• Genomics & Informatics
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• 제16권4호
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• pp.33.1-33.9
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• 2018

Recently, there have been many studies in medicine related to genetic analysis. Many genetic studies have been performed to find genes associated with complex diseases. To find out how genes are related to disease, we need to understand not only the simple relationship of genotypes but also the way they are related to phenotype. Multi-block data, which is a summation form of variable sets, is used for enhancing the analysis of the relationships of different blocks. By identifying relationships through a multi-block data form, we can understand the association between the blocks in comprehending the correlation between them. Several statistical analysis methods have been developed to understand the relationship between multi-block data. In this paper, we will use generalized canonical correlation methodology to analyze multi-block data from the Korean Association Resource project, which has a combination of single nucleotide polymorphism blocks, phenotype blocks, and disease blocks.

• Asian-Australasian Journal of Animal Sciences
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• 제18권9호
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• pp.1217-1220
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• 2005

Random amplified polymorphic DNA (RAPD-PCR) analysis of 56 animals of four different genetic groups of dwarf cattle in Kerala was done as a single step analysis. Bandsharing (BS) values were calculated for animals of each group and between groups as an analytical tool to find out genetic variation among animals. The different factors affecting BS values were estimated using Harvey''s Least squares analysis. The effects of genetic group, Guanine-cytosine (GC) content of primer and gel on BS values were found significant. Bandsharing values of Kasargode-Highrange dwarf animals were significantly different from Vechur, Vatakara and their combinations. The Vechur, Vatakara and Vechur-Vatakara combinations were found to be more uniform (high BS value) compared with other combinations. The bandsharing value was lowest with primers of GC content 90% and highest with 80% GC content. The effect of gel on BS value points to the need of adjustments of gel factor for calculation of BS values.

• Asian-Australasian Journal of Animal Sciences
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• 제8권4호
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• pp.357-364
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• 1995

A biochemical genetic study on blood enzyme/protein systems in some breeds/crosses of sheep in Malaysia was carried out using horizontal starch gel electrophoresis. Blood samples were collected from 435 sheep, representing 8 breeds/crosses. These included 5 wool sheep breeds (Thai Longtail, wiltshire, Suffolk, Dorsimal and cMBLx), 1 hair sheep breed (Barbados Blackbelly) and 2 hybrids between wool sheep and hair sheep (Cameroon ${\times}$ Thai Longtail and Bali Bali ${\times}$ Malin). Twenty loci systems were examined. Of these, ten ($HB{\beta}$, ALB, TF, XP, CAT, DIA1, EsA, GPI, ME and NP) exhibited genetic variation whereas the other ten (AAT, CA, DIA2, ${\alpha}GLO$, ${\alpha}GLU$, LDH, MDH, PEP[leu-gly-gly], 6PGD and SOD) were monomorphic. The allelic frequencies which were obtained in 10 polymorphic markers are assessed and compared with the results obtained by previous workers. The estimations of inbreeding coefficient, intrabreed variation and breed relationships have been critically discussed and are used to reveal some important recommendations.

• 정보처리학회논문지D
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• 제18D권2호
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• pp.89-100
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• 2011

인간 유전체에 존재하는 유전적 구조 변이(genetic structural variation) 중 하나인 유전체 단위반복변이(Copy Number Variation, CNV)은 유전자의 기능 발현과 밀접한 관련이 있다. 특히 특정 유전 질병이 있는 사람들을 대상으로 CNV와 유전자발현의 관계를 밝히는 연구가 계속 진행되고 있지만, 정상인 유전체에 대한 CNV의 기능적 분석은 아직 활발히 이루어지고 있지 않다. 본 논문에서는 다수의 정상인 샘플에서 찾아낸 공통된 CNV에 대하여 유전자들과의 기능적 관계를 유전자의 분자적 위치와 상관없이 밝힐 수 있는 분석 방법을 제시한다. 이를 위해 서로 다른 이질적인 생물학데이터를 통합하는 방법을 제시하고 공통된 CNV와 유전자와의 연관성을 분자적 위치와 상관없이 계산할 수 있는 새로운 방법을 제시한다. 제안된 방법의 유의성을 보이기 위해서 유전자 온톨로지 (Gene Ontology) 데이터베이스를 이용한 다양한 검증 실험들을 수행하였다. 실험결과 새롭게 제안된 연관성 측정방법은 유의성이 있으며 공통된 CNV와 강한 연관성을 갖는 유전적 기능의 후보들을 시스템적으로 제시할 수 있는 것으로 나타났다.

• Genomics & Informatics
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• 제21권4호
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• pp.48.1-48.8
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• 2023

Liver cancer is the fourth leading cause of death worldwide. Well-known risk factors include hepatitis B virus and hepatitis C virus, along with exposure to aflatoxins, excessive alcohol consumption, obesity, and type 2 diabetes. Genomic variants play a crucial role in mediating the associations between these risk factors and liver cancer. However, the specific variants involved in this process remain under-explored. This study utilized a bioinformatics approach to identify genetic variants associated with liver cancer from various continents. Single-nucleotide polymorphisms associated with liver cancer were retrieved from the genome-wide association studies catalog. Prioritization was then performed using functional annotation with HaploReg v4.1 and the Ensembl database. The prevalence and allele frequencies of each variant were evaluated using Pearson correlation coefficients. Two variants, rs2294915 and rs2896019, encoded by the PNPLA3 gene, were found to be highly expressed in the liver tissue, as well as in the skin, cell-cultured fibroblasts, and adipose-subcutaneous tissue, all of which contribute to the risk of liver cancer. We further found that these two SNPs (rs2294915 and rs2896019) were positively correlated with the prevalence rate. Positive associations with the prevalence rate were more frequent in East Asian and African populations. We highlight the utility of this population-specific PNPLA3 genetic variant for genetic association studies and for the early prognosis and treatment of liver cancer. This study highlights the potential of integrating genomic databases with bioinformatic analysis to identify genetic variations involved in the pathogenesis of liver cancer. The genetic variants investigated in this study are likely to predispose to liver cancer and could affect its progression and aggressiveness. We recommend future research prioritizing the validation of these variations in clinical settings.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제11권sup2호
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• pp.59-66
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• 2008

