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RISS 인기검색어
- 검색키워드
- 주제어 : Single Nucleotide Polymorphisms (SNPs) (검색결과 29 건)
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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.
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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.
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Kim, Jung Eun,Lee, Young Mee,Lee, Jeong-Ho,Noh, Jae Koo,Kim, Hyun Chul,Park, Choul-Ji,Park, Jong-Won,Kim, Kyung-Kil The Korean Society of Developmental Biology 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.
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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.
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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.
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de los Angeles Rivera-Juarez, Maria,Rosas-Murrieta, Nora Hilda,Mendieta-Carmona, Victoriano,Hernandez-Pacheco, Raquel Esneidy,Zamora-Ginez, Irma,Rodea-Avila, Carlos,Apresa-Garcia, Teresa,Garay-Villar, Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.3
Sialyltransferase gene expression is altered in several cancers, including examples in the cervix. Transcriptional regulation of the responsible genes depends on different promoters. We aimed to determine the association of single-nucleotide polymorphisms in the B3 promoter of the ST3GAL4 gene and the P1 promoter of the ST6GAL1 gene with cervical premalignant lesions or cervical cancer. A blood sample and/or cervical scrapes were obtained from 104 women with normal cytology, 154 with premalignant lesions and 100 with cervical cancer. We also included 119 blood samples of random donors. The polymorphisms were identified by sequencing from PCR products. For the B3 promoter, a fragment of 506 bp (from nucleotide -408 to +98) was analyzed, and for the P1 promoter a 490 bp (-326 to +164) fragment. The polymorphism analysis showed that at SNP rs10893506, genotypes CC and CT of the ST3GAL4 B3 promoter were associated with the presence of premalignant lesions (OR=2.89; 95%CI 1.72-4.85) and cervical cancer (OR=2.23; 95%CI 1.27-3.91). We detected only one allele of each polymorphism in the ST6GAL1 P1 promoter. We did not detect any genetic variability in the P1 promoter region in our study population. Our results suggest that the rs10893506 polymorphism -22C/T may increase susceptibility to premalignant and malignant lesions of the cervix.
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Rattikan Suwannasing,Monchai Duangjinda,Wuttigrai Boonkum,Rutjawate Taharnklaew,Komson Tuangsithtanon 아세아·태평양축산학회 2018 Animal Bioscience Vol.31 No.12
Objective: The purpose of this study was to investigate a single step genome-wide association study (ssGWAS) for identifying genomic regions affecting reproductive traits in Landrace and Large White pigs. Methods: The traits included the number of pigs weaned per sow per year (PWSY), the number of litters per sow per year (LSY), pigs weaned per litters (PWL), born alive per litters (BAL), non-productive day (NPD) and wean to conception interval per litters (W2CL). A total of 321 animals (140 Landrace and 181 Large White pigs) were genotyped with the Illumina Porcine SNP 60k BeadChip, containing 61,177 single nucleotide polymorphisms (SNPs), while multiple traits single-step genomic BLUP method was used to calculate variances of 5 SNP windows for 11,048 Landrace and 13,985 Large White data records. Results: The outcome of ssGWAS on the reproductive traits identified twenty-five and twenty-two SNPs associated with reproductive traits in Landrace and Large White, respectively. Three known genes were identified to be candidate genes in Landrace pigs including retinol binding protein 7, and ubiquitination factor E4B genes for PWL, BAL, W2CL, and PWSY and one gene, solute carrier organic anion transporter family member 6A1, for LSY and NPD. Meanwhile, five genes were identified to be candidate genes in Large White, two of which, aldehyde dehydrogenase 1 family member A3 and leucine rich repeat kinase 1, associated with all of six reproduction traits and three genes; retrotransposon Gag like 4, transient receptor potential cation channel subfamily C member 5, and LHFPL tetraspan subfamily member 1 for five traits except W2CL. Conclusion: The genomic regions identified in this study provided a start-up point for marker assisted selection and estimating genomic breeding values for improving reproductive traits in commercial pig populations.
