• Asian-Australasian Journal of Animal Sciences
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• 제20권5호
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• pp.653-660
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• 2007

In this study, we have investigated sequence variants in the PRNP gene of 20 individuals belonging to the Korean cattle, and have analyzed and compared genetic features between varieties of other cattle breeds. Of the 73 sequence variants identified in Korean cattle, 27 were identified for the first time in this study, whereas 46 of these polymorphisms had previously been isolated. We discovered a 2.6 kb SNP hot spot region localized on the putative promoter region of the PRNP gene. Furthermore, the copy numbers of the octapeptide repeat (24 bp indel) which is detected on the coding sequence (CDS) of the PRNP exhibited a completely homozygous 6/6 genotype which is dominant in other cattle breeds. We also characterized a new 19 bp/10 bp allele located on the putative promoter region of the PRNP gene, which represented 0.71 in allele frequency. To the best of our knowledge, this report is the first to address polymorphisms of the PRNP gene structure in Korean cattle in which BSE has yet to be discovered. Therefore, our findings may prove useful with regard to our current understanding of allelic diversity in bovine species, and may also provide new insights into the genetic factors associated with susceptibility or resistance to BSE.

• The Korean Journal of Physiology and Pharmacology
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• 제3권5호
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• pp.501-505
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• 1999

Tryptophan hydroxylase (TPH), the rate-limiting enzyme in serotonin biosynthesis, is primarily expressed in serotonergic neurons of the raphe nuclei. Simple tandem repeat polymorphisms, typically one to four nucleotides long, are tandemly repeated several times and often characterized by many alleles. To identify the presence of polymorphic repeats, we sequenced the 5'-upstream region of the mouse TPH gene. For the detection of any allelic variants, polymerase chain reaction, nonisotopic single-strand conformation polymophism, and DNA sequencing analyses of the tandem repeat sequences were performed using genomic DNA extracted from 60 ICR mice. Two dinucleotide repeats, $5'-(AC/TG)_{22}-3'$ and $5'-(GT/CA)_{17}3',$ were identified at approximately - 5.7 kb and - 3.4 kb upstream from the transcriptional initiation site of the mouse TPH gene, respectively. Minor allelic variants, $5'-(AC/TG)_{21}-3'$ and $5'-(GT/CA)_{18}-3',$ were observed in heterozygous pairs from 3 of 60 and 1 of 60 ICR mice, respectively. The identification of these microsatellites in the mouse TPH promoter raises the possibility that identical and/or other polymorphic sequences might exist in the upstream region of the human TPH gene.

• 약학회지
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• 제54권1호
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• pp.49-54
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• 2010

SLC6A19 which reported as a neurotransmitter was composed of seven minisatellites. In previous our study, the minisatellites variants of SLC6A19-MS7 showed the susceptibility for hypertension. When this minisatellte sequences were analyzed using the bioinformatic tool, USF1 (upstream transcription factor 1) was found in this region as a putative transcription factor binding site. USF1 is binding with E-boxes which has a consensus sequence of CACGTG. USF1 is a ubiquitously expressed transcription factor and involved in the transcriptional control of many genes including the molecular pathogenesis of cardiovascular disease. Thus, we investigated that the putative functional relationship between the minisatellites variants and susceptibility for myocardial infarction. A case-control study was performed that compared genomic DNA from 400 controls and 225 cases with myocardial infarction. There were no significant differences observed in the overall allelic distribution of minisatellites between controls and cases, which indicates that this polymorphism is not responsible for myocardial infarction susceptibility. Hence, we analyzed the five different minisatellites alleles from this study and characterized 14 different repeats units (Unit1~Unit14). Then, we evaluated the DNA composition, phylogenic tree, and pairwise distances of its repeats. The variability of each repeats differed from 2.33% to 16%. The phylogenic trees for the four SLC6A19-MS7 minisatellites exhibited very different shapes in their braches and distances, and present most common 8 repeats allele was the longest 14 repeats allele. Therefore, this result may help to understand for the evolutional level of the length of minisatellites.

