• 응용통계연구
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• 제16권2호
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• pp.195-202
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• 2003

복합성유전질환 연구에 있어서 단일염기변이를 이용한 일배체형 분석은 개별적인 단일염기변이 분석에 비하여 비용 및 효율 면에서 훨씬 유용하며, 생물학적으로도 기능적 중요성을 갖는 것으로 평가되고 있다. 그러나 일반적인 유전형분석방법을 이용한 단일염기변이군 자료는 이배체형(diploid)으로서 위상(phase)을 확인할 수 없으므로 일배체형 비율을 예측하기 어렵다. 본 연구에서는 고형종양 환자군과 정상군의 단일염기변이군 이배체형 자료가 주어졌을 때 단일염기변이군 일배체형 비율의 우도함수에 EM알고리듬을 적용하여 각 일배체형의 비율을 추정하였다. 이로부터 단일염기변이간의 연관불균형(linkage disequilibrium)을 분석하여 고형 종양과 연관 가능성이 있는 단일염기변이를 살펴보았다.

• Journal of Korean Neurosurgical Society
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• 제57권6호
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• pp.422-427
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• 2015

Moyamoya disease (MMD) is a chronic, progressive, cerebrovascular occlusive disorder that displays various clinical features and results in cerebral infarct or hemorrhagic stroke. Specific genes associated with the disease have not yet been identified, making identification of at-risk patients difficult before clinical manifestation. Familial MMD is not uncommon, with as many as 15% of MMD patients having a family history of the disease, suggesting a genetic etiology. Studies of single nucleotide polymorphisms (SNPs) in MMD have mostly focused on mechanical stress on vessels, endothelium, and the relationship to atherosclerosis. In this review, we discuss SNPs studies targeting the genetic etiology of MMD. Genetic analyses in familial MMD and genome-wide association studies represent promising strategies for elucidating the pathophysiology of this condition. This review also discusses future research directions, not only to offer new insights into the origin of MMD, but also to enhance our understanding of the genetic aspects of MMD. There have been several SNP studies of MMD. Current SNP studies suggest a genetic contribution to MMD, but further reliable and replicable data are needed. A large cohort or family-based design would be important. Modern SNP studies of MMD depend on novel genetic, experimental, and database methods that will hopefully hasten the arrival of a consensus conclusion.

• Asian-Australasian Journal of Animal Sciences
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• 제27권12호
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• pp.1691-1694
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• 2014

Copy number variation (CNV) or single nucleotide phlyorphism (SNP) is useful genetic resource to aid in understanding complex phenotypes or deseases susceptibility. Although thousands of CNVs and SNPs are currently avaliable in the public databases, they are somewhat difficult to use for analyses without visualization tools. We developed a web-based tool called the VCS (visualization of CNV or SNP) to visualize the CNV or SNP detected. The VCS tool can assist to easily interpret a biological meaning from the numerical value of CNV and SNP. The VCS provides six visualization tools: i) the enrichment of genome contents in CNV; ii) the physical distribution of CNV or SNP on chromosomes; iii) the distribution of log2 ratio of CNVs with criteria of interested; iv) the number of CNV or SNP per binning unit; v) the distribution of homozygosity of SNP genotype; and vi) cytomap of genes within CNV or SNP region.

• Molecules and Cells
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• 제43권8호
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• pp.728-738
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• 2020

Time and cost-effective production of next-generation sequencing data has enabled the performance of population-scale comparative and evolutionary studies for various species, which are essential for obtaining the comprehensive insight into molecular mechanisms underlying species- or breed-specific traits. In this study, the evolutionary and functional analysis of Korean native pig (KNP) was performed using single nucleotide polymorphism (SNP) data by comparative and population genomic approaches with six different mammalian species and five pig breeds. We examined the evolutionary history of KNP SNPs, and the specific genes of KNP based on the uniqueness of non-synonymous SNPs among the used species and pig breeds. We discovered the evolutionary trajectory of KNP SNPs within the used mammalian species as well as pig breeds. We also found olfaction-associated functions that have been characterized and diversified during evolution, and quantitative trait loci associated with the unique traits of KNP. Our study provides new insight into the evolution of KNP and serves as a good example for a better understanding of domestic animals in terms of evolution and domestication using the combined approaches of comparative and population genomics.

• 생명과학회지
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• 제33권12호
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• pp.1025-1035
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• 2023

본 연구에서는 한국산과 중국산 새꼬막(Scapharca subcrenata) 사이의 원산지 판별을 위하여 quantitative real-time PCR (qPCR) 분석을 기반으로 하는 Single-nucleotide polymorphism (SNP) 마커의 primer set를 개발 및 검증하였다. 총 180개의 새꼬막 sample을 genotyping by sequencing으로 분석하여 원산지 판별에 유용할 것이라 판단되는 7개의 후보 MS 마커와 15개의 후보 SNP 마커를 선정하였다. 후보 SNP 마커는 PCR과 sanger sequencing, SYBR green-based qPCR을 통해 원산지별 분리 여부를 확인하였다. 이 중 Insertion 1, SNP 21 마커가 qPCR 증폭 양상에서 집단이 확연히 분리되었으며 예상과 실제 증폭 형태가 일치하였다. 추가적으로 새꼬막을 무작위로 섞어서 진행한 blind test에서 Insertion 1은 새꼬막 100개에 대하여 74%의 정확도, 52%의 민감도, 96%의 특이도를 보였고, SNP 21은 새꼬막 137개에 대하여 86%의 정확도, 79%의 민감도, 93%의 특이도를 보였다. 따라서 개발된 두 개의 SNP 마커는 독립적 또는 복합적으로 사용하면 새꼬막 원산지 판별의 진위 여부를 검증하는 데 유용할 것으로 기대된다.

