• Asian-Australasian Journal of Animal Sciences
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• 제28권8호
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• pp.1066-1074
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• 2015

In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five YSNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (${\pi}=5.6{\times}10^{-4}$) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (${\pi}=0.00000$) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses.

• Journal of Genetic Medicine
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• 제12권1호
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• pp.6-11
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• 2015

Intellectual disability (ID) is the most common disability among people under the age of 20 years. In the absence of obvious non-genetic causes of ID, the majority of cases of severe ID are thought to have a genetic cause. The advent of technologies such as array comparative genomic hybridization, single nucleotide polymorphism genotyping arrays, and massively parallel sequencing has shown that de novo copy number variations and single nucleotide variations affecting coding regions are major causes of severe ID. This article reviews the genetic causes of ID along with diagnostic approaches for this disability.

• 동의생리병리학회지
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• 제21권5호
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• pp.1307-1312
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• 2007

This study was designed to investigate effectiveness of korean medicine therapy and the relation between effectiveness of that and single nucleotide gene polymorphism in stroke patients. This study was carried out on 92 stroke patients who were admitted to the department of acupuncture & moxibustion, college of Oriental medicine, Daegu Haany University and 112 healthy Korean. All patients were received Korean medicine therapy including acupuncture and herbal medicine for stroke and assessed by National Institutes of Health Stroke Scale(NIHSS). Blood samples from all subjects were obtained for DNA extraction. The extracted DNA was amplified by polymerase chain reaction(PCR). PCR products were visualized by 1.5% agarose gel electrophoresis. Through Pyrosequencing of PCR product, the polymorphism of single nucleotide gene was genotyped automatically. There were significant difference between before and after Korean medicine therapy in NIHSS. Genotypes were AA, AG, GG, but there was no significant difference between control and stroke groups. And there was not any statistical significant allelic frequency difference between control and stroke groups. We concluded that Korean medicine therapy in stroke patient can improve NIHSS, but there is no definite relation between effectiveness of Korean medicine therapy and single nucleotide gene polymorphism in stroke patients. This study need to be confirmed in large patients and further studies about relation with gene polymorphism are required.

• 한국정보과학회논문지:시스템및이론
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• 제34권7호
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• pp.276-281
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• 2007

본 논문에서는 한국인의 대표질환 중 하나인 만성 간염에 대한 질환 감수성을 예측하기 위해서 Single Nucleotide Polymorphism 데이타와 대표적인 기계학습 기술인 Support Vector Machine을 이용하였다. 실험을 위한 데이타로 만성간염 환자 173명과 정상인 155명의 SNP 데이타를 사용하였으며, 평가를 위한 방법으로는 Leave-One-Out Cross Valication을 사용하였다. 실험결과 SNP 데이터만으로는 67.1%의 예측 결과를 얻었으며 기본적인 건강요소인 나이와 성별을 특징요소로 사용함으로서 74.9%의 예측 결과를 보였다. 향후 보다 많은 SNP 데이타와 건강관련정보 그리고 생활패턴에 대한 요소들을 특징요소로 감수성 예측에 함께 사용한다면, SVM은 만성 간염 예측을 위한 보다 효과적인 도구가 될 것이다.

• 한국발생생물학회지:발생과생식
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• 제18권4호
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• pp.275-286
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• 2014

To successful molecular breeding, identification and functional characterization of breeding related genes and development of molecular breeding techniques using DNA markers are essential. Although the development of a useful marker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breeding and developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely used for genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. We identified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of a total 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and 217 transversions. As a result, 144 SNP markers were developed on the basis of 514 SNP to selection of useful gene region, and then applied to each of eight wild and culture olive flounder (total 16 samples). In our experimental result, only 32 markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was not detected in polymorphic SNPs. Heterozygosity of wild and cultured olive flounder using the 32 SNP markers is 0.34 and 0.29, respectively. In conclusion, we identified SNP and polymorphism in olive flounder using newly designed marker, it supports that developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study can be basic data for researches for immunity gene and characteristic with SNP.

