• Animal Bioscience
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• v.34 no.7
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• pp.1105-1115
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• 2021

Objective: To conserve and utilize the genetic resources of a traditional Chinese indigenous pig breed, Liangshan pig, we assessed the genetic diversity, genetic structure, and genetic distance in this study. Methods: We used 50K single nucleotide polymorphism (SNP) chip for SNP detection of 139 individuals in the Liangshan Pig Conservation Farm. Results: The genetically closed conserved population consisted of five overlapping generations, and the total effective content of the population (Ne) was 15. The whole population was divided into five boar families and one non-boar family. Among them, the effective size of each generation subpopulation continuously decreased. However, the proportion of polymorphic markers (P_N) first decreased and then increased. The average genetic distance of these 139 Liangshan pigs was 0.2823±0.0259, and the average genetic distance of the 14 boars was 0.2723±0.0384. Thus, it can be deduced that the genetic distance changed from generation to generation. In the conserved population, 983 runs of homozygosity (ROH) were detected, and the majority of ROH (80%) were within 100 Mb. The inbreeding coefficient calculated based on ROH showed an average value of 0.026 for the whole population. In addition, the inbreeding coefficient of each generation subpopulation initially increased and then decreased. In the pedigree of the whole conserved population, the error rate of paternal information was more than 11.35% while the maternal information was more than 2.13%. Conclusion: This molecular study of the population genetic structure of Liangshan pig showed loss of genetic diversity during the closed cross-generation reproduction process. It is necessary to improve the mating plan or introduce new outside blood to ensure long-term preservation of Liangshan pig.

• Korean Journal of Clinical Laboratory Science
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• v.55 no.4
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• pp.291-297
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• 2023

Gastritis is an inflammation of the gastric mucosa and gastric ulcers are a break in the mucosa of the stomach lining. Past research on gastritis and gastric ulcers has been mainly conducted from the perspective that environmental factors are the primary cause of these gastric diseases. However, recently the importance of genetic factors has been emphasized due to current developments in genetic research. The SLC25A26 gene is believed to be associated with the accumulation of reactive oxygen species. Oxidative stress promotes an inflammatory response, which increases the production of free radicals and causes cellular damage, and these lead to the development of gastric diseases. In this study, the correlation between SLC25A26 and gastric diseases was analyzed. Polymorphisms in SLC25A26 were analyzed in 1,369 domestic gastric disease patients and 7,471 healthy controls. As a result, 11 single nucleotide polymorphisms (SNPs) (in the genotype) and 13 SNPs (in the imputation) showed statistical significance (P<0.05), and high relative risk of gastric diseases. Among them, the rs13874 allele of SLC25A26 showed a highly significant association with gastric diseases. In the genotype-based mRNA expression analysis, the minor allele (C) group showed increased mRNA expression and this could increase oxidative stress. In conclusion, SLC25A26 polymorphisms are associated with gastric diseases. These results may provide a basis for new guidelines for gastric disease management in the Korean population.

• Korean Journal of Clinical Laboratory Science
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• v.56 no.1
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• pp.66-72
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• 2024

Lipid metabolic disorders are commonly encountered in clinical practice. Dyslipidemia and its prevalence rate are strongly associated with the morbidity and mortality of cardiovascular disease worldwide. We conducted a genetic analysis to determine the association between genetic polymorphisms of the ABO gene in adults middle-aged (40~69 years) with dyslipidemia in the Korean population. A total of 6,750 subjects from the Korea Association REsource (KARE) were selected for this study. Using the genetic and epidemiologic data of 4,403 dyslipidemia cases and 2,347 normal controls from the KARE, single nucleotide polymorphisms (SNPs) in ABO gene were analyzed for their genetic correlation. Eleven SNPs out of the ABO gene demonstrated a statistically significant association with dyslipidemia. Among them, rs8176707 in ABO gene statistically showed the most significant correlation with dyslipidemia (P-value=0.002, odds ratio=0.82, 95% confidence interval=0.78~0.86). The minor allele of T polymorphism within the ABO intron genetic region was associated with a decreased risk of dyslipidemia. This study uncovered a significant association between genetic polymorphism in the ABO gene and dyslipidemia. This finding suggest that ABO SNPs markers have a genetic correlation with the etiology of dyslipidemia.

