• Title, Summary, Keyword: SNP

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The Usage of an SNP-SNP Relationship Matrix for Best Linear Unbiased Prediction (BLUP) Analysis Using a Community-Based Cohort Study

  • Lee, Young-Sup;Kim, Hyeon-Jeong;Cho, Seoae;Kim, Heebal
    • Genomics & Informatics
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    • v.12 no.4
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    • pp.254-260
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    • 2014
  • Best linear unbiased prediction (BLUP) has been used to estimate the fixed effects and random effects of complex traits. Traditionally, genomic relationship matrix-based (GRM) and random marker-based BLUP analyses are prevalent to estimate the genetic values of complex traits. We used three methods: GRM-based prediction (G-BLUP), random marker-based prediction using an identity matrix (so-called single-nucleotide polymorphism [SNP]-BLUP), and SNP-SNP variance-covariance matrix (so-called SNP-GBLUP). We used 35,675 SNPs and R package "rrBLUP" for the BLUP analysis. The SNP-SNP relationship matrix was calculated using the GRM and Sherman-Morrison-Woodbury lemma. The SNP-GBLUP result was very similar to G-BLUP in the prediction of genetic values. However, there were many discrepancies between SNP-BLUP and the other two BLUPs. SNP-GBLUP has the merit to be able to predict genetic values through SNP effects.

Accuracy of genomic-polygenic estimated breeding value for milk yield and fat yield in the Thai multibreed dairy population with five single nucleotide polymorphism sets

  • Wongpom, Bodin;Koonawootrittriron, Skorn;Elzo, Mauricio A.;Suwanasopee, Thanathip;Jattawa, Danai
    • Asian-Australasian Journal of Animal Sciences
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    • v.32 no.9
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    • pp.1340-1348
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    • 2019
  • Objective: The objectives were to compare variance components, genetic parameters, prediction accuracies, and genomic-polygenic estimated breeding value (EBV) rankings for milk yield (MY) and fat yield (FY) in the Thai multibreed dairy population using five single nucleotide polymorphism (SNP) sets from GeneSeek GGP80K chip. Methods: The dataset contained monthly MY and FY of 8,361 first-lactation cows from 810 farms. Variance components, genetic parameters, and EBV for five SNP sets from the GeneSeek GGP80K chip were obtained using a 2-trait single-step average-information restricted maximum likelihood procedure. The SNP sets were the complete SNP set (all available SNP; SNP100), top 75% set (SNP75), top 50% set (SNP50), top 25% set (SNP25), and top 5% set (SNP5). The 2-trait models included herd-year-season, heterozygosity and age at first calving as fixed effects, and animal additive genetic and residual as random effects. Results: The estimates of additive genetic variances for MY and FY from SNP subsets were mostly higher than those of the complete set. The SNP25 MY and FY heritability estimates (0.276 and 0.183) were higher than those from SNP75 (0.265 and 0.168), SNP50 (0.275 and 0.179), SNP5 (0.231 and 0.169), and SNP100 (0.251and 0.159). The SNP25 EBV accuracies for MY and FY (39.76% and 33.82%) were higher than for SNP75 (35.01% and 32.60%), SNP50 (39.64% and 33.38%), SNP5 (38.61% and 29.70%), and SNP100 (34.43% and 31.61%). All rank correlations between SNP100 and SNP subsets were above 0.98 for both traits, except for SNP100 and SNP5 (0.93 for MY; 0.92 for FY). Conclusion: The high SNP25 estimates of genetic variances, heritabilities, EBV accuracies, and rank correlations between SNP100 and SNP25 for MY and FY indicated that genotyping animals with SNP25 dedicated chip would be a suitable to maintain genotyping costs low while speeding up genetic progress for MY and FY in the Thai dairy population.