• 대한치과보철학회지
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• 제49권4호
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• pp.341-345
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• 2011

DNA 복제과정에서의 오류(error)에 의한 유전적 변이(genetic variation)를 통해 개개인이 가지고 있는 유전변이형을 조사하고 특정 질환에 대한 감수성의 차이를 밝히는 유전체 연관성 연구가 의학계 전반에 활발히 진행되고 있다. 개인 간의 DNA 상에 존재하는 염기서열의 차이를 보이는 유전적 변이를 통해 개인간의 형질이 다르게 표현 되는 것을 다형성이라고 하는데 다형성의 원인 중 염기 서열 한 쌍의 변이에 의하여 다른 형질로 표현되는 것을 단일염기다형성(Single Nucleotide Polymorphism; SNP)이라고 정의한다. 유전자 분석 기술의 놀랄만한 발전과 컴퓨터를 이용한 분석 프로그램의 개발에 의해 SNP과 질병의 연관성에 관한 연구는 의학계 모든 분야에서 가속화 되고 있다. 최근 급격하게 빨리 진척되는 연구들에 힘입어 특정 질병에 대한 특정 유전자가 가지는 위험도를 분석하고 환자를 유전적 위험도에 따라 분류하여 진단, 예방 및 치료하는 환자 맞춤식의 진료가 모든 의약학 분야에 적용 될 것으로 생각 된다. 치과 영역에서는 충치와 치주 질환과의 관련성에 대해서 초기 단계의 연구가 진행되고 있는 수준이다. 본 종설에서는 유전체 질병 연구의 현황과 치과 영역에서 시작된 연구를 소개 하고자 한다.

• Journal of Genetic Medicine
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• 제19권1호
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• pp.7-13
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• 2022

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.

• Bulletin of the Korean Chemical Society
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• 제31권7호
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• pp.2011-2014
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• 2010

The fluorescence intensity of a single-stranded oligonucleotide containing a fluorene-labeled deoxyuridine $(U^{Fl})$ unit increases by only 1.5-fold upon formation of its perfectly matched duplex. To increase the fluorescence signal during hybridization, we positioned a quencher strand containing a deoxyguanine (dG) nucleobase, functioning as an internal quencher, opposite to the $U^{Fl}$ unit to reduce the intrinsic fluorescence upon hybridization with a probe. From an investigation of the optimal length of the quencher strand and the effect of the neighboring base sequence, we found that a short strand (five-nucleotide) containing all natural nucleotides and dG as an internal quencher was effective at reducing the intrinsic fluorescence of a linear beacon; it also exhibited high total discrimination factors for the formation of perfectly matched and single base-mismatched duplexes. Such assays that function based on clear changes in fluorescence in response to single-base nucleotide mutations would be useful tools for accelerating diagnoses related to various diseases.

• 한국균학회지
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• 제43권4호
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• pp.231-238
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• 2015

팽이버섯(Flammulina velutipes) 25품종의 유전체 재분석 데이터를 표준유전체(KACC42781)와 비교하여 genomewide single nucleotide polymorphism (SNP)를 선발하였다. 균주에 따른 mapping율의 차이는 균주간 변이를 반영하였으며, genome-wide SNP분포는 homozygous SNP, heterozygous SNP로 구분되었으며 모두 균주에 따른 변이가 크게 나타났다. 수집균주들 사이의 유연관계를 살펴보기 위해, 계통수를 그려본 결과, Group I은 F. velutipes var. 계통인 ASI 4062, 4148, 4195이 묶여지고, Group II는 ASI 4188 F. elastica, ASI 4190 F. fennae, ASI 4194 F. rossica의 다른 종이 별도의 그룹을 형성하였다. 그 외 F. velutipes 19개 계통은 같은 그룹으로 나타났으며 그 유전적 자리를 잘 반영하였다. 한편 백색 group과 갈색 group을 유연관계로 분석하고자 시도하였으나 색깔에 따른 group은 이루어지지 않았다. 한국 백색 품종인 ASI 4210, 4166, 4178과 일본 백색 품종인 ASI 4209, 4167을 분석한 결과 phylogenetic tree상에서 한국 백색 품종과 일본 백색 품종간의 유전적 상동성이 매우 높음을 확인할 수 있었다.

• Bulletin of the Korean Chemical Society
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• 제31권7호
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• pp.1902-1906
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• 2010

A microchip electrophoresis (ME) method was developed using a programmed field strength gradients (PFSG) for the single nucleotide polymorphism (SNP) based fast identification of cattle breeds. Four different Korean cattle (Hanwoo) and Holstein SNP markers amplified by allele-specific polymerase chain reaction were separated in a glass microchip filled with 0.5% poly(ethyleneoxide) ($M_r$ = 8 000 000) by PFSG as follows: 750 V/cm for 0 - 14 s, 166.7 V/cm for 14 - 31 s, 83.3 V/cm for 31 - 46 s, and 750 V/cm for 46 - 100 s. The cattle breeds were clearly distinguished within 45 s. The ME-PFSG method was 7 times and 5 times faster than the constant electric field ME method and the capillary electrophoresis- PFSG method, respectively, with a high resolving power ($R_s$ = 5.05 - 9.98). The proposed methodology could be a powerful tool for the fast and simultaneous determination of SNP markers for various cattle breeds with high accuracy.