• Genomics & Informatics
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• 제20권2호
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• pp.18.1-18.7
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• 2022

According to long-term projections, by 2030, the world's population is predicted to reach 7.5 billion individuals, and there will be roughly 27 million new cancer cases diagnosed. The global burden of breast cancer (BC) is expected to rise. According to the Ministry of Health-Iraqi Cancer Registry, cancer is the second largest cause of death after cardiovascular disease. This study investigated the interleukin-18 (IL18) single-nucleotide polymorphisms (SNPs) -607C/A rs1946518 and -137G/C rs187238 using the sequence-specific amplification-polymerase chain reaction approach. Regarding the position -607C/A, there was a highly significant difference between the observed and expected frequencies in patients and controls (χ² = 3.16 and χ² = 16.5), respectively. The AA and CA genotypes were associated with significantly increased BC risk (odds ratio [OR], 3.68; p = 0.004 and OR, 2.83; p = 0.04, respectively). Women with the A allele had a 5.03-fold increased susceptibility to BC. The C allele may be a protective allele against BC (OR, 0.19). Although position -137G/C showed no significant differences in the CC genotype distribution (p = 0.18), the frequency of the CC genotype was significantly higher in patients than in controls. In contrast, patients had a significantly higher frequency of GC genotypes than controls (p = 0.04), which was associated with an increased risk of developing BC (OR, 2.63). The G allele frequency was significantly lower in patients than in controls (55.0% vs. 76.2%, respectively). This SNP may be considered a common genotype in the Iraqi population, with the wild-type G allele having a protective function (OR, 0.19) and the mutant C allele having an environmental effect (OR, 2.63).

• Journal of Interdisciplinary Genomics
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• 제6권1호
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• pp.6-13
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• 2024

Background: ABO typing is crucial for ensuring safe blood transfusion and is commonly performed by examining antigen-antibody interactions. Determining ABO blood group can be difficult when dealing with ABO discrepancy and ABO subgroups. ABO genotyping may be necessary to resolve ABO discrepancy. ABO genotyping primarily involves direct sequencing, with the possibility of using other molecular methods. Methods: PCR and direct sequencing of exons 6 and 7 were performed for total 108 samples from June 2010 to December 2019. Also, other molecular methods including cloning sequencing and short tandem repeat analysis were carried out just in case. Sequencing data were compared with allele information of blood group antigen mutation databases. Results: The predominant causal allele among 108 ABO discrepant cases was cis-AB01, with 28 cases. This was followed by rare ABO alleles (B309, B306, A204, Bw29, and Ax01) with 14 cases, and blood chimera with 5 cases. Five new alleles were identified during the investigation. Conclusion: This study reaffirms that cis-AB is the most common cause of inherited ABO discrepancies, and cis-AB01 is the most prevalent cis-AB allele in the Korean population, also in the southeastern region. In addition, we discovered five new alleles and five blood chimeras by adopting sequencing analysis and additional molecular techniques to resolve ABO discrepancies, which provide regional data on rare alleles. This study presents rare and new ABO alleles and blood chimeras identified over a ten-year period at two major university hospitals in Southeastern Korea.

• Genomics & Informatics
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• 제5권4호
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• pp.152-160
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• 2007

Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.

• Journal of Genetic Medicine
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• 제10권1호
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• pp.1-6
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• 2013

Chronic granulomatous disease (CGD) is a rare inherited disorder of a defective NADPH oxidase enzyme, resulting in very low or no production of superoxide and subsequent reactive oxygen species. Consequently, patients with CGD are highly susceptible to severe bacterial and fungal infections. CGD is a genetically heterogeneous disease caused by defects in any one of the genes encoding the NADPH oxidase components. CGD generally affects about 3-4 per 1,000,000 individuals; thus, it is surprising that the prevalence of CGD on Jeju Island is 34.3 per 1,000,000 individuals. At present, 20 patients with CGD from 14 unrelated families on Jeju Island have been identified; nine males and 11 females. All patients with CGD tested on Jeju Island had an identical and homozygous mutation (c.7C>T in CYBA, p.Q3X in $p22^{phox}$). Therefore, all patients were autosomal recessive form of CGD. This strongly suggests that the unique and identical mutation in CYBA may be inherited from a common proband. Using mutation-specific primers to detect the mutated allele in CYBA, the frequency of subjects carrying a mutated allele was 1.3% of enrolled subjects from Seogwipo City. Further studies are necessary to elucidate how frequently this mutant allele occurs in the population on Jeju Island. Additionally, it is important to construct a national registry system to understand the pathophysiology of CGD and develop a strategy for long-term therapy.

