• Journal of Genetic Medicine
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• 제5권1호
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• pp.41-46
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• 2008

목 적 : 취약 X 증후군(fragile X syndrome)은 FMR1 유전자의 5' 비해독부위에 있는 CGG 3염기 반복의 확장에 의해 발생되는 유전성 질환이다. 방 법 : 본 연구에서는 임상 소견과 핵형분석에서 취약 X 증후군으로 진단 받은 여아 환자와 그 부모를 대상으로 Abbott Molecular Fragile X PCR Kit를 이용하여 CGG 3염기 영역을 PCR로 증폭하여 normal, premutation, full mutation의 CGG 반복의 유형을 확인하였으며, premutation과 normal allele의 경우에는 정확한 CGG 반복수를 분석하였다. 결 과 : 환자는 30회와 >200회의 CGG 3염기가 반복된 FMR1 대립유전자를 갖고 있는 것으로 확인되어 취약 X 증후군으로 진단되었다. 또한 환자의 어머니에서 30과 98회의 반복 allele을 확인함으로써, 이 환자의 full mutation allele은 모계의 premutation allele로부터 유래한 것임을 알 수 있었다. 결 론 : Abbott Molecular Fragile X PCR Kit를 사용한 진단방법은, 취약 X 증후군환자의 경우에서 통상적으로 시행되고 있는 PCR, MS-PCR, Southern blotting을 병행하는 방법에 비해 신속하고 정확한 분자유전학적 진단이 가능한 유용한 방법이라 생각된다.

• Asian Pacific Journal of Cancer Prevention
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• 제16권8호
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• pp.3101-3109
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• 2015

Background: Methylenetetrahydrofolate reductase (MTHFR) is involved in amino acid synthesis and DNA function. Two common polymorphisms are reported, C677T and A1298C, that are implicated in a number of human diseases, including cancer. Objective: The association between MTHFR C677T and A1298C genotype and haplotype frequencies in risk for lung cancer (LC) was investigated in the Jordanian population. Materials and Methods: A total of 98 LC cases were studied for MTHFR C677T and A1298C polymorphisms, compared to 89 controls taken from the general population, employing the PCR-RFLP technique. Results: The frequency of the genotypes of MTHFR C677T among Jordanians was: CC, 59.6%, CT, 33%; and TT, 7.4% among LC cases and 49.4%, 40.2% and 10.3% among controls. No significant association was detected between genetic polymorphism at this site and LC. At MTHFR A12987C, the genotype distribution was AA, 29.5%; AC, 45.3%, and CC 25.3% among LC cases and 36.8%, 50.6% and 12.6% among controls. Carriers of the CC genotype were more likely to have LC (OR=2.5; 95%CI: 1.04-6; p=0.039) as compared to AA carriers. Smokers and males with the CC genotype were 9.9 and 6.7 times more likely to have LC, respectively ($OR_{smokers}=9.9$; 95%CI: 1.2-84.5, p=0.018; $OR_{men}=6.6$; 95%CI: 1.7-26.2, p=0.005). Haplotype analysis of MTHFR polymorphism at the two loci showed differential distribution of the CC haplotype (677C-1298C) between cases and controls. The CC haplotype was associated with an increased risk for lung cancer (OR=1.6; 95% CI: 1.03-2.4, p=0.037). Conclusions: The genetic polymorphism of MTHFR at 1298 and the CC haplotype (risk is apparently lower with the C allele at position 677) may modulate the risk for LC development among the Jordanian population. Risk associated with the 1298C allele is increased in smokers and in males. The results indicate that a critical gene involved in folate metabolism plays a modifying role in lung cancer risk, at least in the Jordanian population.

