• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2004년도 춘계학술발표대회
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• pp.993-996
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• 2004

사람들 사이에는 DNA 서열의 변이로 인한 유전적 차이가 있으며, 가끔 이러한 차이가 유전 질병의 원인이 되기도 한다. 일반적으로 DNA에서 가장 잘 알려진 변이가 바로 SNP(Single Nucleotide Polymorphism : 스닙)이다. SNP는 보통 블록단위로 유전되어지며 한쪽 부모로부터 유전되어진 SNP 블록을 SNP 하플로타입이라고 부른다. 생물학 실험을 통하여 추출되어진 결과물은 부모로부터 유전되어진 대립 유전자가 혼합되어진 지노타입(genotype)의 정보이다. 지노타입은 직관적으로 정확한 SNP 하플로타입을 추정하기가 힘들고, 생물학 실험을 통하여 하플로타입(haplotype)을 분석하는데 많은 비용이 들기때문에, 이를 컴퓨터 계산을 통하여 추론하는 연구가 Clark[1]에 의해서 제안되어진 이후 활발하게 진행되고 있다. 본 논문에서는 하플로타입을 효과적으로 추론하기 위해 유전자 알고리즘을 이용한 새로운 방법을 설명하고, 실험 결과를 기존의 연구 결과와 비교 분석한다.

• Asian-Australasian Journal of Animal Sciences
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• 제21권8호
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• pp.1073-1079
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• 2008

The objectives of this study were to identify polymorphisms of insulin-like growth factor I (IGF-I) gene and to investigate their association with growth traits in Nanjiang Huang goats. Five hundred and ninety-two animals were used to detect the polymorphisms in the complete coding sequence, part of introns and the 5'-regulatory region of the IGF-I gene by means of PCR-SSCP. A new single nucleotide polymorphism (G to C transversion) was identified at intron 4 of the IGF-I gene in the goats. Two alleles and three genotypes were observed in this group. The frequency of G and C alleles was 54.6 and 45.4%, respectively. The statistical analysis showed that polymorphism of the IGF-I gene had a significant association (p<0.05) with birth weight (BW), body weight at 6 months (W6) and at 12 months (W12), heart girth at 2 months (G2), body length at 6 months (L6), wither height at 6 months (H6) and at 12 months (H12) and heart girth at 12 months (G12). The goats with genotype CC had significantly higher BW, W6, W12, G2, L6, H6, H12 and G12 than those with genotype GC and had significantly higher W12, H6, H12 and G12 than those with genotype GG. Therefore, genotype CC may be the most advantageous for growth traits in the Nanjiang Huang goat. However, no significant association between SNP genotypes and other growth traits was observed. These results indicated that the SNP marker of the IGF-I gene may be a potential molecular marker for growth traits in Nanjiang Huang goats.

• 대한한의학회지
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• 제25권2호
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• pp.207-219
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• 2004

Objectives : We investigated to find the relationship between single-nucleotide polymorphism (SNP) of IL4R, IL-10 and bee venom therapy efficacy in patients with RA treated with bee venom for 8 weeks. Methods : Korean RA patients (n=114) and healthy subjects (n=109) were included in this prospective study. Korean bee venom was dissolved in saline (diluted 1:3000) and administrated into acupuncture points. Bee venom therapy was applied twice a week and continued for 8 weeks. The clinical response was evaluated using various assessments before and after treatment. Disease severity was measured by determining the number of tender joints and swollen joints. Laboratory studies included ESR, CRP, and rheumatoid factor. Genotyping for IL-4R and IL-10 polymorphism was done by pyrosequencing analysis. Results : 1. In IL4R genotypes, there was significant difference between RA ptitients tind controls group. 2. In IL4R genotypes, there was significant difference among Good, Mild and Bad responders to in RA patients, but in the frequency of alleles and carriers, there were no significant difference. 3. There was no significant difference between RA patients and controls group in IL-10 gene genotypes. 4. In IL-10 genotypes, there was no significant difference among Good, Mild and Bad responders to in RA patients. 5. There was no significant difference in the improvement of ESR, CRP and KHAQ scores after bee venom therapy in RA patients among the IL4R or IL-10 genotypes. Conclusions : In IL-4R genotypes, there was significant difference between RA patients and control group, and among Good, Mild and Bad responders in RA patients. However, in IL-10 genotypes, there was no significant difference between RA patients and controls group and among Good, Mild and Bad responders in RA patients.

• 한국축산식품학회:학술대회논문집
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• 한국축산식품학회 2005년도 제36차 추계 학술발표대회
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• pp.123-126
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• 2005

본 연구는 고등동물의 불포화지방산 생합성의 핵심 효소로 알려져 있는 Stearoyl-CoA desaturase(SCD) 유전자의 특정한 단일염기다형(single nucleotide polymorphism; SNP)이 한우의 도체 및 육질형질에 미치는 영향을 분석하기 위해 SCD 유전자의 Intron 7번 영역의 특정부위를 포함하는 primer를 제작하고, 염기서열 분석을 통하여 유전자 구조를 해석한 결과 총 211bp 크기를 갖는 염기서열의 122번째에서 아데닌(A)${\leftrightarrow}$구아닌(G) 염기치환으로 발생한 단일염기다형(SNP) 부위를 발견하였다. 이들 단일염기다형 염기서열 부위를 PCR-SSCP(single-strand conformation polymorphism) 기법을 이용하여 분석한 결과 3종류의 SNP 유전자형(A/A, A/G 및 G/G)을 검출하였다. 이 가운데 A/G 유전자형이 한우의 근내지방도와 등지방두께와 고도의 유의적 연관성이 있다는 새로운 사실을 발견하였다. 따라서, 본 연구를 통해 개발된 한우 SCD 유전자의 특정한 단일 염기다형 표지인자는 한우의 연령 및 성별에 관계없이 육질이 우수한 고급육을 생산하는 우량 한우의 조기식별에 매우 유용한 DNA 표지인자로 활용할 수 있을 것으로 기대된다.