• 운동영양학회지
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• 제24권1호
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• pp.24-28
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• 2020

[Purpose] Recent studies have demonstrated a probable association between ACE I/D polymorphism and obesity. Thus, this study aimed to investigate whether ACE I/D polymorphism influenced the susceptibly of developing obesity in Korean adults. [Methods] A total of 353 healthy Korean adults aged between 30 and 82 years were recruited, including 157 males and 196 females. Among the participants, 103 (29.2 %) were classified as normal (BMI < 23 kg/m²), 117 (33.1 %) as overweight (23 kg/m² ≤ BMI < 25 kg/m²), and 133 (37.7 %) as obese (BMI ≥ 25 kg/m²). ACE polymorphism (rs1799752) analysis was performed using the MGB TaqMan® SNP Genotyping assay with 3 types of primers and 2 types of probes. The distributions of the ACE genotypes and allele frequencies were analyzed among the three groups using the Hardy-Weinberg equilibrium, chi-square tests, and multiple regression analysis. [Results] The distribution of the ACE genotypes were as follows: normal [II: n=38 (36.9 %), ID: n=46 (36.8 %), DD: n=19 (18.4 %)], overweight [II: n=43 (36.8 %), ID: n=55 (47.0 %), DD: n=19 (16.2 %)], and obese [II: n=41 (30.8 %), ID: n=76 (57.0 %), DD: n=16 (12.0 %)]. Unexpectedly, the I allele, rather than the D allele, was common in the obese group. [Conclusion] ACE I/D polymorphism is not associated with BMI in Korean adults. Thus, it is unlikely to be a powerful candidate gene for obesity in Korean adults.

• 미생물학회지
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• 제29권6호
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• pp.392-396
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• 1991

Pseudomonas sp. DJ77의 chromosomal DNA로부터 6.9kb XhoI 절편 상에 존재하는 phenanthrene 분해에 관련된 유전자군을 vector pBLUESCRIPT SK(+)에 클로닝하였다. 이렇게 얻은 재조합 plasmid인 pHENX7을 가지고 있는 JM101 균주는 3-methylcarechol을 노란색의 meta-cleavage 화합물로 전환할 수 있었다. 그러나 삽입된 절편의 방향이 반대가 되도록 제조한 pHENX7은 extradiol dioxygenase 활성을 나타내지 않기 때문에 전사방향을 알 수 있었다. pHENX7과 이의 듀도체들을 지니는 JH101균주에서 PhnC(24kDa), PhnD(31KDa), PhnE(34kDa), PhnF(KDa)의 4 polypeptide를 확인 할 수 있었고 개개의 유전자의 위치와 범위를 알 수 있었다. 유전자 순서는 phnC-phnD-phnE-phnF-phnG이었으며, phnC, phnD, phnE, phnF, phnG는 각기 glutathione S-transferase, meta-cleavage compound hydrolase extradiol dioxygenase, meta-cleavage compound dehydrogenase의 유전자이었다.

• Clinical and Experimental Pediatrics
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• 제58권1호
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• pp.20-27
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• 2015