• Asian-Australasian Journal of Animal Sciences
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• v.28 no.7
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• pp.926-935
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• 2015

The efficiency of genome-wide association analysis (GWAS) depends on power of detection for quantitative trait loci (QTL) and precision for QTL mapping. In this study, three different strategies for GWAS were applied to detect QTL for carcass quality traits in the Korean cattle, Hanwoo; a linkage disequilibrium single locus regression method (LDRM), a combined linkage and linkage disequilibrium analysis (LDLA) and a $BayesC{\pi}$ approach. The phenotypes of 486 steers were collected for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area, and marbling score (Marb). Also the genotype data for the steers and their sires were scored with the Illumina bovine 50K single nucleotide polymorphism (SNP) chips. For the two former GWAS methods, threshold values were set at false discovery rate <0.01 on a chromosome-wide level, while a cut-off threshold value was set in the latter model, such that the top five windows, each of which comprised 10 adjacent SNPs, were chosen with significant variation for the phenotype. Four major additive QTL from these three methods had high concordance found in 64.1 to 64.9Mb for Bos taurus autosome (BTA) 7 for WWT, 24.3 to 25.4Mb for BTA14 for CWT, 0.5 to 1.5Mb for BTA6 for BFT and 26.3 to 33.4Mb for BTA29 for BFT. Several candidate genes (i.e. glutamate receptor, ionotropic, ampa 1 [GRIA1], family with sequence similarity 110, member B [FAM110B], and thymocyte selection-associated high mobility group box [TOX]) may be identified close to these QTL. Our result suggests that the use of different linkage disequilibrium mapping approaches can provide more reliable chromosome regions to further pinpoint DNA makers or causative genes in these regions.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.11
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• pp.4727-4732
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• 2015

Background: Folylpolyglutamate synthetase (FPGS), an important enzyme in the folate metabolic pathway, plays a central role in intracellular accumulation of folate and antifolate in several mammalian cell types. Loss of FPGS activity results in decreased cellular levels of antifolates and consequently to polyglutamatable antifolates in acute lymphoblastic leukemia (ALL). Materials and Methods: During May 1997 and December 2003, 134 children diagnosed with ALL were recruited from one hospital in Thailand. We performed a mutation analysis in the coding regions of the FPGS gene and the association between single nucleotide polymorphisms (SNPs) within FPGS in a case-control sample of childhood ALL patients. Mutation screening was conducted by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and subsequently with direct sequencing (n=72). Association analysis between common FPGS variants and ALL risk was done in 98 childhood ALL cases and 95 healthy volunteers recruited as controls. Results: Seven SNPs in the FPGS coding region were identified by mutation analysis, 3 of which (IVS13+55C>T, g.1297T>G, and g.1508C>T) were recognized as novel SNPs. Association analysis revealed 3 of 6 SNPs to confer significant increase in ALL risk these being rs7039798 (p=0.014, OR=2.14), rs1544105 (p=0.010, OR= 2.24), and rs10106 (p=0.026, OR=1.99). Conclusions: These findings suggested that common genetic polymorphisms in the FPGS coding region including rs7039789, rs1544105, and rs10106 are significantly associated with increased ALL risk in Thai children.

• Journal of Digital Contents Society
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• v.19 no.9
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• pp.1795-1801
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• 2018

Genome-Wide Association Study (GWAS) have been used to identify susceptibility genes for complex human diseases and many recent studies succeed to report common genetic factors for various diseases. Unfortunately, it is hard to understand all biological functions and mechanisms around the complex disease with GWAS only although the number of known associated genes with diseases is increased drastically because GWAS is a single locus based approach while not a gene but numerous factors may affect a disease associated pathways. PRaDA generates a combined report with genes, pathways and Gene Ontology (GO) using single nucleotide polymorphism (SNP) analysis output. The PRaDA reports not only directly associated pathways but also functionally related ones for identifying accumulated effects of low p-value SNPs. Through integrated information including indirect functional effects, user could have insights of overall disease mechanisms and markers.

