• Genomics & Informatics
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• v.11 no.3
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• pp.129-134
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• 2013

Orthostatic hypotension (OH) is defined by a 20-mm Hg difference of systolic blood pressure (dtSBP) and/or a 10-mm Hg difference of diastolic blood pressure (dtDBP) between supine and standing, and OH is associated with a failure of the cardiovascular reflex to maintain blood pressure on standing from a supine position. To understand the underlying genetic factors for OH traits (OH, dtSBP, and dtDBP), genome-wide association studies (GWASs) using 333,651 single nucleotide polymorphisms (SNPs) were conducted separately for two population-based cohorts, Ansung (n = 3,173) and Ansan (n = 3,255). We identified 8 SNPs (5 SNPs for dtSBP and 3 SNPs for dtDBP) that were repeatedly associated in both the Ansung and Ansan cohorts and had p-values of < $1{\times}10^{-5}$ in the meta-analysis. Unfortunately, the SNPs of the OH case control GWAS did not pass our p-value criteria. Four of 8 SNPs were located in the intergenic region of chromosome 2, and the nearest gene (CTNNA2) was located at 1 Mb of distance. CTNNA2 is a linker between cadherin adhesion receptors and the actin cytoskeleton and is essential for stabilizing dendritic spines in rodent hippocampal neurons. Although there is no report about the function in blood pressure regulation, hippocampal neurons interact primarily with the autonomic nervous system and might be related to OH. The remaining SNPs, rs7098785 of dtSBP trait and rs6892553, rs16887217, and rs4959677 of dtDBP trait were located in the PIK3AP1 intron, ACTBL2-3' flanking, STAR intron, and intergenic region, respectively, but there was no clear functional link to blood pressure regulation.

• Biomedical Science Letters
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• v.19 no.3
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• pp.239-244
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• 2013

Serum liver enzyme levels are widely used in the clinical diagnosis of liver diseases and the assessment of liver status. They also have epidemiological significance to be prospective risk factors for type 2 diabetes, cardiovascular disease. In the previous study, single nucleotide polymorphisms (SNPs) in several genes have been reported to be associated with serum liver enzyme levels in American population. We aimed to confirm whether the genetic variation of C16orf47 (chromosome 16 open reading frame 47) gene also influence the serum liver enzyme levels in Korean population. We genotyped variants in or near C16orf47 in a population-based sample including 994 unrelated Korean adult. Here, we performed association analysis to elucidate the possible relations of genetic polymorphisms in C16orf47 gene with serum liver enzyme levels. By examining genotype data of a total of 944 subjects in 5 hospital health promotion center, we discovered the C16orf47 gene polymorphisms are associated with serum liver enzyme levels. The common and highest significant polymorphism was rs7203412 (${\beta}$=3.68, P=3.66E-06) with glutamic oxaloacetic transferase (GOT) and rs7203412 (${\beta}$=6.2, P=7.06E-05) with glutamic pyruvate transaminase (GPT) in all group. Furthermore, the SNP rs7203412 was consistently associated with GOT (${\beta}$=6.41, P=6.78E-08) and GPT (${\beta}$=11.53, P=2.81E-06) in men group. Consequently, we found statistically significant SNP in C16orf47 gene that are associated with serum levels of GOT and GPT. In addition, these results suggest that the individuals with the minor alleles of the SNP in the C16orf47 gene may be more elevated serum liver enzyme levels in the Korean population.

