• Proceedings of the Korean Society of Crop Science Conference
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• 2022.10a
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• pp.290-290
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• 2022

Powdery mildew is known to be one of the serious diseases in C. moschata cultivation. Plants infected with powdery mildew cause damage to cultivation areas such as occurrence of deformity fruit and decrease in quantity. also, it has been reported that many farms have difficulties in controlling powdery mildew due to the outbreak under various conditions throughout the year. Therefore, this study intends to perform a phenotype test and a genotype test for C. moschata 60 lines grown in Jenong S&T. Podospareaxanthii, known as a pathogen that causes powder mildew disease in pumpkins in Korea, was collected and used as an inoculation source, phenotype test was performed by examining the infection area rate(%) of powdery mildew disease that occurred in leaves 25 days after inoculation. It was determined that 0% of the infection area rate was in the first stage, 1 to 5% in the second stage, 6 to 15% in the third stage, 16 to 30% in the fourth stage, and 31% or more in the fifth stage, The first and second stages were judged as resistance, the third as moderate resistance, and the fourth and fifth stages as sensitivity. As a result of the phenotype test, it was confirmed that the resistance was 21 points, moderate resistance was 14 points, and sensitivity was 25 points. After searching for the genes related to powdery mildew resistance resistance, pm-0, CmbHLH87, and LOC111453072, 21 points of resistance and 9 points of moderate resistance identified through phenotype tests were identified through gel electrophoresis after polymerase chain reaction(PCR) using 5 primers related to 3 genes. As a result of genotype testing of a total 30 points, the CmbHLH87 and LOC111453072 gene were found to be resistant bands in all points, PMR1 was identified as 20 points for resistance, 4 points for moderate resistance, and 6 points for sensitivity, PMR2 was not identified in the entire band, and PMR5 was identified as 18 point for resistance, 3 points for moderate resistance, and 9 points for sensitivity. As a result, when comparing the phenotype test results and genotype test results, CmbHLH87 and LOC111453072 genes was 100% consistent in resistance and moderate resistance, PMR1 was 95.2% in resistance, 44.4% in moderate resistance, and PMR5 was 90% in resistance and 33.3% in moderate resistance, PMR2 was not consistent in resistance and moderate resistance. Therefore, it is expected that more accurate PMR test will be possible by using molecular markers(PMR1, PMR5) and by developing CmbHLH87 and LOC111453072 gene-related molecular markers.

• Annals of Laboratory Medicine
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• v.38 no.6
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• pp.585-590
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• 2018

Background: Although testing to detect weak D antigens using the antihuman globulin reagent is not required for D- patients in many countries, it is routinely performed in Korea. However, weak D testing can be omitted in D- patients with a C-E- phenotype as this indicates complete deletion of the RHD gene, except in rare cases. We designed a new algorithm for weak D testing, which consisted of RhCE phenotyping followed by weak D testing in C+ or E+ samples, and compared it with the current algorithm with respect to time and cost-effectiveness. Methods: In this retrospective study, 74,889 test results from January to July 2017 in a tertiary hospital in Korea were analyzed. Agreement between the current and proposed algorithms was evaluated, and total number of tests, time required for testing, and test costs were compared. With both algorithms, RHD genotyping was conducted for samples that were C+ or E+ and negative for weak D testing. Results: The algorithms showed perfect agreement (agreement=100%; ${\kappa}=1.00$). By applying the proposed algorithm, 29.56% (115/389 tests/yr) of tests could be omitted, time required for testing could be reduced by 36% (8,672/24,084 min/yr), and the test cost could be reduced by 16.53% (536.11/3,241.08 USD/yr). Conclusions: Our algorithm omitting weak D testing in D- patients with C-E- phenotype may be a cost-effective testing strategy in Korea.

