• Tuberculosis and Respiratory Diseases
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• 제76권2호
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• pp.59-65
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• 2014

Background: Variable-number tandem repeat (VNTR) typing is a promising method to discriminate the Mycobacterium tuberculosis isolates in molecular epidemiology. The purpose of this study is to determine the optimal VNTR combinations for discriminating isolated M. tuberculosis strains in Korea. Methods: A total of 317 clinical isolates collected throughout Korea were genotyped by using the IS6110 restriction fragment length polymorphism (RFLP), and then analysed for the number of VNTR copies from 32 VNTR loci. Results: The results of discriminatory power according to diverse combinations were as follows: 25 clusters in 83 strains were yielded from the internationally standardized 15 VNTR loci (Hunter-Gaston discriminatory index [HGDI], 0.9958), 25 clusters in 65 strains by using IS6110 RFLP (HGDI, 0.9977), 14 clusters in 32 strains in 12 hyper-variable VNTR loci (HGDI, 0.9995), 6 clusters in 13 strains in 32 VNTR loci (HDGI, 0.9998), and 7 clusters in 14 strains of both the 12 hyper-variable VNTR and IS6110 RFLP (HDGI, 0.9999). Conclusion: The combination of 12 hyper-variable VNTR typing can be an effective tool for genotyping Korean M. tuberculosis isolates where the Beijing strains are predominant.

• The Plant Pathology Journal
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• 제35권6호
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• pp.644-653
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• 2019

The genetic variability of 'Candidatus Liberibacter asiaticus' (CLas) population associated with huanglongbing (HLB) disease of citrus in North Eastern (NE) region of India, a geographically locked region, and home for the diversity of many citrus species was analyzed on the basis of tandem repeat numbers (TRN) in variable CLIBASIA_01645 genomic loci. Fifty-five CLas strains sampled from different groves of NE Hill (NEH) region of India were in single amplicon group, but there was remarkable genetic variability in TRNs. The TRN in HLB-associated CLas strains varied from 0-21 and two novel repeat motifs were also identified. Among the NE population of CLas, TRN5 and TRN9 were most frequent (total frequency of 36.36%) followed by TRN4 (14.55%) and TRN6, TNR7 with a frequency of 12.73% each. Class II type CLas genotypes (5 < TRN ≤ 10) had highest prevalence (frequency of 60.00%) in the samples characterized in present study. Class I (TRN ≤ 5) genotypes were second highest prevalent (29.09%) in the NEH region. Further analysis of genetic diversity parameters using Nei's measure (H value) indicated wide genetic diversity in the CLas strains of NE India (H value of 0.58-0.86). Manipur CLas strains had highest genetic variability (0.86) as compared to Eastern, Southern and Central India. The R₁₀ values (TRN ≤ 10/TRN > 10) of NE CLas population was 10.43 (73/7), higher from other regions of India. Present study conclusively reported the occurrence of high genetic variability in TRN of CLas population in North East Indian citrus groves which have evolved to adapt to the specific ecological niche.

• 한국군사과학기술학회지
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• 제27권4호
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• pp.507-515
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• 2024

Microbial forensics is a scientific discipline for analyzing evidence related to biological crimes by identifying the origin of microorganisms. Multiple locus variable number tandem repeat analysis(MLVA) is one of the microbiological analysis methods used to specify subtypes within a species based on the number of tandem repeat in the genome, and advances in next generation sequencing(NGS) technology have enabled in silico anlysis of full-length whole genome sequences. In this paper, we analyzed unknown samples provided by Robert Koch Institute(RKI) through The United Nations Secretary-General's Mechanism(UNSGM)'s external quality assessment exercise(EQAE) project, which we officially participated in 2023. We confirmed that the 3 unknown samples were B. anthracis through nucleic acid isolation and genetic sequence analysis studies. MLVA results on 32 loci of B. anthracis were analysed by using genome sequences obtained from NGS(NextSeq and MinION) and Sanger sequencing. The MLVA typing using short-reads based NGS platform(NextSeq) showed a high probability of causing assembly error when a size of the tandem repeats was grater than 200 bp, while long-reads based NGS platform(MinION) showed higher accuracy than NextSeq, although insertion and deletion was observed. We also showed hybrid assembly can correct most indel error caused by MinION. Based on the MLVA results, genetic identification was performed compared to the 2,975 published MLVA databases of B. anthracis, and MLVA results of 10 strains were identical with 3 unkonwn samples. As a result of whole genome alignment of the 10 strains and 3 unknown samples, all samples were identified as B. anthracis strain A4564 which is associated with injectional anthrax isolates in heroin users.