• Journal of Ginseng Research
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• v.34 no.1
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• pp.41-46
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• 2010

Expensive herbs such as ginseng are always a possible target for fraudulent labeling. New mountain ginseng strains have occasionally been found deep within mountain areas and commercially traded at exorbitant prices. However, until now, no scientific basis has existed to distinguish such ginseng from commonly cultivated ginseng species other than by virtue of being found within deep mountain areas. Polymerase chain reaction (PCR) analysis of the internal transcribed spacer has been shown to be an appropriate method for the identification of the most popular species (Panax ginseng) in the Panax ginseng genus. A single nucleotide polymorphism (SNP) has been identified between three newly found mountain ginseng (KGD4, KGD5, and KW1) and already established Panax species. Specific PCR primers were designed from this SNP site within the sequence data and used to detect the mountain ginseng strains via multiplex PCR. The established multiplex-PCR method for the simultaneous detection of newly found mountain ginseng strains, Korean ginseng, and foreign ginseng in a single reaction was determined to be effective. This study is the first report of scientific discrimination of "mountain ginsengs" and describes an effective method of identification for fraud prevention and for uncovering the possible presence of other, cheaper ginseng species on the market.

• Horticultural Science & Technology
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• v.33 no.5
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• pp.730-736
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• 2015

Tomato spotted wilt virus (TSWV) causes one of the most destructive viral diseases that threatens global tomato production. Sw-5b was reported as the resistance gene effective against TSWV. The objective of this research was to develop a single-nucleotide polymorphism (SNP) marker to distinguish tomato cultivars resistant to TSWV from susceptible cultivars for marker-assisted breeding. First, we determined genotypes for TSWV resistance in 32 commercial tomato cultivars using the previously reported Sw-5b gene-based marker. Then, DNA sequences of Sw-5b alleles in tomato cultivars showing resistant or susceptible genotypes were analyzed; a single SNP was found to distinguish tomato cultivars resistant to TSWV from susceptible cultivars. Based on the confirmed SNP, a SNP primer pair was designed. Using this new SNP sequence and high-resolution melting analysis, the same 32 tomato cultivars were screened. The results were perfectly correlated with those from screening with the Sw-5b gene-based marker. These results indicate that the SNP maker developed in this study will be useful for better tracking of resistance to TSWV in tomato breeding.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.11
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• pp.4917-4920
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• 2016

For advanced non-small-cell lung cancer (NSCLC) cases, a platinum-based regimen is the first-line chemotherapy treatment. The excision repair cross-complementing group 1 (ERCC1) plays an important role in DNA repair and has been related to resistance to platinum chemotherapy. This study aimed to investigate the effects of the ERCC1 (C118T) polymorphism on treatment response in 26 Thai advanced NSCLC patients receiving first line platinum-based chemotherapy during January to July 2015 at King Chulalongkorn Memorial Hospital (KCMH). DNA was extracted from peripheral blood lymphocytes and the single nucleotide polymorphism of ERCC1 was genotyped using a real-time PCR method with the TaqMan assay. The distribution of C/C, C/T and T/T genotypes was 57.7 %, 34.6 % and 7.7 %, respectively. The response rate to platinum-based chemotherapy in the wild type (C/C) of ERCC1 (C118T) was better than with the variant types (C/T and T/T) but the difference was not statistically significant (29.7% vs 9.1%, P=0.274). The results showed that a genetic polymorphism in ERCC1 might influence patient response to platinum-based chemotherapy. Further multicenter studies are now required to confirm the results of our study.

• Genomics & Informatics
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• v.9 no.2
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• pp.64-68
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• 2011

Monomelic amyotrophy (MA), also known as Hirayama disease, occurs mainly in young men and manifests as weakness and wasting of the muscles of the distal upper limbs. Here, we sought to identify a genetic basis for MA. Given the predominance of MA in males, we focused on candidate neurological disease genes located on the X chromosome, selecting two X-linked candidate genes, androgen receptor (AR ) and ubiquitin-like modifier activating enzyme 1 (UBA1). Screening for genetic variants using patients' genomic DNA revealed three known genetic variants in the coding region of the AR gene: one nonsynonymous single-nucleotide polymorphism (SNP; rs78686797) encoding Leu57Gln, and two variants of polymorphic trinucleotide repeat segments that encode polyglutamine (CAG repeat; rs5902610) and polyglycine (GGC repeat; rs3138869) tracts. Notably, the Leu57Gln polymorphism was found in two patients with MA from 24 MA patients, whereas no variants were found in 142 healthy male controls. However, the numbers of CAG and GGC repeats in the AR gene were within the normal range. These data suggest that the Leu57Gln polymorphism encoded by the X-linked AR gene may contribute to the development of MA.