• Asian Pacific Journal of Cancer Prevention
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• v.15 no.4
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• pp.1797-1802
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• 2014

Background: The prostaglandin-endoperoxide synthase 2 (PTGS2) and phospholipase A2 group IIA (PLA2G2A) genes encode enzymes that are involved in arachidonic acid and prostaglandin biosynthesis. Dysregulation of both genes is associated with inflammation and carcinogenesis, including esophageal squamous cell carcinoma (ESCC). We therefore hypothesized that there is an association between single nucleotide polymorphisms (SNPs) in these genes and susceptibility to ESCC. Methods: We performed a gene-wide tag SNP-based association study to examine the association of SNPs in PTGS2 and PLA2G2A with ESCC in 269 patients and 269 healthy controls from Taihangshan Mountain, Henan and Hebei Provinces, the rural area of China which has the highest incidence of esophageal cancer in the world. Thirteen tag SNPs in PLA2G2A and 4 functional SNPs in PTGS2 were selected and genotyped using a high-throughput Mass Array genotyping platform. Results: We found a modest increased risk of ESCC in subjects with the PTGS2 rs12042763 AA genotype (OR=1.23; 95% CI, 1.00-3.04) compared with genotype GG. For PLA2G2A, a decreased risk of ESCC was observed in subjects with the rs11677 CT (OR=0.51, 95%CI, 0.29-0.85) or TT genotype (OR=0.51, 95%CI, 0.17-0.96) or the T carriers (CT+TT) (OR=0.52, 95%CI, 0.31-0.85) when compared with the CC genotype. Also for PLA2G2A, rs2236771 C allele carriers were more frequent in the control group (P=0.02). Subjects with the GC (OR=0.55, 95%CI, 0.33-0.93) or CC genotype (OR=0.38, 95% CI, 0.16-0.94) or the C carriers (GC+CC) (OR=0.52, 95%CI, 0.32-0.85) showed a negative association with ESCC susceptibility. Conclusions: Our results suggest that PTGS2 and PLA2G2A gene polymorphisms may modify the risk of ESCC development.

• Korean Journal of Biological Psychiatry
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• v.13 no.4
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• pp.289-298
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• 2006

Objectives : Autism is a complex neurodevelopmental spectrum disorder with a strong genetic component. Previous neurochemical and genetic studies suggested the possible involvement of glutamate N-methyl-D-aspartate(NMDA) receptor in autism. The aim of study was to investigate the association between the NMDA2B receptor gene(GRIN2B) and autism spectrum disorders(ASD) in the Korean population. Methods : The patients with ASD were diagnosed with Autism Diagnostic Interview-Revised and Autism Diagnostic Observation Schedule based on DSM-IV diagnostic classification. The present study was conducted with the detection of four single nucleotide polymorphisms(SNPs) in GRIK2 and family-based association analysis of the single nucleotide polymorphisms in Korean ASD trios using transmission disequilibrium test (TDT). Results : One hundred twenty six patients with ASD and their biological parents were analyzed. 86.5% were male and 85.1% were diagnosed as autistic disorder. The mean age was $71.9{\pm}31.6$ months(range : 26-185 months). We found that rs1805247 showed significantly preferential transmission(TDT ${\chi}^2$=12.8, p<0.001) in ASD. Conclusion : One SNP in GRIN2B gene was significantly associated with ASD in the Korean population. This result suggests the possible involvement of glutamate NMDA receptor gene in the development of ASD.

• Asian-Australasian Journal of Animal Sciences
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• v.22 no.10
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• pp.1351-1358
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• 2009

Parentage tests using polymorphic DNA marker are commonly performed to avoid incorrect recording of the parental information of livestock animals, and single-nucleotide polymorphisms (SNPs) are becoming the method of choice. In Japanese Black cattle, parentage tests based on the exclusion method using microsatellite markers are currently conducted; however, an alternative SNP system aimed at parentage tests has recently been developed. In the present study, two types of simulations were conducted using the pedigree data of two subpopulations in the breed (subpopulations of Hyogo and Shimane prefectures) in order to examine the effect of actual genetic and breeding structures. The first simulation (simulation 1) investigated the usefulness of SNPs for excluding a close relative of the true sire; the second one (simulation 2) investigated the accuracy of sire identification tests for multiple full-sib putative sires by a combined method of exclusion and paternity assignment based on the LOD score. The success rates of excluding a single fullsib and sire of the true sires were, respectively, 0.9915 and 0.9852 in Hyogo and 0.9848 and 0.9852 in Shimane, when 50 SNPs with minor allele frequency (MAF: q) of 0.25${\leq}$q${\leq}$0.35 were used in simulation 1. The success rates of sire identification tests based solely on the exclusion method were relatively low in simulation 2. However, assuming that 50 SNPs with MAF of 0.25${\leq}$q${\leq}$0.35 or 0.45${\leq}$q${\leq}$0.5 were available, the total success rates including achievements due to paternity assignment were, respectively, 0.9430 and 0.9681 in Hyogo and 0.8999 and 0.9399 for Shimane, even when each true sire was assumed to compete with 50 full-sibs.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.1
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• pp.41-48
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• 2012

