• Asian Pacific Journal of Cancer Prevention
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• v.15 no.1
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• pp.123-127
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• 2014

A recent study summarized several published genome-wide association studies (GWASs) of cancer and reported two pleiotropic loci at 6p21.1 and 7p15.3 contributing to multiple cancers including lung cancer, noncardia gastric cancer (NCGC), and esophageal squamous-cell carcinoma (ESCC) in Han Chinese. However, it is not known whether such genetic variants have similar effects on the risk of gynecologic cancers, such as ovarian cancer. Hence, we explored associations between genetic variants in 6p21.1 and 7p15.3 and ovarian cancer risk in Han Chinese women. We performed an independent case-control study by genotyping the two loci (rs2494938 A > G at 6p21.1 and rs2285947 A > G at 7p15.3) in a total of 377 ovarian cancer cases and 1,034 cancer-free controls using TaqMan allelic discrimination assay. We found that rs2285947 at 7p15.3 was significantly associated with risk of ovarian cancer with per allele odds ratio (OR) of 1.33 [95% confidence interval (CI): 1.08-1.64, P=0.008]. However, no significant association was observed between rs2494938 and ovarian cancer risk. Our results showed that rs2285947 at 7p15.3 may also contribute to the development of ovarian cancer in Han Chinese women, further suggesting pleiotropy of 7p15.3 in multiple cancers.

• BMB Reports
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• v.43 no.6
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• pp.445-449
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• 2010

Aspirin-intolerant asthma (AIA) is characterized by severe asthmatic attack after ingestion of aspirin and/or non-steroidal anti-inflammatory drugs. In this study, we investigated the relationship between Prostaglandin E2 receptor (PTGER) gene family polymorphisms and AIA in 243 AIA patients and 919 aspirin-tolerant asthma (ATA) controls of Korean ethnicity in two separate study cohorts. After genotyping 120 SNPs of the PTGER gene family for the $1^{st}$ cohort study, four SNPs in PTGER1, ten in PTGER3, six in PTGER3, and a haplotype of PTGER2 showed association signals with decreased or increased risk of AIA. Among the positively associated SNPs, one in PTGER1 and four in PTGER3 were analyzed in the $2^{nd}$ cohort study. The results show that rs7543182 and rs959 in PTGER3 retained their effect, although no statistical significance was retained in the $2^{nd}$ cohort study. Our findings provide further evidence that polymorphisms in PTGER3 might play a significant role in aspirin hypersensitivity among Korean asthmatics.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.9
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• pp.5415-5420
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• 2013

Background: Cell cycle deregulation is a major component of carcinogenesis. The p53 tumor suppressor gene plays an important role in regulating cell cycle arrest, and mouse double minute 2 (MDM2) is a key regulator of p53 activity and degradation. Abnormal expression of p53 and MDM2 occurs in various cancers including lung cancer. Methods: We investigated the distribution of the p53 Arg72Pro (rs1042522) and MDM2 SNP309 (rs2279744) genotypes in patients and healthy control subjects to assess whether these single nucleotide polymorphisms (SNPs) are associated with an increased risk of lung adenocarcinomas in Chinese female non-smokers. Genotypes of 764 patients and 983 healthy controls were determined using the TaqMan SNP genotyping assay. Results: The p53 Pro/Pro genotype (adjusted OR = 1.55, 95% CI = 1.17-2.06) significantly correlated with an increased risk of lung adenocarcinoma, compared with the Arg/Arg genotype. An increased risk was also noted for MDM2 GG genotype (adjusted OR = 1.68, 95% CI = 1.27-2.21) compared with the TT genotype. Combined p53 Pro/Pro and MDM2 GG genotypes (adjusted OR = 2.66, 95% CI = 1.54-4.60) had a supermultiplicative interaction with respect to lung adenocarcinoma risk. We also found that cooking oil fumes, fuel smoke, and passive smoking may increase the risk of lung adenocarcinomas in Chinese female non-smokers who carry p53 or MDM2 mutant alleles. Conclusions: P53 Arg72Pro and MDM2 SNP309 polymorphisms, either alone or in combination, are associated with an increased lung adenocarcinoma risk in Chinese female non-smokers.

