• Asian-Australasian Journal of Animal Sciences
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• 제19권7호
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• pp.931-937
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• 2006

The full-length cDNA of the porcine SMPX gene was obtained by the rapid amplification of cDNA ends (RACE). The nucleotide sequences and the predicted protein sequences share high sequence identity with both human and mouse. The promoter of SMPX was sequenced and then analyzed to find the promoter binding sites. The reverse transcriptase-polymerase chain reaction (RT-PCR) revealed that SMPX has a high level of expression in heart and skeletal muscle, a very low expression in lung and spleen and no expression in liver, kidney, fat and brain. Moreover, SMPX has a differential expression level in skeletal muscle, the expression in 65-day embryos being higher than other stages. The porcine SMPX was mapped to SSCXp24 by using a somatic cell hybrid panel (SCHP) and was found closely linked to SW1903 using the radiation hybrid panel IMpRH. An A/G single nucleotide polymorphism (PCR-RFLP) in the 3'-untranslated region (3'-UTR) was detected in eight breeds. The analysis of allele frequency distribution showed that introduced pig breeds (Duroc and Large White) have a higher frequency of allele A while in the Chinese indigenous pig breeds (Qingping pig, Lantang pig, YushanBlack pig, Large Black-White pig, Small Meishan) have a higher frequencies of allele G. The association analysis using an experimental population (188 pigs), which included two cross-bred groups and three pure-blood groups, suggested that the SNP genotype was associated with intramuscular fat content.

• Animal cells and systems
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• 제1권1호
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• pp.123-128
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• 1997

The characteristics of allelic polymorphisms of the two (CA)n microsatellite (p599 and ㅅ599) markers spanning the long arm of chromosome 5 were studied in 52 DNA samples from unrelated inhabitants of Seoul (Korea) by using the polymerase chain reaction (PCR) to investigate differences in allele frequencies between Korean and Caucasian populations. The 6 alleles were observed for p599 (CA)n with a polymorphism informative content (PIC) value of 0.71 and 9 alleles for ㅅ599 (CA)n with a PIC value of 0.82. The observed heterozygote frequencies of the loci were estimated to 0.730 and 0.846, respectively. Several allele frequencies of two loci showed significant differences between Korean and Caucasian populations. Genotype data from the two loci were consistent with the Hardy-Weinberg equilibrium by x2 test. Linkage disequilibrium between p599 (CA)n and ㅅ599 (CA)n loci was observed in x2 test between the observed and expected frequency of allelic association. The probability of matching calculated at each locus was 0.104 for p599 (CA)n and 0.043 for ㅅ599 (CA)n, respectively. These results demonstrate the need to determine populationspecific allele frequency distributions for polymorphic markers when performing genetic linkage studies in racially defined several populations.

• Genes and Genomics
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• 제40권12호
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• pp.1309-1317
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• 2018

It is well known that dopaminergic genes affect the development of attention deficit hyperactivity disorder (ADHD) in various populations. Many studies have shown that variable number tandem repeats (VNTRs) located within the 3′-untranslated region of DAT1 and in exon 3 of DRD4 are associated with ADHD development; however, these results were inconsistent. Therefore, we investigated the genetic association between two VNTRs and ADHD in Korean children. We determined the VNTRs using PCR. We examined genotype and allele frequency differences between the experimental and control groups, along with the odds ratios, using Chi square and exact tests. We observed a significant association between the children with ADHD and the control group in the 10R/10R genotype of DAT1 VNTRs (p=0.025). In addition, the 11R allele of DAT1 VNTRs showed a higher frequency in the control group than in the ADHD group (p=0.023). Also, the short repeat (without 11R) and long repeat alleles (including 11R) were associated with ADHD (p<0.05). The analysis of DRD4 VNTRs revealed that the 2R allele is associated with ADHD (p=0.025). A significant result was also observed in long and short repeats (p<0.05). Additionally, ADHD subtypes showed that the DRD4 VNTRs are associated with combined and hyperactive-impulsive subtype groups (p<0.05). Therefore, our results suggest that DAT1 VNTRs and DRD4 VNTRs play a role in the genetic etiology of ADHD in Korean children.

