• Genomics & Informatics
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• 제14권4호
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• pp.187-195
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• 2016

In genetic association studies with high-dimensional genomic data, multiple group testing procedures are often required in order to identify disease/trait-related genes or genetic regions, where multiple genetic sites or variants are located within the same gene or genetic region. However, statistical testing procedures based on an individual test suffer from multiple testing issues such as the control of family-wise error rate and dependent tests. Moreover, detecting only a few of genes associated with a phenotype outcome among tens of thousands of genes is of main interest in genetic association studies. In this reason regularization procedures, where a phenotype outcome regresses on all genomic markers and then regression coefficients are estimated based on a penalized likelihood, have been considered as a good alternative approach to analysis of high-dimensional genomic data. But, selection performance of regularization procedures has been rarely compared with that of statistical group testing procedures. In this article, we performed extensive simulation studies where commonly used group testing procedures such as principal component analysis, Hotelling's $T^2$ test, and permutation test are compared with group lasso (least absolute selection and shrinkage operator) in terms of true positive selection. Also, we applied all methods considered in simulation studies to identify genes associated with ovarian cancer from over 20,000 genetic sites generated from Illumina Infinium HumanMethylation27K Beadchip. We found a big discrepancy of selected genes between multiple group testing procedures and group lasso.

• 한국자원식물학회지
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• 제22권3호
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• pp.242-247
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• 2009

Randomly Amplified Polymorphic DNA (RAPD) was performed to define the genetic variation and relationships of Artemisia capillaris. Fifteen populations by the distributions and habitat were collected to conduct RAPD analysis. RAPD markers were observed mainly between 300bp and 1600bp. Total 72 scorable markers from 7 primers were applied to generate the genetic matrix, and 69 bands were polymorphic and only 3 bands were monomorphic. The genetic dissimilarity matrix by Nei's genetic distance (1972) and UPGMA phenogram were produced from the data matrix. Populations of Artemisia capillaris were clustered with high genetic affinities and cluster patterns were correlated with distributional patterns. Two big groups were clustered as southern area group and middle area group. The closest OTUs were GW2 and GG1 in middle area group, and GB1 from southern area group was clustered with OTUs in middle area group. RAPD data was useful to define the genetic variations and relationships of A. capillaris.

• Journal of Genetic Medicine
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• 제18권1호
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• pp.38-43
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• 2021

Purpose: Demand for genetic counseling on cancer predisposition syndrome is increasing. We evaluated the psychological effect on counselees after genetic counseling at a clinic in a single center. Materials and Methods: We surveyed a total of 72 enrolled participants who visited a genetic counseling clinic at the Samsung Medical Center (SMC). The initial survey was conducted before the first genetic counseling session, and the second survey was conducted after the second genetic counseling session. A total of 43 participants completed both the initial and second surveys. Results: The initial survey of 72 participants indicated higher feelings of guilt in the group with religion, higher depression and anxiety in the group with a diagnosis of self, and higher anxiety in the group on self-referral to the genetic counseling clinic. In the completed survey of 43 participants, overall decreased depression was observed after the second genetic counseling session (P=0.013). Risk perception and anxiety decreased in the group diagnosed with benign variant/variant of uncertain significance (BV/VUS, 25/3) and increased in the group diagnosed with pathogenic variant (PV, 15). Risk perception and anxiety differed between the BV/VUS and PV groups (P<0.001 and P=0.03, respectively). Conclusion: The genetic counseling clinic at the SMC was effective in ameliorating the depression score. Assessment of survey results revealed different depression scores, feelings of guilt and anxiety, and different effects of the genetic counseling clinic, depending on the subgroups. Understanding the needs and psychological characteristics of different groups is necessary for improving genetic counseling services.

• Applied Biological Chemistry
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• 제37권2호
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• pp.110-114
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• 1994

토양에서 분리된 방선균에서 생산되는 살충성 물질을 스크리닝하는 연구과정중 선발된 no. 46균주가 생산하는 살충성 물질을 분리하였다. 분리된 물질 4가지는 UV, $^1H-NMR$, $^{13}C-NMR$, C-H COSY 방법으로 구조 분석한 결과, Piericidin $C_1$, $C_2$, $C_3$ 그리고 $D_1$으로 각각 동정되었다.

