• Genomics & Informatics
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• 제3권4호
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• pp.149-153
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• 2005

Asthma is an inflammatory airways disease characterized by bronchial hyperresponsiveness and airways obstruction, which results from a complex interaction of genetic and environmental factors. Interleukin (IL)-13 and IL-4 are important in IgE synthesis and allergic inflammation, therefore genes encoding IL-13 and IL-4 are candidates for predisposition to asthma. In the present study, we screened single-nucleotide polymorphisms (SNPs) in IL-13 and IL-4 and examined whether they are risk factors for asthma. We resequenced all exons and the promoter region in 12 asthma patients and 12 normal controls, and identified 18 SNPs including 2 novel SNPs. The linkage disequilibrium(LD) pattern was evaluated with 16 common SNPs, and haplotypes were also estimated within the block. Although IL-13 and IL-4 are localized within 27 kb on chromosome 5q31 and share many biological profiles, this region was partitioned into 2 blocks. One SNP and three SNPs were determined as haplotype-taggingSNPs (htSNPs) within IL-13 and IL-4 haplotype-block, respectively. No significant associations were observed between any of the SNPs or haplotypes and development of asthma in small number of Korean subjects. However, the genetic variants of IL-13 and IL-4 would provide valuable strategies for the genotyping studies in large population.

• 정보처리학회논문지A
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• 제13A권1호
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• pp.79-86
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• 2006

최근 인간의 다양성과 SNP과의 연관연구에 드는 비용을 줄이기 위해서, 최소의 tagSNP을 선택하는 문제를 해결하기 위한 연구가 이루어지고 있다. 일반적으로 많은 수의 SNP들을 여러 블록으로 분할하여 각 블록 내에서 tagSNP을 선택하는 접근방법이 사용되고 있다. 본 논문에서 구현된 MarSel은 기존의 블록분할 접근 방법의 문제로 볼 수 있는 생물학적 의미의 부족을 해결하고자, 연관불균형(Linkage Disequilibrium, LD)의 개념을 도입한 시스템이다. 기존의 접근방법에서는 생물학적으로 재조합(recombination)이 일어나지 않는 연속된 구간에서도 여러 블록으로 나누어지는 문제가 생겼던 반면, MarSel에서는 연관불균형 계수 |D'|에 의해서 연속된 구간이 하나의 블록으로 유지된 상태에서 tagSNP을 선택하게 된다. 또한 MarSel에서는 각 블록 내에서 tagSNP을 선택 할 때에 엔트로피(entropy) 기반의 최적해 알고리즘을 이용함으로써 최소한의 tagSNP 선택을 보장하게 되며, 기존의 구현된 시스템들보다 더 많은 양의 데이터를 효율적으로 처리할 수 있도록 구현되었기 때문에 염색체 레벨의 연관 연구도 가능하게 해준다.

• Clinical and Experimental Pediatrics
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• 제55권10호
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• pp.388-392
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• 2012

Purpose: Single-nucleotide polymorphism (SNP) markers within LIN28B have been reported to be related to the timing of pubertal growth. However, no study has investigated the frequency of genetic markers in girls with precocious puberty (PP) or early puberty (EP). This study aimed to determine the frequency of putative genetic markers in girls with PP or EP. Methods: Genomic DNAs were obtained from 77 and 109 girls that fulfilled the criteria for PP and EP, respectively. The controls in this study were 144 healthy volunteers between 20 and 30 years of age. The haplotypes were reconstructed using 11 SNPs of LIN28B, and haplotype association analysis was performed. The haplotype frequencies were compared. Differences in the clinical and laboratory parameters were analyzed according to the haplotype dosage. Results: Eleven SNPs in LIN28B were all located in a block that was in linkage disequilibrium. The haplotype could be reconstructed using 2 representative SNPs, rs4946651 and rs369065. The AC haplotype was less frequently observed in the PP group than in the controls (0.069 vs. 0.144, P=0.010). The trend that girls with non-AC haplotypes tended to have earlier puberty onset (P=0.037) was illustrated even in the EP+PP patient group by Kaplan-Meier analysis. Conclusion: The results of the present study showed that non-AC haplotypes of LIN28B had a significant association with PP in girls.

