• Title, Summary, Keyword: SNPs

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SNPchaser : A Web-based Program for Detecting SNPs Substitution and Heterozygosity Existence (SNPchaser : DNA서열의 SNPs 치환 및 Heterozygosity 확인 프로그램)

  • Jang, Jin-Woo;Lee, Hyun-Chul;Lee, Myung-Hoon;Choi, Yeon-Shik;Choo, Dong-Won;Park, Kie-Jung;Lee, Dae-Sang
    • KSBB Journal
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    • v.24 no.4
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    • pp.410-414
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    • 2009
  • 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. SNPchaser 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.

Synthesis and Characterization of Epoxy Silane-modified Silica/Polyurethane-urea Nanocomposite Films (에폭시 변성 실리카 나노입자/폴리우레탄-우레아 나노복합체 필름의 제조 및 특성 연구)

  • Joo, Jin;Kim, Hyeon Seok;Kim, Jin Tae;Yoo, Hye Jin;Lee, Jae Ryung;Cheong, In Woo
    • Korean Chemical Engineering Research
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    • v.50 no.2
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    • pp.371-378
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    • 2012
  • Hydrophilic silica nanoparticles (SNPs) were treated by using 3-glycidoxypropyltrimethoxy silane (GPTMS) and then they were blended with polyurethane-urea (PUU) emulsions to obtain SNPs/PUU nanocomposite films. Thermo-mechanical properties of the nanocomposite films were investigated by varying the grafted amount of GPTMS onto SNPs and the contents of SNPs in the PUU matrix. The thermo-mechanical properties of the nanocomposite films were also compared in terms of the dispersibility of SNPs in the PUU matrix and thermal curing of the GPTMS-grafted SNPs. The maximum amount of grafted GPTMS was $1.99{\times}10^{-6}\;mol/m^2$, and which covered ca. 53% of the total SNP surface area. $^{29}Si$ CP/MAS NMR analyses with the deconvolution of peaks revealed the details of polycondensation degree and patterns of GPTMS in the surface modification of SNPs. The surface modification did not significantly affect colloidal stability of the SNPs in aqueous medium; however, the hydrophobic modification of SNPs offered a favorable effect on the dispersibility of SNPs in the PUU matrix as well as better thermal stability. XRD patterns revealed that GPTMS-grafted SNPs broadened the reduced the characteristic peak of polyol in PUU matrix. The composite films became rigid and less flexible as the SNP content increased from 5 wt.% to 20 wt.%. Particularly, Young's modulus and tensile modulus significantly increased after the thermal curing reaction of the epoxy groups in the SNPs.

Replication Association Study between RBC Indices and Genetic Variants in Korean Population

  • Lee, Sang In;Park, Sangjung;Jin, Hyun-Seok
    • Biomedical Science Letters
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    • v.25 no.2
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    • pp.190-195
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    • 2019
  • Hemoglobin (Hb) concentrations and hematocrit (Hct) values can be changed by factors such as erythrocyte production, destruction, and bleeding. In addition, variants in the protein expression involved in the amount of red blood cells that determine Hb metabolism or Hct value can increase susceptibility to complex blood diseases. Previous studies have reported significant single nucleotide polymorphisms (SNPs) by applying a genome-wide association study (GWAS) on Hb levels and Hct values in European population. In this study, we confirmed whether the significant SNPs are replicated in Koreans. In previous studies, 26 and 18 SNPs with a significant correlation Hb and Hct were identified in Korean genotype data, and 21 and 12 SNPs were selected, respectively. The SNPs of PRKCE (rs10495928), TMPRSS6 (rs2235321, rs5756505, rs855791) were significantly associated with Hb (P<0.05). In the association analysis of Hct, the SNPs of HBS1L (rs6920211, rs9389268, rs9483788), PRKCE (rs4953318), SCGN (rs9348689) and TMPRSS6 (rs2413450) genes showed a significant correlation (P<0.05). Replicated SNPs and not replicated SNPs showed the difference of genetic distance calculated by Fst. The replicated SNPs with a significant correlation showed similar allele frequencies, whereas the not replicated SNPs showed a large difference in allele frequency. All replicated SNPs with significant correlations had Fst values less than 0.05, indicating that the genetic distance between the groups was close. On the other hand, the not replicated SNPs showed that the Fst value was 0.05 or more and the genetic distance was relatively large.

