• Genomics & Informatics
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• 제10권2호
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• pp.117-122
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• 2012

A sample size with sufficient statistical power is critical to the success of genetic association studies to detect causal genes of human complex diseases. Genome-wide association studies require much larger sample sizes to achieve an adequate statistical power. We estimated the statistical power with increasing numbers of markers analyzed and compared the sample sizes that were required in case-control studies and case-parent studies. We computed the effective sample size and statistical power using Genetic Power Calculator. An analysis using a larger number of markers requires a larger sample size. Testing a single-nucleotide polymorphism (SNP) marker requires 248 cases, while testing 500,000 SNPs and 1 million markers requires 1,206 cases and 1,255 cases, respectively, under the assumption of an odds ratio of 2, 5% disease prevalence, 5% minor allele frequency, complete linkage disequilibrium (LD), 1:1 case/control ratio, and a 5% error rate in an allelic test. Under a dominant model, a smaller sample size is required to achieve 80% power than other genetic models. We found that a much lower sample size was required with a strong effect size, common SNP, and increased LD. In addition, studying a common disease in a case-control study of a 1:4 case-control ratio is one way to achieve higher statistical power. We also found that case-parent studies require more samples than case-control studies. Although we have not covered all plausible cases in study design, the estimates of sample size and statistical power computed under various assumptions in this study may be useful to determine the sample size in designing a population-based genetic association study.

• 한국작물학회지
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• 제54권4호
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• pp.441-451
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• 2009

In this study, 29 simple sequence repeat (SSR) markers were used to analyze the genetic diversity and population structure of 125 rice accessions from 40 different origins in Africa, Asia, Europe, South America, and Oceania. A total of 333 alleles were detected, with an average of 11.5 per locus. The mean values of major allele frequency, expected heterozygosity, and polymorphism information content (PIC) for each SSR locus were 0.39, 0.73, and 0.70, respectively. The highest mean PIC was 0.71 for Asia, followed by 0.66 for Africa, 0.59 for South America, 0.53 for Europe, and 0.47 for Oceania. Model-based structure analysis revealed the presence of five subpopulations, which was basically consistent with clustering based on genetic distance. Some accessions were clearly assigned to a single population in which >70% of their inferred ancestry was derived from one of the model-based populations. In addition, 12 accessions (9.6%) were categorized as having admixed ancestry. The results could be used to understanding the genetic structure of rice cultivars from these regions and to support effective breeding programs to broaden the genetic basis of rice varieties.

• 대한두경부종양학회지
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• 제22권2호
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• pp.117-122
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• 2006

Background and Objectives : Thyroid carcinoma is the sixth commonest cancer in Korea and the papillary carcinoma is the most common type(88%) of the malignant thyroid tumors. Bulky DNA adducts formed by the carcinogens are repaired by DNA repair process, but failure to repair this DNA damage can cause mutations in oncogenes and tumor suppressor genes resulting in tumor formation. The xeroderma pigmentosum group C(XPC) gene is essential for this repair procedure and the XPC-PolyAT(PAT) polymorphisms may alter DNA repair capacity(DRC) and genetic susceptibility to cancer. Subjects and Methods : In a case-control study of 113 Korean patients with pathologically diagnosed thyroid papillary carcinoma and 65 control subjects, we investigated the association between the three XPC-PAT gene polymorphisms and thyroid papillary cancer susceptibility. Results : The frequency of the variant XPC-PAT allele was lower in the cases(0.349) than in the controls (0.423), but the difference was not significant(p=0.140). Using logistic regression adjusting for age and sex, risk for thyroid papillary cancer was not increased in the XPC-PAT-/+ and XPC-PAT+/+ compared to XPCPAT-/-(adjusted overall odds ratio[95% confidence intervals;95%CI]=0.52[0.26-1.03] and 0.62 [0.22-1.75], respectively; trend test, p=0.167). Conclusion : There are no relationship between the XPC-PAT polymorphism and the risk of thyroid papillary carcinoma in Korean population. Based on our results, XPC-PAT polymorphism do not modulate genetic susceptibility to thyroid papillary cancer.

• Mycobiology
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• 제45권2호
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• pp.105-109
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• 2017

Sixteen genomic DNA simple sequence repeat (SSR) markers of Lentinula edodes were developed from 205 SSR motifs present in 46.1-Mb long L. edodes genome sequences. The number of alleles ranged from 3-14 and the major allele frequency was distributed from 0.17-0.96. The values of observed and expected heterozygosity ranged from 0.00-0.76 and 0.07-0.90, respectively. The polymorphic information content value ranged from 0.07-0.89. A dendrogram, based on 16 SSR markers clustered by the paired hierarchical clustering' method, showed that 33 shiitake cultivars could be divided into three major groups and successfully identified. These SSR markers will contribute to the efficient breeding of this species by providing diversity in shiitake varieties. Furthermore, the genomic information covered by the markers can provide a valuable resource for genetic linkage map construction, molecular mapping, and marker-assisted selection in the shiitake mushroom.

