• Journal of the Korean Data and Information Science Society
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• v.21 no.3
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• pp.387-395
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• 2010

It is important to identify the interaction of genes about human disease and characteristic value. Many studies as like logistic analysis, have associated being pursued, but, previous methods did not consider the sub-group of the genotypes. So, QTL interactions and the GMM (genotype matrix mapping) have been developed. In this study, we detect the superior genotype combination to have an impact on economic traits of Korean cattle based on the study over GMM method. Thus, we identified interaction effects of single nucleotide polymorphisms (SNPs) responsible for average daily gain(ADG), marbling score (MS), carcass cold weight (CWT), longissimus muscle dorsiarea (LMA) using GMM method. In addition, we examine significance of the major genotype combination selected by implementing permutation test of the F-measure which was not obtained by Sachiko et al.

• The Korean Journal of Applied Statistics
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• v.23 no.4
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• pp.693-703
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• 2010

Diseases of human or economical traits of cattles are occured by interaction of genes. We introduce expanded multifactor dimensionality reduction(E-MDR), dummy multifactor dimensionality reduction(D-MDR) and SNPHarvester which are developed to find interaction of genes. We will select interaction of outstanding gene combinations and select final best genotype groups.

• Journal of Life Science
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• v.25 no.1
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• pp.84-92
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• 2015

Interferon inducible transmembrane protein (IFITM) family genes have been implicated in various cellular processes such as the homotypic cell adhesion functions of IFNs and cellular anti-proliferative activities. The present study aimed to investigate whether the polymorphisms of the IFITM2 and IFITM5 genes are associated with susceptibility to UC. We identified a total of thirteen polymorphisms (eleven SNPs and two variations) in the IFITM2 gene and twelve polymorphisms (eleven SNPs and one variation) in the IFITM5 gene, by the direct sequencing method. Genotype analysis in the IFITM2 and IFITM5 SNPs was performed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and Taq-Man probe analysis, and the haplotype frequencies of IFITM2 and IFITM5 SNPs for multiple loci were estimated using the expectation maximization (EM) algorithm. The genotype and allele frequencies of IFITM2 SNPs, as well as IFITM5 SNPs, in UC patients were not significantly different from those of the healthy controls. We also analyzed the combined frequencies of rs77537847 of IFITM1, rs909097 of IFITM2, and rs56069858 of IFITM5 in the UC patients and the healthy controls. Although the distribution of the major combined genotype frequency did not differ significantly between the healthy controls and the UC patients, the GGT combined frequency in the healthy controls was significantly different from that in the UC patients (P=0.002). This result suggests that the combined genotype of the IFITMs polymorphisms may be associated with a susceptibility to UC and could be a useful genetic marker for UC.

• Journal of the Korean Data and Information Science Society
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• v.23 no.3
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• pp.467-474
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• 2012

Human diseases and livestock economic traits are not typically the result of variation of a single genetic locus, but are rather the result of interplay between interactions among multiple genes and a variety of environmental exposures. We have used linear regression model for adjusted environmental effects and multifactor dimensionality reduction (MDR) method to identify gene-gene interaction effect of statistical model in general. Of course, we use 5 SNPs (single uncleotide polymorphism) which were studied recently by Oh et al. (2011). We apply the MDR (multifactor demensionality reduction) method on the identify major interaction effects of single nucleotide polymorphisms responsible for economic traits in a Korean cattle population.

• Journal of the Korean Data and Information Science Society
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• v.20 no.4
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• pp.639-647
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• 2009

From development of computer science, genetic algorithm has been applied to many fields for search like non-linear problem based on various variables and optimization process. Among others, in the data mining field, there are methods to select the best input variables for model accuracy and various predict models which were merged by using the genetic algorithm. In the meantime, to improve and preserve quality of the Hanwoo (Korean cattle) which is represented the agricultural industry in our country, we need to find out outstanding economical traits of Hanwoo in having specific genotype of single nucleotide polymorphism (SNP) which is inherited to next generation. According to, This research proposed the selecting method to find genotype of SNPs marker which affects economical traits of the Hanwoo by using the genetic algorithm. And we selected the best genotypes of the principal SNPs marker by applying to real data on Hanwoo genetic.

• The Korean Journal of Applied Statistics
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• v.24 no.5
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• pp.861-869
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• 2011

One of the main objects of recent genetic studies is to understand genetic factors that induce complex diseases. If there are interactions between loci, it is difficult to find such associations through a single-locus analysis strategy. Thus we need to consider the gene-gene interactions and/or gene-environment interactions. The MDR(multifactor dimensionality reduction) method is being used frequently; however, it is not appropriate to detect interactions caused by a small fraction of the possible genotype pairs. In this study, we propose a relative risk interaction explorer that detects interactions through the calculation of the relative risks between the control and disease groups from each genetic combinations. For illustration, we apply this method to MDR open source data. We also compare the MDR and the proposed method using the simulated data eight genetic models.

