• Proceedings of the Korean Society of Crop Science Conference
• /
• 2022.10a
• /
• pp.273-273
• /
• 2022

The increasing number of Westernized eating patterns based on wheat flour in Korea has led to an increase in the rate of diseases such as obesity and diabetes, which has become a social problem. Wheat consumption is increasing due to changes in eating habits, but domestic wheat has low price competitiveness and has stagnated recently, so it is necessary to secure new resources to differentiate from imported wheat. Resistant starch, a newly created resource in domestic wheat, can act as a prebiotic similar to dietary fiber in the body, inducing microbial changes in the gut and having beneficial effects on metabolic syndrome. Wheat research on resistant starch was carried out based on the breeding of high amylose. A genome-wide association study (GWAS) was used to perform SNP identification and expression analysis related to wheat amylose through phenotype and genotype. 561 wheat core collection gene sources were investigated for amylose content in wheat, and related genes were extracted and analyzed. In the GWAS analysis, the model formulas BLIMK, FarmCPU, GLM, MLM, and MLMM were used to derive results such as QQ plots and Manhattan plots through phenotypic data. Among these models, BLAST was conducted to find the association between the SNPs identified using FarmCPU and genes related to starch, and 15 were found. Using the identified markers, it becomes easier to develop and browse related wheat cultivars according to their amylose content.

• Korean Journal of Biological Psychiatry
• /
• v.22 no.4
• /
• pp.173-178
• /
• 2015

Objectives Previous genome-wide association studies have indicated the association between ankyrin 3 (ANK3) and the vulnerability of schizophrenia. We investigated the association between single nucleotide polymorphisms (SNPs) covering the whole ANK3 locus and schizophrenia in the Korean population. Methods The study subjects were 582 patients with schizophrenia and 502 healthy controls. Thirty-eight tag SNPs on ANK3 and five additional SNPs showing significant association with schizophrenia in previous studies were genotyped. Results Three (rs10994181, rs16914791, rs1938526) of 43 SNPs showed a nominally significant association (p < 0.05) with at least one genotype model. But none of these associations remained significant after adjusting for multiple testing errors with Bonferroni's correction. Conclusions We could not identify a significant association between ANK3 and schizophrenia in the Korean population. However, three SNPs showing an association signal with nominal significance need to be investigated in future studies with higher statistical power and more specific phenotype crossing the current diagnostic categories.

• Journal of Gastric Cancer
• /
• v.20 no.2
• /
• pp.127-138
• /
• 2020

Purpose: Mucin 1 (MUC1) was identified as a gastric cancer (GC) susceptibility gene by genome-wide association studies in Asians and candidate gene studies in Europeans. This study aimed to investigate the association between the MUC1 rs4072037 polymorphism and GC in terms of the Lauren classification and long-term clinical outcomes. Materials and Methods: A total of 803 patients with GC and 816 unrelated healthy controls were enrolled in the study. The association between the MUC1 rs4072037 variant and GC histological types and clinical outcomes, including tumor recurrence and prognosis was investigated. Results: The major A allele of rs4072037 was associated with increased GC risk (P<0.05). In subtype analysis, the association was most significant for diffuse-type GC (P<0.05) and in a dominant model (P<0.05), whereas there was no association with intestinal-type GC (P>0.05). Cox proportional hazards analysis revealed the heterozygote AG rs4072037 allele as an independent risk factor influencing tumor recurrence and disease-related death in diffusetype GC (P<0.05). but not in intestinal-type GC (P>0.05). Conclusions: The exonic single nucleotide polymorphism rs4072037 in MUC1 was associated with diffuse-type GC and was an independent risk factor influencing tumor recurrence and disease-related death in diffuse-type GC.

• Journal of Animal Science and Technology
• /
• v.55 no.4
• /
• pp.231-235
• /
• 2013

Carcass weight (CW) is one of the most important economic traits in pigs, directly affecting the income of farmers. In this study, a genome wide association study was performed to detect significant single nucleotide polymorphisms (SNPs) affecting CW in pigs derived from a $F_2$ intercross between Landrace and Korean native pig (KNP). Using high-density porcine SNP chips, highly significant SNPs were identified on SSC12. Two candidate genes, LOC100523510 and LOC100621652, were subsequently selected within this region and further investigated. Within these candidate genes, five SNPs were identified and genotyped using the VeraCode GoldenGate assay. The results revealed that one SNP in the LOC100621652 gene and four SNPs in the LOC100523510 gene are highly associated with CW. These SNP markers can thus have significant applications for improving CW in KNP. However, the functions of these candidate genes are not fully understood and require further study.

• Communications for Statistical Applications and Methods
• /
• v.17 no.5
• /
• pp.667-678
• /
• 2010

It is important to detect the gene-gene interaction in GWAS(Genome-Wide Association Study). There are many studies about detecting gene-gene interaction. The one is Multifactor dimensionality reduction method. But MDR method is not applied continuous data and expanded multifactor dimensionality reduction(E-MDR) method is suggested. The goal of this study is to evaluate the power of E-MDR for identifying gene-gene interaction by simulation. Also we applied the method on the identify interaction e ects of single nucleotid polymorphisms(SNPs) responsible for economic traits in a Korean cattle population (real data).