• The korean journal of orthodontics
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• v.44 no.2
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• pp.96-102
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• 2014

Objective: A recent study suggested that rs6504340, a polymorphism within the homeobox B (HOXB) gene cluster, is associated with the susceptibility for malocclusions in Europeans. The resulting malocclusions require orthodontic treatment. The aim of this study was to investigate the association of rs6504340 and other dentition-implicated polymorphisms with dental and occlusal traits in Korean and Japanese populations. Methods: The study participants included 223 unrelated Koreans from the Busan area and 256 unrelated Japanese individuals from the Tokyo metropolitan area. DNA samples were extracted from saliva specimens. Genotyping for rs6504340 and four single nucleotide polymorphisms (SNPs) that have been shown to be associated with the timing of first tooth eruption and the number of teeth at 1 year of age (rs10506525, rs1956529, rs9674544, and rs8079702) was performed using TaqMan assays. The Index of Orthodontic Treatment Need (IOTN), overjet, overbite, arch length discrepancy, crown sizes, and length and width of the dental arches were measured. Spearman's correlation coefficients were calculated to evaluate relationships between rs6504340 and these dental/occlusal traits. Results: We evaluated the aesthetic components and dental health components of the IOTN in the Korean and Japanese populations and found that neither rs6504340 nor the other four SNPs showed any association with dental and occlusal traits in these East Asian populations. Conclusions: These negative results suggest that further research is needed to identify the genetic determinants of malocclusions in order to reach a consensus.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• v.22 no.4
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• pp.287-293
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• 2011

Objectives : The region of chromosome 5p14 is known to be associated with autism spectrum disorder (ASD). The cadherin9 (CDH9) and cadherin10 (CDH10) genes are located in the region of chromosome 5p14 and reported to be associated with ASD in the Caucasian population. We performed an association study to identify if single nucleotide polymorphisms (SNPs) located on the CDH9 and CDH10 genes are associated in the Korean population. Methods : Genomic DNA was extracted from the blood of 214 patients with ASD and 258 controls. SNPs selected from two genes were genotyped using an Illumina Golden-Gate Genotyping assay with VeraCode technology. Statistical analysis was performed using SAS and Plink software. Results : All controls and ASD patients were in Hardy-Weinberg equilibrium. In the results of logistic regression analyses for the genotype model and the chi-square test for the allele model, we found that SNPs on the CDH9 and CDH10 genes were not associated with ASD. Conclusion : Our data suggests that the CDH9 and CDH10 genes are not associated with ASD in the Korean population.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.4
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• pp.494-500
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• 2019

Objective: Feed consumption contributes a large percentage for total production costs in the poultry industry. Detecting genes associated with feeding traits will be of benefit to improve our understanding of the molecular determinants for feed efficiency. The objective of this study was to identify candidate genes associated with feed conversion ratio (FCR) via genomewide association study (GWAS) using sequence data imputed from single nucleotide polymorphism (SNP) panel in a Chinese indigenous chicken population. Methods: A total of 435 Chinese indigenous chickens were phenotyped for FCR and were genotyped using a 600K SNP genotyping array. Twenty-four birds were selected for sequencing, and the 600K SNP panel data were imputed to whole sequence data with the 24 birds as the reference. The GWAS were performed with GEMMA software. Results: After quality control, 8,626,020 SNPs were used for sequence based GWAS, in which ten significant genomic regions were detected to be associated with FCR. Ten candidate genes, ubiquitin specific peptidase 44, leukotriene A4 hydrolase, ETS transcription factor, R-spondin 2, inhibitor of apoptosis protein 3, sosondowah ankyrin repeat domain family member D, calmodulin regulated spectrin associated protein family member 2, zinc finger and BTB domain containing 41, potassium sodium-activated channel subfamily T member 2, and member of RAS oncogene family were annotated. Several of them were within or near the reported FCR quantitative trait loci, and others were newly reported. Conclusion: Results from this study provide valuable prior information on chicken genomic breeding programs, and potentially improve our understanding of the molecular mechanism for feeding traits.

