• Journal of Animal Science and Technology
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• v.45 no.4
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• pp.523-528
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• 2003

This study was performed to investigate a possible association of the porcine estrogen receptor(ER) locus with the total number of born(TNB) and number of born alive(NBA) in Yorkshire pigs. Using DNAs extracted from 242 Yorkshire pigs, the ER genotype was determined by PvuII PCR-RFLP. The ER allele frequencies of two types of A and B were 0.39 and 0.61, respectively. The least squares means of the litter size by ER genotype was evaluated. The TNB and NBA were found to be associated with an specific ER allele. The genotype at the porcine ER locus has an application potential for marker-assisted selection for litter size in pigs.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.22
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• pp.10009-10013
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• 2014

Background: Vitamin D receptor (VDR) gene has been a subject of extensive pharmacogenetic research recently. Association studies between different types of cancers including prostate cancer (PCa) and VDR gene polymorphism have also been conducted. The objective of this study was to find possible associations between PCa and VDR gene polymorphisms in the Pakistani population. Materials and Methods: A total of 162 subjects, including prostate cancer patients and controls, were genotyped for Apa I, Taq I and Fok I polymorphisms in the VDR gene using allele specific PCR, PCR-RFLP and direct DNA sequencing. Allelic frequencies were tested for Hardy-Weinberg equilibrium and associations between the genetic markers and PCa were calculated using logistic regression. Results: Apa I CC genotype was found to have strongest association with PCa risk, and "A" genotype was found to have protective effect. Fok I and Taq I did not have appreciable levels of association with PCa, although Taq I "TC" heterozygotes seemed to have some protective effect. Similarly the "C" allele of Fok I also seemed to have protective effect. Conclusions: To our knowledge, this is the first report showing association between VDR gene polymorphisms and PCa in Pakistan. Our findings may be somewhat skewed because of small sample size and tendency of consanguineous marriages in Pakistani society; nevertheless, it shows the trend of association and protective effects of certain VDR gene polymorphisms against PCa.

• Asian Pacific Journal of Cancer Prevention
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• v.17 no.2
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• pp.815-821
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• 2016

Background: Development of chronic myeloid leukemia (CML) involves formation of double strand breaks (DSBs) which are initially sensed by the ataxia telangiectasia mutated (ATM) signal kinase to induce a DNA damage response (DDR). Mutations or single nucleotide polymorphisms in ATM gene are known to influence the signaling capacity resulting in susceptibility to certain genetic diseases such as cancers. Materials and Methods: In the present study, we have analyzed -5144A>T (rs228589) and C4138T (rs3092856) polymorphisms of theATM gene through polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in 925 subjects (476 CML cases and 449 controls). Results: The A allele of -5144A>T polymorphism and T allele of C4138T polymorphism which were known to be influencing ATM signaling capacity are significantly associated with enhanced risk for CML independently and also in combination (evident from the haplotype and diplotype analyses). Significant elevation in the frequencies of both the risk alleles among high risk groups under European Treatment and Outcome Study (EUTOS) score suggests the possible role of these polymorphisms in predicting the prognosis of CML patients. Conclusions: This study provides the first evidence of association of functional ATM gene polymorphisms with the increased risk of CML development as well as progression.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.1
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• pp.179-182
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• 2013

Human cytochrome P4502E1 (CYP2E1) is a well-conserved xenobiotic-metabolizing enzyme expressed in liver, kidney, nasal mucosa, brain, lung, and other tissues. CYP2E1 is inducible by ethanol, acetone, and other low-molecular weight substrates and may mediate development of chemically-mediated cancers. CYP2E1 polymorphisms alter the transcriptional activity of the gene. This study was conducted in order to investigate the allele frequency variation in different populations of Andhra Pradesh. Two hundred and twelve subjects belonging to six populations were studied. Genotype and allele frequency were assessed through TaqMan allelic discrimination (rs6413419) and polymerase chain reaction-sequencing (-1295G>C and -1055C>T) after DNA isolation from peripheral leukocytes. The data were compared with other available world populations. The SNP rs6413419 is monomorphic in the present study, -1295G>C and -1055C>T are less polymorphic and followed Hardy-Weinberg equilibrium in all the populations studied. The -1295G>C and -1055C>T frequencies were similar and acted as surrogates in all the populations. Analysis of HapMap populations data revealed no significant LD between these markers in all the populations. Low frequency of $CYP2E1^*c2$ could be useful in the understanding of south Indian population gene composition, alcohol metabolism, and alcoholic liver disease development. However, screening of additional populations and further association studies are necessary. The heterogeneity of Indian population as evidenced by the different distribution of $CYP2E1^*c2$ may help in understanding the population genetic and evolutionary aspects of this gene.

