SNPchaser:DNA서열의 SNPs 치환 및 Heterozygosity 확인 프로그램

장진우(Jin-Woo Jang),이현철(Hyun-Chul Lee),이명훈(Myung-Hoon Lee),최연식(YeonShik Choi),추동원(Dongwon Choo),박기정(Kiejung Park),이대상(Daesang Lee) 한국생물공학회 2009 KSBB Journal Vol.24 No.4

단염기 다양성 (Single-Nucleotide Polymorphisms, SNPs) 은 핵산수준에서의 개개인의 유전 서열간의 차이를 나타내는 말로 최근 맞춤의약 분야에서 각광 받고 있다. 일반적으로 NPs존재 유무를 확인하는데 주로 사용되는 방법은 ABI automated DNA sequencer와 같은 대용량 염기서열 결정 기계에서 산출되는 결과물 파일로부터 DNA서열을 추출하여 BLAST와 같은 상동성 검색을 수행하는 것이다. 본 논문에서는 사용자로부터 참조서열, AB1파일, SNPs 존재 가능성을 가진 염기의 위치 정보를 입력 값으로 받아 해당 위치에 존재하는 염기의 SNPs 치환 및 heterozygosity 여부를 확인 할 수 있는 프로그램인 SNPchaser를 개발하였다. 특정 유전자 서열 내에서 SNPs를 보이는 염기의 위치에 대한 정보를 사용자가 알고 있는 경우, 전체 유전자 서열에 대해 SNPs유무를 조사할 필요 없이 SNPs를 보인다고 보고된 위치의 염기를 조사하여 SNPs유무를 판단하고, 해당지역의 염기의 chromatogram정보를 사용자에게 제공하는 기능을 가지고 있다. 또한 SNPchaser는 사람과 같은 2배체의 염색체를 가진 생명체에 존재 하는 SNPs지역의 염기에 대한 heterozygosity여부를 사용자가 손쉽게 판별 할 수 있도록 하였다. 본 논문에서 개발한 SNPchaser는 http://www.bioinformatics.ac.kr/SNPchaser에서 사용 가능하다. Single-nucleotide polymorphisms (SNPs) are the DNA sequences difference among the same species in the level of nucleic acids and are widely applied in clinical fields such as personalized medicine. The routine and labor-intensive methods to determine SNPs are performing the sequence homology search by using BLAST and navigating the trace of chromatogram files generated by high-throughput DNA sequencing machine by using Chromas program. In this paper, we developed SNPchaser, a web-based program for detecting SNPs substitution and heterozygosity existence, to improve the labor-intensive method in determining SNPs. NPchaser performed sequence alignment and visualized the suspected region of SNPs by using user"s reference sequence, AB1 files, and positional information of SNPs. It simultaneously provided the results of sequences alignment and chromatogram of relevant area of SNPs to user. In addition, SNPchaser can easily determine existence of heterozygosity in SNPs area. SNPchaser is freely accessible via the web site http://www.bioinformatics.ac.kr/SNPchaser and the source codes are available for academic research purpose.

다이아몬드 FETs에서 전기적 바이어스 방법을 이용한 단일염기 다형성(SNPs) 검출

송광섭(Kwang Soup Song) 대한전자공학회 2015 전자공학회논문지 Vol.52 No.3

한국인 정신분열병환자에서 MTHFR 유전자의 단일 염기 다형성인 C677T와 A1298C의 연관성 분석

김제원(Je-Won Kim),강호진(Ho Jin Kang),김병권(Byoung Gwon Kim),홍영습(Young-Seoub Hong),김성환(Seong Hwan Kim),최병무(Byeong Moo Choe) 대한생물치료정신의학회 2009 생물치료정신의학 Vol.15 No.2

Objectives: Methylenetetrahydrofolate reductase (MTHFR) plays an important role in folate metabolism, and the C677T and A1298C single nucleotide polymorphisms(SNPs) of the MTHFR gene may be associated with schizophrenia. The relationship between MTHFR SNPs and schizophrenia is unclear in Korean schizophrenic patients. The purpose in this study was to determine the association between the MTHFR gene SNPs and schizophrenia in Korean patients. Methods: Three hundred and sixty six patients with schizophrenia and 359 normal control subjects were used to identify the SNPs. Genetic analysis was carried out in the C677T and A1298C SNP regions using the SNP-IT™ assay. The allele, genotype and haplotype frequencies were compared between the two groups. The subgroups were divided on the basis of the onset age, and the allele frequencies and genotype frequencies were individually compared among the subgroups. Results: Gene variation of the MTHFR C677T and A1298C SNPs did not show significant differences between the schizophrenic patients and controls. In addition, no association between their SNPs and the onset age of schizophrenia was found. Conclusion: A genetic association between the C677T and A1298C SNPs on the MTHFR gene and Korean schizophrenic patients was not found in this study.

