• Communications for Statistical Applications and Methods
• /
• 제29권1호
• /
• pp.65-83
• /
• 2022

Although various statistical methods have been developed to map time-dependent genetic factors, most identified genetic variants can explain only a small portion of the estimated genetic variation in longitudinal traits. Gene-gene and gene-time/environment interactions are known to be important putative sources of the missing heritability. However, mapping epistatic gene-gene interactions is extremely difficult due to the very large parameter spaces for models containing such interactions. In this paper, we develop a Gaussian process (GP) based nonparametric Bayesian variable selection method for longitudinal data. It maps multiple genetic markers without restricting to pairwise interactions. Rather than modeling each main and interaction term explicitly, the GP model measures the importance of each marker, regardless of whether it is mostly due to a main effect or some interaction effect(s), via an unspecified function. To improve the flexibility of the GP model, we propose a novel grid-based method for the within-subject dependence structure. The proposed method can accurately approximate complex covariance structures. The dimension of the covariance matrix depends only on the number of fixed grid points although each subject may have different numbers of measurements at different time points. The deviance information criterion (DIC) and the Bayesian predictive information criterion (BPIC) are proposed for selecting an optimal number of grid points. To efficiently draw posterior samples, we combine a hybrid Monte Carlo method with a partially collapsed Gibbs (PCG) sampler. We apply the proposed GP model to a mouse dataset on age-related body weight.

• 한국수의병리학회:학술대회논문집
• /
• 한국수의병리학회 2000년도 추계학술대회 및 정기총회
• /
• pp.19-19
• /
• 2000

Most renal diseases progress by consecutive cell responses such as hypertrophy, hyperplsia, proliferation, defferentiation, sclerosis, fibrosis and other cellular degenerative process. These cellular responses are mediated by the activation of various mitogens such as vasoconstrictors, growth factors, hormone, genotoxins and cytokines through mechanical, hemodynamic, immunological injury as well as metabolic abnormality. (omitted)

• 미생물학회지
• /
• 제29권4호
• /
• pp.215-220
• /
• 1991

MudJ(Km.lac) operon fusions were used in the identification of osmotic-inducible genetic(osi) loci in Salmonella typhimurium. Expression of osi::lacZ(osi5001, 5027) genes were dramatically induced 39-189 fold when the osmolarity was increased. Seven osm::lacZ genes were constituvely expressed under both low and high osmotic strength. The osi5001::lacZ fusion strains showed the enhanced osmotolerance and the reduced expression of the osi5001::lacZ in the presence of 1mM proline or betaine as osmoprotectants. Four osmotic inducible genetic loci were mapped into 36 (YK531), 44 (YK504), 57 (YK501) and 84 (YK528) map unit by testing the cotransduction frequency.

• Asian-Australasian Journal of Animal Sciences
• /
• 제14권3호
• /
• pp.302-306
• /
• 2001

This study was carried out to construct mapping population and to evaluate the methods involved, including polymorphic DNA marker system and appropriate statistical analysis. As an initial step to establish chicken genome mapping project, White Leghorn (WL) and Korean Ogol chicken (KOC) were used for generating backcross population. From 8 initial parents, total 280 backcross progenies were obtained and 40 were used for genotyping and linkage analysis. For development of novel polymorphic markers for KOC, Random Amplified Polymorphic DNA (RAPD) markers specific for this chicken line were generated. Also included in this study were six microsatellite markers from East Lansing map as reference loci. For segregation analysis, 15 RAPD markers and 6 microsatellites were used to genotype the backcross population. Among the RAPD markers that we developed, 2 pairs of markers were identified to be linked and another 4 RAPD markers showed linkage with microsatellites of known map. In summary, this study showed that our backcross population generated from the mating of KOC to WL serves as a valuable genetic resource for genotyping. Furthermore, RAPD markers are proved to be valuable in linkage mapping analysis.