• Journal of the Korean Data and Information Science Society
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• v.23 no.1
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• pp.1-11
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• 2012

When the microarray experiment developed, main interest was limited to detect differentially expressed genes associated with a phenotype of interest. However, as human diseases are thought to occur through the interactions of multiple genes within a same functional category, the unit of analysis of the microarray experiment expanded to the set of genes. For the phenotype of censored survival time, Gene Set Enrichment Analysis(GSEA), Global test and Wald type test are widely used. In this paper, we modified the Wald type test by adopting normal score transformation of gene expression values and developed a parametric test which requires much less computation than others. The proposed method is compared with other methods using a real data set of ovarian cancer and a simulation data set.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.2
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• pp.113-120
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• 2023

The hypertriglyceridemic-waist (HTGW) phenotype can predict the risk of coronary artery disease. This study evaluated the relationship between the HTGW phenotype and metabolic abnormalities in hypertensive adults. The test was conducted on adult hypertension patients aged 20 or older who underwent health checkups from January 2018 to December 2021 at general hospitals in Gyeonggi Province. The HTGW phenotype was triglyceride ≥150 mg/dL and waist circumference ≥90 cm for men and ≥85 cm for women. The prevalence of the HTGW phenotype in the study subjects was 17.9%. After adjusting for age, gender, and BMI, the odds ratio of the HTGW group was 5.09 (95% confidence interval [CI]: 3.545~7.309) for low HDL-cholesterol, 1.68 (95% CI: 1.176~2.411) for high LDL-cholesterol, was 2.92 (95% CI: 2.009~4.235) for high total cholesterol, 3.39 (95% CI: 2.124~5.412) for diabetes and 1.85 (95% CI: 1.286~2.674) for hyperuricemia compared to the normal triglyceride levels with the normal waist (NTNW) group. The area under curve values of the HTGW phenotype for diagnosing metabolic syndrome were 0.849 for all subjects, 0.858 for men, and 0.890 for women. In conclusion, the HTGW phenotype is closely related to metabolic abnormalities and is a useful indicator for monitoring adult hypertensive patients with metabolic syndrome.

• Genomics & Informatics
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• v.14 no.4
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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.

• Journal of Preventive Medicine and Public Health
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• v.27 no.3 s.47
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• pp.569-579
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• 1994

The genetically determined ability to metabolize debrisoquine (DBR) is related to risk of lung cancer and DBR hydroxylation exhibits wide inter-individual variation. In this study, 100 korean adults were tested for their ability to metabolize DBR. The DBR metabolic phenotype were determined by metabolic ratio (MR, DBR / 4-HDBR) which is the percent dose excreted as unchanged DBR divided by the percent dose excreted as 4-hydroxyebrisoquine(4-HDBR) in a aliquot of an eight hour urine sample, after 10mg DBR test dose administration. Analysis was performed on a capillary gas chromatograph fitted with electron capture detector. The results were as follows; 1 Geometric mean of DBR MR was 0.32 in male,0.27 in female,0.30 in total and the distribution of log (MR) was seemed to follow normal distribution. 2. Metabolic ratio of DBR was higher in non-smoker and non-drinker than in smoker and drinker without any statistically significant difference. 3. None of personal factors was significantly related to DBR MR except age. 4. The DBR metabolic phenotype was extensive metabolizer(EM) 93, intermediate metabolizer(IM) 7 by traditional method and EM 98, IM 3 by Caporaso's method. The poor metabolizer (PM) phenotype was not found by either method. 5. Maximal expected PM phenotype was 0.36% by traditional method and 0.04% by Caporaso's method.

• Clinical and Experimental Pediatrics
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• v.55 no.11
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• pp.430-437
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• 2012

Purpose: Mucopolysaccharidosis IVA (MPS IVA; Morquio A syndrome) is rare lysosomal storage disorder caused by N-acetylgalactosamine-6-sulfatase (GALNS) deficiency. Only a few MPS IVA cases have been reported in the Korean literature; there is a paucity of research about clinical or radiologic findings for this disorder. Therefore, we studied clinical findings, radiological features, and genetic data of Korean MPS IVA patients for determining factors that may allow early diagnosis and that may thus improve the patients' quality of life. Method: MPS IVA was confirmed via assay for enzymatic activity of leukocytes in 10 patients. The GALNS gene was analyzed. Patients' charts were retrospectively reviewed for obtaining clinical features and evaluated for radiological skeletal surveys, echocardiography, pulmonary function test, and ophthalmologic test results. Result: Nine patients had severe clinical phenotype, and 1 had an intermediate phenotype, on the basis of clinical phenotype criteria. Radiologic findings indicated skeletal abnormalities in all patients, especially in the hips and extremities. Eight patients had an odontoid hypoplasia, and 1 showed mild atlantoaxial subluxation and cord myelopathy. Genetic analysis indicated 10 different GALNS mutations. Two mutations, c.451C>A and c.1000C>T, account for 37.5% (6/16) and 25% (4/16) of all mutations in this samples, respectively. Conclusion: An understanding of the clinical and radiological features involved in MPS IVA may allow early diagnosis of MPS IVA. Adequate evaluations and therapy in the early stages may improve the quality of life of patients suffering from skeletal abnormalities and may reduce life-threatening effects of atlantoaxial subluxation.