• 수면정신생리
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• 제15권1호
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• pp.39-43
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• 2008

목 적 : 하지불안증후군(restless legs syndrome ; RLS)의 병인은 아직 불명확하지만, 도파민 결핍과 유전적 소인이 흔히 제기된다. RLS는 도파민수용체를 차단하는 항정신 병약물을 복용하는 환자들에서 더 흔히 발생하는 것으로 보인다. 본 연구에서는 정신분열병환자에서 항정신병약물에 의해 유발된 RLS와 도파민 수송체(dopamine transporter gene ; DAT1) 유전자가 연관이 있는지 알아보고자 하였다. 방 법: International Restless Legs Syndrome Study Group의 진단기준으로 190명의 한국인 정신분열병 환자들을 대상으로 RLS에 대해서 평가하였다. 유전자형분석은 중합효소연쇄반응기법을 사용하여 DAT1 유전자의 40 염기쌍(basepair) variable number of tandem repeat(VNTR)에 대해서 시행되었다. 결 과 : 우리는 44명의 RLS군과 146명의 비RLS군으로 환자들을 분류하였다. 두 군간의 유전자형과 대립유전자 빈도의 차이를 분석한 결과 유의한 차이를 발견할 수 없었다. 결 론 : 이 연구는 DAT1 유전자의 40 bp VNTR 다형성이 항정신병약물로 유발된 RLS와 연관이 없다는 것을 시사한다. 이 결과를 확증하기 위해서는 향후 보다 대규모의 연합연구가 필요할 것이다.

• 대한화학회지
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• 제50권2호
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• pp.123-128
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• 2006

혈관염이 특징적인 질환으로 구강궤양, 음부궤양, 안구염증과 관절, 피부, 중추신경계, 위장관 등 여러 장기를 침범할 수 있는 만성 염증성 질환이다. 베체트병의 발병원인이나 기전에 대해 확실히 밝혀지지는 않았으나 유전적인 소인이 있는 사람에서 감염 등 환경적인 요인이 면역 반응에 이상을 일으켜 질병의 여러 증상이 발현된다. 주조직복합체 (major histocompatibility complex, MHC)와 non-MHC gene등 다양한 유전자들이 베체트병의 병인으로 관여한다. 이 연구에서는 IL-6의 유전적 다형성이 한국인 베체트병의 감수성에 관여하는지를 확인하였다. 유전자 다형성은 VNTR (variable number of tandem repeat), RFLP (restriction fragment length polymorphism), DHPLC (denaturing high performance liquid chromatography) 방법을 이용하여 확인하였다. 실험 결과, 베체트 환자와 대조군에서 IL-6prom의 유전적 다형성은 관련성이 없었지만 IL-6vntr에서는 유전형과 대립형질의 빈도가 다르게 나타났다. IL-6vntr*C 대립유전자가 한국인 베체트병과 연관성이 높게 나타났다. 이런 결과를 확인하기 위해 앞으로 여러 집단과 다른 유전자의 연구가 필요하다.

• 생물정신의학
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• 제25권1호
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• pp.16-20
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• 2018

Objectives Psychological resilience is the ability to cope with stress. The genetic background behind psychological resilience is not much known. The serotonin transporter and dopamine transporter are implicated in stress related psychology and emotional processing. The aim of this study is to investigate a possible genetic role of functional polymorphisms of serotonin and dopamine transporters for psychological resilience. Methods A total of 951 healthy adult subjects were included. Psychological resilience was measured using Connor-Davidson Resilience Scale (CD-RISC). Genotyping was performed for serotonin transporter gene(SERT) promoter variable number tandem repeat (VNTR) and dopamine transporter gene(DAT1) 3'-untranslated region (UTR) VNTR. Genetic association analysis was conducted between genotypes and the CD-RISC score. Results No genetic association was observed for SERT promoter VNTR or DAT1 3'-UTR VNTR with CD-RISC score. No genetic interaction between SERT promoter VNTR and DAT1 3'-UTR VNTR with CD-RISC score was detected. Conclusions Either serotonin or dopamine transporter did not seem to play a significant role for psychological resilience in this sample.

• 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.

• Journal of the Korean Academy of Child and Adolescent Psychiatry
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• 제16권2호
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• pp.199-210
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• 2005