• 한국발생생물학회:학술대회논문집
• /
• 한국발생생물학회 2001년도 발생공학 국제심포지움 및 학술대회 발표자료집
• /
• pp.14-17
• /
• 2001

Positional clonging (map-based cloning) of mutations or genetic variations has been served as an invaluable tool to understand in-vivo functions of genes and to identify molecular components underlying phenotypes of interest. Mice homozygous for the cerebellar deficient folia (cdf) mutation are ataxic, with cerebellar hypoplasia and abnormal lobulation of the cerebellum. In the cdf mutant cerebellum approximately 40% of Purkinje cells are ectopically located within the white matter and the inner granule cell layer (IGL). To identify the cdf gene, a high-resolution genetic map for the cdf-gene-encompassing region was constructed using 1997 F2 mice generated from C3H/HeSnJ-cdf/cdf and CAST/Ei intercross. The cdf gene showed complete linkage disequilibrium with three tightly linked markers D6Mit208, D6Mit359, and D6Mit225. A contig using YAC, BAC, and P1 clones was constructed for the cdf critical region to identify the gene. A deletion in the cdf critical region on chromosome 6 that removes approximately 150 kb of DNA selection. cdf mutant mice with the transgenic copy of the identified gene restored the brain abnormalities of the mutant mice. The positional cloning of cdf gene provides a good example showing the identification of a gene could lead to finding a new component of important molecular pathways.

• 한국작물학회:학술대회논문집
• /
• 한국작물학회 2017년도 9th Asian Crop Science Association conference
• /
• pp.117-117
• /
• 2017

The onion (Allium cepa L.) is the most widely cultivated species of the genus Allium, especially it has been valued because of the pungent flavor and aroma. Allium species including onion has very large genome sizes ranging from approximately 10 to 20 Gbp, which have complicated genomic studies and precluded genome sequencing until recently. A population of 186 F2 individuals derived from a cross of 'Umjinara' ${\times}$ 'Sinsunhwang' and the two parental lines were used for this study. For the development of framework map, various types of markers including SSRs, RAPD, SNPs, and CAPS makers have been used for polymorphism test. Especially, a lot of SNP and CAPS loci were developed from the onion transcriptome sequence by RNASEQ of two parental lines. The GBS libraries have been constructed based on a modified protocol from Poland Lab using a two-enzyme system. We have been developing markers showing polymorphism between two parental lines, and genotyping for all F2 individuals were finished for a number of polymorphic markers. For the construction of GBS libraries, a set of 192 barcoded adapters were generated from complementary oligonucleotides with XhoI overhang sequence and unique barcodes of length 4-8 bp and they have been tested using two parental linesto determine the optimum conditions for GBS analysis.

• 한국동물번식학회:학술대회논문집
• /
• 한국동물번식학회 2001년도 발생공학 국제심포지움 및 학술대회 발표자료집
• /
• pp.14-17
• /
• 2001

Positional cloning (map-based cloning) of mutations or genetic variations has been served as an invaluable tool to understand in-vivo functions of genes and to identify molecular components underlying phenotypes of interest. Mice homozygous for the cerebellar deficient folia (cdf) mutation are ataxic, with cerebellar hypoplasia and abnormal lobulation of the cerebellum. In the cdf mutant cerebellum approximately 40% of Purkinje cells are ectopically located within the white matter and the inner granule cell layer (IGL). To identify the cdf gene, a high-resolution genetic map for the cdf-gene-encompassing region was constructed using 1997 F2 mice generated from C3H/HeSnJ-cdf/cdf and CAST/Ei intercross. The cdf gene showed complete linkage disequilibrium with three tightly linked markers D6Mit208, D6Mit359, and D6Mit225. A contig using YAC, BAC, and P1 clones was constructed for the cdf critical region to identify the gene. A deletion in the cdf critical region on chromosome 6 that removes approximately 150kb of DNA was identified. A gene associated with this deletion was identified using cDNA selection. cdf mutant mice with the transgenic copy of the identified gene restored the brain abnormalities of the mutant mice. The positional cloning of cdf gene provides a good example showing the identification of a gene could lead to finding a new component of important molecular pathways.