• 한국양식학회지
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• 제17권1호
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• pp.69-80
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• 2004

The objective of the present study was to analyze genetic distances, variation and characteristics of individuals in rainbow trout, Oncorhynchus mykis using amplified fragment length polymorphism (AFLP) method as molecular genetic technique, to detect AFLP band patterns as genetic markers, and to compare the efficiency of agarosegel electrophoresis (AGE) and polyacrylamide gel electrophoresis (PAGE), respectively. Using 9 primer combinations, a total of 141 AFLP bands were produced, 108 bands (82.4%) of which were polymorphic in AGE. In PAGE, a total of 288 bands were detected, and 220 bands (76.4%) were polymorphic. The AFLP fingerprints of AGE were different from those of PAGE. Separation of the fragments with low molecular weight and genetic polymorphisms revealed a distinct pattern in the two gel systems. In the present study, the average bandsharing values of the individuals between two populations apart from the geographic sites in Kangwon-do ranged from 0.084 to 0.738 of AGE and PAGE. The bandsharing values between individuals No.9 and No. 10 showed the highest level within population, whereas the bandsharing values between individuals No.5 and No.7 showed the lowest level. As calculated by bandsharing analysis, an average of genetic difference (mean$\pm$SD) of individuals was approximately 0.590$\pm$0.125 in this population. In AGE, the single linkage dendrogram resulted from two primers (M11+H11 and M13+H11), indicating six genetic groupings composed of group 1 (No.9 and 10), group 2 (No. 1, 4, 5, 7, 10, 11, 16 and 17), group 3 (No. 2, 3, 6, 8, 12, 15 and 16), group 4 (No.9, 14 and 17), group 5 (No. 13, 19, 20 and 21) and group 6 (No. 23). In AGE, the genetic distances among individuals of between-population ranged from 0.108 to 0.392. In AGE, the shortest genetic distance (0.108) displaying significant molecular differences was between individuals No.9 and No. 10. Especially, the genetic distance between individuals No. 23 and the remnants among individuals within population was highest (0.392). Additionally, in the cluster analysis using the PAGE data, the single linkage dendrogram resulted from two primers (M12+H13 and M11+H13), indicating seven genetic groupings composed of group 1 (No. 15), group 2 (No. 14), group 3 (No. 11 and 12), group 4 (No.5, 6, 7, 8, 10 and 13), group 5 (No.1, 2, 3 and 4), group 6 (No.9) and group 7 (No. 16). By comparison with the individuals in PAGE, genetic distance between No. 10 and No. 7 showed the shortest value (0.071), also between No. 16 and No. 14 showed the highest value (0.242). As with the PAGE analysis, genetic differences were certainly apparent with 13 of 16 individuals showing greater than 80% AFLP-based similarity to their closest neighbor. The three individuals (No. 14, No. 15 and No. 16) of rainbow trout between two populations apart from the geographic sites in Kangwon-do formed distinct genetic distances as compared with other individuals. These results indicated that AFLP markers of this fish could be used as genetic information such as species identification, genetic relationship or analysis of genome structure, and selection aids for genetic improvement of economically important traits in fish species.

• Asian-Australasian Journal of Animal Sciences
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• 제18권8호
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• pp.1075-1079
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• 2005

The main objective of this study is to examine genetic changes in growth rate and carcass composition traits in group housed, ad libitum fed pigs, from lines of Large White divergently selected over four years for high and low post-weaning daily gain on a fixed but restricted ration. Genetic parameters for production and carcass traits were also estimated by using average information-restricted maximum likelihood applied to a multivariate individual animal model. All analyses were carried out on 1,728 records of group housed ad libitum fed pigs, and include a full pedigree of 5,324 animals. Estimates of heritability (standard errors in parentheses) were 0.11 (0.04) for lifetime daily liveweight gain (LDG), 0.13 (0.04) for daily carcass weight gain (CDG) and 0.28 (0.06) for carcass backfat (CFT). Genetic correlations between LDG and CDG were highly positive and between LDG and CFT negative, suggesting that selection for lifetime daily gain under commercial conditions of group housing with ad libitum feeding would result in favourable improvement in carcass traits. CFT showed negative genetic correlations with CDG. Correlated genetic responses evaluated as estimated breeding values (EBVs) were obtained from a multivariate animal model-best linear unbiased prediction analysis. After four years of divergent selection for 6 week post-weaning growth rate on restricted feeding, pigs performance tested on ad libitum feeding in groups exhibited changes in EBVs of 6.77 and -9.93 (g/d) for LDG, 4.25 and -7.08 (g/d) for CDG, and -1.42 and 1.55 (mm) for CFT, in the high and low lines, respectively. It is concluded that selection for growth rate on restricted feeding would significantly improve genetic performance and carcass composition of their descendants when group housed and ad libitum fed as is a common commercial practice.

• 한국양식학회지
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• 제17권1호
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• pp.12-23
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• 2004