• Journal of Genetic Medicine
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• v.1 no.1
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• pp.27-31
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• 1997

Steroid 21 hydroxylase deficiency is a major cause of congenital adrenal hyperplasia (CAH) and is caused by genetic impairment of the gene (CYP21B). In the human genome, CYP21B is located within the MHC class III region on the short arm of chromosome 6. Most of the genes in this region are highly polymorphic and crowded. Also the CYP21B gene is accompanied by its pseudogene (CYP21A) and tandemly arranged with two genes of fourth component of complement. This highly complex gene cluster in this area may predispose genetic instability of CYP21, i.e. mutations. In this study, tried to investigate the frequency of duplication and deletion of CYP21 and patterns of the genetic alterations of these genes.We also compared the genetic alteration in normal subjects with those of the CAH patients. The results showed that 15% of the normal korean population have duplication or deletion of CYP21. There was one normal subject with heterozygous deletion of CYP21B. Of the 5 CAH patients examined, 2 were found to show abnormal patterns. One was a large-scale gene conversion and the other a gene conversion associated with deletion involving both CYP21B and C4 locus II gene. Through this study, we carne to the conclusion that the duplication or even deletion of CYP21 and C4 might be quite a common event in the Korean population and these rearrangements must be regarded as polymorphisms. It could contribute to a high incidencs of CAH by providing a genetic pool of instable CYP21.

• KOREAN JOURNAL OF CROP SCIENCE
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• v.49 no.1
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• pp.69-72
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• 2004

Somaclonal variation, defined as phenotypic and genetic variations among regenerated plants from a parental plant, could be caused by changes in chromosome structure, single gene mutation, cytoplasm genetic mutation, insertion of transposable elements, and DNA methylation during plant regeneration. The objective of this study was to evaluate DNA variations among somaclonal variants from the cotyledonary node culture in soybean. A total of 61 soybean somaclones including seven $\textrm{R}_1$ lines and seven $\textrm{R}_2$ lines from Iksannamulkong as well as 27 $\textrm{R}_1$ lines and 20 $\textrm{R}_2$ lines from Jinju 1 were regenerated by organogenesis from the soybean cotyledonary node culture system. Field evaluation revealed no phenotypic difference in major agronomic traits between somaclonal variants and their wild types. AFLP and SSR analyses were performed to detect variations at the DNA level among somaclonal variants of two varieties. Based on AFLP analysis using 36 primer sets, 17 of 892 bands were polymorphic between Iksannamulkong and its somaclonal variants and 11 of 887 bands were polymorphic between Jinju 1 and its somaclonal variants, indicating the presence of DNA sequence change during plant regeneration. Using 36 SSR markers, two polymorphic SSR markers were detected between Iksannamulkong and its somaclonal variants. Sequence comparison amplified with the primers flanking Satt545 showed four additional stretches of ATT repeat in the variant. This suggests that variation at the DNA level between somaclonal variants and their wild types could provide basis for inducing mutation via plant regeneration and broadening crop genetic diversity.

• Korean Journal of Veterinary Research
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• v.55 no.2
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• pp.105-110
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• 2015

A real-time PCR assay using hybridization probe (HybProbe) has been developed to detect Brucella (B.) melitensis strains. The primer and HybProbe sets were designed based on the gap gene of chromosome I with a specific single nucleotide polymorphism of B. melitensis. Specificity of the assay was confirmed by comparison to reference Brucella species and other related strains. In the melting curve analysis, B. melitensis generated a peak at $67^{\circ}C$ unlike those for other Brucella species observed at $61^{\circ}C$. Sensitivity of the assay for B. melitensis ranged from 20 ng to 200 fg of genomic DNA. The ability to identify 94 Mongolian B. melitensis isolates using the real-time PCR assay was identical to that of classical biotyping methods and differential multiplex PCR. These data showed that this new molecular technique is a simple and quick method for detecting B. melitensis, which will be important for the control and prevention of brucellosis.