• Asian Pacific Journal of Cancer Prevention
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• 제16권3호
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• pp.1123-1127
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• 2015

Uterine leiomyomas (ULM), are benign tumors of the smooth muscle cells of the myometrium. They represent a common health problem and are estimated to be present in 30-70% of clinically reproductive women. Abnormal angiogenesis and vascular-related growth factors have been suggested to be associated with ULM growth. The angiotensin-I converting enzyme (ACE) is related with several tumors. The aim of this study was to identify possible correlation between ULM and the ACE I/D polymorphism, to evaluate whether the ACE I/D polymorphism could be a marker for early diagnosis and prognosis. ACE I/D was amplified with specific primer sets recognizing genomic DNA from ULM (n=72) and control (n=83) volunteers and amplicons were separated on agarose gels. The observed genotype frequencies were in agreement with Hardy-Weinberg equilibrium ($x^2=2.162$, p=0.339). There was no association between allele frequencies and study groups ($x^2=0.623$; p=0.430 for ACE I allele, $x^2=0.995$; p=0.339 for ACE D allele). In addition, there were no significant differences between ACE I/D polymorphism genotype frequencies and ULM range in size and number ($X^2=1.760;$ p=0.415 for fibroid size, $X^2=0.342;$ p=0.843 for fibroid number). We conclude that the ACE gene I/D polymorphism is not related with the size or number of ULM fibroids in Turkish women. Thus it cannot be regarded as an early diagnostic parameter nor as a risk estimate for ULM predisposition.

• Asian Pacific Journal of Cancer Prevention
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• 제15권8호
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• pp.3667-3673
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• 2014

Background: colorectal cancer (CRC) is the third most common type of cancers and the fourth leading cause of death worldwide. In Saudi Arabia, CRC accounts for 8.5% of all tumors; it ranks first among all cancers in males and third among females. The aim of this study was to link between different PARP-1 mutations and risk of CRC in Saudi population and to determine common variants of PARP-1 in Saudi CRC patients and normal individuals. Materials and Methods: DNA samples were isolated from fifty CRC patients and from a comparable number of control subjects then sequenced to detect different variations present in exons 3, 17, and 21 of the PARP-1 gene. Results and Conclusions: When comparing the genotype and allele frequencies of all detected SNPs in CRC patients with those in controls, we found none were significantly different for all variants even the most common SNP in PARP-1 gene (Val762Ala). However, two novel alterations in exon 21 were found to be associated with increased risk of CRC. The variants identified as (1) Lys933Asn [p-value 0.0318] and (2) Lys945Asn [p-value 0.0257]. Our results suggest that PARP-1 Lys933Asn and Lys945Asn alterations could be associated with increased risk of CRC in the Saudi population.

• IMMUNE NETWORK
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• 제2권4호
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• pp.242-247
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• 2002

Background: Tumor necrosis factor-alpha (TNF-$\alpha$) is known to play an important role in various conditions such as inflammation, autoimmunity, apoptosis, insulin resistance and sleep induction. Five single nucleotide polymorphisms (SNPs) have been known to affect the transcriptional activities of TNF-$\alpha$: -1,031T/C, -863C/A, -857C/T, -308G/A and -238G/A. Methods: We have investigated 5 SNPs of the promoter region of TNF-$\alpha$ gene, the distribution of 5-locus TNF-$\alpha$ haplotypes, and their haplotypic associations with previously typed HLA-A, -B and -DRB1 loci in 107 healthy unrelated Koreans. TNF-$\alpha$ SNPs were typed using PCR-single-strand conformation polymorphism (SSCP) and PCR-restriction fragment length polymorphism (RFLP) methods. Results: The allele frequencies of -1,031C, -863A, -857T, -308A, and-238A, which are known as the high-producer-type, were 19.3%, 15.9%, 14.0%, 5.9%, and 2.9%, respectively. The frequency of -308A allele, known to be associated with autoimmune diseases, was 5.9% in Koreans which was lower than Caucasians (14~17%) and somewhat higher than Japanese (1.7%). Five most common TNF-$\alpha$ haplotypes (-1,031/-863/-857/-308/-238) comprised over 95% of total haplotypes: TCCGG (58.4%), CACGG (14.8%), TCTGG (13.7%), TCCAG (5.3%), and CCCGA (3.1%). Strong positive associations (P<0.001) were observed between TCCGG and B62; between CACGG and B51, $DRB1^*0901$; between TCTGG and B35, B54, B59, $DRB1^*1201$; and between TCCAG and A33, B58, $DRB1^*0301$, $DRB1^*1302$. Five most common extended haplotypes (>3%) comprised around 16% of total haplotypes: A33-B58-TCCAG-$DRB1^*1302$, A24-B52-TCCGG-$DRB1^*1502$, A33-B44-TCCGG-$DRB1^*1302$, A24-B7-TCCGG-$DRB1^*0101$, and A11-B62-TCCGG-$DRB1^*0406$. The distribution of extended HLA and TNF-$\alpha$ haplotypes showed that most of HLA haplotypes were almost exclusively associated with particular TNF-$\alpha$ haplotypes. Conclusion: The results obtained in this study would be useful as basic data for anthropologic studies and disease association studies in Koreans.