Purpose: We investigated the molecular types of uropathogenic Escherichia coli (UPEC) by using conventional phylogrouping, multilocus sequence typing (MLST), and fimH genotyping. Methods: Samples of patients younger than 18 years of age were collected from the Chung-Ang University Hospital over 2 years. Conventional phylogenetic grouping for UPEC strains was performed by polymerase chain reaction (PCR). Bacterial strain sequence types (STs) were classified on the basis of the results of partial sequencing of seven housekeeping genes. In addition, we analyzed nucleotide variations in a 424-base pair fragment of fimH, a major virulence factor in UPEC. Results: Sixty-four UPEC isolates were analyzed in this study. Phylogenetic grouping revealed that group B2 was the most common type (n=54, 84%). We identified 16 distinctive STs using MLST. The most common STs were ST95 (35.9%), ST73 (15.6%), ST131 (12.5%), ST69 (7.8%), and ST14 (6.3%). Fourteen fimH allele types were identified, of which 11 had been previously reported, and the remaining three were identified in this study. f1 (n=28, 45.2%) was found to be the most common allele type, followed by f6 and f9 (n=7, 11.3% each). Comparative analysis of the results from the three different molecular typing techniques revealed that both MLST and fimH typing generated more discriminatory UPEC types than did PCR-based phylogrouping. Conclusion: We characterized UPEC molecular types isolated from Korean children by MLST and fimH genotyping. fimH genotyping might serve as a useful molecular test for large epidemiologic studies of UPEC isolates.

• Childhood Kidney Diseases
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• 제4권1호
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• pp.33-39
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• 2000

목 적 : IgA 신병증은 혈뇨와 단백뇨를 보이는 사구체 질환으로 세계적으로 가장 빈도가 높은 질환중의 하나 이며 우리 나라를 포함한 아시아 지역에서도 높은 발생율을 보이고 있으나 아직 정확한 발생기전이나 원인은 불분명한 상태이다. IgA 신병증은 발병 10년 후 $20-30\%$가 말기 신부전증으로 진행됨이 보고되고 있으나 신부전으로 진행속도는 환자에 따라 매우 다양하기 때문에 특이적인 조직적합항원을 찾아냄으로서 치료 및 예후 결정에 도움을 주기 위하여 본 연구를 시행하였다. 대상 및 방법 : 세브란스 병원에 입원하여 IgA 신병증으로 진단 받은 환자를 대상으로 정상 신기능을 유지하고 있었던 소아환아 69명(Group A)과 이미 신부전으로 진행하여 신이식을 시행 받은 70명(Group B)을 포함한 신기능 저하군으로 분류하여 HLA대립유전자의 결정은 SSOP (sequence specific oligonucleotide probe)법으로 분석하여 HLA-class II(DR, DQ)대립유전자의 발현빈도와 IgA 신병증의 예후와의 관계를 분석하였다. 결 과 : 대상 환자의 진단 당시의 평균나이는 A군은 $8.8{\pm}2.9$세, B군은 $35.0{\pm}15.5$세였고, 남녀비는 각각 2.8:1과 2.5:1이었다. HLA-DQB1 유전자중 139명중 $47.5\%$로 $03^{**}$의 발현빈도가 가장 증가되어 있었고 $06^{**}(32.4\%),\;04^{**}(28.7\%),\;05^{**}(20.1\%),\;02^{**}(8.6\%)$순이 었다. DQ7의 HLA-DQB1*0301 이 전체 환자의 20.1$\%$(28/139)로 가장 흔한 대립유전자였으나 두군간에 유의한 차이는 없었다. 대립유전자중 HㄴA-$DQBI^*03^{**}과\;DQB1^*05^{**}$가 이미 말기신부전으로 진행된 Group B에서 유의하게 증가되어 있었으며(P<0.05), $03^{**}$ 아형중 $DQB1^{*}0302와\;05^{**}중\;DQB1^{*}05031$이 신기능이 정상인 A군에 비해 유의하게 증가되어 있었다(P<0.05). DR 유전자형의 low-frequency type상 HLA-$DRB1^*03과\;HLA-DRB1^*15$가 Group B에서 유의 있게 증가되어 있었으나, high-frequency type상에서는 양군 사이에 유의한 차이가 없었다. A군의 경우 신조직 검사의 소견에 따라 4등급으로 분류하여 대립유전자의 발현빈도를 분석하였으나 의미 있는 관계가 없었다. 곁 론 : IgA신병증의 예후를 예측하기 위한 여러 조사에서 발병 초기의 심한 단백뇨, 고혈압, 조직 병리학상의 심한 변화 등이 있을 경우 예후가 나쁘다고 하였으며 이런 위험 인자외에 유전적 요인에 대해 알아보고자 하였다. 본 연구에서 신부전으로 진행하여 신대체요법을 받은 IgA신병증환자군에서 HLA-$DQB1^*0302와\;^*05031$ 대립유전자의 발현빈도가 유의하게 증가되어 있어 이 결과를 바탕으로 치료후의 경과 및 예후를 진단초기에 예측하여 환자의 관리에 적용할수 있는 중요한 자료로 이용될 수 있을 것으로 사료된다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권8호
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• pp.3339-3344
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• 2015