• Korean Journal of Biological Psychiatry
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• v.11 no.2
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• pp.110-116
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• 2004

Objectives:Recently, polymorphisms of several serotonin genes have been suggested to be associated with suicide, but the results are still unclear. We examined whether the T102C polymorphisms of the serotonin 2A receptor gene and the G861C polymorphisms of the serotonin 1B receptor gene were associated with suicidal behavior using drug intoxication. Methods:The subjects were 52 patients who visited emergency room with suicidal behaviors. Fifty controls were selected from healthy volunteers matched for sex and age to the suicide subjects. The polymorphisms were analyzed with TaqMan$^{(R)}$ assay using primers based on previous studies. Results:The T102C polymorphism of the serotonin 2A receptor gene showed no significant difference between the suicidal attempters and controls in both genotype and allele frequency analyses(p=0.179 and p=0.422, respectively). There was no statistically significant difference between the suicidal attempters and the controls in the G861C polymorphism of the serotonin 1B receptor gene and any significant effect of the genotype distributions or the allele frequencies was not observed(p=0.092 and p=0.987, respectively). Conclusion:These findings suggest that the T102C polymorphism in serotonin 2A receptor gene and the G861C polymorphism in serotonin 1B receptor gene are not related to the susceptibility to suicide attempts using drugs. To clarify the genetic influences of the serotonergic system on suicidal behavior, the polymorphisms of other candidate genes in the serotonergic system should be studied with larger numbers of subjects.

• Molecules and Cells
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• v.25 no.2
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• pp.301-304
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• 2008

Microsatellites, short tandem repeats, are useful markers for genetic analysis because of their high frequency of occurrence over the genome, high information content due to variable repeat lengths, and ease of typing. To establish a panel of microsatellite markers useful for genetic studies of the Korean population, the allele frequencies and heterozygosities of 207 microsatellite markers in 119 unrelated Korean, Indian and Pakistani individuals were compared. The average heterozygosity of the Korean population was 0.71, similar to that of the Indian and Pakistani populations. More than 80% of the markers showed heterozygosity of over 0.6 and were valuable as genetic markers for genome-wide screening for disease susceptibility loci in these populations. To identify the allelic distributions of the multilocus genetic data from these microsatellite markers, the population structures were assessed by clustering. These markers supported, with the most probability, three clustering groups corresponding to the three geographical populations. When we assumed only two hypothetical clusters (K), the Korean population was separate from the others, suggesting a relatively deep divergence of the Korean population. The present 207 microsatellite markers appear to reflect the historical and geographical origins of the different populations as well as displaying a similar degree of variation to that seen in previously published genetic data. Thus, these markers will be useful as a reference for human genetic studies on Asians.

• Journal of The Korean Society of Inherited Metabolic disease
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• v.4 no.1
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• pp.5-12
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• 2004

Purpose Phenylketonuria is an inborn error of metabolism, which is inherited as an autosomal recessive trait. PKU is resulting from deficiency of phenylalanine hydroxylase. PAH gene spans about 90 kb on chromosome 12q and comprises 13 exons. In order to define the genetic basis of PKU and the frequencies and distribution of PAH mutations in the Korean population, we analyzed PAH gene in independent 80 patients with PKU. Methods All 13 exons including exon-intron boundaries and 2 kb of 5' upstream region of the PAH gene were analyzed by PCR-direct sequencing methods. Results PAH gene analysis revealed 39 different mutations including 10 novel mutations. The novel mutations consisted of 9 missense mutations (P69S, G103S, N207D, T278S, P281A, L293M, G332V, S391I and A447P) and a novel splice site variant (IVS10-3C>G). R243Q, IVS4-1G>A, and E6-96A>G were the most relevant mutations and they accounted in the whole for 38% of the mutant alleles identified in this study. We also observed that. $BH_4$ responsibility was. associated with genotype of R241C, R53H and R408Q. Conc1ustion Our present study with 80 participants extends the previous results to more comprehensive understanding of PAH allele distribution and frequency in Koreans. Although Korean mutation profile of PAH is similar to those of the nearest oriental populations (Japanese, Chinese, and Taiwanese), several different characteristic features are revealed. The characterization of the genotype-phenotype relationship was also performed. Our data would be very useful information for diagnosis, genetic counseling and planning of dietary and therapeutic strategies in Korean PAH patients.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.9
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• pp.1342-1348
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• 2007