Genomic DNAs were extracted from the muscle of twenty-two specimens of two shortnecked clam, Ruditapes phifippinarum populations collected in Anmyeondo and Seocheon. Genetic differences within and between populations were analysed by random amplified polymorphic DNAs-polymerase chain reaction (RAPD-PCR) using twenty arbitrary decamer primers. Out of 20 primers, 6 generated a total of 1,111 major and minor RAPD bands from individuals of two sites, producing approximately 4.2 average polymorphic bands per primer in individuals from Anmyeondo and ranging in size from less than 50 to larger than 1,500 base pairs (bp). The electrophoretic analysis of RAPD products amplified showed moderate levels of similarity among the different individuals in Seo-cheon population. The average bandsharing values (BS value) of the samples within population from Anmyeondo ranged from 0.155 to 0.684, whereas it was 0.143∼0.782 within population from Seocheon. The average BS value between individuals No. 13 and No. 14 from Seocheon was 0.782 which was higher than that of those from Anmyeondo. The single linkage dendrogram resulted from three primers (OPA-08, -09 and -20), indicating six genetic groupings composed of group 1 (No.4, 8 and 10), group 2 (No. 18), group 3 (No.2, 5 and 7), group 4 (No. 1, 3, 6, 9, 11, 12, 13, 14, 15 and 17), group 5 (16, 19 and 20) and group 6 (No. 21 and 22). In the Seocheon population, the individual No. 18 clustered distinctly from the others of this population. The observed genetic distance between the two populations from Anmyeondo and Seocheon was more than 0.209 (0.247 and 0.275). The shortest genetic distance (0.094) displaying significant molecular differences was between individuals No. 13 and No. 14. Especially, the genetic distance between individuals No. 22 and the remnants among individuals in two geographical populations was highest (0.275). This result illustrated that individual No.22 is distinct from other individuals within two shortnecked populations. The different geographical features of two sites may have caused the genetic diversity in two shortnecked clam populations.

• Asian-Australasian Journal of Animal Sciences
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• 제15권6호
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• pp.772-776
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• 2002

This study was made with 631 does of 3 genetic groups and 1,112 of their kids allocated into 3 different locations to examine gestation length, litter size and litter weight in goats. Attributes studied were genetic group, parity, age of dam at kidding, weight of dam at breeding, season and location. Genetic group of dam affected significantly (p<0.01) size of litter but not gestation length and weight of litter. Selected Black Bengal (SBB) genetic group performed better in litter size and litter weight than random bred Black Bengal (RBB) and its crossbreds with Jamunapari ♂ (JBB). Litter size and weight were significantly affected by age of dam at kidding (p<0.01), weight of dam at service (p<0.001) and parity (p<0001). Size and weight of litter were found highest in SBB does, or does having 35-40 months of age at kidding, or does with 19-20 kg live weight at service, or at 4th parity. Season, location and parity also affected significantly (p<0.05) gestation length. Shortest gestation length was found in 5th parity or in summer season, whereas the longest was in 2nd parity or in winter season.

• 한국경영과학회지
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• 제32권1호
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• pp.61-75
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• 2007

The purpose of this paper is to develop a new group classification method based on genetic algorithm and to com-pare its prediction performance with those of existing methods in the area of bond rating. To serve this purpose, we conduct various experiments with pilot and general models. Specifically, we first conduct experiments employing two pilot models : the one searching for the cluster center of each group and the other one searching for both the cluster center and the attribute weights in order to maximize classification accuracy. The results from the pilot experiments show that the performance of the latter in terms of classification accuracy ratio is higher than that of the former which provides the rationale of searching for both the cluster center of each group and the attribute weights to improve classification accuracy. With this lesson in mind, we design two generalized models employing genetic algorithm : the one is to maximize the classification accuracy and the other one is to minimize the total misclassification cost. We compare the performance of these two models with those of existing statistical and artificial intelligent models such as MDA, ANN, and Decision Tree, and conclude that the genetic algorithm-based group classification method that we propose in this paper significantly outperforms the other methods in respect of classification accuracy ratio as well as misclassification cost.

• 한국작물학회지
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• 제56권4호
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• pp.322-328
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• 2011

우리나라에서 수집한 재래종 조 26계통들에 대하여 9개의 AFLP primer조합을 사용하여 유전적 다양성 및 계통유연관계를 분석한 결과는 다음과 같다. 1. 분석에 이용한 9개의 AFLP primer조합들은 국내에서 수집한 조 26계통들에서 총 170개의 DNA단편을 나타내었고, 이중에서 145개의 단편(85.3%)들은 다형성을 나타내었다. 9개의 AFLP primer조합들에서 측정된 유전적 다양성 값(Hs)은 1.84에서 6.80의 범위로 나타나, 평균 3.85값을 나타내었다. 강원지역에서 수집한 조 계통(Group 1)들은 평균 3.39의 유전적 다양성 값을 나타내었고, 경기도 등 타 지역에서 수집한 조 계통들(Group 2)은 평균 2.99의 유전적 다양성 값을 나타내었다. 2. 국내에서 수집된 재래종 조 26계통들은 유전적 유사성 73% 수준에서 크게 두 개의 그룹으로 구분되었다. Group I은 유전적 유사성 76.8% 수준에서 강원도에서 수집한 13계통들과 경기도에서 수집한 1계통을 포함하고 있었으며, Group II는 유전적 유사성 78.9% 수준에서 강원도에서 수집한 2계통들과 타 지역에서 수집한 10계통들을 포함하고 있었다. 본 연구결과는 우리나라에서 수집한 재래종 조 계통들에 대한 유전적 다양성 및 계통유연관계 이해 그리고 이들 자원의 수집 및 보존 등에 유용한 정보를 제공할 것으로 기대된다.