Background: This case-control study aimed to determine if there were any associations between the two single nucleotide polymorphisms (SNPs) in Gc, rs7041 (Asp416Glu) and rs4588 (Thr420Lys) and 3 common cancers (breast, lung and colorectal) in Thai patients. Materials and Methods: Two hundred and eighty two colorectal, 101 breast and 113 lung cancer patients were recruited from one institute during 2011-2013. The controls were age-matched volunteers who had a negative history of index cancers. In addition, vitamin D levels were compared among different genotypes in the 2 SNPs. Results: The minor allele frequencies of rs7041 (G) and rs4588 (A) were 0.32 and 0.24, respectively. Under the dominant model, the study found significant associations between minor-allele genotypes of the SNP rs7041 (TG/GG) and lung cancer (odds ratio [OR] 1.78, 95% CI 1.05-3.03). When subgroup analysis was performed according to sex and age at diagnosis, the study found that the minor-allele genotypes of rs7041 (TG/GG) were significantly associated with colorectal cancer in patients whose age at diagnosis was more than 60 years (OR 1.67, 95%CI 1.06-2.61) and the minor-allele genotypes of rs4588 (CA/AA) were significantly associated with colorectal cancer in males aged 60 years or less (OR 2.34, 95%CI 1.25-4.37). When SNP combinations (rs7041-rs4588) were examined, the TT-CA combination had a significant protective association with lung cancer (OR 0.44, 95% CI 0.22-0.85). On evaluation of serum 25(OH)D levels in 205 individuals without cancer (males 144, females 61), the proportion of subjects with low serum vitamin D (< 20 ng/ml) in those harboring CA or AA genotypes of rs4588 (41.7%) was significantly higher than the CC genotype (15.5%, p-value < 0.01). Conclusions: Genetic polymorphisms in Gc were associated with lung and colorectal cancers in Thai patients. Lower serum 25(OH)D in minor variants of rs4588 may explain this association.

• Nutrition Research and Practice
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• 제9권1호
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• pp.79-86
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• 2015

BACKGROUND/OBJECTIVES: It is well-known that alcohol consumption is associated with stroke risk as well as with aldehyde dehydrogenase 2 gene (ALDH2) polymorphisms. However, it is unclear whether ALDH2 polymorphisms are associated with stroke risk independent of alcohol consumption and whether such association is modified by sex. We evaluated sex-specific associations of a common ALDH2 polymorphism and alcohol consumption with stroke risk in a Korean population. SUBJECTS/METHODS: We conducted a prospective cohort study involving 8,465 men and women, aged 40-69 years and free of stroke between June, 2001 and January, 2003, and followed for the development of stroke. We identified new cases of stroke, which were self-reported or ascertained from vital registration data. Based on genome-wide association data, we selected a single-nucleotide polymorphism (rs2074356), which shows high linkage disequilibrium with the functional polymorphism of ALDH2. We conducted Cox proportional hazards regression analysis considering potential risk factors collected from a baseline questionnaire. RESULTS: Over the median follow-up of 8 years, 121 cases of stroke were identified. Carrying the wild-type allele of the ALDH2 polymorphism increased stroke risk among men. The multivariate hazard ratio [95% confidence interval] of stroke was 2.02 [1.03-3.99] for the wild-type allele compared with the mutant alleles, but the association was attenuated after controlling for alcohol consumption. Combinations of the wild-type allele and other risk factors of stroke, such as old age, diabetes mellitus, and habitual snoring, synergistically increased the risk among men. Among women, however, the ALDH2 polymorphism was not associated with stroke risk. CONCLUSIONS: The prospective cohort study showed a significant association between a common ALDH2 polymorphism and stroke risk in Korean men, but not in Korean women, and also demonstrated that men with genetic disadvantages gain more risk when having risk factors of stroke. Thus, these men may need to make more concerted efforts to control modifiable risk factors of stroke.