• Pediatric Gastroenterology, Hepatology & Nutrition
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• 제17권1호
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• pp.37-40
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• 2014

Purpose: Crigler-Najjar syndrome type II (CN-2) is characterized by moderate non-hemolytic unconjugated hyperbilirubinemia as a result of severe deficiency of bilirubin uridine diphosphate-glucuronosyltransferase (UGT1A1). The study investigated the mutation spectrum of UGT1A1 gene in Korean children with CN-2. Methods: Five Korean CN-2 patients from five unrelated families and 50 healthy controls were enrolled. All five exons and flanking introns of the UGT1A1 gene were amplified by polymerase chain reaction (PCR) and the PCR products were directly sequenced. Results: All children initially presented with neonatal jaundice and had persistent indirect hyperbilirubinemia. Homozygous p.Y486D was identified in all five patients. Three patients had an associated homozygous p.G71R and two a heterozygous p.G71R. The allele frequency of p.Y486D and p.G71R in healthy controls was 0 and 0.16, respectively. No significant difference in mean serum bilirubin levels was found between homozygous carriers of p.G71R and heterozygous carriers. Conclusion: The combination of homozygous p.Y486D and homozygous or heterozygous p.G71R is identified. The p.Y486D and p.G71R can be screened for the mutation analysis of UGT1A1 in Korean CN-2 patients.

• Ocean and Polar Research
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• 제26권4호
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• pp.551-557
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• 2004

Polymorphism of the lipoprotein lipase (LPL) gene which plays an important role in regulation of lipid deposition was analysed in two red seabream (pagrus major) populations (KF4, cultured KORDI line, n=100 : JPN, imported from Japan, n=100). We amplified a DNA fragment (1,091 bp) including the exon 2 region of the LPL gene, and conducted PCR-RFLP analysis using MspI and AluI. The PCR products were also sequenced. Two alleles (A and B) were found in MspI digestion and Sve alleles (A, B, C, D and E) in AluI digestion. The sequenced data revealed four nucleotide substitutions including one transversion at the MspI recognition site (nt 2,235, $C{\rightarrow}10$) and three transitions at the AluI recognition sites (nt 1,721, $A{\rightarrow}G;$ nt 2,319, $C{\rightarrow}T;$ nt 2,319, $T{\rightarrow}C$). Among them, substitutions at the nt 2,235 and 2,319 sites which are located in the exon 2 were proved to be silent point mutations. MspI polymorphism resulted in 3 genotypes, and the allele frequency was significantly different between the two fish populations, KF4 and JPN. In the case of AluI polymorphism, the 5 alleles (A, B, C, D, E) comprised 12 genotypes of the 5 alleles. KF4 population, alleles D and I were specific to the LPL gene Polymorphisms would be useful DNA markers for red seabream population.

• Asian-Australasian Journal of Animal Sciences
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• 제28권9호
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• pp.1354-1361
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• 2015

The complement system is a part of the natural immune regulation mechanism against invading pathogens. Complement activation from three different pathways (classical, lectin, and alternative) leads to the formation of C5-convertase, an enzyme for cleavage of C5 into C5a and C5b, followed by C6, C7, C8, and C9 in membrane attack complex. The C9 is the last complement component of the terminal lytic pathway, which plays an important role in lysis of the target cells depending on its self-polymerization to form transmembrane channels. To address the association of C9 with traits related to disease resistance, the complete porcine C9 cDNA was comparatively sequenced to detect single nucleotide polymorphisms (SNPs) in pigs of the breeds Hampshire (HS), Duroc (DU), Berlin miniature pig (BMP), German Landrace (LR), Pietrain (PIE), and Muong Khuong (Vietnamese potbelly pig). Genotyping was performed in 417 $F_2$ animals of a resource population (DUMI: $DU{\times}BMP$) that were vaccinated with Mycoplasma hyopneumoniae, Aujeszky diseases virus and porcine respiratory and reproductive syndrome virus at 6, 14 and 16 weeks of age, respectively. Two SNPs were detected within the third exon. One of them has an amino acid substitution. The European porcine breeds (LR and PIE) show higher allele frequency of these SNPs than Vietnamese porcine breed (MK). Association of the substitution SNP with hemolytic complement activity indicated statistically significant differences between genotypes in the classical pathway but not in the alternative pathway. The interactions between eight time points of measurement of complement activity before and after vaccinations and genotypes were significantly different. The difference in hemolytic complement activity in the both pathways depends on genotype, kind of vaccine, age and the interaction to the other complement components. These results promote the porcine C9 (pC9) as a candidate gene to improve general animal health in the future.

