Allele-specific, Hybridization-based, Washing-free Fluorescence Signal Production Platforms for Quantitation of Single-Base Change (C?

박성민,하상수 대한화학회 2015 Bulletin of the Korean Chemical Society Vol.36 No.1

A single nucleotide polymorphism (SNP) is a single base-pair substitution that commonly constitutes the genetic variation in individuals. Because of its association with disease susceptibility and drug resistance, SNP detection is of great value in studying the variation in drug responses. Here we report four types of washing- free (i.e., separation-free or sequential addition of reagents) and polymerase chain reaction (PCR)-free fluorescence signal production platforms for quantitative detection of a single-base mismatch inRNAand compare their analytical efficiency. The RNA-templated SNP detection methods in this study are based on the allelespecific hybridization approach and/or on the allele-specific oligonucleotide ligation approach, and have been successfully applied to the quantitation of single-base mutation (C→U) inRNAof the BCR–ABL fusion gene, by endpoint measurements of fluorescence intensity. These methods have several advantages for practical applications, such as direct discrimination of single-base mismatch of theRNAextracted from cells, no requirement of PCR amplification, performance of homogeneous detection, easy design of detection probes, and suitability for large-scale genotyping.

정상 한국인의 항간질약 내성기전에 관여할 것으로 추정되는 유전자변이 정보

김명규,최강호,남태승,김준태,최성민,박만석,김병채,조기현 대한신경과학회 2010 대한신경과학회지 Vol.28 No.2

Background: The completion of the human genome project means that a high-quality reference sequence of the gene-rich portion of the human genome is now available. However, the strong influence of ethnic, geographical, and other characteristics of study populations on the frequencies of different single-nucleotide polymorphisms (SNPs) makes it questionable whether foreign SNP data should be used in domestic studies. Methods: Twenty-seven possible candidate genes of antiepileptic drug (AED) resistance were resequenced in a DNA pool from 200 healthy Koreans to identify SNPs and calculate their minor allele frequencies (MAFs). Results: A total of 98 SNPs were present in 22 of the 27 genes: 28 were in the coding regions, 34 were in introns, 23 were in 5’ near genes, 10 were in 5’ untranslated regions, and 3 were in 3’ near genes. Conclusions: The comparative analysis using the pooled DNA adopted in the present study was highly reliable in estimating MAFs and was compatible with the common disease/common variant hypothesis. The reported data on 98publicly available SNPs of genes possibly associated with AED resistance that be useful to researchers with limited availability of domestic SNP data.

Highly selective detection of single nucleotide polymorphism (SNP) using a dumbbell DNA probe with a gap-filling approach

Jooyeong Kim,Jin Kyung Ahn,Ji Su Kim,Boram Choi,Juyeon Cho,Hyukjin Lee 한국공업화학회 2020 Journal of Industrial and Engineering Chemistry Vol.88 No.-

Single nucleotide polymorphism (SNP) is the most common type of genetic sequence variations andknown to associate with the development of various diseases including cancer. Accurate detection of SNPis often necessary to determine the susceptibility of patients to diseases as well as their response to themedical treatments. Molecular inversion probe (MIP) has been widely utilized as an alternative methodto detect the SNP as compared to the conventional PCR/genome sequencing method. However, basepairingbased detection of SNP fundamentally lacks target specificity toward the single mismatch of basesand often fails to meet the accuracy requirement for SNP detection. In this study, we report thedevelopment of new SNP detection method using a dumbbell-probe with a gap-filling approach. Twoseparate DNA strands are designed to self-assemble to form a dumbbell DNA probe for the selectivedetection of EGFR 21 point mutation. Unlike the direct binding of MIP to the target sequence, our systemhas an additional process for the enhancement of sequence specificity through a base matched gapfilling. In the presence of target sequences, the dumbbell-probe undergoes base-pair hybridization to thetarget sequence followed by sequence specific gap-filling and ligation in single-step. The detection ofEGFR 21 point mutation is achieved with a highly specific and selective manner. This simple and robustdetection method offers promising future potential in the diagnosis of various genetic mutations.

Effect of Single-Nucleotide Polymorphisms on Decline of Dopamine Transporter Availability in Parkinson’s Disease

신승현,김근영,이재민,김은주,김성장,김인주,박경준,이명준 대한신경과학회 2019 Journal of Clinical Neurology Vol.15 No.1