• The Korean Journal of Physiology and Pharmacology
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• 제12권3호
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• pp.125-129
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• 2008

The aim of this study was to determine whether single nucleotide polymorphisms (SNPs) of matrix metallopeptidase 2 (MMP2) are associated with obesity. MMP2 is an enzyme with proteolytic activity against matrix and nonmatrix proteins, particularly basement membrane constituents. To identify the relationship between polymorphisms of MMP2 and overweight/obese, we genotyped 5 SNPs (rs17242319, rs1053605, rs243849, rs2287074, and rs10775332) of the coding region of MMP2 using the Golden Gate assay on an Illumina BeadStation 500 GX. One hundred and forty two overweight/obese ($BMI\;{\ge}\;23$) and 145 normal (BMI 18 to < 23) subjects were analyzed. SNPStats, Haploview, HapAnalyzer, SNPAnalyzer, and Helixtree programs were used for the analysis of genetic data. A linkage disequilibrium (LD) block was discovered among the 5 SNPs selected, including rs17242319, rs1053605, rs243849, and rs2287074. Of the 5 polymorphisms, 2 synonymous SNPs [rs17242319 (Gly226Gly) and rs10775332 (Phe602Phe)] were found significant associations with overweight/obese. Recently, rs1132896 replaced rs17242319 as a new number (SNP database, BUILD 129). In haplotype analysis using Haploview, a haplotype (haplotype: CCCA) containing a meaningful polymorphism (rs17242319) was found to be significantly different. The results suggest that MMP2 may be associated with overweight/obese in Korean population.

• Molecular & Cellular Toxicology
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• 제4권2호
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• pp.124-131
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• 2008

The growing problem of obesity is associated with numerous medical conditions. Several studies have reported that activation of thyroid hormone receptor beta $(THR{\beta})$ is involved in lipid metabolism and thermogenesis. To identify the relationship between the $THR{\beta}$ gene and obesity, we genotyped eighty two single nucleotide polymorphisms (SNPs) in the gene using the Affymetrix array chip in 209 overweight/obese and 155 normal subjects in Korean population. Of the eighty two polymorphisms, the seven SNPs exhibited a significant association with overweight/obesity in three alternative models (codominant, dominant, and recessive models; P<0.05 after adjusting for age and sex) were rs826221 (+267878 T>C), rs4858604 (+186399 A>G), rs1158265 (+200152 T>C), rs1868575 (+206031 G>A), rs1700939 (+238467 T>A), rs1505301 (+241933 T>C), and rs1924768 (+126491 T>C). During haplotype analysis using HapAnalyzer software, 2 haplotypes (block 13: TTAT; block 15: CTGC) containing significant polymorphisms (rs1700939 +238467 T>A and rs4858604 +186399 A>G) were detected to be significantly different. The results suggest that the $THR{\beta}$ gene may be associated with overweight/obesity in Korean population.

• Genomics & Informatics
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• 제5권4호
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• pp.188-193
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• 2007

The Functional Element SNPs Database (FESD) categorizes functional elements in human genic regions and provides a set of single nucleotide polymorphisms (SNPs) located within each area. Users may select a set of SNPs in specific functional elements with haplotype information and obtain flanking sequences for genotyping. Our previous version of FESD has been improved in several ways. We regenerated all the data in FESD II from recently updated source data such as HapMap, UCSC GoldenPath, dbSNP, OMIM, and $TRANSFAC^{(R)}$. Users can obtain information about tagSNPs and simulate LD blocks for each gene from four ethnicities in the HapMap project on the fly. FESD II employs a Java/JSP web interface for better platform portability and higher speed than PHP in the previous version. As a result, FESD II provides its users with more powerful information about functional element SNPs of human ethnicities.

• Asian-Australasian Journal of Animal Sciences
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• 제25권7호
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• pp.913-920
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• 2012

In this study, we investigated the relationship between unsaturated fatty acids influencing beef flavor and four types of SNPs (c.280A>G, c.388G>A, c.408G>C and c.456A>G) located at exon 2, 3 and 4 of the FABP4 gene, which is a fatty acid binding protein 4 in Korean cattle (n = 513). When analyzing the relationship between single genotype, fatty acids and carcass trait, individuals of GG, GG, CC and GG genotypes that are homozygotes, had a higher content of unsaturated fatty acids and marbling scores than other genotypes (p<0.05). Then, haplotype block showed strong significant relationships not only with unsaturated fatty acids (54.73%), but also with marbling scores (5.82) in $ht1{\times}ht1$ group (p<0.05). This $ht1{\times}ht1$ group showed significant differences with unsaturated fatty acids and marbling scores that affected beef flavor in Korean cattle. Therefore, it can be inferred that the $ht1{\times}ht1$ types might be valuable new markers for use in the improvement of Korean cattle.

• Genomics & Informatics
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• 제12권4호
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• pp.165-170
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• 2014

Genome-wide association (GWA) studies have found many important genetic variants that affect various traits. Since these studies are useful to investigate untyped but causal variants using linkage disequilibrium (LD), it would be useful to explore the haplotypes of single-nucleotide polymorphisms (SNPs) within the same LD block of significant associations based on high-density variants from population references. Here, we tried to make a haplotype catalog affecting body mass index (BMI) through an integrative analysis of previously published whole-genome next-generation sequencing (NGS) data of 7 representative Korean individuals and previously known Korean GWA signals. We selected 435 SNPs that were significantly associated with BMI from the GWA analysis and searched 53 LD ranges nearby those SNPs. With the NGS data, the haplotypes were phased within the LDs. A total of 44 possible haplotype blocks for Korean BMI were cataloged. Although the current result constitutes little data, this study provides new insights that may help to identify important haplotypes for traits and low variants nearby significant SNPs. Furthermore, we can build a more comprehensive catalog as a larger dataset becomes available.