• Asian-Australasian Journal of Animal Sciences
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• 제18권8호
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• pp.1061-1065
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• 2005

Growth rate is one of the economically important quantitative traits that affect carcass quantity in beef cattle. Two genes, bovine insulin-like growth factor I (IGF-I) and myogenic factor 5 (MYF5), were chosen as candidate genes for growth traits due to their important role in growth and development of mammals. The objectives of this study were to determine gene-specific single nucleotide polymorphism (SNP) markers of the IGF-I and MYF5 positional candidate genes and to investigate their associations with growth traits in Korean cattle. Genotyping of the SNP markers in these candidate genes was carried out using the single strand conformation polymorphism (SSCP) analysis. The frequencies of A and B alleles were 0.72 and 0.28 for IGF-I gene and 0.39 and 0.61 for MYF5 gene, respectively, in Korean cattle population examined. The gene-specific SNP marker association analysis indicated that the SNP genotype in IGF-I gene showed a significant association (p<0.05) with weight at 3 months (W3), and cows with AB genotype had higher W3 than BB genotype cows. The SNP genotype of MYF5 gene was found to have a significant effect (p<0.05) on the weight at 12 months (W12) and average daily gain (ADG), and cows with BB and AB genotypes had higher W12 and ADG compared with cows with AA genotype, respectively. However, no significant association between the SNP genotypes and any other growth traits was detected. The gene-specific SNP markers in the IGF-I and MYF5 candidate genes may be useful for selection on growth traits in Korean cattle.

• BMB Reports
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• 제38권5호
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• pp.555-562
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• 2005

Single nucleotide polymorphisms (SNPs) are becoming the most common type of markers used in genetic analysis. In the present report a SNP has been chosen to test the applicability of Real Time PCR to discriminate and quantify SNPs alleles on DNA pools. Amplification Refractory Mutation System (ARMS) and Mismatch Amplification Mutation Assay (MAMA) has been applied. Each assay has been pre-validated testing specificity and performances (linearity, PCR efficiency, interference limit, limit of detection, limit of quantification, precision and accuracy). Both the approaches achieve a precise and accurate estimation of the allele frequencies on pooled DNA samples in the range from 5% to 95% and don't require standard curves or calibrators. The lowest measurement that could be significantly distinguished from the background noise has been determined around the 1% for both the approaches, allowing to extend the range of quantifications from 1% to 99%. Furthermore applicability of Real Time PCR assays for general diagnostic purposes is discussed.

• 한국자원식물학회:학술대회논문집
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• 한국자원식물학회 2010년도 정기총회 및 춘계학술발표회
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• pp.15-15
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• 2010

Koran ginseng(Pnax ginseng) is one of the most important medicinal plants in Orient. Among the nine cultivars of Korea ginseng, Chunpoong commands a much greater market value and has been planted widely. A rapid and reliable method for discriminating the Chunpoong cultivar was developed by exploiting a single nucleotide polymorphism (SNP) in the mitochondrial nad7 intron 4 region of nine Korea ginseng cultivars using universal primers. A SNP was detected between Chunpoong and other cultivars and modified allele-specific primers were designed from this SNP site to effective method for the geneic identification of the Chunpoong cultivar of ginseng.

• 한국균학회지
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• 제50권3호
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• pp.225-233
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• 2022

Pyogo (Shiitake, Lentinula edodes) is one of the most important edible mushrooms because of its outstanding nutritive and medicinal value. In the registration and protection procedure for newly developed mushroom cultivars, the application of molecular markers that can supplement the morphological characteristic-based distinction has been strongly requested. Sanjo 701 and Chamaram, newly developed at the Federation Forest Mushroom Research Center of Korea, have been characterized as innovative cultivars suitable for customer demands because of their high yields and cultivation rates. However, no technical tools can protect the rights to these important cultivars. In this study, using comparative genomic information from 23 commercially available pyogo cultivars, we identified single nucleotide polymorphisms (SNPs) that accurately differentiated Sanjo701 and Chamaram from the other cultivars. We also developed high-resolution melting analysis (HRM)-based SNP markers that discriminate among the tested 23 pyogo cultivars. The developed SNP markers can be utilized for rapid, accurate identification of pyogo cultivars with low genetic diversity and to prevent cultivar contamination caused by illegally distributed inocula. In addition, these markers can serve as a crucial scientific basis for securing the right to conserve new cultivars in international markets.

• Genomics & Informatics
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• 제12권4호
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• pp.254-260
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• 2014

Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

• Animal cells and systems
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• 제5권2호
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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.