Genome-wide association studies using large case-control samples and several hundred thousand genetic markers efficiently and powerfully assay common genetic variations. The application of these studies to inflammatory bowel disease has led to the identification of susceptibility genes and affirmed the importance of innate and adaptive immunity in the pathogenesis of disease. Efforts directed towards the identification of environmental factors have implicated commensal bacteria as determinants of dysregulated immunity and inflammatory bowel disease. Host genetic polymorphisms most likely interact with functional bacterial changes to stimulate aggressive immune responses that lead to chronic tissue injury.

• Asian-Australasian Journal of Animal Sciences
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• 제15권12호
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• pp.1822-1830
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• 2002

The microsatellites are the short tandem repeats of 1 to 6 bp long monomer sequences that are repeated several times. These short tandem repeats are considered to be generated by the slipped strand mispairing. Based on the unique capability of alternating purine-pyrimidine residues to form Z-DNA, the possible role of the microsatellites in gene regulation has been proposed. The microsatellites are highly polymorphic, follow Mendelian inheritance and are evenly distributed throughout the genomes of eukaryotes. They are easy to isolate and the polymerase chain reaction based typing of the alleles can be readily automated. These properties make them the preferred markers for comparison of the genetic structure of the closely related breeds/populations; very high-resolution genetic mapping and parentage testing etc. The microsatellites have rapidly replaced the restriction fragment length polymorphism (RFLP) and the random amplified polymorphic DNA (RAPD) in most applications in the population genetics studies in most species, including the various farm animals viz. cattle, buffalo, goat, sheep and pigs etc. More and more reports are now available describing the use of microsatellites in pigs ranging from measurement of genetic variation between breeds/populations, developing high resolution genetic maps to identifying and mapping genes of biological and economic importance.

• Genomics & Informatics
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• 제8권3호
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• pp.101-102
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• 2010

During the last decade, large community cohorts have been established by the Korea National Institutes of Health (KNIH), and enormous epidemiological and clinical data have been accumulated. Using these information and samples in the cohorts, KNIH set out to do a large-scale genome-wide association study (GWAS) in 2007, and the Korea Association REsource (KARE) consortium was launched to analyze the data to identify the underlying genetic risk factors of diseases and diverse health indexes, such as blood pressure, obesity, bone density, and blood biochemical traits. The consortium consisted of 6 research divisions, formed by 25 principal investigators in 19 organizations, including 18 universities, 2 institutes, and 1 company. Each division focused on one of the following subjects: the identification of genetic factors, the statistical analysis of gene-gene interactions, the genetic epidemiology of gene-environment interactions, copy number variation, the bioinformatics related to a GWAS, and a GWAS of nutrigenomics. In this special issue, the study results of the KARE consortium are provided as 9 articles. We hope that this special issue might encourage the genomics community to share data and scientists, including clinicians, to analyze the valuable Korean data of KARE.

• Asian-Australasian Journal of Animal Sciences
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• 제22권1호
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• pp.124-130
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• 2009

Estimating genetic interaction effects in animal genomics would be one of the most challenging studies because the phenotypic variation for economically important traits might be largely explained by interaction effects among multiple nucleotide sequence variants under various environmental exposures. Genetic improvement of economic animals would be expected by understanding multi-locus genetic interaction effects associated with economic traits. Most analyses in animal breeding and genetics, however, have excluded the possibility of genetic interaction effects in their analytical models. This review discusses a historical estimation of the genetic interaction and difficulties in analyzing the interaction effects. Furthermore, two recently developed methods for assessing genetic interactions are introduced to animal genomics. One is the restricted partition method, as a nonparametric grouping-based approach, that iteratively utilizes grouping of genotypes with the smallest difference into a new group, and the other is the Bayesian method that draws inferences about the genetic interaction effects based on their marginal posterior distributions and attains the marginalization of the joint posterior distribution through Gibbs sampling as a Markov chain Monte Carlo. Further developing appropriate and efficient methods for assessing genetic interactions would be urgent to achieve accurate understanding of genetic architecture for complex traits of economic animals.

• Asian-Australasian Journal of Animal Sciences
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• 제19권4호
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• pp.475-481
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• 2006

The genetic polymorphism and relationships of Muscovy, Cherry Valley Meat ducks, Partridge ducks and their crossbreds $F_1$ and $F_2$, respectively, were studied using a random amplified polymorphic DNA (RAPD) technique. The results showed that RAPD markers were effective for the analysis of genetic relationships among ducks. Amplification with 20-primers gave 760 reproducible amplified fragments. The percentage of polymorphic marker band was 74.70%, which indicates that the RAPD technique had higher efficiency of polymorphism detection and sensitivity in studying the genetic variations among ducks and showed that the genetic polymorphism was abundant between two species of duck populations. The average index of genetic distance in hybrid $F_2$ was 0.2341 and higher than that of its parents, which indicates that the genetic diversity was improved by crossbreeding with Muscovy.