• 생명과학회지
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• 제29권1호
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• pp.1-8
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• 2019

한우(한국 재래 소)에서 반수체형 페이징을 위한 고밀도 시퀀싱을 이용한 비교 분석 논문은 많지가 않다. 이런 고밀도 시퀀싱 플랫폼 중에서, 일루미나에서 서비스 하는 Truseq Synthetic Long-Read Haplotyping 시퀀싱 플랫폼(TSLRH)과 10X Genomics에서 서비스하는 The Chromium Genome 시퀀싱 플랫폼을 특별히 비교 분석하는 논문은 없다. 우리는 한우 연구소의 한우 종모우(아이디: TN1505D2184 or 27214)의 정액에서 DNA를 추출하였으며, 이 DNA로부터 각각의 시퀀싱 플랫폼을 이용하여 시퀀싱 데이터를 생산하였다. 그 후, 우리는 각각의 시퀀싱 플랫폼에 맞는 분석 방법을 이용하여 단일염기서열변이들은 찾아냈다. 그 결과, TSLRH과 10XG의 전체 리드 수는 각각 355,208,304, 1,632,772,004, 맵핑 리드의 개수는 351,992,768(99.09%), 1,526,641,824(93.50%), Q30(%)은 89.04%, 88.60%, 평균 밀도는 13.04X, 74.3X, 가장 긴 페이즈 블락은 1,982,706bp, 1,480,081 bp, N50 페이즈 블락은 57,637 bp, 114,394 bp, 전체 단일염기서열변이는 4,534,989, 8,496,813, 전체 페이징 비율은 72.29%, 87.67%였다. 더욱이, 우리는 각각의 시퀀싱 플랫폼을 비교해서 각각의 시퀀싱 플랫폼의 고유한 단일염기서열변이와 두 시퀀싱 플랫폼에서 공통적으로 존재하는 단일염기서열변이를 각 염색체 별로 확인하였으며, 단일염기서열변이의 개수는 염색체 길이에 정비례한다는 결과를 확인하였다. 결론적으로, 본 연구에서 추천하는 바는 연구비가 충분하지 않을 시에는 TSLRH 보다 10XG을 사용하는 것을 추천한다. 왜냐하면 전체 리드 및 단일염기서열변이 개수, N50 페이즈 블락, 가장 긴 페이즈 블락, 페이즈 비율 그리고 평균 밀도 등이 TSLRH 보다 10XG가 더 높거나 좋기 때문이다.

• Journal of Animal Science and Technology
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• 제51권3호
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• pp.185-192
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• 2009

소 염색체 19번에 존재하는 유지방 함량 및 지방산 조성에 영향을 미치는 양적경제 형질 유전자 좌위에서 발견된 지방산 합성 효소인 FASN 유전자는 포화지방산과 불포화지방산의 함량을 조절하는 강력한 후보유전자이다. 본 연구에서 FASN 유전자의 g.17924 A>G 변이를 한우집단과 미국산 육우 집단에서 분석하였고 그 결과는 한우에서는 GG형의 개체빈도가(71%)로 매우 높았으며, 미국산육우에서는 GG형 빈도는 불과(35%)밖에 되지 않았다. 한우 품종에서 FASN 유전자의 염기서열 분석을 하여 27 개의 단일염기 변이를 발견 하였고, 그 중 9개는 본 연구에서 처음으로 밝혀지는 단일염기 변이이다. 한우 집단 100두와 수입우 집단 96에 대하여 유전자형 분석을 수행한 결과, FASN 유전자 내의 4개의 단일염기 변이의 연관 불평형 및 반수체 구역을 연구하였다. g.10568 C>T와 g.11280 G>A 단일염기 변이의 다형성은 한우집단에서 고기의 육색(P=0.004)과 고기의 조직감(P=0.0114)에 고도의 유의성이 통계적인 분석에 의하여 나타났다. 그리고 g.13125 C>T와 g.17924 G>A 다형성은 등지방두께 및 육량지수에 유의성을 관찰할 수 있었다(P=0.0179, 0.0495). 이상의 결과는 소 FASN 유전자 내의 변이들이 한우집단의 불포화 지방산 함량과 도체 형질에 연관성은 차별화된 고급한우육을 생산하기 위한 중요한 DNA 마커로써 활용가치가 있을 것으로 사료된다.