• 한국육종학회지
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• 제41권3호
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• pp.194-204
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• 2009

Cytoplasmic male sterility (CMS) and fertility restoration have been utilized as valuable tools for $F_1$-hybrid seed production in many crops despite laborious breeding processes. Molecular markers for the selection of CMS-related genes help reduce the expenses and breeding times. A previously reported genomic region containing the Ppr-B gene, which is responsible for restoration of fertility and corresponds to the Rfo locus, was used to develop gene-based or so-called "functional" markers for allelic selection of the restorer-of-fertility gene (Rfo) in $F_1$-hybrid breeding of radish (Raphanus sativus L.) Polymorphic sequences among Rfo alleles of diverse breeding lines of radish were examined by sequencing the Ppr-B alleles. However, presence of Ppr-B homolog, designated as Ppr-D, interferes on specific PCR amplification of Ppr-B in certain breeding lines. The organization of Ppr-D, resolved by genome walking, revealed extended homology with Ppr-B even in the promoter region. Interestingly, PCR amplification of Ppr-D was repeatedly unsuccessful in certain breeding lines implying the lack of Ppr-D in these radishes. Ppr-B could only be successfully amplified for analysis through designing primers based on the sequences unique to Ppr-B that exclude interference from Ppr-D gene. Four variants of Rfo alleles were identified from 20 breeding lines. A combination of three molecular markers was developed in order to genotype the Rfo locus based on polymorphisms among four different variants. These markers will be useful in facilitating $F_1$-hybrid cultivar development in radish.

• Genes and Genomics
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• 제40권12호
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• pp.1279-1285
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• 2018

Interdigitating dendritic cell sarcoma (IDCS) is an aggressive neoplasm and is an extremely rare disease, with a challenging diagnosis. Etiology of IDCS is also unknown and most studies with only case reports. In our case, immunohistochemistry showed that the tumor cells were positive for S100, CD45, and CD68, but negative for CD1a and CD21. This study aimed to investigate the causative factors of IDCS by sequencing the protein-coding regions of IDCS. We performed whole-exome sequencing with genomic DNA from blood and sarcoma tissue of the IDCS patient using the Illumina Hiseq 2500 platform. After that, we conducted Sanger sequencing for validation of sarcoma-specific variants and gene ontology analysis using DAVID bioinformatics resources. Through comparing sequencing data of sarcoma with normal blood, we obtained 15 nonsynonymous single nucleotide polymorphisms (SNPs) as sarcoma-specific variants. Although the 15 SNPs were not validated by Sanger sequencing due to tumor heterogeneity and low sensitivity of Sanger sequencing, we examined the function of the genes in which each SNP is located. Based on previous studies and gene ontology database, we found that POLQ encoding DNA polymerase theta enzyme and FNIP1 encoding tumor suppressor folliculin-interacting protein might have contributed to the IDCS. Our study provides potential causative genetic factors of IDCS and plays a role in advancing the understanding of IDCS pathogenesis.

• 한국임상수의학회지
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• 제36권4호
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• pp.190-195
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• 2019

We aimed to identify genomic variations as well as the marker genes related with chronic mitral valve disease (CMVD) in Canis lupus familiaris using whole genome resequencing, which provides valuable resources for further study. Two ten-year old female Canis lupus familiaris English cocker spaniels were used for this study, one control and one who had been diagnosed as CMVD. For the whole genome resequencing, muscles from the left ventricular wall were collected from each dog. With the HiSeq DNA Shotgun library and $HiSeq^{TM}$ 2000 platform, whole genome resequencing was performed. From the results, we identified 5 million and 6 million variants in gene expression in the control and CMVD-diagnosed subject, respectively. We then selected the top 1,000 genes from the SNP, INS, and DEL mutation and 675 genes among them were overlapped for every mutation between the control and CMVD-diagnosed patient. Interestingly, in both groups, the intron variant (91.16 and 91.18%) and upstream variant (3.10 and 3.08%) are most highly related. Among the overlapped 675 genes, gene ontology for intracellular signal transduction is highly counted in INS, and DEL, and SNPs (35, 33, 31, respectively). In this study, we found that the COL and CDH gene families could be key molecules in identifying the difference in gene expression between control and CMVD-diagnosed dogs. We believe further studies will prove the importance of variants in key molecule expression and that these data will serve as a valuable foundation stone the study of canine CMVD.

• Asian Pacific Journal of Cancer Prevention
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• 제16권2호
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• pp.775-781
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• 2015

Background: RB1 (retinoblastoma 1) was reportedly one of the major determinative factors for sensitivity to taxanes in previous studies. In this study, we investigated the influence of RB1 single nucleotide polymorphisms (SNPs) on the efficacy of platinum-taxane regimens in advanced NSCLC patients. Materials and Methods: 234 cases of patients with advanced NSCLC who were treated with first-line platinum-taxane agents were enrolled in this study. Genomic DNA was extracted from patients' peripheral blood samples using a QIAamp DNA Maxi Kit, and genotyped by iSelect HD Bead-Chip. Results: Regression analyses were conducted through the univariate and multivariate Cox proportional hazards model in the 234 patients. The results showed that of the eight RB1 tagSNPs, only rs4151510 was a positive predictive factor for the advanced NSCLC patients treated with platinum taxanes regimen. The patients with G/G genotype of RB rs4151510 had longer overall survival (OS) than the non-G/G genotype (p=0.018). The histology was also correlated with OS in the whole advanced NSCLC patients. Three tagSNPs of RB1, rs4151510, rs4151465, rs9568036 were significantly associated with OS in the advanced NSCLC patients with squamous cell histology using Kaplan-Meier overall survival analysis stratified by histology. Conclusions: RB1 genomic variants were correlated with the efficacy of platinum-taxanes regimen. RB rs4151510 is an independent factor of the prognosis of NSCLC patients receiving platinum-taxane chemotherapy.