연구목표 : 주의력결핍과잉행동장애 (attention deficit hyperactivity disorder : 이하 ADHD)는 역학적 유전연구를 통해 강한 유전적 요인이 작용하는 질환으로 알려져 왔다. 최근에는 이에 근거하여 질환관련 취약유전자를 규명하려는 노력이 시작되었다. 본 연구는 소아정신과에 내원하여 ADHD 진단을 받은 아동과 정상 대조군을 대상으로, 도파민 운반체 유전자 제 1 형 (dopamine transporter gene type 1 ; 이하 DAT1)과 ADHD간의 연합 여부를 규명하는 것을 목적으로 하였다. 연구내용 : 본 연구의 대상이 된 ADHD 아동은 임상적인 면담과 K-SADS-PL을 통한 확진과정을 거쳐 진단되었으며, 모든 ADHD 아동을 대상으로 소아청소년 행동평가척도(Korean Child Behavior Checklist ; K-CBCL), 부모 및 교사용 코너스 척도, 듀폴 ADHD 임상척도 등 다양한 임상척도를 시행하여, 그 심각도를 평가하였다. 이러한 과정을 통해, 최종 진단된 85명의 ADHD 환아와 독립적으로 모집된 100명의 정상대조군을 대상으로 분자유전연구를 시행하였다. 각 대상으로부터 얻은 전혈 1ml로 유전자분석 (genotyping)이 시행되었고, DAT1 variable number of tandem repeat(VNTR)의 다형성을 확인하였다. 이를 통해, ADHD군과 정상군사이의 DAT1 대립유전자의 다형성 빈도차이를 분석하였고, 두 번째로, ADHD군내에서의 다형성 분포 및 유전형에 따른 임상척도, 신경심리변인과의 차이를 규명하였다. 연구결과 : 소아 환자군 및 대조군의 DAT1-VNTR 분석에서는 7, 9, 10, 11 repeat의 4가지 대립유전자가 발견되었다. 먼저 환자-대조군 모델을 적용하여, 각 대립유전자 빈도에 대하여 ADHD 환자군과 대조군 비교를 시행하였다. 그 결과, 9/10 genotype의 빈도가 환자군에서 대조군에 비해 유의하게 높은 빈도로 나타났다(p<0.05). 또한 9 repeat allele 존재여부에 따라 환아군을 나누고, 각 군에서의 주의력장애 진단시스템(attentional deficit diagnostic system ; ADS)의 결과를 비교한 결과, 9 repeat allele를 갖는 군에서 유의하게 높은 오경보 오류(commission error)점수를 보였다. 결론 : 본 연구에서는 첫째, 대조군-환자군 사이에서는 ADHD와 DAT1 9/10 genotype간에 유의한 연관관계를 보여주었다. 그리고 DAT1 9 repeat allele와 ADS결과에 대한 비교 분석에서 높은 충동성 (오경보오류)과 9 repeat allele이 연관되어 있다는 것이 확인되었다. 그러므로 본 연구 결과를 종합할 때, DAT1 9 repeat allele는 한국 아동 ADHD와 연관성이 있으며, 특히 충동성을 가진 ADHD와 유의한 연관관계를 나타낸다고 할 수 있을 것이다. 이러한 연구결과에 대해 향후 보다 큰 규모의 추시가 필요하리라 생각된다.

• Journal of Microbiology and Biotechnology
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• 제28권2호
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• pp.338-346
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• 2018

Two molecular epidemiologic methods, IS6110 restriction fragment length polymorphism (IS6110-RFLP) and 24-locus mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR), are used worldwide in studies of Mycobacterium tuberculosis (MTB). Conversely, because of its poor resolution, pulsed-field gel electrophoresis (PFGE) is not widely used for MTB. In this study, we improved the 24-locus MIRU-VNTR and PFGE protocols and compared the effectiveness of these approaches for the molecular typing of MTB using 75 clinical isolates obtained from a cohort investigation of high-risk populations infected with MTB. The 24-locus MIRU-VNTR method demonstrated superior discriminatory ability, followed by PFGE and IS6110-RFLP. Next, we analyzed six isolates with clear epidemiologic connections; that is, isolates from patients who attended the same school. IS6110-RFLP and PFGE identified these samples as the same type. By contrast, according to MIRU-VNTR, two isolates differed from four other isolates at one locus each; one isolate was identified as Mtub29 and the other as QUB-26. In summary, the 24-locus MIRU-VNTR assay was the most useful molecular typing method among the three methods investigated due to its discriminatory power, short time required, and availability as an epidemiologic investigation tool. PFGE was the second-best method. Compared with the other loci assessed in the 24-locus MIRU-VNTR assay, the Mtub29 and QUB-26 loci appeared to exhibit greater variability during transmission.

• Clinical and Experimental Reproductive Medicine
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• 제24권1호
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• pp.51-56
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• 1997

Recently, through the development of the primer extension preamplification(PEP) method which amplifies the whole genome, simultaneous multiple DNA analysis has become possible. Whole genome from each single cell can be amplified using 15 base oligonucleotide random primer. The greatest advantage of PEP-PCR is the ability to investigate several loci simultaneously and confirm results by analysing multiple aliquots for each locus. This technique led to the development of preimplantation genetic disease diagnosis using blastomere from early embryo, sperm, polar body and oocyte. In this study, we applied PEP-PCR in 20 cases of single amniocyte and 20 cases of single chorionic villus cell for the clinical application of the prenatal and preimplantational genetic diagnosis. We analysed 7 gene loci simultaneously which are 46, 47 exons related to dystrophin gene, two VNTR (variable number tandem repeat) markers using 5'dysIII, 3'CA related to dystrophin gene and DYZ1, DYZ3, DYS14 regions on chromosome Y. In all the tests, 97.5% of PEP-PCR amplifications with single cells were successful. We obtained 38/40 (95%) accuracy in gender determination through chromosome analysis comparison. Therefore, these results have significant implications for a sperm or oocyte analysis and prenatal or preimplantational genetic diagnosis.