• Genomics & Informatics
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• v.20 no.4
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• pp.46.1-46.7
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• 2022

Influenza A virus (IAV) is the most widespread pathogen causing human respiratory infections. Although polymerase chain reaction (PCR)-based methods are currently the most commonly used tools for IAV detection, PCR is not ideal for point-of-care testing. In this study, we aimed to develop a more rapid and sensitive method than PCR-based tools to detect IAV using loop-mediated isothermal amplification (LAMP) technology. We designed reverse-transcriptional (RT)-LAMP primers targeting the hemagglutinin gene. RNAs from reference H1N1 and H3N2 showed specific RT-LAMP signals with the designed primers. We optimized the reaction conditions and developed universal reaction conditions for both LAMP assays. Under these conditions, the detection limit was 50 copies for both RT-LAMP assays. There was no non-specific signal to 19 non-IAV respiratory viruses, such as influenza B virus, coronaviruses, and respiratory syncytial viruses. Regarding the reaction time, a positive signal was detected within 25 min after starting the reaction. In conclusion, our RT-LAMP assay has high sensitivity and specificity for the detection of the H1 and H3 subtypes, making it suitable for point-of-care IAV testing.

• BMB Reports
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• v.40 no.2
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• pp.135-141
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• 2007

Conjugation of the methyl group at the fifth carbon of cytosines within the palindromic dinucleotide 5'-CpG-3' sequence (DNA methylation) is the best studied epigenetic mechanism, which acts together with other epigenetic entities: histone modification, chromatin remodeling and microRNAs to shape the chromatin structure of DNA according to its functional state. The cancer genome is frequently characterized by hypermethylation of specific genes concurrently with an overall decrease in the level of 5-methyl cytosine, the pathological implication of which to the cancerous state has been well established. While the latest genome-wide technologies have been applied to classify and interpret the epigenetic layer of gene regulation in the physiological and disease states, the epigenetic testing has also been seriously explored in clinical practice for early detection, refining tumor staging and predicting disease recurrence. This critique reviews the latest research findings on the use of DNA methylation in cancer diagnosis, prognosis and staging/classification.

• YAKHAK HOEJI
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• v.48 no.6
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• pp.364-368
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• 2004

The prevalence of resistance to a range of macrolides was determined for clinical isolates of common respiratory pathogens using NCCLS testing methods and interpretative criter ia.71.4% of Streptococcus pneumoniae, 62.3% of Staphylococcus aureus, 50.8% of coagulase-negative staphylococci and 4.4% of Strpetococcus pyogenes were erythromycin resistant. Also, the rates of resistance to other macrolides and clindamycin in these clinical isolates were as high as to eryth -romycin. Almost all of the macrolide-resistant isolates were positive for erm of the methylase gene, or mef of the efflux gene.

• Communications for Statistical Applications and Methods
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• v.25 no.5
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• pp.559-568
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• 2018

Gene classification can involve complex order-restricted inference. Examining gene expression pattern across groups with order-restriction makes standard statistical inference ineffective and thus, requires different methods. For this problem, Roy's union-intersection principle has some merit. The M-estimator adjusting for outlier arrays in a microarray study produces a robust test statistic with distribution-insensitive clustering of genes. The M-estimator in conjunction with a union-intersection principle provides a nonstandard robust procedure. By exact permutation distribution theory, a conditionally distribution-free test based on the proposed test statistic generates corresponding p-values in a small sample size setup. We apply a false discovery rate (FDR) as a multiple testing procedure to p-values in simulated data and real microarray data. FDR procedure for proposed test statistics controls the FDR at all levels of ${\alpha}$ and ${\pi}_0$ (the proportion of true null); however, the FDR procedure for test statistics based upon normal theory (ANOVA) fails to control FDR.

• Journal of Genetic Medicine
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• v.9 no.1
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• pp.31-34
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• 2012

Spondyloepiphyseal dysplasia tarda (SEDT) is an X-linked skeletal dysplasia. Patients show disproportionate short stature with short trunk and barrel-shaped chest, which usually become pronounced in late childhood. The radiologic findings are characterized by narrow intervertebral disc spaces and moderate epiphyseal dysplasia of long bones. Here we report a case of SEDT with a novel frameshift mutation in TRAPPC2, the disease-causing gene of SEDT. This is the first Korean report with SEDT confirmed by genetic testing.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.8
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• pp.3879-3887
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• 2012

