• 한국정보과학회논문지:시스템및이론
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• 제35권11호
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• pp.509-516
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• 2008

Minimum Letter Flips(MLF) 모델과 Weighted Minimum Letter Flips(WMLF) 모델은 일배체형 조합문제(haplotype assembly problem)를 해결하기 위한 모델들이다. 그러나 MLF 모델이나 WMLF 모델은 SNP(Single Nucleotide Polymorphism) 단편들에 손실과 오류가 적은 경우에만 효과적이다. 본 논문은 WMLF 모델의 개선을 목적으로 유전자형 정보를 추가한 WMLF/GI 모델과 문제를 제시한다. 새로 제시한 문제가 NP-hard임을 증명하고, 정확성이 높고 효율적인 문제 해결을 위해 유전자 알고리즘을 설계한다. 실험 결과를 통해 새로운 모델이 기존의 모델들에 비해 SNP 단편들에 손실과 오류가 많은 경우에도 높은 정확성을 가짐과 유전자형 정보가 유전자 알고리즘의 수렴속도를 크게 개선함을 보인다.

• Journal of Animal Science and Technology
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• 제49권5호
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• pp.577-584
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• 2007

본 연구는 후대검정 한우 295두의 혈액으로부터 genomic DNA를 추출하여 PCR 방법에 의한 증폭과 염기서열 분석을 통하여 ADSF/resistin 유전자의 단일염기다형을 발굴하고 이들과 한우 육질관련형질과의 상관관계를 분석하기 위하여 실시하였다. 확보된 DNA로부터 염기서열을 결정한 결과 promoter와 4개의 exon영역에서는 SNP를 찾지 못하였으나 intron 영역에서 7개의 SNP를 발굴하였다. 발굴된 SNP의 출현 빈도는 0.027에서 0.16까지 그 차이가 많았다. 육질형질과의 상관분석에서 이들 SNP 중 intron 2에서 발굴된 764A ins 만이 근내지방도와 상관관계가 발견되었다(P<0.05). 근내지방도는 유전력이 매우 높기 때문에 이번에 발굴된 ADSF/resistin 유전자의 SNP 764A ins와 같이 유전표지인자를 이용하는 것이 근내 지방도의 개량을 위해 우수한 결과를 가지는 것으로 사료된다. 가축의 경제형질의 경우 다수의 유전자가 관여하기 때문에 한 개의 유전자를 이용한 가축의 선발 또는 개량에 이용한다는 것은 제한적일 수 있다. 따라서 다수의 관련 유전자를 이용한 다형현상과 경제형질과의 연관성 연구가 동반될 때 육질개선 및 가축개량에 실질적인 증대효과가 있을 것으로 사료된다.

• Asian-Australasian Journal of Animal Sciences
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• 제28권7호
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• pp.926-935
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• 2015

The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a $BayesC{\pi}$ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

• Asian-Australasian Journal of Animal Sciences
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• 제20권6호
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• pp.817-820
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• 2007

The effects of diacylglycerol O-acyltransferase (DGAT1) candidate gene polymorphism on the economic traits of Hanwoo were studied. Through sequencing analysis, two polymorphism sites at K232A and T11993C were established and were analyzed by PCR-RFLP. The PCR-RFLP analysis for K232A showed that the frequencies of alleles K and A were 0.75 and 0.25, respectively, and the frequencies of genotypes for K/K, K/A and A/A were estimated as 0.509, 0.491 and 0, respectively. In the PCR-RFLP analysis for T11993C, we found allele frequencies of 0.773 and 0.227 for T and A, respectively, and 0.546, 0.454 and 0 for the T/T, T/C and C/C genotype frequencies, respectively. No significant effects on economic traits in Hanwoo were found in the separate analysis of K232A and T11993C polymorphisms, but the interaction between K232A and T11993C showed a significant effect (p<0.005) on marbling score. The DGAT1 candidate gene was found to have a significant effect not only on milk yield and component traits but also on the metabolism of intramuscular fat.

• Asian Pacific Journal of Cancer Prevention
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• 제13권10호
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• pp.4943-4946
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• 2012

Studies have reported an association between the TERT rs2736098 single nucleotide polymorphism (SNP) and cancer susceptibility, but the results remain inconclusive. Toprovide a more precise estimation of the relationship, a meta-analysis of 8 published studies including 8,070 cases and 10,239 controls was performed. Stratification by sample size, genotyping method, source of controls and ethnicity were used to explore the source of heterogeneity. In the overall analysis, no significant association was found between the TERT rs2736098 polymorphism and cancer risk. However, the result showed the rs2736098 was significantly associated with an increased cancer risk and the heterogeneity was effectively decreased for homozygote comparison by removal of two studies: OR = 1.337 (95% CI = 1.183-1.511; Pheterogeneity = 0.087). In the subgroup analysis by ethnicity, a significantly increased risk of cancers was found among Asians (OR = 1.413, 95% CI = 1.187-1.683 for AA versus GG). Our meta-analysis did not show that the TERT rs2736098 plays an important role in cancer risk. More studies with larger sample size and well-matched controls are needed to confirm the findings.