Introduction: Breast cancer is the second leading cancer in Korean women. To assess potential genetic associations between the prostate stem cell antigen (PSCA) gene in the chromosome 8q24 locus and breast cancer risk in Korean women, 13 SNPs were selected and associations with breast cancer risk were analyzed with reference to hormone receptor (HR) and menopausal status. Methods:We analyzed DNA extracted from buffy coat from 456 patients and 461 control samples, using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) based upon region-specific PCR followed by allelespecific single base primer extension reactions. Risks associated with PSCA genotypes and haplotypes were estimated with chi-square test (${\chi}^2$-test), and polytomous logistic regression models using odds ratios (OR) and 95% confidence intervals (CIs), by HR and menopausal status. Results: In case-control analysis, odds ratios (OR) of rs2294009, rs2294008, rs2978981, rs2920298, rs2976395, and rs2976396 were statistically significant only among women with estrogen receptor (ER) negative cancers, and those of rs2294008, rs2978981, rs2294010, rs2920298, rs2976394, rs10216533, and rs2976396 were statistically significant only in pre-menopausal women, and not in postmenopausal women. Risk with the TTGGCAA haplotype was significantly elevated in ER (-) status (OR= 1.48, 95% CI= 1.03~2.12, p<0.05). Especially risk of allele T of rs2294008 is significantly low in pre-menopausal breast cancer patients and AA genotype of rs2976395 in ER (-) status represents the increase of OR value. Conclusion: This report indicated for the first time that associations exist between PSCA SNPs and breast cancer susceptibility in Korean women, particularly those who are pre-menopausal with an estrogen receptor negative tumor status.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.50 no.5
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• pp.361-367
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• 2005

Single nucleotide polymorphisms (SNPs) are valuable DNA markers due to their abundance and potential for use in automated high-throughput genotyping. Numerous SNP genotyping assays have been developed. In this report, one of effective and high throughput SNP genotyping assays, which was named the template-directed dye-terminator incorporation with fluorescence polarization detection (FP-TDI) was described. Although the most of this assay succeed, the objective of this work was to deter­mine the reasons for the failures, find ways to improve the assay and reduce the running cost. Ninety $F_2$-derived soybean, Glycine max (L.) Merr., RILs from a cross between 'Pureunkong' and 'Jinpumkong 2' were genotyped at four SNPs. FP measurement was done on $Victot^3$ microplate reader (perkinelmer Inc., Boston, MA, USA). Increasing the number of thermal cycles in the single-base extension step increased the separation of the FP values between the products corresponding to different genotypes. But in some assays, excess of heterozygous genotypes was observed with increase of PCR cycles. We discovered that the excess heterozygous was due to misincorporation of one of the dye­terminators during the primer extension reaction. After pyrophosphatase incubation and thermal cycle control, misincoporation can be effectively prevented. Using long amplicons instead of short amplicons for SNP genotyping and decreasing the amount of dye terminator and Acyclopol Taq polymerase to 1/2 or 1/3 decreased the cost of the assay. With these minor adjustments, the FP-TDI assay can be used more accurately and cost-effectively.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.11
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• pp.1491-1495
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• 2004

Small Tail Han Sheep has significant characteristics of high prolificacy and non-seasonal ovulatory activity and is an excellent local sheep breed in P. R. China. Recently a novel member of the transforming growth factor $\beta$ (TGF$\beta$) superfamily termed bone morphogenetic protein 15 (BMP15) was shown to be specifically expressed in oocytes and to be essential for female fertility. Therefore, BMP15 is a candidate gene for reproductive performance of Small Tail Han Sheep. The whole genomic nucleotide sequence of BMP15 gene in Small Tail Han Sheep was searched for polymorphisms by PCR-SSCP and direct sequencing, and only one polymorphism was found. The polymorphism was a result of a 3 base pair deletion, which eliminated a single Leu codon (CTT). The allelic frequencies for A (without deletion) and B (with a codon deletion) are 0.73 and 0.27 respectively. The effects of BMP15 genotype on litter size were evaluated using the least squares model. This indicated that there was a significant association between litter size of Small Tail Han Sheep and a deletion in BMP15 gene (p=0.02<0.05). Small Tail Han Sheep ewes with AA and AB genotype produce on average 0.5 and 0.3 more lambs per litter than those ewes with BB genotype.

