• Journal of the Korea Society of Computer and Information
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• v.17 no.11
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• pp.141-148
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• 2012

The advance of technologies for human genome makes it possible that the analysis of association between genetic variants and diseases and the application of the results to predict risk or susceptibility to them. Many of those studies carried out in case-control study. For quantitative traits, statistical analysis methods are applied to find single nucleotide polymorphisms (SNP) relevant to the diseases and consider them one by one. In this study, we presented methods to select informative single nucleotide polymorphisms and predict risk for quantitative traits and compared their performance. We adopted two SNP selection methods: one considering single SNP only and the other of all possible pairs of SNPs.

• The Korean Journal of Applied Statistics
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• v.16 no.2
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• pp.195-202
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• 2003

Haplotype analysis in SNP is very useful for the study of complex genetic disease due to low cost and high efficiency comparing to individual analysis of each SNP, and is functionally important in biological view. But, the gametic phase of haplotypes is usually unknown in SNP group, and it is difficult to predict haplotype proportions. In this study, haplotype proportions were estimated using EM algorithm from diploid data of SNP group in solid tumor group and normal group. From these results, linkage disequilibrium among SNPs was analyzed.

• BMB Reports
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• v.37 no.3
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• pp.269-274
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• 2004

DNA polymerases without the 3' exonuclease function ($exo^-$ pol) have been widely used in sequencing and SNP genotyping. As a major player that expedited the coming of the postgenomic era, $exo^-$ polymerases worked remarkably well in the Human Genome Sequencing Project. However, it has become a challenge for this class of polymerases to efficiently screen the large number of SNPs that are found in the human genome. For more than three decades it has been recognized that polymerase fidelity varied according to the presence of proofreading activity that is mediated by its internal 3' exonuclease. Polymerases with proofreading function are famous for their high fidelity in DNA replication both in vivo and in vitro, but this well-known class of polymerases has been almost completely neglected in genetic analysis in the postgenomic era. We speculate that $exo^+$ polymerases may exhibit higher nucleotide identification ability when compared to $exo^-$ polymerases for an in vitro genetic analysis. With the application of $exo^+$ polymerases in SNP assays, a novel mechanism for the maintenance of DNA replication, the on/off switch, was discovered. Two new SNP assays have been developed to carry out genome-wide genotyping, taking advantage of the enzymatic properties of $exo^+$ polymerases. Furthermore, the on/off switch mechanism embodies a powerful nucleotide identification ability, which can be used to discriminate the bases that are upstream of the 3' terminus, and thus defines a new concept in de novo sequencing technology. Application of $exo^+$ polymerases to genetic analysis, and especially SNP assays, will greatly accelerate the pace to personalized medicine.

• Asian-Australasian Journal of Animal Sciences
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• v.21 no.12
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• pp.1703-1709
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• 2008

As genetic markers, single nucleotide polymorphisms (SNP) are very appropriate for the development of genetic tests for economic traits in livestock. Several microsatellite markers have been identified as useful markers for the genetic improvement of Hanwoo. Among those markers, ILSTS035 was recently mapped at a similar position with four SNPs (AH1_11, AH1_9, 31465_446, and 12273_165) in a linkage map of EST-based SNP in BAT6. Among the four SNPs, two SNPs (31465_446 and 12273_165) were analyzed using BLAST at the NCBI web site. The sequences including the 12273_165 SNP were identified at the intron region within the LOC534614 gene on the gene sequence map (Bos taurus NCBI Map view, build 3.1). The LOC534614 gene represents a protein similar to myosin heavy chain, fat skeletal muscle, embryonic isoform 1 in the dog, and myosin_1 (Myosin heavy chain D) in Macaca mulatta. In cattle, the myosin heavy chain was associated with muscle development. The phenotypic data for growth and carcass traits in the 415 animals were analyzed by the mixed ANCOVA (analysis of covariance) linear model using PROC GLM module in SAS v9.1. By the genotyping of Hanwoo individuals (n = 415) to evaluate the association of SNP with growth and carcass traits, it was shown that the 12273_165 SNP region within LOC534614 may be a candidate marker for growth. The results of the statistical analyses suggested that the genotype of the 12273_165 SNP significantly affected birth weight, weight of the cattle at 24 months of age, average daily gain and carcass cold weight (p<0.05). Consequently, the 12273_165 SNP polymorphisms at the LOC534614 gene may be associated with growth in Hanwoo, and functional validation of polymorphisms in LOC534614 should be performed in the future.

• BMB Reports
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• v.41 no.1
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• pp.29-34
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• 2008

The aim of this study was to determine whether single nucleotide polymorphisms (SNP) in the beef cattle adipocyte fatty-acid binding protein 3 and 4 (FABP3 and FABP4) genes are associated with carcass weight (CW) and back fat thickness (BF) of beef cattle. By direct DNA sequencing in 24 unrelated Korean native cattle, we identified 20 SNPs in FABP3 and FABP4. Among them, 10 polymorphic sites were selected for genotyping in our beef cattle. We performed SNP, haplotype and linkage disequilibrium studies on 419 Korean native cattle with the 10 SNPs in the FABP genes. Statistical analysis revealed that 220A>G (I74V) and 348+303T>C polymorphisms in FABP4 showed putative associations with BF traits (P=0.02 and 0.01, respectively). Our findings suggest that the polymorphisms in FABP4 may play a role in determining one of the important genetic factors that influence BF in beef cattle.