Important SNPs Identification from the Economic Traits for the High Quality Korean Cattle (고품질 한우를 위한 여러 경제형질에서의 주요 SNP 규명)

  • Lee, Jea-Young;Kim, Dong-Chul
    • Communications for Statistical Applications and Methods
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    • v.16 no.1
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    • pp.67-74
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    • 2009
  • In order to make the high quality Korean cattle, it has been identified the gene markers which influence to various economic traits. To identify statistically significances among SNP markers, Lee et. al. (2008b) identified SNP(19_1)$^*$SNP(28_2) marker was an important marker in LMA(longissimus muscle dorsi area). In addition, CWT(carcass cold weight) and ADG(average daily gain) are applied for expanded multifactor dimensionality reduction (expanded MDR) method from the comprehensive economic traits. The results showed that SNP(19_1)$^*$SNP(28_2) interaction marker was good and a very meaningful for economic traits.

MarSel : LD based tagSNP Selection System for Large-scale SNP Haplotype Dataset (MarSel : 대용량 SNP 일배체형 데이터에 대한 연관불균형기반의 tagSNP 선택 시스템)

  • Kim Sang-Jun;Yeo Sang-Soo;Kim Sung-Kwon
    • The KIPS Transactions:PartA
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    • v.13A no.1
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    • pp.79-86
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    • 2006
  • Recently the tagSNP selection problem has been researched for reducing the cost of association studies between human's diversities and SNPs. General approach for this problem is that all of SNPs are separated into appropriate blocks and then tagSNPs are chosen in each block. Marsel in this paper is the system that involved the concept of linkage disequilibrium for overcoming the problem that the existing block partitioning approaches have short of biological meanings. In most approaches, the contiguous regions, which recombinations have LD coefficient |D'| and then tagSNP selection step is performed. And MarSel guarantees the minimum tagSNP selection using entropy-based optimal selection algorithm when tagSNPs are chosen in each block, and enables chromosome-level association studies using efficient memory management technique when input is very large-scale dataset that is impossible to be processed in the existing systems.

Main SNP Identification of Hanwoo Carcass Weight with Multifactor Dimensionality Reduction(MDR) Method (MULTIFACTOR DIMENSIONALITY REDUCTION(MDR)을 이용한 한우 도체중에서의 주요 SNP 규명)

  • Lee, Jea-Young;Kim, Dong-Chul
    • The Korean Journal of Applied Statistics
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    • v.21 no.1
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    • pp.53-63
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    • 2008
  • It is commonly believed that disease of human or economic traits of livestock are caused not by single gene acting alone, but by multiple genes interacting with one an-other. This issue is difficult due to the limitations of parametric statistical method like as logistic regression for detection of gene effects that are dependent solely on interactions with other genes and with environmental exposures. Multifactor dimensionality reduction (MDR) nonparametric statistical method, to improve the identification of single nucleotide polymorphism (SNP) associated with the Hanwoo(Korean cattle) carcass cold weight, is applied and compared with ANOVA results.

Effective Analysis Of SNP Related Chronic Hepatitis Using SNP (SVM을 이용한 만성간염 환자 예측진단을 위한 SNP 정보분석)

  • Kim Dong-Hoi;Ham Ki-Baek;Kim Jin
    • Proceedings of the Korean Information Science Society Conference
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    • pp.19-21
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    • 2006
  • Single Nucleotide Polymorphism(SNP)는 인간 유전자 서열의 0.1%에 해당하는 부분으로 이는 각 개인의 체질 및 각종 유전질환과 밀접한 관련이 있다고 알려져 있다. 최근 이 SNP정보의 패턴을 이용 질병의 진단 및 치료에 연관지으려는 노력이 시도되고 있다. 그러나 아직 SNP를 이용한 효율적인 분석방법에 대한 전산학적 연구는 많지 않다. 본 논문에서는 대표적인 패턴인식기 중 하나인 Support Vector Machine(SVM)을 이용 한국인의 대표적인 유전질환으로 알려진 만성간염에 대해서 관련된 SNP에 대한 패턴 인식율 측정을 실험하였다. 실험 데이터는 간 및 소화기 질환 유전체 센터에서 얻어진 만성간염 환자와 관련 SNP정보를 사용하였으며, 실험 결과 전체 SNP 정보를 모두 가지는 환자그룹에 대한 학습인식율이 66.46%로 나타났으며, 부분그룹에서는 72.91%로 높은 인식율을 보였다. 이 결과는 SNP 정보를 이용한 만성간염의 초기진단예측에 SVM을 효율적으로 사용할 수 있음을 보인다.