• Animal Bioscience
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• v.37 no.7
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• pp.1168-1176
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• 2024

Objective: As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future. Methods: Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations. Results: Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations. Conclusion: The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.9
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• pp.116-123
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• 2018

The sperm quality is determined by the kinetic characteristics and acrosome integrity of the sperm. In the previous studies, analysis of semen quality had large errors because those experiments by using microscope had been conducted by people. In recent years, the molecular biological methods have been newly developed to complement the previous techniques. The ZAR1 gene is known to be a gene that affects early embryonic development in vertebrates, but there is no study of the association with semen. In this study, we analyzed the association between the kinetic characteristics and ZAR1 single nucleotide polymorphism (SNP) genotype. To detect the SNPs, we performed sequencing using genomic DNA from the whole bloods of Duroc pigs. We identified an SNP in the ZAR1 gene g.2540T>C. ZAR1 SNP genotypeing in 105 pigs revealed that the major and minor alleles were T and C, respectively. After we analyzed the association between the kinetic characteristics of sperm and the ZAR1 SNP genotype, we found a significant association in MOT (p<0.01), VSL (p<0.05) of the kinetic characteristics in the Duroc boars. It was confirmed that the boars with T allele were lower in MOT and VSL than C allele. Therefore, pigs with C allele are judged to be better at the MOT and VSL of semen. Based on these results, ZAR1 SNP genotyping may be a useful molecular biomarker to improve semen quality by applying molecular breeding technology.

• Genomics & Informatics
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• v.16 no.2
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• pp.36-41
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• 2018

Kawasaki disease (KD) is an acute febrile vasculitis predominately affecting infants and children. The dominant incidence age of KD is from 6 months to 5 years of age, and the incidence is unusual in those younger than 6 months and older than 5 years of age. We tried to identify genetic variants specifically associated with KD in patients younger than 6 months or older than 5 years of age. We performed an age-stratified genome-wide association study using the Illumina HumanOmni1-Quad BeadChip data (296 cases vs. 1,000 controls) and a replication study (1,360 cases vs. 3,553 controls) in the Korean population. Among 26 candidate single nucleotide polymorphisms (SNPs) tested in replication study, only a rare nonsynonymous SNP (rs4365796: c.1106C>T, p.Thr369Met) in the lymphoid enhancer binding factor 1 (LEF1) gene was very significantly associated with KD in patients younger than 6 months of age (odds ratio [OR], 3.07; $p_{combined}=1.10{\times}10^{-5}$), whereas no association of the same SNP was observed in any other age group of KD patients. The same SNP (rs4365796) in the LEF1 gene showed the same direction of risk effect in Japanese KD patients younger than 6 months of age, although the effect was not statistically significant (OR, 1.42; p = 0.397). This result indicates that the LEF1 gene may play an important role as a susceptibility gene specifically affecting KD patients younger than 6 months of age.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.68 no.3
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• pp.134-146
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• 2023

Phytophthora root rot (PRR) is a major soybean disease caused by an oomycete, Phytophthora sojae. PRR can be severe in poorly drained fields or wet soils. The disease management primarily relies on resistance genes called Rps (resistance to P. sojae). This study aimed to identify resistance loci associated with resistance to P. sojae isolate 40468 in Daepung × CheonAl recombinant inbred line (RIL) population. CheonAl is resistant to the isolate, while Daepung is generally susceptible. We genotyped the parents and RIL population via high-throughput single nucleotide polymorphism genotyping and constructed a set of genetic maps. The presence or absence of resistance to P. sojae was evaluated via hypocotyl inoculation technique, and phenotypic distribution fit to a ratio of 1:1 (R:S) (χ² = 0.57, p = 0.75), indicating single gene mediated inheritance. Single-marker association and the linkage analysis identified a highly significant genomic region of 55.9~56.4 megabase pairs on chromosome 18 that explained ~98% of phenotypic variance. Many previous studies have reported several Rps genes in this region, and also it contains nine genes that are annotated to code leucine-rich repeat or serine/threonine kinase within the approximate 500 kilobase pairs interval based on the reference genome database. CheonAl is the first domestic soybean genotype characterized for resistance against P. sojae isolate 40468. Therefore, CheonAl could be a valuable genetic source for breeding resistance to P. sojae.