• Genomics & Informatics
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• v.20 no.2
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• pp.16.1-16.12
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• 2022

Various methodologies for the genetic analysis of longitudinal data have been proposed and applied to data from large-scale genome-wide association studies (GWAS) to identify single nucleotide polymorphisms (SNPs) associated with traits of interest and to detect SNP-time interactions. We recently proposed a grid-based Bayesian mixed model for longitudinal genetic data and showed that our Bayesian method increased the statistical power compared to the corresponding univariate method and well detected SNP-time interactions. In this paper, we further analyze longitudinal obesity-related traits such as body mass index, hip circumference, waist circumference, and waist-hip ratio from Korea Association Resource data to evaluate the proposed Bayesian method. We first conducted GWAS analyses of cross-sectional traits and combined the results of GWAS analyses through a meta-analysis based on a trajectory model and a random-effects model. We then applied our Bayesian method to a subset of SNPs selected by meta-analysis to further discover SNPs associated with traits of interest and SNP-time interactions. The proposed Bayesian method identified several novel SNPs associated with longitudinal obesity-related traits, and almost 25% of the identified SNPs had significant p-values for SNP-time interactions.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.6
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• pp.2841-2846
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• 2012

Background: Many studies have investigated the association between the MDM2 promoter SNP309 T/G polymorphism and liver cancer risk, but inconsistencies make drawwing definitive conclusions difficult. Methods: We therefore searched main databases for articles relating MDM2 SNP309 T/G polymorphism to risk of liver cancer in humans and estimated summary odds ratio (OR) with 95% confidence intervals (95% CI) to assess the possible association in a meta-analysis. Results: The main analysis revealed no significant heterogeneity, and the pooled ORs of fixed-effects were all significant (for G versus T, OR = 1.59, 95% CI 1.42-1.78; for GG versus TT, OR = 2.45, 95% CI 1.93-3.12; for GT versus TT, OR = 1.70, 95% CI 1.38-2.09; for GG versus GT, OR = 1.49, 95% CI 1.24-1.79; for GG and GT versus TT, OR = 1.95, 95% CI 1.61-2.38; for GG versus TT and GT, OR = 1.73, 95% CI 1.46-2.07). Subgroup analyses by ethnicity and sensitivity analyses both showed associations to remain significant. Conclusion: The present meta-analysis of available data showed a significant association between the MDM2 SNP309 T/G polymorphism and liver cancer risk, the MDM2 SNP309 G allele contributing to increased risk in both Asians and Caucasians in a graded, dose-dependent fashion.

• Journal of Apiculture
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• v.32 no.3
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• pp.147-154
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• 2017

Honeybees (Apis mellifera) are common pollinators and important insects studied in agriculture, ecology and basic research. Recently, RDA (Rural Development Administration) and YIRI (Yecheon-gun Industrial Insect Research Institute) have been breeding a triple crossbred honey bee named Jangwon, which have the ability to produce superior quality honey. In this study, we identified a single nucleotide polymorphism (SNP) marker in the genome of Jangwon honeybee, particularly, in the paternal line (D line). Initially, we performed Sequence-Based Genotyping (SBG) using the Illumina Hiseq 2500 in 5 honeybee inbred lines; A, C, D, E, and F; and obtained 1,029 SNPs. Seventeen SNPs for each inbred line were generated and selected after further filtering of the SNP dataset. The 17 SNP markers validated by performing TaqMan probe-based real-time PCR and genotyping analysis was conducted. Genotyping analysis of the 5 honeybee inbred lines and one hybrid line, $D{\times}F$, revealed that one set of SNP marker, AmD9, precisely discriminated the inbred line D from the others. Our results suggest that the identified SNP marker, AmD9, is successful in distinguishing the inbred honeybee lines D, and can be directly used for genotyping and breeding applications.

• Asian-Australasian Journal of Animal Sciences
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• v.18 no.11
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• pp.1548-1551
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• 2005

The leptin, an anti-obesity protein, is a hormone protein expressed and secreted mainly from adipocyte tissue, and involved in regulation of body weight, food intake and energy metabolism. In an effort to discover polymorphism(s) in genes whose variant(s) might be implicated in phenotypic traits of growth, we have sequenced exons and their boundaries of leptin gene including 1,000 bp upstream of promoter region with twenty-four unrelated Korean cattle. Fifty-seven sequence variants were identified: fourteen in 5' flanking region, twenty-seven in introns, eight in exons, and eight in 3' flanking region. By pair-wise linkage analysis among polymorphisms, ten sets of SNPs were in absolute linkage disequilibrium (LD) (|D'| = 1 and $r^2$ = 1). Among variants identified, thirty-six SNPs were newly identified, and twenty-one SNPs, which were reported in other breeds, were also confirmed in Korean cattle. The allele frequencies of variants were quite different among breeds. The information from SNPs of bovine leptin gene could be useful for further genetic studies of this gene.

• Asian-Australasian Journal of Animal Sciences
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• v.24 no.11
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• pp.1504-1513
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• 2011

It is important to identify genetic interactions related to human diseases or animal traits. Many linear statistical models have been reported but they did not consider genetic interactions. Genotype matrix mapping (GMM) has been developed to identify genetic interactions. This study uses the GMM method to detect superior SNP combinations of the CCDC158 gene that influences average daily gain, marbling score, cold carcass weight and longissimus muscle dorsi area traits in Hanwoo. We evaluated the statistical significance of the major SNP combinations selected by implementing the permutation test of the F-measure. The effect of g.34425+102 A>T (AA), g.8778G>A (GG) and g.4102+36T>G (GT) SNP combinations produced higher performance of average daily gain, marbling score, cold carcass weight and the longissimus muscle dorsi area traits than the effect of a single SNP. GMM is a fast and reliable method for multiple SNP analysis with potential application in marker-assisted selection. GMM may prospectively be used for genetic assessment of quantitative traits after further development.