Detection of SNPs using electrical biased method on diamond FETs (다이아몬드 FETs에서 전기적 바이어스 방법을 이용한 단일염기 다형성(SNPs) 검출)

  • Song, Kwang Soup
    • Journal of the Institute of Electronics and Information Engineers
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    • v.52 no.3
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    • pp.190-195
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    • 2015
  • The detection of single nucleotide polymorphisms (SNPs) caused of mutant or genetic diseases is important to diagnosis and medicine. There are many methods have been proposed to detect SNPs. However the detection of SNPs is difficulty, because the difference of energy between complementary DNA (cDMA) and SNPs is very small. In this work, we detect the SNPs using field-effect transistors (FETs) which based on the detection of negative charge of DNA. We bias -0.3 V on the drain-source electrode at the target DNA hybridization process. The efficiency of hybridization and the amplitude of signal decrease by repulsive force between negative charge of DNA and negative bias on the electrode. However, the sensitivity of SNPs increases about 5 times from 1.7 mV to 8.7 mV.

Analysis of Single Nucleotide Polymorphisms of Leptin Gene in Hanwoo(Korean Cattle) (한우 Leptin 유전자의 단일 염기 다형성 분석)

  • Lee, J.-Min;Song, G.C.;Lee, J.Y.;Kim, Young-Bong
    • Journal of Animal Science and Technology
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    • v.49 no.3
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    • pp.295-302
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    • 2007
  • Leptin, the product of the obese(ob) gene, is an adipocyte-derived hormone for the regulation of whole- body energy storage and energy usage. It has been reported that the homozygous mutations in the gene for leptin(LEP) induce obesity and reduce energy expenditure. In cattle, LEP has significant roles directly or indirectly related with phenotypes such as body weight and fat deposits, therefore SNPs of LEP have been considered important genetic marker to estimate carcass fat content in cattle. In this study, SNPs were screened in LEP(2,222 bp) between intron 1 to 3'-UTR from 24 independent Hanwoo(Korean cattle) by PCR and DNA sequencing. Total 25 SNPs were found and two nonsynonymous SNPs including T1163A(V19E) and G3256A(G132D) were newly detected only from Hanwoo. Among 20 SNPs previously reported in cattle, 16 SNPs were found in Hanwoo; however, the frequencies of some SNPs were significantly different between Hanwoo and western cattle breeds. The other 4 SNPs were not detected from Hanwoo. These Hanwoo specific SNP patterns in LEP will be used in development of molecular marker and application to genetic improvement of Hanwoo.

A Scheme for Filtering SNPs Imputed in 8,842 Korean Individuals Based on the International HapMap Project Data

  • Lee, Ki-Chan;Kim, Sang-Soo
    • Genomics & Informatics
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    • v.7 no.2
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    • pp.136-140
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    • 2009
  • Genome-wide association (GWA) studies may benefit from the inclusion of imputed SNPs into their dataset. Due to its predictive nature, the imputation process is typically not perfect. Thus, it would be desirable to develop a scheme for filtering out the imputed SNPs by maximizing the concordance with the observed genotypes. We report such a scheme, which is based on the combination of several parameters that are calculated by PLINK, a popular GWA analysis software program. We imputed the genotypes of 8,842 Korean individuals, based on approximately 2 million SNP genotypes of the CHB+JPT panel in the International HapMap Project Phase II data, complementing the 352k SNPs in the original Affymetrix 5.0 dataset. A total of 333,418 SNPs were found in both datasets, with a median concordance rate of 98.7%. The concordance rates were calculated at different ranges of parameters, such as the number of proxy SNPs (NPRX), the fraction of successfully imputed individuals (IMPUTED), and the information content (INFO). The poor concordance that was observed at the lower values of the parameters allowed us to develop an optimal combination of the cutoffs (IMPUTED${\geq}$0.9 and INFO${\geq}$0.9). A total of 1,026,596 SNPs passed the cutoff, of which 94,364 were found in both datasets and had 99.4% median concordance. This study illustrates a conservative scheme for filtering imputed SNPs that would be useful in GWA studies.

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

  • Shin, Seung-Wook;Kim, Young-Joo;Kim, Byung-Dong
    • Genomics & Informatics
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    • v.5 no.2
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    • pp.68-76
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    • 2007
  • 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.

Characterization of Single Nucleotide Polymorphisms in 55 Disease-Associated Genes in a Korean Population

  • Lee, Seung-Ku;Kim, Hyoun-Geun;Kang, Jason-J.;Oh, Won-Il;Oh, Berm-Seok;Kwack, Kyu-Bum
    • Genomics & Informatics
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    • v.5 no.4
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    • pp.152-160
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    • 2007
  • Most common diseases are caused by multiple genetic and environmental factors. Among the genetic factors, single nucleotide polymorphisms (SNPs) are common DNA sequence variations in individuals and can serve as important genetic markers. Recently, investigations of gene-based and whole genome-based SNPs have been applied to association studies for marker discovery. However, SNPs are so population-specific that the association needs to be verified. Fifty-five genes and 384 SNPs were selected based on association with disease. Genotypes of 337 SNPs in candidate genes were determined using Illumina Sentrix Array Matrix (SAM) chips by an allele-specific extension method in 364 unrelated Korean individuals. Allelic frequencies of SNPs were compared with those of other populations obtained from the International HapMap database. Minor allele frequencies, linkage disequilibrium blocks, tagSNPs, and haplotypes of functional candidate SNPs in 55 genetic disease-associated genes were provided. Our data may provide useful information for the selection of genetic markers for gene-based genetic disease-association studies of the Korean population.

