• Genomics & Informatics
• /
• 제5권2호
• /
• pp.61-67
• /
• 2007

The allele frequencies of markers as well as linkage disequilibrium (LD) can be changed in cases due to the LD between markers and the disease allele, exhibiting spurious associations of markers. To identify the true association, classical statistical tests for dealing with confounders have been applied to draw a conclusion as to whether the association of variants comes from LD with the known disease allele. However, a more direct test considering LD using estimated haplotype frequencies may be more efficient. The null hypothesis is that the different allele frequencies of a variant between cases and controls come solely from the increased disease allele frequency and the LD relationship with the disease allele. The haplotype frequencies of controls are estimated using the expectation maximization (EM) algorithm from the genotype data. The estimated frequencies are applied to calculate the expected haplotype frequencies in cases corresponding to the increase or decrease of the causative or protective alleles. The suggested method was applied to previously published data, and several APOE variants showed association with Alzheimer's disease independent from the APOE ${\varepsilon}4$ variant, rs429358, regardless of LD showing significant simulated p-values. The test results support the possibility that there may be more than one common disease variant in a locus.

• 한국동물위생학회지
• /
• 제31권4호
• /
• pp.485-492
• /
• 2008

Salmonella enterica serovars Gallinarum(SG, causative agent of fowl typhoid) and S Pullorum(SP, causative agent of pullorum disease) are very important bacterial pathogens in poultry industry. They share some common antigenic properties though the characteristics of outbreaks are quite different. To discriminate between SG and SP, we developed two rapid diagnostic methods, allele-specific real-time PCR and 3'-tailed PCR over 2 single nucleotide polymorphisms ($237^{th}\;and\;598^{th}$). In both methods, $237^{th}$ allele was found to be a good target for differential diagnosis, while $598^{th}$ allele produced some non-specific reactions.

• Genomics & Informatics
• /
• 제20권4호
• /
• pp.42.1-42.11
• /
• 2022

Breast cancer (BC) is a significant threat to female health, with both modifiable and non-modifiable risk factors. It is essential to monitor patients regularly and to raise population awareness. Increasing research also suggests that E-selectin (SELE) may increase tumor angiogenesis and the development of cancer. This study investigated SELE single-nucleotide polymorphisms (SNPs) in the following positions: rs5367T/C, rs5368C/T, rs5362T/G, and rs5362T/C. Using polymerase chain reaction, significant differences in allele and genotype frequencies were found between BC patients and controls. Position rs5368 was associated with an increased risk of BC for the CT and TT genotypes, with odds ratios (ORs) of 16.3 and 6.90 (Fisher probability = 0.0001, p = 0.005). Women with the T allele had a 19.3-fold higher incidence of BC, while allele C may be a protective allele against BC (OR, 0.05). Heterozygous genotypes at rs5367, rs5362, and rs5362 were significantly more common in BC patients, with ORs of 5.70, 4.50, and 3.80, respectively. These SNPs may be associated with the risk of BC, because the frequency of mutant alleles was significantly higher in patients (OR: 4.26, 3.83, and 4.30, respectively) than in controls (OR: 0.23, 0.30, and 0.20, respectively). These SNPs may be considered a common genotype in the Iraqi population, with the wild-type allele having a protective fraction and the mutant allele having an environmental fraction. The results also revealed a 2-fold increase in gene expression in BC patients compared to controls, with a significant effect (p = 0.017). This study's findings confirm the importance of SELE polymorphisms in cancer risk prediction.

• Asian Pacific Journal of Cancer Prevention
• /
• 제15권10호
• /
• pp.4207-4210
• /
• 2014

Several lines of evidence suggest that genetic variation in MUC5AC gene might contribute to the risk of gastric cancer. We conducted a case-control study to evaluate the relationship between common genetic variations in MUC5AC gene and non-cardia gastric cancer using an LD-based tagSNP approach in Baotou, north-western China. We genotyped 12 tagSNPs by TaqMan method among 288 cases with non-cardia gastric cancer and 281 normal controls. Unconditional logistic regression was used to calculate odds ratios (ORs) and 95% confidence intervals (CIs) for non-cardia gastric cancer risk in association with alleles, genotypes and haplotypes. We observed that the frequencies of rs3793964 C allele and rs11040869 A allele were significantly lower in cases than in controls. Meanwhile, minor allele homozygotes of rs3793964 and rs11040869 were significantly associated with a decreased risk of non-cardia gastric cancer when compared with their major allele homozygotes. Furthermore, a statistically significantly protective effect of rs885454 genotypes on non-cardia gastric cancer was also observed (for CT vs. CC: OR=0.581, 95%CI=0.408-0.829; for CT/TT vs. CC: OR=0.623, 95%CI=0.451-0.884). Our results indicated that some common genetic variations in the MUC5AC gene might have effects on the risk of non-cardia gastric cancer in our studied population.

• Animal cells and systems
• /
• 제2권2호
• /
• pp.281-285
• /
• 1998

We examined Y chromosomal DNA polymorphisms at the DYS19 and DXYS5Y loci in a total of 480 unrelated male samples from the Korean population. All five common alleles were identified at the tetranucleotide microsatellite locus DYS19 in this study. The C allele was the most frequent (212/480), followed by D (136/480), B (75/480), E (36/480) and A (21/480) allele. The frequency of Y2 allele at the DXYS5Y locus was found to be 4.6% (22/480). Combining the allelic variation at these two loci resulted in a total of 9 combination haplotypes. The mean combination haplotype diversity wIns 0.72. Based on the results of these two loci, Korean and Japanese populations may share some common genetic structure that is rare or absent in the other ethnic groups. The genetic similarity between Korean and Japanese populations may be due to the large infusion of Y chromosomes through the Yayoi migration starting 2,300 years ago from Korea to Japan.