A Statistical Analysis of SNPs, In-Dels, and Their Flanking Sequences in Human Genomic Regions

Shin, Seung-Wook,Kim, Young-Joo,Kim, Byung-Dong Korea Genome Organization 2007 Genomics & informatics Vol.5 No.2

Due to the increasing interest in SNPs and mutational hot spots for disease traits, it is becoming more important to define and understand the relationship between SNPs and their flanking sequences. To study the effects of flanking sequences on SNPs, statistical approaches are necessary to assess bias in SNP data. In this study we mainly applied Markov chains for SNP sequences, particularly those located in intronic regions, and for analysis of in-del data. All of the pertaining sequences showed a significant tendency to generate particular SNP types. Most sequences flanking SNPs had lower complexities than average sequences, and some of them were associated with microsatellites. Moreover, many Alu repeats were found in the flanking sequences. We observed an elevated frequency of single-base-pair repeat-like sequences, mirror repeats, and palindromes in the SNP flanking sequence data. Alu repeats are hypothesized to be associated with C-to-T transition mutations or A-to-I RNA editing. In particular, the in-del data revealed an association between particular changes such as palindromes or mirror repeats. Results indicate that the mechanism of induction of in-del transitions is probably very different from that which is responsible for other SNPs. From a statistical perspective, frequent DNA lesions in some regions probably have effects on the occurrence of SNPs.

Mutual information and linkage disequilibrium based SNP association study by grouping case‐control

Xiguo Yuan,Junying Zhang,Yue Wang 한국유전학회 2011 Genes & Genomics Vol.33 No.1

Two main reasons for the difficulties to search for susceptibility single‐nucleotide polymorphisms (SNPs) underlying genetic diseases are that the findings are not easy to be confirmed and the interactions between potential susceptibility SNPs are not clear. Many available association studies usually presented results with significance levels but did not illustrate the stability of the results. In some sense, their performances might be unclear in real practice. In this paper, we develop a novel method based on mutual information theory and linkage disequilibrium by grouping case‐control. Mutual information (MI)is used to test multiple SNPs in combining with disease status. Those SNPs contributing the maximum MI are selected as potential susceptibility SNPs. Linkage disequilibrium (LD) analysis is used to extend MI detected result so that both direct and indirect factors can be included in the final result. The purpose of case‐control grouping is to generate a number of data groups by randomly sampling from target samples. Each group is assumed to have almost the same number of individuals (cases and controls), and overlap is allowed among the groups. We apply the method to each data group, and then make comparisons and intersections between the results obtained from each of the groups so as to give the final result. We implement the method by continuously grouping until the final result reaches a stable state and a highly significance level. The experimental results indicate that our method to detect susceptibility SNPs in simulated and real data sets has shown remarkable success.

Elucidating breed-specific variants of native pigs in Korea: insights into pig breeds’ genomic characteristics

이영섭,손승우,이학교,이라함,신동현 한국통합생물학회 2022 Animal cells and systems Vol.26 No.6

Although conserving native pig breeds is important in Korea, research on the genomic aspects to identify breed-specific variations in native pig breeds is uncommon. Single nucleotide polymorphisms (SNPs) can be a powerful source for identifying breed-specific variants. We used whole genome sequencing data, including Jeju Native Pig (JNP), Korean Native Pig (KNP), Korean Wild Boar (KWB), and other western commercial pig breeds to determine native pig breed-specific SNPs. Furthermore, the goal was not only to determine the genomic specificity of native pig breeds but also to identify SNPs that carry breed-specific information (breedinformative SNPs) that can be related to breed characteristics. The representative characteristics of native pigs are their unique meat quality and disease resistance. We surveyed the gene ontology (GO) of native pigs with breed-specific SNPs. Examining the genes associated with GO may contribute to revealing the reasons for the unique characteristics of native pig breeds. The enriched GOs terms were neuron projection development, cell surface receptor signaling pathway, ion homeostasis in JNP, cell adhesion and wound healing in KNP, and DNA repair and reproduction in KWB. We expect that this study of breed-specific SNPs will enable us to gain a deeper understanding of native pigs in Korea.