Background and Purpose We aimed to determine the association between the annual changes in dopamine transporter (DAT) availability as measured by 123I-ioflupane (123I-FP-CIT) single-photon-emission computed tomography and single-nucleotide polymorphisms (SNPs) known to be risk factors in Parkinson’s disease (PD). Methods In total, 150 PD patients were included from the Parkinson’s Progression Markers Initiative database. Specific SNPs that are associated with PD were selected for genotyping. SNPs that were not in Hardy-Weinberg equilibrium or whose minor allele frequency was less than 0.05 were excluded. Twenty-three SNPs met the inclusion criteria for this study. The Kruskal- Wallis test was used to compare annual percentage changes in DAT availability for three subgroups of SNP. Results None of the 23 SNPs exerted a statistically significant effect (p<0.0022) on the decline of DAT availability in PD patients. However, we observed trends of association (p<0.05) between three SNPs of two genes with the annual percentage change in DAT availability: 1) rs199347 on the putamen (p=0.0138), 2) rs356181 on the caudate nucleus (p=0.0105), and 3) rs3910105 on the caudate nucleus (p=0.0374). A post-hoc analysis revealed that DAT availability was reduced the most for 1) the putamen in the CC genotype of rs199347 (vs. CT, p=0.0199; vs. TT, p= 0.0164), 2) the caudate nucleus in the TT genotype of rs356181 (vs. CC, p=0.0081), and 3) the caudate nucleus in the CC genotype of rs3910105 (vs. TT, p=0.0317). Conclusions Significant trends in the associations between three SNPs and decline of DAT availability in PD patients have been discovered.

Alteration in Cngb1 Expression upon Maternal Immune Activation in a Mouse Model and Its Possible Association with Schizophrenia Susceptibility

Hwa-Young Lee,Sung Wook Kang,Hyeonjung Jeong,권준택,Young Ock Kim,김학재 대한정신약물학회 2021 CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE Vol.19 No.4

Objective: The cyclic nucleotide-gated channel (Cng) regulates synaptic efficacy in brain neurons by modulating Ca2+ levels in response to changes in cyclic nucleotide concentrations. This study investigated whether the expression of Cng channel, cyclic nucleotide-gated channel subunit beta 1 (Cngb1) exhibited any relationship with the pathophysiology of schizophrenia in an animal model and whether genetic polymorphisms of the human gene were associated with the progression of schizophrenia in a Korean population. Methods: We investigated whether Cngb1 expression was related to psychiatric disorders in a mouse model of schizophrenia induced by maternal immune activation. A case-control study was conducted of 275 schizophrenia patients and 410 controls with single-nucleotide polymorphisms (SNPs) in the 5′-near region of CNGB1. Results: Cngb1 expression was decreased in the prefrontal cortex in the mouse model. Furthermore, the genotype frequency of a SNP (rs3756314) of CNGB1 was associated with the risk of schizophrenia. Conclusion: Our results suggest that CNGB1 might be associated with schizophrenia susceptibility and maternal immune activation. Consequently, it is hypothesized that CNGB1 may be involved in the pathophysiology of schizophrenia.

The identification of novel regions for reproduction trait in Landrace and Large White pigs using a single step genome-wide association study

Rattikan Suwannasing,Monchai Duangjinda,Wuttigrai Boonkum,Rutjawate Taharnklaew,Komson Tuangsithtanon 아세아·태평양축산학회 2018 Animal Bioscience Vol.31 No.12

Objective: The purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs. Methods: The traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records. Results: The outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL. Conclusion: The genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.

Genome-wide single-nucleotide polymorphism data and mitochondrial hypervariable region 1 nucleotide sequence reveal the origin of the Akhal-Teke horse

Zhoucairang Kang,Jinping Shi,Ting Liu,Yong Zhang,Quanwei Zhang,Zhe Liu,Jianfu Wang,Shuru Cheng Asian Australasian Association of Animal Productio 2023 Animal Bioscience Vol.36 No.10

Objective: The study investigated the origin of the Akhal-Teke horse using genome-wide single-nucleotide polymorphism (SNP) data and mitochondrial hypervariable region 1 (HVR-1) nucleotide sequences Methods: Genome-wide SNP data from 22 breeds (481 horses) and mitochondrial HVR-1 sequences from 24 breeds (544 sequences) worldwide to examine the origin of the Akhal-Teke horse. The data were analyzed using principal component analysis, linkage disequilibrium analysis, neighbor-joining dendrograms, and ancestry inference to determine the population relationships, ancestral source, genetic structure, and relationships with other varieties. Results: A close genetic relationship between the Akhal-Teke horse and horses from the Middle East was found. Analysis of mitochondrial HVR-1 sequences showed that there were no shared haplotypes between the Akhal-Teke and Tarpan horses, and the mitochondrial data indicated that the Akhal-Teke horse has not historically expanded its group. Ancestral inference suggested that Arabian and Caspian horses were the likely ancestors of the Akhal-Teke horse. Conclusion: The Akhal-Teke horse originated in the Middle East.