• Genomics & Informatics
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• 제6권1호
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• pp.18-28
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• 2008

Single nucleotide polymorphisms (SNPs) are the most abundant forms of human genetic variations and resources for mapping complex genetic traits and disease association studies. We have constructed a linkage disequilibrium (LD) map of chromosome 22 in Korean samples and compared it with those of other populations, including Yorubans in Ibadan, Nigeria (YRI), Centre d'Etude du Polymorphisme Humain (CEPH) reference families (CEU), Japanese in Tokyo (JPT) and Han Chinese in Beijing (CHB) in the HapMap database. We genotyped 4681 of 111,448 publicly available SNPs in 90 unrelated Koreans. Among genotyped SNPs, 4167 were polymorphic. Three hundred and five LD blocks were constructed to make up 18.6% (6.4 of 34.5 Mb) of chromosome 22 with 757 tagSNPs and 815 haplotypes (frequency $\geq$ 5.0%). Of 3430 common SNPs genotyped in all five populations, 514 were monomorphic in Koreans. The CHB + JPT samples have more than a 72% overlap with the monomorphic SNPs in Koreans, while the CEU + YRI samples have less than a 38% overlap. The patterns of hot spots and LD blocks were dispersed throughout chromosome 22, with some common blocks among populations, highly concordant between the three Asian samples. Analysis of the distribution of chimpanzee-derived allele frequency (DAF), a measure of genetic differentiation, Fst levels, and allele frequency difference (AFD) among Koreans and the HapMap samples showed a strong correlation between the Asians, while the CEU and YRI samples showed a very weak correlation with Korean samples. Relative distance as a quantitative measurement based upon DAF, Fst, and AFD indicated that all three Asian samples are very proximate, while CEU and YRI are significantly remote from the Asian samples. Comparative genome-wide LD studies provide useful information on the association studies of complex diseases.

• 대한치과교정학회지
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• 제34권3호
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• pp.261-267
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• 2004

