• Journal of Animal Science and Technology
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• 제64권5호
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• pp.830-841
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• 2022

Genetic analysis has great potential as a tool to differentiate between different species and breeds of livestock. In this study, the optimal combinations of single nucleotide polymorphism (SNP) markers for discriminating the Yeonsan Ogye chicken (Gallus gallus domesticus) breed were identified using high-density 600K SNP array data. In 3,904 individuals from 198 chicken breeds, SNP markers specific to the target population were discovered through a case-control genome-wide association study (GWAS) and filtered out based on the linkage disequilibrium blocks. Significant SNP markers were selected by feature selection applying two machine learning algorithms: Random Forest (RF) and AdaBoost (AB). Using a machine learning approach, the 38 (RF) and 43 (AB) optimal SNP marker combinations for the Yeonsan Ogye chicken population demonstrated 100% accuracy. Hence, the GWAS and machine learning models used in this study can be efficiently utilized to identify the optimal combination of markers for discriminating target populations using multiple SNP markers.

• 생명과학회지
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• 제30권7호
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• pp.614-624
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• 2020

최근 next-generation sequencing technology의 발달로 유전체 분석 사례는 증가하고 있으나, 단감에 있어 적용 가능한 Single Nucleotide Polymorphism (SNP) 마커 및 적용 결과는 거의 없는 실정이다. 이에 우리나라 고유 떫은감 5품종으로부터 개발된 SNP primer 들을 단감 품종에 적용하여 사용 가능성을 검증하고자 수행하였다. Jung 등에 의해 개발된 19개 SNP primer들의 PCR 조건을 확인 한 후 본 실험의 전기영동 방식으로는 분석이 매우 어려웠던 8개의 primer를 제외한 11개의 SNP primer들을 최종 선발하였다. 1, 2차 검증을 통해 최종 선발된 11개의 SNP primer 들을 76품종 및 계통(불완전단감 20, 완전단감 30, 완전떫은감 20, 불완전떫은감 6)에 적용한 결과 38품종 및 계통(불완전단감 8, 완전단감 18, 완전떫은감 9, 불완전떫은감 3품종)은 각 품종 및 계통 간 구분을 할 수가 없었다. 그러나 최종 선발된 11개의 SNP primer 들을 신품종에 적용한 결과만를 보면 '감누리', '단누리', '홍추'와 '자미시', '미감조생'을 동시에 구분할 수 있어 단감 신품종 판별을 위한 특이적 마커로 사용될 수 있을 것으로 판단된다.

• International Journal of Oral Biology
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• 제31권3호
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• pp.107-112
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• 2006

Aldehyde dehydrogenase (ALDH) plays an important role in alcohol metabolism; ALDH is responsible for the oxidation of acetaldehyde generated during alcohol oxidation. ALDH is also known to oxidize various other endogenous and exogenous aldehydes. Cytochrome P-450 2E1 (CYP2E1), a liver microsomal enzyme, also metabolizes acetaldehyde and ethanol and can be induced by other inducers including acetone and ethanol. We examined single nucleotide polymorphisms (SNP) of ALDH and CYP2E1 genotypes in Korean. Restriction fragment length polymorphism (RFLP) method was used to determine ALDH and CYP2E1 SNP. Mutation in ALDH was 60% (heterozygote 46.7% and homozygote 13.3%) among 15 cases. CYP2E1 mutation was 52.7% (heterozygote 47.4% and homozygote 5.3%) among 19 cases.

• Asian-Australasian Journal of Animal Sciences
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• 제16권1호
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• pp.100-103
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• 2003

Higher environmental temperature affects the economic performance of pigs. Heat shock protein 70 has been shown to play an important role in thermoresistance. The purpose of this study was to assess the effect of a single nucleotide polymorphism in the 5'-flanking region of porcine HSP70.2 on growth performance in Taiwanese Duroc. The genotype of this nt 393 polymorphic site could be verified by digestion with Bsa WI restriction enzyme of a PCR product. Pigs with TT and TC genotypes have thinner backfats than those with CC type (p<0.05). The result suggested that the polymorphic Bsa WI site in the 5'flanking region of porcine HSP70.2 may be used as a marker for the early selection of ultrasonic backfat thickness in Duroc pigs.