• Animal Bioscience
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• v.36 no.9
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• pp.1327-1335
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• 2023

Objective: When evaluating individuals with the same parent and no phenotype by pedigree best linear unbiased prediction (BLUP), it is difficult to explain carcass grade difference and select individuals because they have the same value in pedigree BLUP (PBLUP). However, single step GBLUP (ssGBLUP), which can estimate the breeding value suitable for the individual by adding genotype, is more accurate than the existing method. Methods: The breeding value and accuracy were estimated with pedigree BLUP and ssGBLUP using pedigree and genotype of 408 Hanwoo cattle from 16 families with the same parent among siblings produced by fertilized egg transplantation. A total of 14,225 Hanwoo cattle with pedigree, genotype and phenotype were used as the reference population. PBLUP obtained estimated breeding value (EBV) using the pedigree of the test and reference populations, and ssGBLUP obtained genomic EBV (GEBV) after constructing and H-matrix by integrating the pedigree and genotype of the test and reference populations. Results: For all traits, the accuracy of GEBV using ssGBLUP is 0.18 to 0.20 higher than the accuracy of EBV obtained with PBLUP. Comparison of EBV and GEBV of individuals without phenotype, since the value of EBV is estimated based on expected values of alleles passed down from common ancestors. It does not take Mendelian sampling into consideration, so the EBV of all individuals within the same family is estimated to be the same value. However, GEBV makes estimating true kinship coefficient based on different genotypes of individuals possible, so GEBV that corresponds to each individual is estimated rather than a uniform GEBV for each individual. Conclusion: Since Hanwoo cows bred through embryo transfer have a high possibility of having the same parent, if ssGBLUP after adding genotype is used, estimating true kinship coefficient corresponding to each individual becomes possible, allowing for more accurate estimation of breeding value.

• Journal of Microbiology and Biotechnology
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• v.19 no.6
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• pp.542-546
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• 2009

Leaves are the major biomass-producing organs in herbaceous plants and mainly develop during vegetative stage by activities of shoot apical meristem. There is a strong correlation between leaf number and bolting, a characteristic phenotype during the transition to reproductive phase in Arabidopsis thaliana. In order to study interactions between leaf number and bolting, we isolated a Landsberg erecta-derived mutant named multifolial (mfo1) that produces increased number of leaves and bolts at the same time as the wild type. Through positional cloning and allelism test, mfo1 was found to be an allele of a previously reported mutant, altered meristem program1-1 (amp1-1) that is defective in a glutamate carboxypeptidase and bolts earlier than its wild type, Columbia ecotype, with the increased number of leaves. The bolting time differences between mfo1 and amp1, despite the same phenotype of many leaves, suggest the existence of genetic factor(s) differently function in each ecotype in the presence of mfo1/amp1 mutation.

• Clinical and Experimental Pediatrics
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• v.59 no.sup1
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• pp.121-124
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• 2016

Turner syndrome (TS) is a genetic disorder in phenotypic females that has characteristic physical features and presents as partial or complete absence of the second sex chromosome. Growth hormone deficiency (GHD) is a condition caused by insufficient release of growth hormone from the pituitary gland. The concomitant occurrence of TS and GHD is rare and has not yet been reported in Korea. Here we report 2 cases of TS and GHD. In case 1, GHD was initially diagnosed. Karyotyping was performed because of the presence of the typical phenotype and poor response to growth hormone therapy, which revealed 45,X/45,X+mar. The patient showed increased growth velocity after the growth hormone dose was increased. In case 2, a growth hormone provocation test and chromosomal analysis were performed simultaneously because of decreased growth velocity and the typical TS phenotype, which showed GHD and a mosaic karyotype of 45,X/46,XX. The patient showed spontaneous pubertal development. In female patients with short stature, it is important to perform a throughout physical examination and test for hormonal and chromosomal abnormalities because diagnostic accuracy is important for treatment and prognosis.