Clinical application of genome-wide single nucleotide polymorphism genotyping and karyomapping for preimplantation genetic testing of Charcot–Marie–Tooth disease

Min Jee Kim,Sun Ok Park,Ye Seul Hong,Eun A Park,Yu Bin Lee,Byung-Ok Choi,Kyung-Ah Lee,Eun Jeong Yu,Inn Soo Kang 대한의학유전학회 2022 대한의학유전학회지 Vol.19 No.1

Purpose: Preimplantation genetic testing for monogenic disorders (PGT-M) has been successfully used to prevent couples with monogenic disorders from passing them on to their child. Charcot–Marie–Tooth Disease (CMT) is a genetic disorder characterized by progressive extremity muscle degeneration and loss of sensory function. For the first time in Korea, we report our experience of applying single nucleotide polymorphism genotyping and karyomapping for PGT-M of CMT disease. Materials and Methods: Prior to clinical PGT-M, preclinical tests were performed using genotypes of affected families to identify informative single-nucleotide polymorphisms associated with mutant alleles. We performed five cycles of in vitro fertilization PGT-M in four couples with CMT1A, CMT2A, and CMT2S in CHA Fertility Center, Seoul Station. Results: From July 2020 through August 2021, five cycles of PGT-M with karyomapping in four cases with CMT1 and CMT2 were analyzed retrospectively. A total of 17 blastocysts were biopsied and 15 embryos were successfully diagnosed (88.2%). Ten out of 15 embryos were diagnosed as unaffected (66.7%). Five cycles of PGT-M resulted in four transfer cycles, in which four embryos were transferred. Three clinical pregnancies were achieved (75%) and the prenatal diagnosis by amniocentesis for all three women confirmed PGT-M of karyomapping. One woman delivered a healthy baby uneventfully and two pregnancies are currently ongoing. Conclusion: This is the first report in Korea on the application of karyomapping in PGT-M for CMT patients. This study shows that karyomapping is an efficient, reliable and accurate diagnostic method for PGT-M in various types of CMT diseases.

Development of a single-nucleotide-polymorphism marker for specific authentication of Korean ginseng (Panax ginseng Meyer) new cultivar "G-1"

Yang, Dong-Uk,Kim, Min-Kyeoung,Mohanan, Padmanaban,Mathiyalagan, Ramya,Seo, Kwang-Hoon,Kwon, Woo-Saeng,Yang, Deok-Chun The Korean Society of Ginseng 2017 Journal of Ginseng Research Vol.41 No.1

Background: Korean ginseng (Panax ginseng) is a well-known medicinal plant of Oriental medicine that is still in practice today. Until now, a total of 11 Korean ginseng cultivars with unique features to Korean ginseng have been developed based on the pure-line-selection method. Among them, a new cultivar namely G-1 with different agricultural traits related to yield and content of ginsenosides, was developed in 2012. Methods: The aim of this study was to distinguish the new ginseng cultivar G-1 by identifying the unique single-nucleotide polymorphism (SNP) at its 45S ribosomal DNA and Panax quinquefolius region than other Korean ginseng cultivars using multiplex amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR). Results: A SNP at position of 45S ribosomal DNA region between G-1, P. quinquefolius, and the other Korean ginseng cultivars was identified. By designing modified allele-specific primers based on this site, we could specifically identified G-1 and P. quinquefolius via multiplex PCR. The unique primer for the SNP yielded an amplicon of size 449 bp in G-1 cultivar and P. quinquefolius. This study presents an effective method for the genetic identification of the G-1 cultivar and P. quinquefolius. Conclusion: The results from our study shows that this SNP-based approach to identify the G-1 cultivar will be a good way to distinguish accurately the G-1 cultivar and P. quinquefolius from other Korean ginseng cultivars using a SNP at 45S ribosomal DNA region.

Genetic predisposition of donors affects the allograft outcome in kidney transplantation: Single-nucleotide polymorphism of aquaporin-11

( Ji In Park ),( Seung Hee Yang ),( Jung Pyo Lee ),( Seong Ho Yoo ),( Yon Su Kim ) 대한신장학회 2015 Kidney Research and Clinical Practice Vol.34 No.1

Background: Aquaporin-11 (AQP11) is a novel member of the aquaporin family. Disruption of the murine Aqp11 gene causes severe proximal tubular injury and renal failure. The rs2276415 (G4A) single-nucleotide polymorphism in the human AQP11 gene results in glycine to serine substitution in a functionally important domain. In this study, the role of the genetic predispositions of AQP11 rs2276415 (G4A) on renal allograft outcomes was evaluated. Methods: A total of 198 pairs of donors and recipients were enrolled in this study. Long-term graft survival was traced and clinical parameters that could have in.uenced graft outcome were collected through the electronic medical record system. Results: The genotype distribution and allele frequency of rs2276415 polymorphism were not different between donors and recipients. Despite similar allele frequencies between donors and recipients, the minor allele rs2276415 (GAþAA) of AQP11 from the donors, but not from the recipients, had a harmful effect on the graft survival compared with the wild-type donor (GG; P¼0.029). This associationwas signi.cant after adjusting for several risk factors including age, sex, human leukocyte antigen mismatch, donor type, hypertension, and diabetes mellitus (P¼0.032). Conclusion: A donor-derived, not recipient-derived, genetic AQP11 polymorphism has different effects on graft outcome. Thus, the genetic in.uence from donors should be carefully considered for proper management of allografts after kidney transplantation. Copyright & 2015. The Korean Society of Nephrology. Published by Elsevier. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).