• Journal of the Korean Data and Information Science Society
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• v.26 no.3
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• pp.677-685
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• 2015

Disease of human and economic traits of livestocks are affected a lot by gene combination effect rather than a single gene effect. In this study, we used SNPHarvester method that supplement existing method in order to investigate the interaction of these genes. The used genes are SREBPs (g.3270+10274 C>T, g.13544 T>C) and FABP4 (g.2634+1018 A>T, g.2988 A>G, g.3690 G>A, g.3710 G>C, g.3977-325 T>C, g.4221 A>G) that are closely related to the fatty acid composition affecting the meatiness of Korean cattle. The economic traits which are used are oleic acid (C18:1), monounsaturated fatty acid (MUFA), marbling score (MS). First, we have utilized the SNPHarvester method in order to find excellent gene combination, and then used the multifactor dimensionality reduction method in order to identify excellent genotype in gene combination.

• Journal of KIISE:Computer Systems and Theory
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• v.35 no.11
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• pp.509-516
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• 2008

The Minimum Letter Flips (MLF) model and the Weighted Minimum Letter Flips (WMLF) model are for solving the haplotype assembly problem. But these two models are effective only when the error rate in SNP fragments is low. In this paper, we first establish a new computational model that employs the related genotype information as an improvement of the WMLF model and show its NP-hardness, and then propose an efficient genetic algorithm to solve the haplotype assembly problem. The results of experiments on random data set and a real data set indicate that the introduction of genotype information to the WMLF model is quite effective in improving the reconstruction rate especially when the error rate in SNP fragments is high. And the results also show that genotype information increases the convergence speed of the genetic algorithm.

• Journal of Genetic Medicine
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• v.4 no.2
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• pp.160-166
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• 2007

Purpose : The ${\beta}$-adrenoceptors are pharmacologically classified into ${\beta}_1$-, ${\beta}_2$- and ${\beta}_3$-adrenoceptor. The gene of each subtype has polymorphisms related to their function (${\beta}_1$-adrenoceptor: Ser49Gly, ${\beta}_2$-adrenoceptor: Gln27Glu, ${\beta}_3$-adrenoceptor: Trp64Arg). The objectives of this study were to analyse the allelic and genotypic distribution of the representative polymorphism of ${\beta}$-adrenoceptors in preeclampsia and to investigate whether combined genotype of ${\beta}$-adrenoceptors may be associated with preeclampsia. Methods : Blood samples were collected from a Korean population (159 preeclamptic pregnancies and 168 normotensive pregnancies). The ${\beta}_1$-, ${\beta}_2$- and ${\beta}_3$-adrenoceptor genotypes was determined using polymerase chain reaction-restriction fragment length polymorphism. Results : There were no differences in allelic and genotypic distribution of ${\beta}_1$- and ${\beta}_2$-adrenoceptor polymorphisms between the two groups. However, the Arg allele of ${\beta}_3$-adrenoceptor polymorphism were more frequent in preecalmpsia than in controls (P<0.05, OR=1.57, 95% CI=1.01-2.46). Moreover, prevalence of genotype carrying heterozygote of ${\beta}_3$-adrenoceptor polymorphism was increased in preeclampsia compared with controls (P<0.05, OR 1.76, 95% CI 1.06-2.92). When combination of the three polymorphisms were evaluated, pregnancies with the particular combined genotype that is consisted of heterozygote of ${\beta}_1$-, ${\beta}_3$-adrenoceptor and wild homozygote of ${\beta}_2$-adrenoceptor (Ser/Gly, Gln/Gln, Trp/Arg), showed a significant increase in the risk of preeclampsia (P<0.05, OR=3.01, 95% CI 1.12-8.08). Conclusion : A particular combined genotype (Ser/Gly, Gln/Gln, Trp/Arg) of - adrenoceptors was associated with the risk of preeclampsia.

• The KIPS Transactions:PartB
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• v.16B no.2
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• pp.157-161
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• 2009

Minimum Letter Flips(MLF) and Weighted Minimum Letter Flips(WMLF) can perform the haplotype reconstruction more accurately from SNP fragments when they have many errors and gaps by introducing the related genotype information. And it is known that WMLF is more accurate in haplotype reconstruction than those based on the MLF. In the paper, we analyze two models under the conditions that the different rates of homozygous site in the genotype information and the different confidence levels according to the sequencing quality. We compare the performance of the two models using neural network and genetic algorithm. If the rate of homozygous site is high and sequencing quality is good, the results of experiments indicate that WMLF/GI has higher accuracy of haplotype reconstruction than that of the MCIH especially when the error rate and gap rate of SNP fragments are high.