• Asian-Australasian Journal of Animal Sciences
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• v.26 no.6
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• pp.766-771
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• 2013

The purpose of this study was to investigate interaction effects of genes using a Harvester method. A sample of Korean cattle, Hanwoo (n = 476) was chosen from the National Livestock Research Institute of Korea that were sired by 50 Korean proven bulls. The steers were born between the spring of 1998 and the autumn of 2002 and reared under a progeny-testing program at the Daekwanryeong and Namwon branches of NLRI. The steers were slaughtered at approximately 24 months of age and carcass quality traits were measured. A SNP Harvester method was applied with a support vector machine (SVM) to detect significant SNPs in the CCDC158 gene and interaction effects between the SNPs that were associated with average daily gains, cold carcass weight, longissimus dorsi muscle area, and marbling scores. The statistical significance of the major SNP combinations was evaluated with $x^2$-statistics. The genotype combinations of three SNPs, g.34425+102 A>T(AA), g.4102636T>G(GT), and g.11614-19G>T(GG) had a greater effect than the rest of SNP combinations, e.g. 0.82 vs. 0.75 kg, 343 vs. 314 kg, 80.4 vs $74.7cm^2$, and 7.35 vs. 5.01, for the four respective traits (p<0.001). Also, the estimates were greater compared with single SNPs analyzed (the greatest estimates were 0.76 kg, 320 kg, $75.5cm^2$, and 5.31, respectively). This result suggests that the SNP Harvester method is a good option when multiple SNPs and interaction effects are tested. The significant SNPs could be applied to improve meat quality of Hanwoo via marker-assisted selection.

• Genomics & Informatics
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• v.10 no.3
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• pp.194-199
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• 2012

In addition to single-nucleotide polymorphisms (SNP), copy number variation (CNV) is a major component of human genetic diversity. Among many whole-genome analysis platforms, SNP arrays have been commonly used for genomewide CNV discovery. Recently, a number of CNV defining algorithms from SNP genotyping data have been developed; however, due to the fundamental limitation of SNP genotyping data for the measurement of signal intensity, there are still concerns regarding the possibility of false discovery or low sensitivity for detecting CNVs. In this study, we aimed to verify the effect of combining multiple CNV calling algorithms and set up the most reliable pipeline for CNV calling with Affymetrix Genomewide SNP 5.0 data. For this purpose, we selected the 3 most commonly used algorithms for CNV segmentation from SNP genotyping data, PennCNV, QuantiSNP; and BirdSuite. After defining the CNV loci using the 3 different algorithms, we assessed how many of them overlapped with each other, and we also validated the CNVs by genomic quantitative PCR. Through this analysis, we proposed that for reliable CNV-based genomewide association study using SNP array data, CNV calls must be performed with at least 3 different algorithms and that the CNVs consistently called from more than 2 algorithms must be used for association analysis, because they are more reliable than the CNVs called from a single algorithm. Our result will be helpful to set up the CNV analysis protocols for Affymetrix Genomewide SNP 5.0 genotyping data.

• Genomics & Informatics
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• v.19 no.2
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• pp.19.1-19.9
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• 2021

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.

• Animal Bioscience
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• v.37 no.4
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• pp.576-590
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• 2024

Objective: The objective of this study was to identify genes associated with 305-day milk yield (MY) and fat yield (FY) that also influence the adaptability of the Thai multibreed dairy cattle population to tropical conditions. Methods: A total of 75,776 imputed and actual single nucleotide polymorphisms (SNPs) from 2,661 animals were used to identify genomic regions associated with MY and FY using the single-step genomic best linear unbiased predictions. Fixed effects included herd-year-season, breed regression, heterosis regression and calving age regression effects. Random effects were animal additive genetic and residual. Individual SNPs with a p-value smaller than 0.05 were selected for gene mapping, function analysis, and quantitative trait loci (QTL) annotation analysis. Results: A substantial number of QTLs associated with MY (9,334) and FY (8,977) were identified by integrating SNP genotypes and QTL annotations. Notably, we discovered 17 annotated QTLs within the health and exterior QTL classes, corresponding to nine unique genes. Among these genes, Rho GTPase activating protein 15 (ARHGAP15) and catenin alpha 2 (CTNNA2) have previously been linked to physiological traits associated with tropical adaptation in various cattle breeds. Interestingly, these two genes also showed signs of positive selection, indicating their potential role in conferring tolerance to trypanosomiasis, a prevalent tropical disease. Conclusion: Our findings provide valuable insights into the genetic basis of MY and FY in the Thai multibreed dairy cattle population, shedding light on the underlying mechanisms of tropical adaptation. The identified genes represent promising targets for future breeding strategies aimed at improving milk and fat production while ensuring resilience to tropical challenges. This study significantly contributes to our understanding of the genetic factors influencing milk production and adaptability in dairy cattle, facilitating the development of sustainable genetic selection strategies and breeding programs in tropical environments.