• Asian Pacific Journal of Cancer Prevention
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• 제13권9호
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• pp.4315-4320
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• 2012

Background: The P53 tumor suppressor gene plays a pivotal role in maintaining cellular homeostasis by preventing the propagation of genome mutations. P53 in its transcriptionally active form is capable of activating distinct target genes that contribute to either apoptosis or growth arrest, like P21. However, the MDM2 gene is a major negative regulator of P53. Single nucleotide polymorphisms (SNP) in codon Arg72Pro of P53 results in impairment of the tumor suppressor activity of the gene. A similar effect is caused by a SNP in codon 31 of P21. In contrast, a SNP in position 309 of MDM2 results in increased expression due to substitution of thymine by guanine. All three polymorphisms have been associated with increased risk of tumorigenesis. Aim of the study: We aimed to study the prevalence of SNPs in the P53 pathway involving the three genes, P53, P21 and MDM2, among acute myeloid leukemia (AML) patients and to compare it to apparently normal healthy controls for assessment of impact on risk. Results: We found that the P21 ser31arg heterozygous polymorphism increases the risk of AML (P value=0.017, OR=2.946, 95% CI=1.216-7.134). Although the MDM2 309G allele was itself without affect, it showed a synergistic effect with P21 ser/arg polymorphism (P value=0.003, OR=6.807, 95% CI=1.909-24.629). However, the MDM2 309T allele abolish risk effect of the P21 polymorphic allele (P value=0.71). There is no significant association of P53 arg72pro polymorphism on the risk of AML. Conclusion: We suggest that SNPs in the P53 pathway, especially the P21 ser31arg polymorphism and combined polymorphisms especially the P21/MDM2 might be genetic susceptibility factors in the pathogenesis of AML.

• Asian Pacific Journal of Cancer Prevention
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• 제17권5호
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• pp.2625-2628
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• 2016

ABCC11 is reported to be associated with breast cancer. However, whether ABCC11 polymorphisms relate to breast cancer risk remains unclear. This study aimed to evaluate any association of a single nucleotide polymorphism (SNP), rs17822931, in ABCC11 with breast cancer in Koreans. Genomic DNA samples of 170 women with breast cancer and 100 controls were assessed for SNP rs17822931 of ABCC11 by single-strand conformation polymorphism (SSCP) and DNA sequencing. A 27-bp deletion (${\Delta}27$) of ABCC11 was analyzed by PCR amplification. The genotype of SNP rs17822931 was confirmed to be AA in all samples from breast cancer patients and ${\Delta}27$ was found in none of the samples. Our finding indicated that the SNP rs17822931 in ABCC11 is not associated with breast cancer. However, this study does provide information on fundamental genetic aspects of ABCC11 with regard to breast cancer risk in Koreans.

• Animal cells and systems
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• 제5권2호
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• pp.153-156
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• 2001

A key aspect of genomic research in the “post-genome era”is to associate sequence variations with heritable phenotypes. The most common variations in the human genome are single nucleotide polymorphisms (SNPs) that occur approximately once in every 500 to 1,000 bases. Although analyzing the phenotypic outcome of these SNPs is crucial to facilitate large-scale association studies of genetic diseases, detection of SNPs from an extended number of human DNA samples is often difficult, labor-intensive and time-consuming. Recent development in SNP detection methods using DNA microarrays and mass spectrophotometry has allowed automated high throughput analyses, but such equipments are not accessible to many scientists. In this study, we demonstrate that a simple PCR-based method using primers with a mismatched base at the 3'-end provides a fast and easy tool to identify known SNPs from human genomic DNA in a regular molecular biology laboratory. Results from this PCR amplification of specific alleles (PASA) analysis efficiently and accurately typed the Q576R polymorphism of human IL4 receptor from the genomic DNAs of 29 Koreans, including 9 samples whose genotype could not be discerned by the conventiona1 PCR-SSCP (single strand conformation polymorphism) method. Given the increasing attention to disease-associated polymorphisms in genomic research, this alternative technique will be very useful to identify SNPs in large-scale population studies.

• 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.

• 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.

• 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.