 2 SNPs in promoter region, a total of 55 SNPs were discovered. In these SNPs, thirty-one common polymorphic sites were selected considering their allele frequencies, haplotype-tagging status and Linkage Disequilibrium (LD) for genotyping in larger-scale subjects. Selected SNPs were confirmed genotype through SNaPshot method (n=274) and were examined for possible genetic association of Fas polymorphisms with carcass weight (CWT), eye muscle area (EMA), and backfat thickness (BF). So, the SNP have been identified significant g.-12T>G, g.1112T>G and g.32548T>C. These results suggest that polymorphism of Fas gene was associated with meat quality traits in Hanwoo.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.7
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• pp.3065-3069
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• 2016

Single nucleotide polymorphism (SNP) detection has been used extensively for genetic association studies of diseases including cancer. For mass, yet accurate and more economic SNP detection we have optimized tetra primer amplification refractory mutation system polymerase chain reaction (ARMS PCR) to detect three SNPs in the cytochrome P450 2E1 (CYP2E1) gene locus; i.e. rs3813865, rs2070672 and rs3813867. The optimization system strategies used were (1) designing inner and outer primers; (2) determining of their optimum primer concentration ratios; and (3) determining of the optimum PCR annealing temperature. The tetra primer ARMS PCR result could be directly observed using agarose gel electrophoresis. The method succesfully determined three SNPs in CYP2E1 locus, the results being consistent with validation using DNA sequencing and restriction fragment length polymorphisms (RFLP).

• Journal of the Institute of Electronics and Information Engineers
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• v.52 no.3
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• pp.190-195
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• 2015

The detection of single nucleotide polymorphisms (SNPs) caused of mutant or genetic diseases is important to diagnosis and medicine. There are many methods have been proposed to detect SNPs. However the detection of SNPs is difficulty, because the difference of energy between complementary DNA (cDMA) and SNPs is very small. In this work, we detect the SNPs using field-effect transistors (FETs) which based on the detection of negative charge of DNA. We bias -0.3 V on the drain-source electrode at the target DNA hybridization process. The efficiency of hybridization and the amplitude of signal decrease by repulsive force between negative charge of DNA and negative bias on the electrode. However, the sensitivity of SNPs increases about 5 times from 1.7 mV to 8.7 mV.