Development and validation of single nucleotide polymorphism (SNP) markers from an expressed sequence tag(EST) database in olive flounder (Paralichthys olivaceus)

Jung Eun Kim,Young Mee Lee,Jae Koo Noh,Hyun Chul Kim,Choul Ji Park,Jong Won Park,Kyung-Kil Kim,Jeong Ho Lee 한국발생생물학회 2014 한국발생생물학회 학술발표대회 Vol.2014 No.9

Molecular markers are useful for selecting to include superior character genetic like as strong immune system and rapid growth in fish. The marker is also very important part of breeding technology in Olive flounder (Paralichthys olivaceus). Single nucleotide polymorphisms (SNPs) marker is already in use widely for genomic research and breeding. But this SNPs marker hardly has been validated for screening functional genes in Olive flounder. We study identify single nucleotide polymorphisms (SNPs) on Expressed sequence tag (EST) database, develop usable SNP marker and apply to wild sample and cultured of olive flounder. As a result, Out of total 4.327 ESTs, 693contigs and 514 SNP from total contigs were detected while these substitutions include 297 transitions and 217 transversions. 144 developed markers were applied in 16 samples (wild 8, culture 8), Out of total marker, only 32 markers had detected polymorphic in sample. Polymorphism of 32 markers was observed in the variety genes region involved in immunity and protein synthesis. And the 32 marker were identified 21 transitions, 11 transversions, and indel was not detected in polymorphic SNPs. The analysis on heterozygosity by sample showed 0.34 in wild sample and 0.29 in cultured sample. In conclusion, we was identified SNP and Polymorphism by designed new marker, it supports that development marker is 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.

Development and Validation of Single Nucleotide Polymorphism (SNP) Markers from an Expressed Sequence Tag (EST) Database in Olive Flounder (Paralichthys olivaceus)

김정은,이정호,이영미,노재구,김현철,박철지,박종원,김경길 한국발생생물학회 2014 발생과 생식 Vol.18 No.4

To successful molecular breeding, identification and functional characterization of breeding related genes anddevelopment of molecular breeding techniques using DNA markers are essential. Although the development of a usefulmarker is difficult in the aspect of time, cost and effort, many markers are being developed to be used in molecular breedingand developed markers have been used in many fields. Single nucleotide polymorphisms (SNPs) markers were widely usedfor genomic research and breeding, but has hardly been validated for screening functional genes in olive flounder. Weidentified single nucleotide polymorphisms (SNPs) from expressed sequence tag (EST) database in olive flounder; out of atotal 4,327 ESTs, 693 contigs and 514 SNPs were detected in total EST, and these substitutions include 297 transitions and217 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 32markers had detected polymorphism in sample, also identified 21 transitions and 11 transversions, whereas indel was notdetected 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 supportsthat developed markers are suitable for SNP detection and diversity analysis in olive flounder. The outcome of this study canbe basic data for researches for immunity gene and characteristic with SNP.

Development and Validation of Single Nucleotide Polymorphism (SNP) Markers from an Expressed Sequence Tag (EST) Database in Olive Flounder (Paralichthys olivaceus)

Jung Eun Kim,Young Mee Lee,Jeong-Ho Lee,Jae Koo Noh,Hyun Chul Kim,Choul-Ji Park,Jong-Won Park,Kyung-Kil Kim 한국발생생물학회 2014 발생과 생식 Vol.18 No.4

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.

유전 및 육종 : 돼지 Melanocortin 4 Receptor(MC4R) 유전자의 육질연관성 분석

노정건 ( Jung Gun Roh ),김상욱 ( Sang Wook Kim ),최정석 ( Jung Suk Choi ),최양일 ( Yang Il Choi ),김종주 ( Jong Joo Kim ),최봉환 ( Bong Hwan Choi ),김태헌 ( Tae Hun Kim ),김관석 ( Kwan Suk Kim ) 한국동물자원과학회 ( 구 한국축산학회 ) 2012 한국축산학회지 Vol.54 No.1