• 한국지능시스템학회논문지
• /
• 제16권5호
• /
• pp.556-561
• /
• 2006

DNA칩 영상의 패턴 분류는 인간의 유전적 질병에 대한 유용한 정보를 획득할 수 있다는 점에서 아주 중요한 것이다. 본 논문에서는 DNA칩 영상의 패턴을 분류하기 위해 신경망의 학습 알고리즘 중 Back-propagation과 Self Organizing Map을 이용하여 패턴을 분류하는 알고리즘을 개발하고 이들의 결과를 비교 분석하였다. 또한 개발한 알고리즘은 PC 환경 및 S3C2440 (ARM920T)을 CPU Core로 사용한 MV2440 보드에서 실험하여 그 결과를 디스플레이 함으로써 사용자가 다양한 환경에서 보다 쉽게 유전자 정보를 얻는데 도움을 줄 수 있도록 하였다.

• 한국가금학회지
• /
• 제42권1호
• /
• pp.77-86
• /
• 2015

닭은 전체 염기서열의 길이가 포유류에 비해 3분의 1 정도로 비교적 작은 유전체를 가지고 있기 때문에 인간의 주요한 단백질 공급원으로써의 중요성뿐 아니라, 동물의 형질연관 유전자 연구 및 발생유전학적 연구에 좋은 모델 동물이다. 따라서 본 연구에서는 한국재래닭 이용성을 증대시키는 목적으로 한국재래닭의 유전적 구조를 이해하고, 다양한 응용연구의 토대를 마련하기 위하여 131개의 microsatellite (MS) 마커와 8개의 SNP 마커 유전자형을 이용하여 한국재래닭의 유전적 연관지도를 작성하였다. 그 결과, 한국재래닭의 유전 연관지도의 총 길이는 2729.4 cM으로 확인되었고, 연관지도 작성에 사용된 각 마커 간의 거리는 평균 19.64 cM으로 계산되었다. 모든 마커의 유전적 거리와 물리적 거리의 순서는 GGA8의 ADL0278과 MCW0351의 물리적 거리의 순서가 바뀐 결과만 제외하고, 이전의 연구결과와 매우 유사한 결과를 나타내었다. 또한 macrochromosome과 microchromosome의 재조합률을 비교해 본 결과, macrochromosome이 microchromosome보다 3.7배 크게 나타나, 이전에 보고와 유사한 결과를 나타내었다. 유전 연관지도의 암수에 따른 차이에서는 GGA1, 7, 13, 27의 네 개의 염색체에서 암, 수의 성별에 따른 차이를 나타내었다. 각 마커의 평균 대립유전자 수와 이형접합도(Hexp), 다형성(PIC) 수치는 각각 5.5, 0.63, 0.58로 유전적 지도를 작성하기에 충분하 다형성을 가진 것을 확인하였다. 따라서 본 연구의 결과는 한국재래닭의 유전적 구조를 이해하고, 유전체 QTL 연구와 같은 응용연구에 기초자료로써 유용하게 사용될 수 있을 것으로 사료된다.

• 한국측량학회지
• /
• 제31권1호
• /
• pp.1-9
• /
• 2013

본 연구는 유전 알고리즘을 이용하여 다대다 면 객체 정합을 수행하는 방법을 제안한다. 동일한 지형 지물을 표현하는 객체 집합의 형상은 서로 동일하다는 가정 하에 형상 유사도를 최적화하는 객체 집합을 두 지도 사이에서 탐색함으로써 정합을 수행한다. 이 때 어떤 객체가 객체 집합에 포함되는지의 여부를 이진 부호로 표현하고, 이진 부호들을 결합한 이진 문자열로 후보해를 표현한다. 초기 후보해들로 해집단을 생성한 뒤, 유전 알고리즘에 의하여 점진적으로 해집단의 품질을 개선함으로써 최적해를 탐색하였다. 제안된 방법을 평가하기 위하여 수원시 도심지역의 수치지형도와 지적도에서 가구계 대응 면 객체 집합을 탐색하였으며 제안된 알고리즘의 효용성을 확인할 수 있었다. 또한 수작업에 의한 탐색결과를 이용하여 평가한 결과 0.946의 정확도를 얻었다.