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AN APPROXIMATE GREEDY ALGORITHM FOR TAGSNP SELECTION USING LINKAGE DISEQUILIBRIUM CRITERIA

  • Wang, Ying;Feng, Enmin;Wang, Ruisheng
    • Journal of applied mathematics & informatics
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    • v.26 no.3_4
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    • pp.493-500
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    • 2008
  • In this paper, we first construct a mathematical model for tagSNP selection based on LD measure $r^2$, then aiming at this kind of model, we develop an efficient algorithm, which is called approximate greedy algorithm. This algorithm is able to make up the disadvantage of the greedy algorithm for tagSNP selection. The key improvement of our approximate algorithm over greedy algorithm lies in that it adds local replacement(or local search) into the greedy search, tagSNP is replaced with the other SNP having greater similarity degree with it, and the local replacement is performed several times for a tagSNP so that it can improve the tagSNP set of the local precinct, thereby improve tagSNP set of whole precinct. The computational results prove that our approximate greedy algorithm can always find more efficient solutions than greedy algorithm, and improve the tagSNP set of whole precinct indeed.

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Effect of prednisolone on rabbit articular chondrocytes treated with sodium nitroprusside

  • Kang, Jin Seok
    • Journal of Biomedical and Translational Research
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    • v.19 no.3
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    • pp.43-48
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    • 2018
  • This study was carried out to investigate the protective effect of prednisolone in rabbit primary cultured articular chondrocytes treated with sodium nitroprusside (SNP), a nitric oxide donor. After a cell phenotype was determined, the MTT assay and Western blot analysis of type II collagen, cylooxygenase-2 (COX-2) and phosphorylated extracellular regulated kinase (pERK) were performed in the control, SNP ($298{\mu}g/ml$) alone or SNP plus prednisolone ($0.05-50{\mu}g/ml$)-treated rabbit articular chondrocytes. Immunofluorescence staining of type II collagen was also performed. Cell morphology indicated that SNP treatment induced cytotoxicity, and that the SNP-induced cytotoxicity was inhibited by prednisolone treatment. MTT assay showed that the SNP treatment resulted in a significant decrease in the level of cell viability compared with that of control (p<0.01), and that the prednisolone treatment resulted in a decrease in the SNP-induced cytotoxicity. SNP treatment resulted in a decrease in the level of type II collagen, compared with the control chondrocytes. The prednisolone treatment recovered the down-regulated expression of type II collagen induced by SNP, showing a significant level in $5{\mu}g/ml$ of the prednisolone treatment group compared to the SNP treatment group (p<0.05). A significant increase in COX-2 was significantly induced by the SNP treatment compared to control chondrocytes (p<0.01). The COX-2 expression was decreased by the prednisolone treatment, showing a significant level in $50{\mu}g/ml$ of the prednisolone treatment group compared to the SNP treatment group (p<0.05). These phenomena was confirmed by immunofluorescence staining. Furthermore, the SNP treatment significantly induced a decrease of pERK expression compared to the control chondrocytes (p<0.01). The prednisolone treatment recovered its expression, showing a significant level in $0.5{\mu}g/ml$ of the prednisolone treatment group compared to the SNP treatment group (p<0.05). Taken the above results together, prednisolone is considered to inhibit SNP-induced cell death and dedifferentiation, and modulated expression of COX-2 and pERK in rabbit articular chondrocytes.

The Effects of Melatonin and Sodium Nitroprusside (SNP) on Development of Porcine IVM/IVF Embryos (돼지 체외수정란의 체외발육에 있어 Melatonin과 Sodium Nitroprusside(SNP) 첨가 효과)

