• Genomics & Informatics
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• 제12권4호
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• pp.289-292
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• 2014

Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases, including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.

• 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.

• Animal Bioscience
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• 제37권4호
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• pp.600-608
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• 2024

Objective: In this study, we aimed to evaluate the usability single nucleotide polymorphisms (SNPs) for parentage testing of horse breeds in Korea. Methods: The genotypes of 93 horse samples (38 Thoroughbred horses, 17 Jeju horses, 20 Quarter horses, and 18 American miniature horses) were determined using 15 microsatellite (Ms) markers (AHT4, AHT5, ASB2, ASB17, ASB23, CA425, HMS1, HMS2, HMS3, HMS6, HMS7, HTG4, HTG10, LEX3, and VHL20) and 101 SNP markers. Results: Paternity tests were performed using 15 Ms markers and 101 SNP markers in Thoroughbred horses and Quarter horses. AHT5, ASB2, ASB17, ASB23, CA425, HMS7, HTG10, and LEX3 did not follow Mendelian inheritance in Thoroughbred horses, whereas in Quarter horses, only AHT4, ASB2, and HMS2 showed Mendelian inheritance, consequently, paternity was not established. Meanwhile, 31 markers, including MNEc_2_2_2_98568918_BIEC2_502451, in Thoroughbred horses, and 30 markers, including MNEc_2_30_7430735_BIEC2_816793, in Quarter horses did not conform with Mendelian inheritance and therefore, could not be used for establishing parentage. Conclusion: The possibility of replacing Ms markers with SNP markers for paternity testing in horses was confirmed. However, further research using more samples is necessary.

• 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.

• 한국잠사학회:학술대회논문집
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• 한국잠사학회 2003년도 International Symposium of Silkworm/Insect Biotechnology and Annual Meeting of Korea Society of Sericultural Science
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• pp.23-23
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• 2003

We made use of 81, 635 expressed sequence tags (ESTs) derived from 12 different cDNA libraries of Bombyx mori to identify high-quality candidate single nucleotide polymorphisms (SNPs). By PHRAP assembling, we obtained 12, 980 contigs containing 11, 531 contigs assembled by more than one reads. From 117 contig sequences, which were assembled by 1, 576 high-quality reads base-called with PHRED, we identified 101 candidate SNPs and 27 single base insertions/deletions based on a neighborhood quality standard(NQS) of SNP. (omitted)

• 미생물학회지
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• 제26권3호
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• pp.155-161
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• 1988

Nucleotide sequence homology between bovine, simian, and porcine rotavirus was determined by the RNA:RNA hybridization technique. Single stranded RNA, prepared in vitro with EDTA activated endogeneous viral RNA polymerase, was hhbridized with tritium labeled bovine rotavirus genomic RNA. The heteroduplex RNA was treated with single stranded RNA specific ribonucleases and the RNase resistant hybrid RNA was precipitated, and collected by filtration on a filter paper. Seventy four percent RNA sequence homology between bovine and simian rotavirus and 8 percent RNA sequence homology between bovine and porcine rotavirus was confirmed by hybridization between tritium labeled single stranded RNA and viral genomic RNA.

• 한국정보과학회:학술대회논문집
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• 한국정보과학회 2002년도 봄 학술발표논문집 Vol.29 No.1 (B)
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• pp.160-162
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• 2002

SNP는 개인과 개인간의 DNA에 존재하는 한 염기 쌍의 차이(single base-pair variation)이다. SNP를 이용하면 사람마다 다른 유전병의 형태 등을 규명할 수 있다. 본 논문에서는 한국생명공학연구원의 유전체 사업단에서 개발해 오고 있는 웹기반 SNP데이터 검색 시스템의 설계와 구현에 대해서 설명한다. 본 시스템은 일반 속성(attribute)을 저장하고 검색하기 위해 PostgreSQL DBMS를 사용하고, DNA 시퀸스 검색을 위해 BLAST검색엔진을 사용한 약결합 아키텍쳐(loosely-coupled architecture)를 채택하고 있다. 즉, 일반 속성으로 저장될 수 있는 데이터들은 데이터베이스의 테이블들의 컬럼 값으로 저장하고 SQL 언어를 통해 검색할 수 있도록 하였으며, DNA 시퀸스 검색을 위해서는 BLAST에서 제공하는 인덱스를 구축하고 BLAST 명령어를 사용하여 검색할 수 있도록 하였다. 또한, 결과 분석 모듈을 구현하여 검색 결과들이 다른 웹 사이트의 데이터를 가리키도록 하였다.

• 한국독성학회:학술대회논문집
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• 한국독성학회 2000년도 국제심포지움 및 추계학술대회
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• pp.167-189
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• 2000

• 한국동물학회:학술대회논문집
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• 한국동물학회 2000년도 공동 춘계학술대회
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• pp.86.2-86
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• 2000

No Abstract, See Full Text

• 한국유전체학회:학술대회논문집
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• 한국유전체학회 2002년도 The 11th Korea Genome Conference
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• pp.45-45
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• 2002