• Asian-Australasian Journal of Animal Sciences
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• v.23 no.12
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• pp.1543-1551
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• 2010

A major aim of cattle genome research is to identify candidate genes associated with meat quantity and quality through QTL analysis for application in the livestock industry. Therefore, this study focused on discovery of useful SNPs within the LOC534614 gene, containing 12273_165 SNP which is located on the same site as the QTL on chromosome 6, and evaluation of the association between SNP and body weight and cold carcass weight in Hanwoo (Korean cattle) As a result of a BLAST search of the NCBI web site, we discovered that the mRNA sequence of the LOC534614 gene was similar to that of the coiled-coil domain containing 158 (CCDC158) for dog and human. According to the direct DNA sequence from the CCDC158 gene, we identified 19 polymorphic SNPs within exons and their flanking regions. Among them, 17 polymorphic SNPs were selected for genotyping in Hanwoo (n = 476) and seventeen marker haplotypes containing 12273_165 SNP (frequency >0.1) were identified. As a result of the association between 17 polymorphic SNPs and Hanwoo (n = 476), g.8778G>A SNP in exon 6 was found to be a non-synonymous SNP, and was significantly associated with body weight and cold carcass weight (p<0.05). We discovered 19 polymorphic SNPs in the CCDC158 gene on the QTL region of BTA 6 in Hanwoo and identified that the g.8778G>A SNP was significantly associated with body weight and cold carcass weight (p<0.05), which causes an amino acid variation from valine to methionine. Furthermore, statistical analysis demonstrated that the CCDC158 gene is strongly associated with body weight and cold carcass weight in Hanwoo. In this regard, the g.8778G>A SNP in the CCDC158 gene can be useful as a positional candidate for body weight and cold carcass weight for marker-assisted selection in Hanwoo.

• Plant Biotechnology Reports
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• v.5 no.3
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• pp.265-271
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• 2011

The cultivated potato as well as its tuber-bearing relatives are considered model plants for cell and tissue culture, and therefore for exploiting the genetic variation induced by in vitro culture. The association between molecular stability and tissue culture in different genetic backgrounds and ploidy levels has already been explored. However, it still remains to be ascertained whether somaclonal variation differs between callus-derived chromosome-doubled and undoubled regenerants. Our research aimed at investigating, through amplified fragment length polymorphism (AFLP) markers, the genetic changes in marker-banding patterns of diploid and tetraploid regenerants obtained from one clone each of Solanum bulbocastanum Dunal and S. cardiophyllum Lindl (both 2n = 2x = 24) and tetraploids from cultivated S. tuberosum L. (2n = 4x = 48). Pairwise comparisons between the banding patterns of regenerants and parents allowed detecting considerable changes associated to in vitro culture both at diploid and tetraploid level. The percentages of polymorphic bands between diploid and tetraploid regenerants were, respectively, 57 and 69% in S. bulbocastanum and 58 and 63% in S. cardiophyllum. On average, the frequencies of lost parental fragments in regenerants were significantly higher than novel bands both in S. bulbocastanum (48 vs. 22%) and S. tuberosum (36 vs. 18%) regenerants. By contrast, in S. cardiophyllum, a similar incidence of the two events was detected (32 vs. 29%). Our results revealed that structural changes after tissue culture process strongly affected the genome of the species studied, but diploid and tetraploids regenerated plants responded equally.

• Journal of Pharmaceutical Investigation
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• v.39 no.5
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• pp.345-351
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• 2009

Organic cation transporters (OCTs) are important for absorption, elimination of many endogenous small organic cations as well as a wide array of drugs and environmental toxins. This gene is located in a cluster on chromosome 6 and OCTs are in major organs such as intestine, liver, kidney, brain and placenta. Therefore, expression levels and function of OCTs directly affect plasma levels and intracellular concentrations of drugs and thereby determine therapeutic response. The aim of this study was to investigate the frequency of the SNPs on OCT1 (C181T and C1022T) and OCT2 (G808T) to analyze haplotype frequency in healthy Korean population. Human subjects have been genotyped for OCT1 (C181T for 195 subjects and C1022T for 825 subjects), using polymerase chain reaction-based diagnostic tests (RFLP). And for OCT2 (G808T), a total of 861 subjects have been genotyped, using pyrosequencing method. Haplotype was statistically inferred using an algorithm based on the expectation-maximization (EM). OCT1 C181T genotyping showed 100% homozygous wild-type (C/C). OCT1 C1022T genotyping showed wild-type (C/C), heterozygous (C/T) and homozygous mutant-type (T/T) and each accounted for 72.1, 24.5 and 3.4%, respectively. OCT2 G808T genotyping results also showed homozygous wild-type (G/G), heterozygous (G/T) and homozygous mutant-type (T/T) and each took 81.8, 17.9 and 0.3%, respectively. Based on these genotype data, haplotype analysis between OCT1 C181T and OCT1 C1022T has proceeded. The result has revealed that linkage disequilibrium between alleles is not obvious (P=0.0122).