• BMB Reports
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• 제35권6호
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• pp.637-641
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• 2002

Only one natural promoter that interacts with bacteriophage K11 RNA polymerase has so far been identified. To identify more, in the present study restriction fragments of the phage genome were individually assayed for transcription activity in vitro. The K11 genome was digested with two 4-bp-recognizing restriction enzymes, and the fragments cloned in pUC119 were assayed with purified K11 RNA polymerase. Eight K11 promoter-bearing fragments were isolated and sequenced. We report that the nine K11 promoter sequences (including the one previously identified) were highly homologous from -17 to +4, relative to the initiation site at +1. Interestingly, five had -10G and -8A, while the other four had -10A and -8C. The consensus sequences with the natural -10G/-8A and -10A/-8C, and their variants with -10G/-8C and -10A/-8A, showed nearly equal transcription activity, suggesting residues at -10 and -8 do not regulate promoter activity. Using hybridization methods, physical positions of the cloned promoter-bearing sequences were mapped on SalI-and KpnI-restriction maps of the K11 genome. The flanking sequences of six cloned K11 promoters were found to be orthologous with T7 or T3 genomic sequences.

• Journal of Genetic Medicine
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• 제17권1호
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• pp.21-26
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• 2020

Purpose: To evaluate the additive value of prenatal chromosomal microarray analysis (CMA) in assessing increased nuchal translucency (NT) (≥3.5 mm) with normal karyotype and the possibility of detecting clinically significant genomic imbalance, based on specific indications. Materials and Methods: Invasive samples from 494 pregnancies with NT ≥3.5 mm, obtained from the Research Center of Fertility & Genetics of Hamchoon Women's Clinic between January 2019 and February 2020, were included in this study and CMA was performed in addition to a standard karyotype. Results: In total, 494 cases were subjected to both karyotype and CMA analyses. Among these, 199 cases of aneuploidy were excluded. CMA was performed on the remaining 295 cases (59.7%), which showed normal (231/295, 78.3%) or non-significant copy number variation (CNV), such as benign CNV or variants of uncertain clinical significance likely benign (53/295, 18.0%). Clinically significant CNVs were detected in 11 cases (11/295, 3.7%). Conclusion: Prenatal CMA resulted in a 3% to 4% higher CNV diagnosis rate in fetuses exhibiting increased NT (≥3.5 mm) without other ultrasound detected anomalies and normal karyotype. Therefore, we suggest using high resolution, non- targeting CMA to provide valuable additional information for prenatal diagnosis. Further, we recommend that a genetics specialist should be consulted to interpret the information appropriately and provide counseling and follow-up services after prenatal CMA.

• Genomics & Informatics
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• 제18권4호
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• pp.44.1-44.7
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• 2020

The severity of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), greatly varies from patient to patient. In the present study, we explored and compared mutation profiles of SARS-CoV-2 isolated from mildly affected and severely affected COVID-19 patients in order to explore any relationship between mutation profile and disease severity. Genomic sequences of SARS-CoV-2 were downloaded from Global Initiative on Sharing Avian Influenza Data (GISAID) database. With the help of Genome Detective Coronavirus Typing Tool, genomic sequences were aligned with the Wuhan seafood market pneumonia virus reference sequence and all the mutations were identified. Distribution of mutant variants was then compared between mildly and severely affected groups. Among the numerous mutations detected, 14408C>T and 23403A>G mutations resulting in RNA-dependent RNA polymerase (RdRp) P323L and spike protein D614G mutations, respectively, were found predominantly in severely affected group (>82%) compared with mildly affected group (<46%, p < 0.001). The 241C>T mutation in the non-coding region of the genome was also found predominantly in severely affected group (p < 0.001). The 3037C>T, a silent mutation, also appeared in relatively high frequency in severely affected group compared with mildly affected group, but the difference was not statistically significant (p = 0.06). We concluded that spike protein D614G and RdRp P323L mutations in SARS-CoV-2 are associated with severity of COVID-19. Further studies will be required to explore whether these mutations have any impact on the severity of disease.