본 연구는 한국재래돼지의 MC4R 유전자 내의 단일염기변이들을 규명하고 그 유전자형 효과가 유전자표지인자를 이용한 선발 (Marker assisted selection, MAS)에 활용 가능한지를 검증하기 위해서 수행되었다. 한국재래돼지의 MC4R 유전자 총 염기서열을 분석하기 위해 6개의 Primer들을 이용하여 증폭산물을 생성하였으며, 염기서열분석을 통해 총 6개(c.-780C>G, c-135C>T, c.175C >T-Leu59Leu, c.707A>G-Arg236His, c.892A>G-Asp298Asn, c.*430A >T)의 단일염기변이를 발견하였다. 한국재래돼지 MC4R 유전자 내의 총 6개의 단일염기변이들간의 연관불균형과 반수체 분석을 통해 단일염기변이들간의 연관성을 분석하였으며, c.-780C >G, c-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His와 c.*430A>T는 완전한 연관불균형을 이루고 있었고, c.892A>G (Asp298Asn) 단일염기변이만 r2-value가 0.028, D`-value가 0.348로 연관불균형 정도가 매우 낮았다. c.707A>G(Arg236His)와 c.892A>G(Asp298Asn) 단일염기변이들을 선발하여 PCR-RFLP 유전자형 분석방법을 이용해 돼지 5품종간의 유전자형 빈도를 추정한 결과, c.707A>G(Arg236His) 단일염기변이는 요크셔 품종 집단에서 오직 A(His) 대립유전자를 관찰할 수 있었으며, 나머지 한국재래돼지, 랜드레이스, 버크셔와 듀록 품종에서는 G 대립유전자의 고정으로 나타났다. c.707A>G 단일염기변이와 육질형질을 484두에서 연관성 분석을 실시한 결과, 조지방, 등심 내의 수분, 육색, 적색도 그리고 황색도 등에서 유의적인 연관성을 관찰할 수 있었다. c.892A>G(Asp298Asn) 단일염기변이의 유전자형 빈도는 품종별로 차이가 났으며, A(Asn) 대립유전자의 빈도가 가장 높은 품종은 듀록으로 나타났고, G(Asp) 대립유전자의 빈도가 가장 높은 품종은 한국재래돼지로 조사되었다. c.892A>G(Asp 298Asn) 단일염기변이와 돼지 4 집단의 육질형질을 1,126두에서 분석한 결과, 등지방두께에 고도의 유의적인 효과를 관찰할 수 있었다(P<0.002). AA 유전자형을 가진 개체가 AG나 GG 유전자형을 가진 개체보다 등지방두께가 두꺼운 것을 확인할 수 있었다. 본 연구의 결과를 통해 MC4R 유전자 내의 c.892A>G(Asp298Asn) 단일염기변이는 돼지의 선발개량에 유전자표지인자로서 충분한 효과가 있음을 검증하였다. This study aimed to investigate the single nucleotide polymorphisms(SNPs) of the porcine MC4R gene and validate the effect of the MC4R genotype for marker assisted selection(MAS). Six amplicons were produced to analyze the entire base sequences of the porcine MC4R gene and six SNPs were detected(c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, c.892A>G-Asp298Asn, and c.*430A>T). Linkage disequilibrium(LD) of the six SNPs was analyzed by performing haploid analysis. There was a perfect linkage disequilibrium in c.-780C>G, c.-135C>T, c.175C>T-Leu59Leu, c.707A>G-Arg236His, and c.*430A>T. Only the c.892A>G(Asp298Asn) SNP showed a very low LD with an r2 value of 0.028 and the D` value of 0.348. As a result, the two SNPs-c.707A>G(Arg236His) and c.892A>G(Asp298Asn)-were selected to extract the genotype frequencies from the 5 pig breeds by using the polymerase chain reaction-restriction fragment length polymorphism(PCR-RFLP) genotype analysis method. The SNP frequency of c.707A>G(Arg236His) indicated the presence of the A(His) allele only in Yorkshire, while the G allele was fixed in the KNP, Landrace, Berkshire, and Duroc. Association analysis was carried out in 484 pigs with the c.707A>G (Arg236His) SNP and the meat quality traits of four different pig cross populations: a significant association was noted in crude fat, sirloin moisture, meat color, and the degree of red and yellow coloration. The frequency of the c.892A>G(Asp298Asn) SNP genotype varied among the breeds; while Duroc showed the highest frequency of the A(Asn) allele, KNP showed the highest frequency of the G(Asp) allele. Association analysis was carried out in 1126 pigs with the c.892A>G(Asp298Asn) SNP and the meat quality traits of four pig populations: a highly significant linkage was noted in the back-fat thickness(P<0.002). It was found that the back-fat thickness was higher in individuals with the AA genotype than in those with the AG or GG genotype. Thus, in this study, we verified that the c.892A>G(Asp298Asn) SNP in the pig MC4R gene has a sufficient effect as a gene marker for MAS in Korean pork industry.