• Proceedings of the Korean Society of Computer Information Conference
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• 2016.07a
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• pp.21-24
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• 2016

전장유전체 연관성 연구에서 상위성 탐색은 많은 단일염기다형성 수로 인해 계산이 어렵기 때문에 네트워크에서의 탐색을 이용한 방법이 사용되고 있다. 그러나 전장유전체 연관성 연구에서 단일염기다형성들의 상위성 네트워크의 구성 역시 큰 계산 비용을 필요로 한다. 본 논문에서는 단일염기다형성과 표현형의 상호정보량을 이용한 네트워크를 구성하는데 드는 시간을 줄이는 알고리즘을 제안한다. 또한 표본 크기별로 계산 시간을 실험해 보았으며, 기존의 방법과 비교해 실행 속도가 향상됨을 보였다.

• Journal of the Korean Data and Information Science Society
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• v.25 no.5
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• pp.1057-1067
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• 2014

Many genetic variants have been identified to be associated with complex diseases such as hypertension, diabetes and cancers throughout genome-wide association studies (GWAS). However, there still exist a serious missing heritability problem since the proportion explained by genetic variants from GWAS is very weak less than 10~15%. Gene-gene interaction study may be helpful to explain the missing heritability because most of complex disease mechanisms are involved with more than one single SNP, which include multiple SNPs or gene-gene interactions. This paper focuses on gene-gene interactions with the survival phenotype by extending the multifactor dimensionality reduction (MDR) method to the accelerated failure time (AFT) model. The standardized residual from AFT model is used as a residual score for classifying multiple geno-types into high and low risk groups and algorithm of MDR is implemented. We call this method AFT-MDR and compares the power of AFT-MDR with those of Surv-MDR and Cox-MDR in simulation studies. Also a real data for leukemia Korean patients is analyzed. It was found that the power of AFT-MDR is greater than that of Surv-MDR and is comparable with that of Cox-MDR, but is very sensitive to the censoring fraction.

• Journal of Convergence for Information Technology
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• v.8 no.6
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• pp.201-207
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• 2018

A genome contains all genetic information of an organism. Within a specific species, unique traits appear for each individual, which can be identified by analyzing nucleotide sequences. Many Genome-Wide Associations Studies have been carried out to find genetic associations and cause of diseases from slightly different base among the individuals. It is important to identify occurrence of slight variations for polymorphisms of individuals. In this paper, we introduce an analysis and visualization tool for specific variation pattern identification of polymorphisms in nucleotide sequences and show the validity of the tool by applying it to analyzing nucleotide sequences of subcultured pOka strain of varicella-zoster virus. The tool is expected to help efficiently explore allele frequency variations and genetic factors within a species.

• The KIPS Transactions:PartD
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• v.18D no.2
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• pp.89-100
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• 2011

The CNV (Copy Number Variation) which is one of the genetic structural variations in human genome is closely related with the function of gene. In particular, the genome-wide association studies for genetic diseased persons have been researched. However, there have been few studies which infer the genetic function of CNV with normal human. In this paper, we propose the analysis method to reveal the functional relationship between common CNV and genes without considering their genomic loci. To achieve that, we propose the data integration method for heterogeneity biological data and novel measurement which can calculate the correlation between common CNV and genes. To verify the significance of proposed method, we has experimented several verification tests with GO database. The result showed that the novel measurement had enough significance compared with random test and the proposed method could systematically produce the candidates of genetic function which have strong correlation with common CNV.

• Journal of Digital Contents Society
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• v.19 no.9
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• pp.1795-1801
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• 2018

Genome-Wide Association Study (GWAS) have been used to identify susceptibility genes for complex human diseases and many recent studies succeed to report common genetic factors for various diseases. Unfortunately, it is hard to understand all biological functions and mechanisms around the complex disease with GWAS only although the number of known associated genes with diseases is increased drastically because GWAS is a single locus based approach while not a gene but numerous factors may affect a disease associated pathways. PRaDA generates a combined report with genes, pathways and Gene Ontology (GO) using single nucleotide polymorphism (SNP) analysis output. The PRaDA reports not only directly associated pathways but also functionally related ones for identifying accumulated effects of low p-value SNPs. Through integrated information including indirect functional effects, user could have insights of overall disease mechanisms and markers.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2019.10a
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• pp.19-19
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• 2019

유전체 전장 연관분석 (GWAS)은 단일염기다형성(SNP)의 유전자형과 표현형 간의 통계적인 연관성을 분석함으로써 품종 선발용 SNP Marker 개발에 응용되고 있다. 본 연구에서는 Tano Red와 Ruby seedless 교배실생 278 계통을 대상으로 여러 과실 특성에 따른 관련 SNP를 동정함으로써 육종 선발에 필요한 DNA marker 개발에 필요한 기초 유전 자료를 얻고자 하였다. 한 계통 당 5~10개의 포도알을 선택하여 과립중, 과육탄성, 과피탄성, 과육경도, 과피경도, 과립당 종자갯수, 과립당 종자무게 및 인장강도를 측정하였다. 각 개체는 Genotyping by sequencing (GBS) 방법으로 Sequencing하여 Reference genome (Vitis vinifera PN40024 12X v2.)과 mapping 하였다. MAF (Minor allele frequency) >5%, Missing Data <30% 의 조건을 가진 SNPs 만 1차 선발하여 TASSEL과 GAPIT 프로그램으로 GWAS 분석을 하였다. Manhattan plot 결과 과립중 형질에서는 33개, 과립당 종자무게 25개와 인장강도에서는 20개의 통계학적으로 유의한 SNPs 가 선발되었고, 특이적으로 이들 모두 18번 염색체에서 발견되었다. 그러나 나머지 형질에서는 유의한 차이를 보이는 SNPs를 선발하지 못하였다. 과실의 인장강도는 수확 후 저장성과 유통과정에 영향을 미치기 때문에 Marker 개발을 통한 품종선별이 중요하다. 향후 이러한 특성과 본 연구를 통해 동정된 SNPs 의 상관관계를 구체적으로 연구하여 Marker 개발에 활용하고자 한다.