Background: Development of effective educational strategies should accompany increases in public awareness and the availability of genetic testing for breast cancer (BC). These educational strategies should be designed to fulfill the knowledge gap while considering factors that influence women's interest in order to facilitate decision making. Objective: To determine the possible correlates of Saudi women's interest in BC genes testing including socio-demographics, the level of awareness towards BC genes, the family history of BC and the perceived personal risk among adult Saudi women in Al Hassa, Saudi Arabia. Subjects and methods: This cross-sectional study was carried out during the second BC community-based campaign in Al Hassa, Saudi Arabia. All Saudi women aged ${\geq}18$ years (n=781) attending the educational components of the campaign were invited to a personal interview. Data collection included gathering information about sociodemographics, family history of BC, the perceived personal risk for BC, awareness and attitude towards BC genes and the women's interest in BC genes testing. Results: Of the included women (n=599), 19.5% perceived higher risk for BC development, significantly more among < 40 years of age, and with positive family history of BC before 50 years of age. The participants demonstrated a poor level of awareness regarding the inheritance, risk, and availability of BC genetic testing. The median summated knowledge score was 1.0 (out of 7 points) with a knowledge deficit of 87.8%. The level of knowledge showed significant decline with age (> 40 years). Of the included women 54.7% expressed an interest in BC genetic testing for assessing their BC risk. Multivariate regression model showed that being middle aged (Odds Ratio 'OR'=1.88, confidence intervals 'C.I'=1.14-3.11), with higher knowledge level (OR=1.67, C.I=1.08-2.57) and perceiving higher risk for BC (OR=2.11, C.I=1.61-2.76) were the significant positive correlates for Saudi women interest in BC genetic testing. Conclusion: Saudi women express high interest in genetic testing for BC risk despite their poor awareness. This great interest may reflect the presence of inappropriate information regarding BC genetic testing and its role in risk analysis.

• The Korean Journal of Applied Statistics
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• v.23 no.4
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• pp.705-713
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• 2010

Predicting survival from microarray data is not easy due to the problem of high dimensionality of data and the existence of censored observations. Also the limitation of individual gene analysis causes the shift of focus to the level of gene sets with functionally related genes. For developing a survival prediction model based on pathway information, the methods for selecting a supergene using principal component analysis and testing its significance for each pathway are discussed. Besides, the performance of gene filtering is compared.

• Fisheries and Aquatic Sciences
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• v.4 no.1
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• pp.39-46
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• 2001

To examine the effect of copy number-dependent transgenic genotype on the expression of foreign gene, stable hemizygous and homozygous transgenic breeding line was established using artificial parthenogenesis. For this purpose, induced diploid gynogenetic transgenesis was optimized in mud loach (Misgurnus mizolepis) using UV-irradiated cyprinid loach (M. anguillicaudatus) sperm and thermal shocks. Optimum UV range for inactivation of cyprinid loach sperm was between 3,150 to $4,050\;ergs/mm^2$ The UV-irradiated sperm were inseminated into eggs from recessive color strain (yellow) or heterozygous transgenic mud loach containing CAT gene. Cold shock at $2^{\circ}C$ for 60 min, 5 min post fertilization successfully restored the diploidy of eggs inseminated with UV-irradiated sperm. Restoration to diploidy was confirmed by flow cytometry and gynogenetic status was verified by examining maternal exclusive inheritance of multi-locus DNA fingerprints, body color and transgenic marker. Putative isogenic transgenic fish clearly showed homozygous status at trans gene locus based on Southern blot hybridization and progeny testing. Further, such homozygous gynogenetic diploids revealed the increased levels of transgene expression, when compared to those of heterozygous (hemizygous) transgenic fish.

• Proceedings of the Korean Society of Crop Science Conference
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• 2017.06a
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• pp.118-118
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• 2017

A high-resolution physical map targeting a cluster of yield-related QTLs on the long arm of rice chromosome 9 was constructed across a 35.5kb region containing the six predicted genes including the probable ascorbate peroxidase (OsApx). The $BC_3F_6$ near isogenic lines (NILs) were derived from a cross between the Oryza sativa Hwaseong and O. rufipogon. The plant height and length of internodes were compared between Hwaseong and NILs. There were significant differences in plant height between Hwaseong and NILs. The NILs internodes were longer than Hwaseong, showing dramatic elongation in the first and fourth internodes; thereby, leading to increased plant height. The antioxidant activity of Hwaseong and NILs was also analyzed by 3,3-diaminobenzidine (DAB) staining and 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay. In order to understand whether or not OsApx gene is important in scavenging $H_2O_2$ in rice, DAB staining was used. Intense dark-brown coloration was observed in Hwaseong than NILs. In addition, DPPH scavenging ability of Hwaseong showed lower value than NILs. These results indicated that the internode elongation and antioxidant activity might possibly be controlled by OsApx. To know the causative relationship of the gene and phenotype, we will further analyze the gene expression and use it for functional studies by complementation transgenic approach.

• Journal of the Korea Society of Computer and Information
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• v.25 no.8
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• pp.1-8
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• 2020

In this paper, we propose a gene family based RNA-seq read distribution method in means to accelerate the overal transcriptome assembly computation time. To measure the performance of our transcriptome sequence data distribution method, we evaluated the performance by testing four types of data sets of the Arabidopsis thaliana genome (Whole Unclassified Reads, Family-Classified Reads, Model-Classified Reads, and Randomly Classified Reads). As a result of de novo transcript assembly in distributed nodes using model classification data, the generated gene contigs matched 95% compared to the contig generated by WUR, and the execution time was reduced by 4.2 times compared to a single node environment using the same resources.