• 한국생명과학회:학술대회논문집
• /
• 한국생명과학회 2007년도 제48회 학술심포지움 및 추계국제학술대회
• /
• pp.116.1-116.1
• /
• 2007

See Full Text

• Asian Pacific Journal of Cancer Prevention
• /
• 제14권2호
• /
• pp.1049-1052
• /
• 2013

Background: Studies have shown that alterations of steroid hormone metabolism, particularly involving testosterone, affect the risk of prostate cancer. Therefore, genetic variation in genes of enzymes which are involved could be of importance. The gene most interest is CYP17, whose enzyme product has an essential role in testosterone hormone synthesis. Some studies have indicated that the A2 allele polymorphism of CYP17 associated with increased risk of prostate cancer that could be affected by ethnicity. Therefore, the aim of this study was determination of presence or absence of the A2 allele in patients with prostate cancer. Materials and Methods: We studied the association of A2 allele and prostate cancer among 74 patients with prostate cancer and 128 healthy men which were referred to hospitals of SBMU. Results: This study revealed a significant association between prostate cancer risk and the A2 allele in an Iranian population so that A1A2 and A2A2 genotypes were more common in cases than controls with P-values of 0.029 and 0.010, respectively. Conclusions: Results of our study support a possible role of the A2 allele in sporadic prostate cancer development in Iran, in line with findings elsewhere.

• Journal of Genetic Medicine
• /
• 제3권1호
• /
• pp.29-32
• /
• 1999

The Apolipoprotein E type 4 allele (ApoE ${\varepsilon}4$) is genetically associated with the common late onset familial and sporadic forms of Alzheimer's disease. The BchE-k variant, which is the common variant of the BchE gene, has been reported to show allelic association with AD in subjects who are also carriers of the ${\varepsilon}4$ allele of the ApoE, especially in subjects over the age of 75. This study was performed to evaluate the distribution of the ApoE and the BchE genotypes in the healthy and AD groups and to evaluate the synergy between the BchE-k variant and the ApoE ${\varepsilon}4$ in AD. The ApoE and the BchE genotypes were determined in DNA samples from 610 healthy people and 60 LOAD patients by using ARMS by standard agarose gel electrophoresis. The effect of the ApoE ${\varepsilon}4$ was closely related to AD(p<0.05). A comparison between the AD patients and the healthy individuals, both with the ${\varepsilon}4$ allele, indicated an interaction between the BchE-k and the ApoE ${\varepsilon}4$(p<0.05). The association of the BchE-k with AD was limited to carriers of the ApoE ${\varepsilon}4$ allele, among whom the presence of the BchE-k gave an odds ratio of AD 3.48 (95% C.I. 1.3-9.2). Therefore, these results suggested that further evidence of an association between the ApoE ${\varepsilon}4$ and LOAD, and the BchE-k acts in synergy with the ApoE ${\varepsilon}4$ as a susceptibility gene for AD.

• 한국동물학회지
• /
• 제36권2호
• /
• pp.193-199
• /
• 1993

The protein po;vmorphisms and allele frequencies of wild house rat (Rattus norvegicus) population in Korea were studied. The studied proteins and enzymes were transferrin (Tf), albumin (Alb), fumarate hvdratase (FH), phospho!loucomutase (PGM), lactate dehvdrogenase A (LDHA) and lactate dehvdrogenase B (LDHB). There were two transferrin alleles, TP and Tf in Korean wild house rat popu1ation. The Tf2 allele was found for the first time by a starch gel, and confirmed by a polvacrvlamide gel isoelectric focusing and immunoblotting. The allele frequencies of TP and TF were 0.985 and 0.015, respectively. Two common alleles fumarate hydratase, FHa and FHb were found, and frequencies of FHa and FPP were calculated to be 0.714 and 0.286, respectively. The kequenw of FH in Korean wild house rat was higher than that of Finnish and Czechoslovakian population. Alb, PGM, LDHA and LDHB are only one phenotype each and all. Therefore, these proteins seem to be monomorphic in Korean wild house rat population.

• Journal of Nutrition and Health
• /
• 제29권6호
• /
• pp.642-650
• /
• 1996

ApoE 유전자의 다형성은 인체 혈중 콜레스테롤 농도의 정상분포를 설명하는 중요한 인자이다. 특히, E2 와 E4 allele들은 고지혈증환자의 혈중에 현저히 나타나며, 각 다른 인종간의 이틀의 상대빈도수가 관상 동맥 질환 유발 위험도와의 상관관계가 아주 높다. Apo E 유전자의 다형성이 혈중 지질 대사변화 에 미치는 영향에 관한 실험은 105명의 건강한 한국여성을 대상으로 시행되었다. Apo E alleles의 한국 인 상대빈도수는 E3가 0.848, E4가 0.087, 그리고 E2는 0.067이었다. 본 연구에서는 E2/2 표현형이 나 타나지 않았지만, 중국 및 일본인과 같이 E4와 E2 allele가 아주 낮았다 최고및 최저혈압, 맥박(p