• Environmental Analysis Health and Toxicology
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• v.20 no.1
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• pp.39-45
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• 2005

Renin-angiotensin system (RAS)은 혈압 조절에 중요한 역할을 수행하는 생리적 조절계로써, 이 system 을 구성하는 유전자들의 이상은 본태성 고혈압의 발병과 유의하게 관련된 것으로 알려졌다. RAS의 주요한 구성 성분인 angiotensin II는 2종류의 수용체인 angiotensin II type I receptor(AT₁R)와 angiotensin II type I receptor(AT₂R)에 의해 그 효과가 매개되기 때문에, 이 수용체를 암호하는 유전자는 본태성 고혈압의 유력한 후보 유전자라고 볼 수 있다. 현재가지의 연구에 의하면, AT₁R 유전자에 존재하는 유전적 변이와 본태성 고혈압과의 관련성에 관해서는 많은 보고들이 있었지만, AT₂R 유전자에 존재하는 유전적 변이 가 본태성 고혈압에 유의한 효과를 나타내는 지에 관해서는 이렇다할 연구 성과가 별로 없는 실정이다. 이에 본 연구에서는 한국인 집단을 대상으로 하여, AT₂R 유전자에 존재하는 C3123A 다형성이 한국인 집단에서 본태성 고혈압과 유의한 관련성이 있는 지를 분석하였다. 이 유전자는 인간의 X 염색체에 존재하기 때문에, 여성인 경우에는 CC, CA및 AA로 이루어진 3유전자형이 존재하지만, 남성인 경우에는 C와 A로 이루어진 2종류의 대립 유전자로 구성되어 있기 때문에, 본 연구에서는 남성과 여성을 개별적으로 나누어서 분석하였다. 연구 결과, AT₂R 유전자에 존재하는 C3123A 다형성은 남녀 모두에서 본태성 고혈압과 유의한 관련성을 나타내지 않았다(P>0.05). 그렇지만, 이 다형성에 대한 대립 유전자 빈도를 서양인 집단과 비교했을 경우에는, 한국인을 대상으로 한 본 연구에서 A 대립 유전자 빈도가 0.33인 반면에 서양인 집단은 그 빈도가 0.43～0.48로 한국인 집단보다 높은 값을 나타내었다. 따라서, AT₂R 유전자에 존재하는 C3123A 다형성과 본태성 고혈압과의 관련성에 대해서는 한국인과 유전적 배경이 다른 서양인 집단을 대상으로 한 추시가 필요할 것으로 사료된다.

• KIPS Transactions on Software and Data Engineering
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• v.2 no.10
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• pp.697-704
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• 2013

The identification of haplotypes, which encode SNPs in a single chromosome, makes it possible to perform haplotype-based association tests with diseases. Minimum Error Correction model, one of models to computationally assemble a pair of haplotypes for a given organism from Single Nucleotide Polymorphism fragments, has been known to be NP-hard even for gapless cases. In the previous work, an improved branch and bound algorithm was suggested and showed that it is more efficient than naive branch and bound algorithm by performing experiments for Apis mellifera (honeybee) data set. In this paper, to show the extensibility of the algorithm to other organisms we apply the improved branch and bound algorithm to the human data set and confirm the efficiency of the algorithm.