• Genomics & Informatics
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• 제2권3호
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• pp.147-148
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• 2004

Recently completed mitochondrial genome databses from public resources provide us with a better understanding of individual mitochondrial genomes for population genomics. By determining the substitution rate of the genomic sequences, it is plausible to derive dates on the phylogenetic tree and build a chronology of events in the evolution of human species. MitGEN is specially designed as a mitochondrial genome browser for analyzing, comparing and visualizing single nucleotide polymorphism for human mitochondrial genomes between human races for comparative genomics. It is a standalone application and is available free for non-commercial work.

• 한국전기전자재료학회:학술대회논문집
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• 한국전기전자재료학회 2003년도 추계학술대회 논문집 Vol.16
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• pp.224-226
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• 2003

In this paper, we succeeded SNP discrimination of DNA hybridization on microarray using new electrochemical system. Using the electrochemical method with a label-free DNA has Performed DNA chip microarray. This method is based on redox of an electrochemical ligand. We developed scanning system with high performance.

• 한국양식학회지
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• 제11권3호
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• pp.295-301
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• 1998

Since the end of the Pliocene, ancestral strains of Astyanax fasciatus have been accidently washed into different caves at the time of flooding and have lost their eyes and body pigments. Availability of this independently derived cave fish and their ancestral form within a single species provided a unique opportunity for studying the process of molecular evolution of the visual pigment gene. The nucleotide sequence comparisons of an ancestral river fish and two cave fish showed that nucleotide polymorphism of a green-like visual pigment gene between the eyed and blind form of A. fasciatus was much higher than that between the same blind form. Considering the number of nucleotide substitutions per nucleotide site and the direction of the nucleotide substitutions, more nucleotide substituions between the different forms of fish rater than the same one were probably due to more frequent mutations in the eyed river form. Nucleotide substitutions per site at the intron have been ocurred more than three times faster than those at the exon. This result indicates that the functional constraint has affected the green-like visual pigment gene of the blind cave fish although its eye sight is no longer required.

• 한국정보과학회논문지:시스템및이론
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• 제34권7호
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• pp.276-281
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• 2007

본 논문에서는 한국인의 대표질환 중 하나인 만성 간염에 대한 질환 감수성을 예측하기 위해서 Single Nucleotide Polymorphism 데이타와 대표적인 기계학습 기술인 Support Vector Machine을 이용하였다. 실험을 위한 데이타로 만성간염 환자 173명과 정상인 155명의 SNP 데이타를 사용하였으며, 평가를 위한 방법으로는 Leave-One-Out Cross Valication을 사용하였다. 실험결과 SNP 데이터만으로는 67.1%의 예측 결과를 얻었으며 기본적인 건강요소인 나이와 성별을 특징요소로 사용함으로서 74.9%의 예측 결과를 보였다. 향후 보다 많은 SNP 데이타와 건강관련정보 그리고 생활패턴에 대한 요소들을 특징요소로 감수성 예측에 함께 사용한다면, SVM은 만성 간염 예측을 위한 보다 효과적인 도구가 될 것이다.

• 한국동물학회:학술대회논문집
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• 한국동물학회 2001년도 한국생물과학협회 학술발표대회
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• pp.249.2-249
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• 2001

• Asian Pacific Journal of Cancer Prevention
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• 제13권12호
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• pp.5981-5984
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• 2012

Background: Numerous studies have investigated the association of matrix metalloproteinase 1 (MMP1) rs1799750 single nucleotide polymorphism with lung cancer susceptibility, but the findings are inconsistent. Therefore, we performed a meta-analysis to comprehensively evaluate any possible association. Methods: We searched publications from MEDLINE, EMBASE and CNKI databases which assessed links between the MMP1 rs1799750 polymorphism and lung cancer risk. We calculated the pooled odds ratio (OR) and its 95% confidence interval (95%CI) using either fixed-effects or random-effects models. Results: The meta-analysis was based on 9 publications encompassing 4,823 cases and 4,298 controls. The overall results suggested there was a significant association between the MMP1 rs1799750 polymorphism and lung cancer risk (1G vs. 2G: OR = 0.83, 95%CI = 0.73-0.94; 1G1G vs. 2G2G: OR = 0.73, 95%CI = 0.59-0.92; 1G1G vs. 1G2G/2G2G: OR = 0.87, 95%CI = 0.79-0.97; 1G1G/1G2G vs. 2G2G: OR = 0.78, 95%CI = 0.64-0.95). In the subgroup analysis by ethnicity, the association was still obvious in Asians (all P values < 0.05), but there was no association in Caucasians (all P values > 0.05). Conclusions: The MMP1 rs1799750 polymorphism is associated with decreased lung cancer risk, and a race-specific effect may exist in this association.