POU1F1 is a positive regulator for GH, PRL and TSH${\beta}$ and its mutations associate with production traits in ruminant animals. We described a DdeI PCR-RFLP method for detecting a silent allele in the goat POU1F1 gene: TCT (241Ser)>TCG (241Ser). Frequencies of $D_1$ allele varied from 0.600 to 1.000 in Chinese 801 goats. Significant associations of DdeI polymorphism with production traits were found in milk yield (*p<0.05), litter size (*p<0.05) and one-year-old weight (*p<0.05) between different genotypes. Individuals with genotype $D_1D_1$ had a superior performances when compared to those with genotype $D_1D_2$ (*p<0.05). Hence, the POU1F1 gene was suggested to the potential candidate gene for superior milk performance, reproduction trait and weight trait. Genotype $D_1D_1$, characterized by a DdeI PCR-RFLP detection, was recommended to geneticists and breeders as a molecular marker for better performance in the goat industry.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.15
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• pp.6327-6330
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• 2015

Background: Glioblastoma is a highly aggressive and malignant brain tumor. Risk factors are largely unknown however, although several biomarkers have been identified which may support development, angiogenesis and invasion of tumor cells. One of these biomarkers is PAI-1.4G/5G and A-844G are two common polymorphisms in the gene promotor of PAI 1 that may be related to high transcription and expression of this gene. Studies have shown that the prevalence of the 4G and 844G allele is significantly higher in patients with some cancers and genetic disorders. Materials and Methods: We here assessed the association of 4G/5G and A-844G polymorphisms with glioblastoma cancer risk in Iranians in a case-control study. All 71 patients with clinically confirmed and 140 volunteers with no history and symptoms of glioblastoma as control group were screened for 4G/5G and A-844G polymorphisms of PAI-1, using ARMS-PCR. Genotype and allele frequencies of case and control groups were analyzed using the DeFinetti program. Results: Our results showed significant associations between 4G/5G (p=0.01824) and A-844G (p = 0.02012) polymorphisms of the PAI-1 gene with glioblastoma cancer risk in our Iranian population. Conclusions: The results of this study supporting an association of the PAI-1 4G/5G (p=0.01824) and A-844G (p = 0.02012) polymorphisms with increasing glioblastoma cancer risk in Iranian patients.

• Asian Pacific Journal of Cancer Prevention
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• v.13 no.12
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• pp.6469-6474
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• 2012

Background: DNA repair is one of the crucial defense mechanism against mutagenic exposure. Inherited SNPs of DNA repair genes may contribute to variation in DNA repair capacity and susceptibility to cancer. Due to the presence of these variants, inter-individual and ethnic differences in DNA repair capacity have been established in various populations. India harbors enormous genetic and cultural diversity. Materials and Methods: In the present study we aimed to determine the genotypes and allele frequencies of XRCC1 Arg399Gln (rs25487), XRCC3 Thr241Met (rs861539), XPD Lys751Gln (rs13181), and OGG1 Ser326Cys (rs1052133) gene polymorphisms in 186 healthy individuals residing in the Hyderabad region of India and to compare them with HapMap and other populations. Results and Conclusions: The genotype and allele frequency distribution at the four DNA repair gene loci among Hyderabad population of India revealed a characteristic pattern. Comparison of these gene polymorphisms with other populations revealed a distinctiveness of Hyderabad population from the Deccan region of India. To the best of our knowledge, this is the first report of such DNA repair gene polymorphisms in the Deccan Indian population.