• Clinical and Experimental Reproductive Medicine
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• 제50권4호
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• pp.253-261
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• 2023

Objective: Azoospermia (the total absence of sperm in the ejaculate) affects approximately 10% of infertile males. Despite diagnostic advances, azoospermia remains the most challenging issue associated with infertility treatment. Our study evaluated transition nuclear protein 2 (TNP2) and synaptonemal complex protein 3 (SYCP3) polymorphisms, azoospermia factor a (AZFa) microdeletion, and gene expression levels in 100 patients with azoospermia. Methods: We investigated a TNP2 single-nucleotide polymorphism through polymerase chain reaction (PCR) restriction fragment length polymorphism analysis using a particular endonuclease. An allele-specific PCR assay for SYCP3 was performed utilizing two forward primers and a common reverse primer in two PCR reactions. Based on the European Academy of Andrology guidelines, AZFa microdeletions were evaluated by multiplex PCR. TNP2, SYCP3, and the AZFa region main gene (DEAD-box helicase 3 and Y-linked [DDX3Y]) expression levels were assessed via quantitative PCR, and receiver operating characteristic curve analysis was used to determine the diagnostic capability of these genes. Results: The TNP2 genotyping and allelic frequency in infertile males did not differ significantly from fertile volunteers. In participants with azoospermia, the allelic frequency of the SYCP3 mutant allele (C allele) was significantly altered. Deletion of sY84 and sY86 was discovered in patients with azoospermia and oligozoospermia. Moreover, SYCP3 and DDX3Y showed decreased expression levels in the azoospermia group, and they exhibited potential as biomarkers for diagnosing azoospermia (area under the curve, 0.722 and 0.720, respectively). Conclusion: These results suggest that reduced SYCP3 and DDX3Y mRNA expression profiles in testicular tissue are associated with a higher likelihood of retrieving spermatozoa in individuals with azoospermia. The homozygous genotype TT of the SYCP3 polymorphism was significantly associated with azoospermia.

• 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.

• 대한한의학회지
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• 제25권4호
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• pp.209-219
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• 2004

The author investigated whether ACE/DD, AGN/TT, and ApoE/ε4 genotypes are associated with CI and whether genetic risk is enhanced by Sasang constitutional classification. The author ascertained these genotypes in patients with CI (n=211), diagnosed by brain computed tomography. Control subjects for the infarction group were randomly selected from 319 subjects matched for age, gender, and history of hypertension with patients. The ACE/DD genotype was not associated with CI. However. there was significant association between ApoE polymorphism and CI (x²=15.089, p<.05). Furthermore, frequency of AGN/TT genotype was higher in the patients with CI than in the controls (x²=20.072, p<.05). The frequency of T allele Was 0.91 in patients and 0.82 in controls (x²=17.237, p<.05). However, the Sasang constitutional classification did not increase the relative risk for CI in the subjects with ApoE/ε4 or AGN/T allele. These results suggest that ApoE and AGN polymorphism predict CI. but Sasang constitutional classification does not enhance the risk for CI associated with ApoE/ε4 or AGN/TT in a Korean population.

• Asian-Australasian Journal of Animal Sciences
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• 제25권1호
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• pp.28-32
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• 2012

In the present study, we evaluated the informativeness of SNPs genotyped by the Illumina Bovine SNP50K assay in different cattle breeds. To investigate these on a genome-wide scale, we considered 52,678 SNPs spanning the whole autosomal and X chromosomes in cattle. Our study samples consists of six different cattle breeds. Across the breeds approximately 72 and 6% SNPs were found polymorphic and fixed or close to fix in all the breeds, respectively. The variations in the average minor allele frequency (MAF) were significantly different between the breeds studied. The level of average MAF observed in Hanwoo was significantly lower than the other breeds. Hanwoo breed also displayed the lowest number of polymorphic SNPs across all the chromosomes. More importantly, this study indicated that the Bovine SNP50K assay will have reduced power for genome-wide association studies in Hanwoo as compared to other cattle breeds. Overall, the Bovine SNP50K assay described in this study offer a useful genotyping platform for mapping quantitative trait loci (QTLs) in the cattle breeds. The assay data represent a vast and generally untapped resource to assist the investigation of the complex production traits and the development of marker-assisted selection programs.