Semantic Modeling for SNPs Associated with Ethnic Disparities in HapMap Samples

  • Kim, HyoYoung;Yoo, Won Gi;Park, Junhyung;Kim, Heebal;Kang, Byeong-Chul
    • Genomics & Informatics
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    • v.12 no.1
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    • pp.35-41
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    • 2014
  • Single-nucleotide polymorphisms (SNPs) have been emerging out of the efforts to research human diseases and ethnic disparities. A semantic network is needed for in-depth understanding of the impacts of SNPs, because phenotypes are modulated by complex networks, including biochemical and physiological pathways. We identified ethnicity-specific SNPs by eliminating overlapped SNPs from HapMap samples, and the ethnicity-specific SNPs were mapped to the UCSC RefGene lists. Ethnicity-specific genes were identified as follows: 22 genes in the USA (CEU) individuals, 25 genes in the Japanese (JPT) individuals, and 332 genes in the African (YRI) individuals. To analyze the biologically functional implications for ethnicity-specific SNPs, we focused on constructing a semantic network model. Entities for the network represented by "Gene," "Pathway," "Disease," "Chemical," "Drug," "ClinicalTrials," "SNP," and relationships between entity-entity were obtained through curation. Our semantic modeling for ethnicity-specific SNPs showed interesting results in the three categories, including three diseases ("AIDS-associated nephropathy," "Hypertension," and "Pelvic infection"), one drug ("Methylphenidate"), and five pathways ("Hemostasis," "Systemic lupus erythematosus," "Prostate cancer," "Hepatitis C virus," and "Rheumatoid arthritis"). We found ethnicity-specific genes using the semantic modeling, and the majority of our findings was consistent with the previous studies - that an understanding of genetic variability explained ethnicity-specific disparities.

A whole genome association study to detect additive and dominant single nucleotide polymorphisms for growth and carcass traits in Korean native cattle, Hanwoo

  • Li, Yi;Gao, Yuxuan;Kim, You-Sam;Iqbal, Asif;Kim, Jong-Joo
    • Asian-Australasian Journal of Animal Sciences
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    • v.30 no.1
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    • pp.8-19
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    • 2017
  • Objective: A whole genome association study was conducted to identify single nucleotide polymorphisms (SNPs) with additive and dominant effects for growth and carcass traits in Korean native cattle, Hanwoo. Methods: The data set comprised 61 sires and their 486 Hanwoo steers that were born between spring of 2005 and fall of 2007. The steers were genotyped with the 35,968 SNPs that were embedded in the Illumina bovine SNP 50K beadchip and six growth and carcass quality traits were measured for the steers. A series of lack-of-fit tests between the models was applied to classify gene expression pattern as additive or dominant. Results: A total of 18 (0), 15 (3), 12 (8), 15 (18), 11 (7), and 21 (1) SNPs were detected at the 5% chromosome (genome) - wise level for weaning weight (WWT), yearling weight (YWT), carcass weight (CWT), backfat thickness (BFT), longissimus dorsi muscle area (LMA) and marbling score, respectively. Among the significant 129 SNPs, 56 SNPs had additive effects, 20 SNPs dominance effects, and 53 SNPs both additive and dominance effects, suggesting that dominance inheritance mode be considered in genetic improvement for growth and carcass quality in Hanwoo. The significant SNPs were located at 33 quantitative trait locus (QTL) regions on 18 Bos Taurus chromosomes (i.e. BTA 3, 4, 5, 6, 7, 9, 11, 12, 13, 14, 16, 17, 18, 20, 23, 26, 28, and 29) were detected. There is strong evidence that BTA14 is the key chromosome affecting CWT. Also, BTA20 is the key chromosome for almost all traits measured (WWT, YWT, LMA). Conclusion: The application of various additive and dominance SNP models enabled better characterization of SNP inheritance mode for growth and carcass quality traits in Hanwoo, and many of the detected SNPs or QTL had dominance effects, suggesting that dominance be considered for the whole-genome SNPs data and implementation of successive molecular breeding schemes in Hanwoo.