• Journal of Life Science
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• v.31 no.6
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• pp.568-573
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• 2021

This study identified genomic factors associated with endoplasmic reticulum protein (ERp)29 gene expression in a genome-wide association study (GWAS) of genetic variants, including single-nucleotide polymorphisms (SNPs). In total, 373 European genes from the 1000 Genomes Project were analyzed. SNPs with an allelic frequency of less than or more than 5% were removed, resulting in 5,913,563 SNPs including in the analysis. The following expression quantitative trait loci (eQTL) from the long noncoding RNA LOC105372577 were strongly associated with ERp29 expression: rs6138266 (p<4.172e10), rs62193420 (p<1.173e10), and rs6138267 (p<2.041e10). These were strongly expressed in the testis and in the brain. The three eQTL were identified through a transcriptome-wide association study (TWAS) and showed a significant association with ERp29 and osteosarcoma amplified 9 (OS9) expression. Upstream sequences of rs6138266 were recognized by ChIP-seq data, while HaploReg was used to demonstrate how its regulatory DNA binds upstream of transcription factor 1 (USF1). There were no changes in the expression of OS9 or USF1 following ER stress.

• Journal of the Korean Data and Information Science Society
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• v.26 no.6
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• pp.1249-1258
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• 2015

DGAT1(diacylglycerol O-acyltransferase1) gene is well known as a major gene of milk production in dairy cattle. This study was conducted to investigate how the DGAT1 gene effect on milk yield was appeared from the genome wide association (GWA) using high density whole genome SNP chip. The data set used in this study consisted of 353 Korean Holstein sires with 50k SNP genotypes and deregressed estimated breeding values of milk yield. After quality control 41,051 SNPs were selected and locations on chromosome were mapped using UMD 3.1. Bayesian regression of BayesB method (pi=0.99) was used to estimate the SNP effects and genomic breeding values. Percentages of variance explained by 1 Mb non-overlapping windows were calculated to detect the QTL region. As the result of this study, top 1 and 3 of 2,516 windows were seen around DGAT1 gene region and 0.51% and 0.48% of genetic variance were explained by these two windows. Although SNPs on the DGAT1 gene region are excluded in commercial 50k SNP chip, the effect of DGAT1 gene seem to be reflected on GWA by the SNPs which are in linkage disequilibrium with DGAT1 gene.

• Journal of Korean Society of Forest Science
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• v.112 no.1
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• pp.40-56
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• 2023

Tree species within the Populus genus grow rapidly and have an excellent capacity to absorb carbon, conferring substantial ability to effective purify the environment. Poplar breeding can be achieved rapidly and efficiently if a genetic linkage map is constructed and quantitative trait loci (QTLs) are identified. Here, a high-density genetic linkage map was constructed for the control pollinated progeny using the genotyping-by-sequencing (GBS) technique, which is a next-generation sequencing method. A search was also performed for the genes associated with quantitative traits located in the genetic linkage map by examining the variables of height and diameter at root collar, and resilience to insect damage. The height and diameter at root collar were measured directly, while the ability to recover from insect damage was scored in a 4-year-old breeding population of aspen hybrids (Odae19 × Bonghyeon4 F1) established in the research forest of Seoul National University. After DNA extraction, paternity was confirmed using five microsatellite markers, and only the individuals for which paternity was confirmed were used for the analysis. The DNA was cut using restriction enzymes and the obtained DNA fragments were prepared using a GBS library and sequenced. The analyzed results were sorted using Populus trichocarpa as a reference genome. Overall, 58,040 aligned single-nucleotide polymorphism (SNP) markers were identified, 17,755 of which were used for mapping genetic linkages. The genetic linkage map was divided into 19 linkage groups, with a total length of 2,129.54 cM. The analysis failed to identify any growth-related QTLs, but a gene assumed to be related to recovery from insect damage was identified on linkage group (chromosome) 4 through genome-wide association study.

• Journal of Nutrition and Health
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• v.43 no.4
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• pp.357-366
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• 2010

There has been no genome-wide association study (GWAS) for macronutrient intake as a quantitative trait. To explore genetic loci associated with total calorie and macronutrient intake, genome-wide association data of autosomal single nucleotide polymorphisms (SNPs) from Korean adults were analyzed. We conducted a GWAS in 3,690 men and women aged 40 to 60 years from an urban population-based cohort. At the baseline examination (June 18, 2001 through January 29, 2003), DNA samples of the study subjects were collected and analyzed for genotyping. The information of average daily consumption of total calorie, carbohydrate, protein, and fat was obtained from a semi-quantitative food frequency questionnaire and transformed by natural logarithm for analyses after adjustment of calorie intake. Using multivariate linear regression analysis adjusted for age, sex, and height, we tested for 352,021 SNPs and found weak associations, which do not reach genome-wide association significance, with calorie and macronutrient intake. However, a number of SNPs were found to have potential associations with macronutrient intake; in particular, signals in SORBS1 and those in PRKCB1 were likely associated with carbohydrate and fat intake, respectively. We observed an inverse association between the minor allele of the SNPs in these genes and the amount of consumption of carbohydrate or fat. Our GWAS identified loci and minor alleles weakly associated with macronutrient intake. Because SORBS1 and PRKCB1 are reportedly associated with the metabolism of glucose and lipid as well as with obesity-related diseases, further investigations on biological and functional roles of polymorphism of these genes in the relation to macronutrient intake are warranted.