• Asian-Australasian Journal of Animal Sciences
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• 제29권3호
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• pp.315-320
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• 2016

Porcine beta-defensin-1 (PBD-1) gene plays an important role in the innate immunity of pigs. The peptide encoded by this gene is an antimicrobial peptide that has direct activity against a wide range of microbes. This peptide is involved in the co-creation of an antimicrobial barrier in the oral cavity of pigs. The objective of the present study was to detect polymorphisms, if any, in exon-1 and exon-2 regions of PBD-1 gene in Large White Yorkshire (LWY) and native Ankamali pigs of Kerala, India. Blood samples were collected from 100 pigs and genomic DNA was isolated using phenol chloroform method. The quantity of DNA was assessed in a spectrophotometer and quality by gel electrophoresis. Exon-1 and exon-2 regions of PBD-1 gene were amplified by polymerase chain reaction (PCR) and the products were subjected to single strand conformation polymorphism (SSCP) analysis. Subsequent silver staining of the polyacrylamide gels revealed three unique SSCP banding patterns in each of the two exons. The presence of single nucleotide polymorphisms (SNPs) was confirmed by nucleotide sequencing of the PCR products. A novel SNP was found in the 5'-UTR region of exon-1 and a SNP was detected in the mature peptide coding region of exon-2. In exon-1, the pooled population frequencies of GG, GT, and TT genotypes were 0.67, 0.30, and 0.03, respectively. GG genotype was predominant in both the breeds whereas TT genotype was not detected in LWY breed. Similarly, in exon-2, the pooled population frequencies of AA, AG, and GG genotypes were 0.50, 0.27, and 0.23, respectively. AA genotype was predominant in LWY pigs whereas GG genotype was predominant in native pigs. These results suggest that there exists a considerable genetic variation at PBD-1 locus and further association studies may help in development of a PCR based genotyping test to select pigs with better immunity.

• 응용통계연구
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• 제21권1호
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• pp.53-63
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• 2008

일반적으로 인간의 질병과 가축의 경제적인 특성은 하나의 유전자가 아닌 여러 유전자의 상호작용으로 일어난다고 믿고 있다. 따라서 본 연구에서는 세대를 거듭할수록 대립유전자의 유전이 안정적으로 발생되어지고 개체의 기능적인 유전적 가치를 직접적으로 추정할 수 있는 single nucleotide polymorphism(SNP)을 한우의 경제적 특성인도체중(carcass cold weight)에 대하여 모수적인 방법인 ANOVA와 비모수적인 방법인 multifactor dimensionality reduction(MDR)을 이용하여 하나의 유전자의 효과와 두 개의 유전자의 상호작용 효과를 비교하였다. ANOVA에서는 하나의 유전자 SNP1이 도체중에 유의한 효과가 있었고 상호작용 효과에서는 도체중에 유의한 효과는 없었다. MDR에서는 하나의 유전자의 효과인 SNP1과 두 개의 유전자의 상호작용인 SNP1*SNP2의 효과가 컸으며 SNP1과 SNP1*SNP2를 비교했을 시에는 SNP1*SNP2의 효과가 더 크게 나타났다. 이는 개별 SNP유전자 보다 복합 SNP유전자의 상호작용이 경제적인 특성인 도체증에 더 영향을 준다는 것을 알 수 있었다.

• Asian-Australasian Journal of Animal Sciences
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• 제27권11호
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• pp.1521-1525
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• 2014

This study investigated heritability for bovine growth estimated with genomewide single nucleotide polymorphism (SNP) information obtained from a DNA microarray chip. Three hundred sixty seven Korean cattle were genotyped with the Illumina BovineSNP50 BeadChip, and 39,112 SNPs of 364 animals filtered by quality assurance were analyzed to estimate heritability of body weights at 6, 9, 12, 15, 18, 21, and 24 months of age. Restricted maximum likelihood estimate of heritability was obtained using covariance structure of genomic relationships among animals in a mixed model framework. Heritability estimates ranged from 0.58 to 0.76 for body weights at different ages. The heritability estimates using genomic information in this study were larger than those which had been estimated previously using pedigree information. The results revealed a trend that the heritability for body weight increased at a younger age (6 months). This suggests an early genetic evaluation for bovine growth using genomic information to increase genetic merits of animals.

• Mycobiology
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• 제43권1호
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• pp.75-80
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• 2015

We identified single nucleotide polymorphism (SNP) markers in the laccase gene to establish a line-diagnostic system for shiitake mushrooms. A total of 89 fungal isolates representing four lines, including Korean registered, Korean wild type, Chinese, and Japanese lines, were analyzed. The results suggest that SNP markers in the laccase gene can be useful for line typing in shiitake mushrooms.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2012년도 제42회 동계 정기 학술대회 초록집
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• pp.540-540
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• 2012

Selective detection of single nucleotide polymorphism (SNP) of Cytochrome P450 2C19 (CYP2C19) was carried out by the PNA chips which were electrically-interfaced with interdigitated nanogap electrodes (INEs). The INEs whose average gap distance and effective gap length were about ~70 nm and ${\sim}140{\mu}m$, respectively, were prepared by the combination of the photo lithography and the surface-catalyzed chemical deposition, without using the e-beam lithography which is almost inevitable in the conventional lab-scale fabrication of the INEs. Four different types of target DNAs were successfully detected and discriminated by the INE-based PNA chips.