• Asian Pacific Journal of Cancer Prevention
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• 제15권18호
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• pp.7731-7735
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• 2014

Colorectal cancer (CRC) is the third most common cause of death due to cancer in the worldwide and the incidence is also increasing in Turkey. Our present aim was to investigate any association between germ-line methylenetetrahydrofolate reductase (MTHFR) C677T and A1298C polymorphisms and CRC risk in Turkey. A total of 86 CRC cases and 212 control individuals of the same ethnicity were included in the current study. Peripheral blood-DNA samples were used for genotyping by StripAssay technique, based on the reverse-hybridization principle and real-time PCR methods. Results were compared in Pearson Chi-square and multiple logistic regression models. The MTHFR 677TT (homozygous) genotype was found in 20.9% and the T allele frequency 4.2-fold increased in CRC when compared with the control group.The second SNP MTHFR 1298CC (homozygous) genotype was found in 14.0% and the C allele frequency 1.4-fold elevated in the CRC group. The current data suggest strong associations between both SNPs of germ-line MTHFR 677 C>T and 1298 A>C genotypes and CRC susceptibility in the Turkish population. Now the results need to be confirmed with a larger sample size.

• Journal of Animal Science and Technology
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• 제56권7호
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• pp.25.1-25.6
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• 2014

This study was carried out to investigate the association of POU1F1 (POU domain, class 1, transcription factor 1, Pit1, renamed as POU1F1) gene with backfat thickness (mm), carcass weight (kg), pH, and color values ($L^*$, $a^*$, $b^*$) in crossbred pigs (Landrace ${\times}$ Yorkshire ${\times}$ Duroc). Frequency of the AA genotype indel was at the highest level (66.67%). Frequency of A allele (0.81) was higher than that of b allele (0.19). This population followed Hardy-Weinberg equilibrium. Carcass weights and $a^*$ values of the three genotypes were all significantly different (p < 0.05), respectively. However, backfat thickness, $L^*$, $b^*$, visual color, and pH of the three genotypes were not significantly different (p > 0.05). Visual color was negatively correlated with $L^*$ (r = -0.521) and $b^*$ (r = -0.390) values, $L^*$ value was correlated with $b^*$ (r = 0.419) value, and $a^*$ value was positively correlated with $b^*$ (r = 0.612) value. These results indicate that the POU1F1 gene affected carcass weight and meat redness.

• 한국육종학회지
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• 제43권1호
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• pp.14-22
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• 2011

In this study, 15 simple sequence repeat (SSR) markers were used to analyze the population structure of 55 mungbean accessions (34 from South Asia, 20 from West Asia, 1 sample from East Asia). A total of 56 alleles were detected, with an average of 3.73 per locus. The mean of major allele frequency, expected heterozygosity and polymorphic information content for 15 SSR loci were 0.72, 0.07 and 0.33 respectively. The mean of major allele frequency was 0.79 for South Asia, and 0.74 for West Asia. The mean of genetic diversity and polymorphic information content were almost similar for South Asian and West Asian accessions (genetic diversity 0.35 and polymorphic information content 0.29). Model-based structure analysis revealed the presence of three clusters based on genetic distance. Accessions were clearly assigned to a single cluster in which >70% of their inferred ancestry was derived from one of the model-based populations. 47 accessions (85.56%) showed membership with the clusters and 8 accessions (14.54%) were categorized as admixture. The results could be used to understanding the genetic structure of mungbean cultivars from these regions and to support effective breeding programs to broaden the genetic basis of mungbean varieties.