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유희정,조인희,박미라,양소영,김순애 대한의학회 2013 Journal of Korean medical science Vol.28 No.9
This study evaluated the family-based genetic association between autism spectrum disorders (ASDs) and 5 single-nucleotide polymorphisms (SNPs) in the catechol-omethyltransferase gene (COMT), which was found among 151 Korean ASDs family trios (dominant model Z = 2.598, P = 0.009, PFDR = 0.045). We found a statistically significant allele transmission or association in terms of the rs6269 SNP in the ASDs trios. Moreover,in the haplotype analysis, the haplotypes with rs6269 demonstrated significant evidence of an association with ASDs (additive model rs6269-rs4818-rs4680-rs769224 haplotype P = 0.004, PFDR = 0.040). Thus, an association may exist between the variants of the COMT gene and the occurrence of ASDs in Koreans.
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Yoo, Hee Jeong,Cho, In Hee,Park, Mira,Yang, So Young,Kim, Soon Ae The Korean Academy of Medical Sciences 2013 JOURNAL OF KOREAN MEDICAL SCIENCE Vol.28 No.9
<P>This study evaluated the family-based genetic association between autism spectrum disorders (ASDs) and 5 single-nucleotide polymorphisms (SNPs) in the catechol-<I>o</I>-methyltransferase gene (<I>COMT</I>), which was found among 151 Korean ASDs family trios (dominant model Z = 2.598, <I>P</I> = 0.009, <I>P</I><SUB>FDR</SUB> = 0.045). We found a statistically significant allele transmission or association in terms of the rs6269 SNP in the ASDs trios. Moreover, in the haplotype analysis, the haplotypes with rs6269 demonstrated significant evidence of an association with ASDs (additive model rs6269-rs4818-rs4680-rs769224 haplotype <I>P</I> = 0.004, <I>P</I><SUB>FDR</SUB> = 0.040). Thus, an association may exist between the variants of the <I>COMT</I> gene and the occurrence of ASDs in Koreans.</P>
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이소연,권기상,고영화,권오유,Lee, Soyeon,Kwon, Kiang,Ko, Younghwa,Kwon, O-Yu Korean Society of Life Science 2021 생명과학회지 Vol.31 No.6
본 연구는 전장 유전체 연관성 분석(genome-wide association study, GWAS)을 통해 ERp29의 mRNA 발현과 관련된 유전좌위(expression quantitative trait loci, eQTL)을 식별하는 것을 목표로 하였다. 대상 유전자는 ERp29이다. ERp29는 소포체(ER)의 lumen에 단백질의 folding & assembly 기능을 가진 분자 chaperone 단백질로서 소포체 스트레스에 의해 발현량이 증가하며, 분비 단백질의 생합성에 관여한다. 최근 연구 결과 발암과 연관성이 알려지면서 주목을 받고 있다. 총 373명의 유럽인의 genome을 대상으로 GWAS 분석 결과, ERp29 유전자 발현은 정소와 뇌에서 강하게 발현하는 long noncoding RNA (LncRNA) LOC105372577과 관계가 있었다. 즉, 3개의 eQTL: rs6138266 (p<4.172e10-9), rs62193420 (p<1.173e10-8), rs6138267 (p<2.041e10-8)와 연관성이 깊은 것으로 밝혀졌다. ERp29의 발현과 연관이 있는 것으로 확인된 3개의 eQTL을 사용한 transcriptome-wide association study (TWAS) 결과 osteosarcoma amplified 9 (OS9) 발현과 유의한 연관성을 보이며 OS9 유전자의 up-stream에 upstream of transcription factor 1 (USF1)이 결합할 수 있는 것을 알았다. This study identified genomic factors associated with endoplasmic reticulum protein (ERp)29 gene expression in a genome-wide association study (GWAS) of genetic variants, including single-nucleotide polymorphisms (SNPs). In total, 373 European genes from the 1000 Genomes Project were analyzed. SNPs with an allelic frequency of less than or more than 5% were removed, resulting in 5,913,563 SNPs including in the analysis. The following expression quantitative trait loci (eQTL) from the long noncoding RNA LOC105372577 were strongly associated with ERp29 expression: rs6138266 (p<4.172e10), rs62193420 (p<1.173e10), and rs6138267 (p<2.041e10). These were strongly expressed in the testis and in the brain. The three eQTL were identified through a transcriptome-wide association study (TWAS) and showed a significant association with ERp29 and osteosarcoma amplified 9 (OS9) expression. Upstream sequences of rs6138266 were recognized by ChIP-seq data, while HaploReg was used to demonstrate how its regulatory DNA binds upstream of transcription factor 1 (USF1). There were no changes in the expression of OS9 or USF1 following ER stress.
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