  • 장현용;오진영;김종택;박춘근;정희태;김정익;이학교;최강덕;양부근
    • Reproductive and Developmental Biology
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    • v.28 no.2
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    • pp.83-87
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    • 2004
  • The objective of this study was performed to establish the in vitro culture system of porcine in vitro maturation and in vitro fertilization(IVM/IVF) embryo. These studies was to determine the effects of melatonin, nitric oxide donor(SNP), and the combination effects of SNP and melatonin in porcine IVM/IVF embryos. In routine porcine IVM/IVF procedure, oocytes were cultured for 40∼44h incubation, and the zygotes were cultured for 40∼44h in NCSU 23 medium. Then 2 to 8 cell embryos were removed cumulus cell and were allotted randomly to NCSU 23 containing different concentration of melatonin, SNP and SNP plus melatonin in 5% $O_2$, 5% $CO_2$ and 90% $N_2$ at 38.5$^{\circ}C$. Cell numbers of blastocyst were also counted using double fluorescence stain method. In NCSU 23 medium treated with melatonin 0, 1, 5 and 10 nM, the developmental rate of morula plus blastocysts were 33.3%, 39.1%, 33.3% and 27.9%, respectivly. This result show that the developmental rate of morula and blascytocys treated with 1 nM melatonin was higher than in any other groups(P<0.05). The developmental rates of morula plus blastocysts were 41.9% in 0 uM SNP, 25.6% in 50 uM and 28.4% in 100 uM, respectively. The developmental rate of morula plus blastocysts were decreased treated with SNP in NCSU 23. In combined effects of SNP plus melatonin (0, SNP 50 uM, SNP 50 uM plus melatonin 1 nM, SNP 50 uM plus melatonin 5 nM and SNP 50 uM plus melatonin 10 nM), the developmental rates beyond morula stage of porcine embryos were 31.3%, 34.1%, 39.5%, 29.4% and 39.5%, respectively. The addition of SNP 50 uM plus maltonin 1 nM, developmental rates of blastocyst was higher rate than in any other groups. Cell numbers of blastocyst in NCSU 23 treated with melatonin 0, 1, 5 and 10 nM were 41.0, 42.6, 39.6 and 33.0, respectively. In combined effects of SNP plus melatonin (0, SNP 50 uM, SNP 50 uM plus melatonin 1 nM , SNP 50 uM plus melatonin 5 nM and SNP 50 uM plus melatonin 10 nM), cell numbers of developed blastocyst were 36.3, 34.6, 39.0, 39.9 and 39.0, respectively. These result show that the cell numbers of blastocyst treated with 0, 1 and 5 nM melatonin were higher than in 10 nM group(P<0.05), but cell numbers of blatocyst produced by SNP plus melatonin were not significantly difference in all experimental groups.

The Eeffect of Sodium Nitroprusside on Muscle Tension in Guinea-pig Ileum (기니 픽 장관 평활근에서 Sodium Nitroprusside가 장력에 미치는 영향)

  • Kwon, Seong-Chun;Kim, Si-Yeon;Kim, Eun-Ju;Kang, Bok-Soon
    • The Korean Journal of Physiology and Pharmacology
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    • v.1 no.6
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    • pp.797-808
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    • 1997
  • Nitric oxide (NO) has been 3mown as a mediator of nonadrenergic, noncholinergic inhibitory neurotransmitter in intestinal smooth muscles. It has been suggested that NO donor such as sodium nitroprusside (SNP) produces relaxation of smooth muscle via activation of guanylate cyclase and elevation of cGMP levels. We have therefore investigated the effects of NO, using SNP, on muscle tension in the longitudinal smooth muscle of guinea-pig ileum. The possible role of cGMP was also investigated as well as the involvement of $K^+$ channel on SNP-induced inhibitory effect. The results are summarized as follows; high KCI-or CCh-activated contractions were inhibited by SNP in a concentration-dependent manner. 8-Br-cGMP also showed a similar effect in that of SNP TEA (1 mM) significantly reduced the SNP-induced inhibitory effect. SNP-induced effect was forther reduced by the presence of 10 mM TEA. On the other hand, 4-AP (0.1 mM), glibenclamide $(10\;{\mu}M)$ and apinain $(0.1\;{\mu}M)$ showed little effects on SNP-induced relaxation. Zaprinast significantly potentiated the SNP-induced inhibitory effect in all ranges. ODQ also significantly decreased the SNP-induced inhibitory effect. Pretreatment with CPA $(10\;{\mu}M)$ slightly reduced the SNP-induced inhibitory effect. From the above results, both effect mediated by NO and cGMP might be responsible for the activation of $Ca^{2+}$-activated $K^+$ channel by SNP in guinea-rig ileum. And this $K^+$ channel activation by SNP also contributes to the SNP-induced membrane hyperpolarization and relaxation.

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