비증후군성 구순구개열은 가장 빈도가 높은 선천성 기형 중의 하나로 특히 한국이나 일본과 같은 극동 지방에서 높은 발생율을 보이고 동유럽에서는 드물게 보고되고 있다. 이러한 인종에 따른 차이는 이 질환에 유전적인 배경이 있음을 의미한다. 본 연구의 목적은 한국인의 비증후군성 구개열과 연관이 있다고 알려진 SfaN1 단일 염기 다형성증의 발현빈도가 한극인 구개열 가족과 루마니아 구순구개열 가족 사이에 통계적으로 유의할만한 차이가 있는지를 알아보기 위하여 시행하였다. 한국인 26가족과 루마니아 18가족을 대상으로 하였다. 전체 인원수는 한국인의 경우 78명이었고 루마니아의 경우 41명이었다. 유전자 서열분석에 사용된 샘플은 각 참여자의 혈액이나 타액을 채취하여 분석하였다. SfaN1 단일 염기 다형성 증은 $TGF-{\beta}3$ 유전자의 5번 인트론에서 관찰된다 (A18141G) 결과를 보면 한국인과 루마니아인의 비증후군성 구개열 가족사이에는 통계적으로 유의할만한 차이 가 인지되었다. 전체 샘플 중에서 AA allele는 한국인에서는 18명(23.1%)이었으나 루마니아는 27명(65.9%)이었다. AS allele는 한국인에서는 27명 (34.6%)이었으나 루마니아에서는 13명 (31.7%)이었다. GG allele는 한국인에서는 33명 (42.3%)이었으나 루마니아에서는 1명 (2.4%)이었다. 두 집단 사이의 차이는 통계적으로 유의하였다 (p<0.001). 결론적으로 한국인과 루마니아인의 비증후군성 구개열 가족 사이에 SfaN1 단일 염기 다형성증의 발현빈도는 한국인에서 통계적으로 유의할만하게 높게 나타났으며, 이는 한국에서 루마니아보다 비증후군성 구개열의 빈도가 높게 나타나는 현상을 부분적으로 설명하여 주는 것으로 사료된다.

• 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.

• Asian Pacific Journal of Cancer Prevention
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• 제15권23호
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• pp.10393-10396
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• 2015

Background: Endometral carcinoma is the most common malignant tumor of the female genital tract and the fourth most common cancer in women after breast, colorectal and lung cancers Hypoxia-inducible factor-1 (HIF-1) is a key transcription factor that regulates cellular response to hypoxia HIF-1 plays important roles in the development and progression of cancer through activation of various genes that are involved in crucial aspects of cancer biology, including angiogenesis, energy metabolism, vasomotor function, erythropoiesis, and cell survival. In this study, we aimed to investigate the association between HIF-1 1772 C/T polymorphisms and endometrial cancer. Materials and Methods: 75 patients with endometrial carcinoma and 75 patients whose underwent hysterectomy for non tumoral indication selected for evaluation of HIF-1 1772 C/T polymorphisms by PCR-RFLP and sequencing. Results: For the 1772 C/T polymorphism, the analysis showed that the T allele and genotype TT were significantly associated with endometrial cancer risk. Conclusions: Our results suggest that the C1772T polymorphism of the HIF-1a may be associated with endometrial cancers.

• Asian Pacific Journal of Cancer Prevention
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• 제14권12호
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• pp.7149-7154
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• 2013

Objective: Increasing scientific evidence suggests that common variants in the PALB2 gene may confer susceptibility to breast cancer, but many studies have yielded inconclusive results. This meta-analysis aimed to derive a more precise estimation of the relationship between PALB2 genetic variants and breast cancer risk. Methods: An extensive literary search for relevant studies was conducted in PubMed, Embase, Web of Science, Cochrane Library, CISCOM, CINAHL, Google Scholar, CNKI and CBM databases from their inception through September 1st, 2013. A meta-analysis was performed using the STATA 12.0 software and crude odds ratios (ORs) with 95% confidence intervals (CIs) were calculated. Results: Six case-control studies were included with a total of 4,499 breast cancer cases and 6,369 healthy controls. Our meta-analysis reveals that PALB2 genetic variants may increase the risk of breast cancer (allele model: OR>1.36, 95%CI: 1.20~1.52, P < 0.001; dominant model: OR>1.64, 95%CI: 1.42~1.91, P < 0.001; respectively). Subgroup analyses by ethnicity indicated PALB2 genetic variants were associated with an increased risk of breast cancer among both Caucasian and Asian populations (all P < 0.05). No publication bias was detected in this meta-analysis (all P > 0.05). Conclusion: The current meta-analysis indicates that PALB2 genetic variants may increase the risk of breast cancer. Thus, detection of PALB2 genetic variants may be a promising biomarker approach.