• Bulletin of the Korean Chemical Society
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• 제31권7호
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• pp.1902-1906
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• 2010

A microchip electrophoresis (ME) method was developed using a programmed field strength gradients (PFSG) for the single nucleotide polymorphism (SNP) based fast identification of cattle breeds. Four different Korean cattle (Hanwoo) and Holstein SNP markers amplified by allele-specific polymerase chain reaction were separated in a glass microchip filled with 0.5% poly(ethyleneoxide) ($M_r$ = 8 000 000) by PFSG as follows: 750 V/cm for 0 - 14 s, 166.7 V/cm for 14 - 31 s, 83.3 V/cm for 31 - 46 s, and 750 V/cm for 46 - 100 s. The cattle breeds were clearly distinguished within 45 s. The ME-PFSG method was 7 times and 5 times faster than the constant electric field ME method and the capillary electrophoresis- PFSG method, respectively, with a high resolving power ($R_s$ = 5.05 - 9.98). The proposed methodology could be a powerful tool for the fast and simultaneous determination of SNP markers for various cattle breeds with high accuracy.

• Genomics & Informatics
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• 제8권4호
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• pp.201-205
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• 2010

The H1 histone family, member N, testis-specific (H1FNT) is exclusively expressed in the testis, and had its possible role for sperm chromatin formation. The purpose of this study is to investigate any genetic association of H1FNT gene with male infertility, especially at the promoter region. We examined the promoter single nucleotide polymorphisms (SNP) of H1FNT gene which is located within transcription factor binding site for its association with male infertility. The statistical analysis showed that the -1129A>T polymorphism was present at a statistically significance in male infertility (p=0.0059 and 0.0349 for hetero and risk type, respectively). The dual-luciferase promoter assay was performed to examine the polymorphic effect of this promoter SNP by the cloning of promoter region (1700bp fragment) into pGL3-basic vector. In our plasmid based reporter system, there is no big difference between wild and risk type. In conclusion, H1FNT -1129A>T promoter SNP is statistically significant with male infertility, especially with subfertile (non-azoospermia) group. Further analysis of its functional polymorphic effect in vivo may provide the biological significance of testis-specific histone with spermatogenesis.

• Asian-Australasian Journal of Animal Sciences
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• 제27권10호
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• pp.1406-1410
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• 2014

Age at first calving is an important trait for achieving earlier reproductive performance. To detect quantitative trait loci (QTL) for reproductive traits, a genome wide association study was conducted on the 96 Hanwoo cows that were born between 2008 and 2010 from 13 sires in a local farm (Juk-Am Hanwoo farm, Suncheon, Korea) and genotyped with the Illumina 50K bovine single nucleotide polymorphism (SNP) chips. Phenotypes were regressed on additive and dominance effects for each SNP using a simple linear regression model after the effects of birth-year-month and polygenes were considered. A forward regression procedure was applied to determine the best set of SNPs for age at first calving. A total of 15 QTL were detected at the comparison-wise 0.001 level. Two QTL with strong statistical evidence were found at 128.9 Mb and 111.1 Mb on bovine chromosomes (BTA) 2 and 7, respectively, each of which accounted for 22% of the phenotypic variance. Also, five significant SNPs were detected on BTAs 10, 16, 20, 26, and 29. Multiple QTL were found on BTAs 1, 2, 7, and 14. The significant QTLs may be applied via marker assisted selection to increase rate of genetic gain for the trait, after validation tests in other Hanwoo cow populations.

• Genomics & Informatics
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• 제12권4호
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• pp.289-292
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• 2014

Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases, including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.