• The Korean Journal of Pain
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• 제29권1호
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• pp.34-39
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• 2016

Background: Although opioids are the most commonly used medications to control postoperative pain in children, the analgesic effects could have a large inter-individual variability according to genotypes. The aim of this study was to investigate the association between single nucleotide polymorphisms and the analgesic effect of morphine for postoperative pain in children. Methods: A prospective study was conducted in 88 healthy children undergoing tonsillectomy, who received morphine during the operation. The postoperative pain score, frequency of rescue analgesics, and side effects of morphine were assessed in the post-anesthesia care unit. The children were genotyped for OPRM1 A118G, ABCB1 C3435T, and COMT Val158Met. Results: Children with at least one G allele for OPRM1 (AG/GG) had higher postoperative pain scores compared with those with the AA genotype at the time of discharge from the post-anesthesia care unit (P = 0.025). Other recovery profiles were not significantly different between the two groups. There was no significant relationship between genotypes and postoperative pain scores in analysis of ABCB1 and COMT polymorphisms. Conclusions: Genetic polymorphism at OPRM1 A118G, but not at ABCB1 C3435T and COMT Val158Met, influences the analgesic effect of morphine for immediate acute postoperative pain in children.

• 한국임상수의학회지
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• 제25권4호
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• pp.227-230
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• 2008

To determine the distribution of feline blood types and then to estimate the risk of neonatal isoerythrolysis (NI) in non-pedigree cats, we typed blood of 482 cats of both genders and various breeds (336 domestic shorthair cat and 146 pedigree) from August 2005 through July 2007. Blood samples from Seoul and Kangwon province were typed within 5 days after collection by the simple tube method. High-titer anti-A antiserum and anti-B reagent, prepared with Triticum vulgaris lectin, were used to determine type A and type B blood, respectively. The majority of cats were type A (n = 465, 96.5%) and only 3.5% (n = 17) were type B. No type AB blood were detected. Blood type distributions among the non-pedigree and pedigree cats were similar: for non-pedigree cats, 96.4% were type A and 3.6% were type B, whereas for pedigree cats, 96.6% were type A and 3.4% were type B. All type B cats had a very strong agglutination reaction to anti-A antiserum: 8 sample for 3+ and 9 for 4+. Assuming 19% of estimated frequency for the type-B allele in domestic cats, the calculated proportion of random mating from this population at risk for developing NI was 3.4%. Based on this finding, it is strongly recommended that blood typing be performed prior to any blood transfusion or breeding to minimize blood type incompatibilities. Further comprehensive studies on the titer of naturally occurring antibodies in cat populations in Korea and the prevalence of possible NI in practice are clearly required.

• Asian Pacific Journal of Cancer Prevention
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• 제16권18호
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• pp.8247-8252
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• 2016

Background: The ubiquitin-proteasome system (UPS) degrades a variety of proteins which attach to specific signals. The ubiquitination pathway facilitates degradation of damaged proteins and regulates growth and stress responses. This pathway is altered in various cancers, including acute lymphoblastic leukemia, head and neck squamous cell carcinoma and breast cancer. Recently it has been reported that expression of newly characterized human genes, UBE2Q1 and UBE2Q2, putative members of ubiquitin-conjugating enzyme family (E2), has been also changed in colorectal cancer. Epigenetics is one of the fastest-growing areas of science and nowadays has become a central issue in biological studies of diseases. According to the lack of information about the role of epigenetic changes on gene expression profiling of UBE2Q1 and UBE2Q2, and the presence of CpG islands in the promoter of these two human genes, we decided to evaluate the promoter methylation status of these genes as a first step. Materials and Methods: The promoter methylation status of UBE2Q1 and UBE2Q2 was studied by methylation-specific PCR (MSP) in tumor samples of 60 colorectal cancer patients compared to adjacent normal tissues and 20 non-malignant controls. The frequency of the methylation for each gene was analyzed by chi-square method. Results: MSP results revealed that UBE2Q2 gene promoter were more unmethylated, while a higher level of methylated allele was observed for UBE2Q1 in tumor tissues compared to the adjacent normal tissues and the non malignant controls. Conclusions: UBE2Q1 and UBE2Q2 genes show different methylation profiles in CRC cases.