• Genomics & Informatics
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• 제8권2호
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• pp.81-85
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• 2010

The aim of the study was to investigate pig reference families, generated from Korean native pigs (KNP) that were crossed with Yorkshire (YS) breeds, which were used to evaluate genetic markers to select breeding animals with superior pork quality. A set of five candidate genes (PRKAG3, MC4R, CAST, ESR, and PRLR ) was analyzed for association with pork quality traits. PRKAG3 (I199V) SNP genotypes were significantly associated with muscle moisture, protein, and fat contents. The MC4R D298N polymorphism was significantly associated with meat tenderness and color traits. The CAST polymorphism was significantly associated with muscle moisture and crude protein traits. These three genes have been associated with pork quality traits in other pig populations, and some of our results are consistent with earlier studies. In addition, two reproductive candidate genes (ESR and PRLR ) did not have significant associations. These results suggest that further study is warranted to investigate and develop more DNA markers associated with pork quality in our KNP-crossed pig families.

• Genomics & Informatics
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• 제12권1호
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• pp.35-41
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• 2014

Single-nucleotide polymorphisms (SNPs) have been emerging out of the efforts to research human diseases and ethnic disparities. A semantic network is needed for in-depth understanding of the impacts of SNPs, because phenotypes are modulated by complex networks, including biochemical and physiological pathways. We identified ethnicity-specific SNPs by eliminating overlapped SNPs from HapMap samples, and the ethnicity-specific SNPs were mapped to the UCSC RefGene lists. Ethnicity-specific genes were identified as follows: 22 genes in the USA (CEU) individuals, 25 genes in the Japanese (JPT) individuals, and 332 genes in the African (YRI) individuals. To analyze the biologically functional implications for ethnicity-specific SNPs, we focused on constructing a semantic network model. Entities for the network represented by "Gene," "Pathway," "Disease," "Chemical," "Drug," "ClinicalTrials," "SNP," and relationships between entity-entity were obtained through curation. Our semantic modeling for ethnicity-specific SNPs showed interesting results in the three categories, including three diseases ("AIDS-associated nephropathy," "Hypertension," and "Pelvic infection"), one drug ("Methylphenidate"), and five pathways ("Hemostasis," "Systemic lupus erythematosus," "Prostate cancer," "Hepatitis C virus," and "Rheumatoid arthritis"). We found ethnicity-specific genes using the semantic modeling, and the majority of our findings was consistent with the previous studies - that an understanding of genetic variability explained ethnicity-specific disparities.

• Communications for Statistical Applications and Methods
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• 제16권4호
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• pp.579-586
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• 2009

통계모형의 상호작용 효과를 분석하기위해 비모수적인 방법인 다중인자 차원 축소(MDR)방법을 사용해 왔다. MDR 방법은 사례-대조 데이터에만 적용 할 수 있다. 본 논문에서는 Regression tree 알고리즘과 더미 변수를 활용한 회귀분석 알고리즘을 사용하여 다중 범주를 High 범주와 Low범주로 분류함으로써, MDR방법에서 연속형 데이터에 적용 할 수 없는 문제를 해결하는 방법으로 제시된 Expanded MDR방법과 Dummy MDR방법을 한우의 주요 경제형질(longissimus muscle dorsi area: LMA, carcass cold weight: CWT, average daily gain: ADG)데이터에 적용하여 한우의 경제형질에 영향을 주는 주요 SNPs 마커를 규명하고, Permutation test를 통해 그 결과를 비교한다.

• Journal of Animal Science and Technology
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• 제62권3호
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• pp.306-312
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• 2020

Korean army dogs are raised for special purposes and have contributed much to society. However, several diseases occur in dogs. Canine hip dysplasia (CHD) is a musculoskeletal disorder that occurs frequently in Korean army dogs and interferes with their activities. If we could control CHD, this would have a positive effect on their performance. This study performed a genome-wide association study (GWAS) in 69 Korean army dogs to find significant loci for CHD using 170K single nucleotide polymorphisms (SNPs). CHD was classified according to the Norberg angle criterion. The control group comprised 62 dogs classified as relatively normal, and 7 dogs with severe CHD formed the case group. From the GWAS analysis, we concluded that SNPs present on chromosome 4 might have a significant impact on the overall expression of canine hip dysplasia.

• Genomics & Informatics
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• 제11권2호
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• pp.93-96
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• 2013

The prediction of externally visible characteristics from DNA has been studied for forensic genetics over the last few years. Externally visible characteristics include hair, skin, and eye color, height, and facial morphology, which have high heritability. Recent studies using genome-wide association analysis have identified genes and variations that correlate with human visible phenotypes and developed phenotype prediction programs. However, most prediction models were constructed and validated based on genotype and phenotype information on Europeans. Therefore, we need to validate prediction models in diverse ethnic populations. In this study, we selected potentially useful variations for forensic science that are associated with hair and eye color, iris pattern, and facial morphology, based on previous studies, and analyzed their frequencies in 1,920 Koreans. Among 20 single nucleotide polymorphisms (SNPs), 10 SNPs were polymorphic, 6 SNPs were very rare (minor allele frequency < 0.005), and 4 SNPs were monomorphic in the Korean population. Even though the usability of these SNPs should be verified by an association study in Koreans, this study provides 10 potential SNP markers for forensic science for externally visible characteristics in the Korean population.