• Asian-Australasian Journal of Animal Sciences
• /
• v.16 no.6
• /
• pp.910-927
• /
• 2003

Transgenesis is a very powerful tool not only to help understanding the basics of life science but also to improve the efficiency of animal production. Since the first transgenic mouse was born in 1980, rapid development and wide application of this technique have been made in laboratory animals as well as in domestic animals. Although pronuclear injection is the most widely used method and nuclear transfer using somatic cells broadens the choice of making transgenic domestic animals, the demand for precise manipulation of the genome leads to the utilization of gene targeting. To make this technique possible, a pluripotent embryonic cell line such as embryonic stem (ES) cell is required to carry genetic mutation to further generations. However, ES cell, well established in mice, is not available in domestic animals even though many attempt to establish the cell line. An alternate source of pluripotent cells is embryonic germ (EG) cells derived from primordial germ cells (PGCs). To make gene targeting feasible in this cell line, a better culture system would help to minimize the unnecessary loss of cells in vitro. In this review, general methods to produce transgenic domestic animals will be mentioned. Also, it will focus on germ cell engineering and methods to improve the establishment of pluripotent embryonic cell lines in domestic animals.

• Journal of Korean Neurosurgical Society
• /
• v.57 no.6
• /
• pp.422-427
• /
• 2015

Moyamoya disease (MMD) is a chronic, progressive, cerebrovascular occlusive disorder that displays various clinical features and results in cerebral infarct or hemorrhagic stroke. Specific genes associated with the disease have not yet been identified, making identification of at-risk patients difficult before clinical manifestation. Familial MMD is not uncommon, with as many as 15% of MMD patients having a family history of the disease, suggesting a genetic etiology. Studies of single nucleotide polymorphisms (SNPs) in MMD have mostly focused on mechanical stress on vessels, endothelium, and the relationship to atherosclerosis. In this review, we discuss SNPs studies targeting the genetic etiology of MMD. Genetic analyses in familial MMD and genome-wide association studies represent promising strategies for elucidating the pathophysiology of this condition. This review also discusses future research directions, not only to offer new insights into the origin of MMD, but also to enhance our understanding of the genetic aspects of MMD. There have been several SNP studies of MMD. Current SNP studies suggest a genetic contribution to MMD, but further reliable and replicable data are needed. A large cohort or family-based design would be important. Modern SNP studies of MMD depend on novel genetic, experimental, and database methods that will hopefully hasten the arrival of a consensus conclusion.

• Journal of the Korean Data and Information Science Society
• /
• v.24 no.2
• /
• pp.277-287
• /
• 2013

It is important to detect the gene-gene interaction in GWAS (genome-wide association study). There have been many studies on detecting gene-gene interaction. The one is D-MDR (dummy multifoactor dimensionality reduction) method. The goal of this study is to evaluate the power of D-MDR for identifying gene-gene interaction by simulation. Also we applied the method on the identify interaction effects of single nucleotide polymorphisms (SNPs) responsible for economic traits in a Korean cattle population (real data).

• Asian Pacific Journal of Cancer Prevention
• /
• v.15 no.15
• /
• pp.6211-6217
• /
• 2014

Previous genome-wide association studies (GWAS) have implicated several single nucleotide polymorphisms (SNPs) in the AT-rich interactive domain 5B (ARID5B) gene with childhood acute lymphoblastic leukemia (ALL). However, replicated studies reported some inconsistent results in different populations. Using meta-analysis, we here aimed to clarify the nature of the genetic risks contributed by the two polymorphisms (rs10994982, rs7089424) for developing childhood ALL. Through searches of PubMed, EMBASE, and manually searching relevant references, a total of 14 articles with 16 independent studies were included. Odds ratios (ORs) with 95% confidence intervals (95%CI) were calculated to assess the associations. Both SNPs rs10994982 and rs7089424 showed significant associations with childhood ALL risk in all genetic models after Bonferroni correction. Furthermore, subtype analyses of B-lineage ALL provided strong evidence that SNP rs10994982 is highly associated with the risk of developing B-hyperdiploid ALL. These results indicate that SNPs rs10994982 and rs7089424 are indeed significantly associated with increased risk of childhood ALL.

• Journal of Gastric Cancer
• /
• v.19 no.3
• /
• pp.235-253
• /
• 2019

Gastric cancer (GC) is one of the deadliest malignancies in the world. Currently, clinical treatment decisions are mostly made based on the extent of the tumor and its anatomy, such as tumor-node-metastasis staging. Recent advances in genome-wide molecular technology have enabled delineation of the molecular characteristics of GC. Based on this, efforts have been made to classify GC into molecular subtypes with distinct prognosis and therapeutic response. Simplified algorithms based on protein and RNA expressions have been proposed to reproduce the GC classification in the clinical field. Furthermore, a recent study established a single patient classifier (SPC) predicting the prognosis and chemotherapy response of resectable GC patients based on a 4-gene real-time polymerase chain reaction assay. GC patient stratification according to SPC will enable personalized therapeutic strategies in adjuvant settings. At the same time, patient-derived xenografts and patient-derived organoids are now emerging as novel preclinical models for the treatment of GC. These models recapitulate the complex features of the primary tumor, which is expected to facilitate both drug development and clinical therapeutic decision making. An integrated approach applying molecular patient stratification and patient-derived models in the clinical realm is considered a turning point in precision medicine in GC.