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snp-single-nucleotide-polymorphism

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Journal Articles
Journal: Diabetes
Diabetes 2005;54(3):893–899
Published: 01 March 2005
... tolerance OGTT, oral glucose tolerance test SNP, single nucleotide polymorphism Adiponectin is a specific protein having 247 amino acids and sharing structural homology with collagen VIII, X, and complement C1q ( 1 , 2 ). It is encoded by the most abundant gene transcript one (apM1) in adipose tissue...
Journal Articles
Journal: Diabetes
Diabetes 2007;56(1):256–264
Published: 01 January 2007
.... Doheny; Elizabeth W. Pugh; Richard M. Watanabe; Thomas A. Buchanan; Timo T. Valle; Richard N. Bergman; Jaakko Tuomilehto; Karen L. Mohlke; Francis S. Collins; Michael Boehnke More than 120 published reports have described associations between single nucleotide polymorphisms (SNPs) and type 2 diabetes...
Includes: Supplementary data
Images
Association of cg08309687 with NAFLD using MR analysis. Plot depicts IVW (s...
Published: 22 February 2019
Figure 5 Association of cg08309687 with NAFLD using MR analysis. Plot depicts IVW (solid line) and MR-Egger estimate (dashed line). No horizontal pleiotropy effect was detected (P value = 0.66). SNP, single nucleotide polymorphism. Figure 5. Association of cg08309687 with NAFLD using MR analysis. Plot depicts IVW (solid line) and MR-Egger estimate (dashed line). No horizontal pleiotropy effect was detected (P value = 0.66). SNP, single nucleotide polymorphism. More
Images
Association of genetically determined plasma adiponectin with risk of type ...
Published: 23 August 2021
Figure 6 Association of genetically determined plasma adiponectin with risk of type 2 diabetes in a two-sample and individual-level one-sample MR setting. The causal risk ratio with 95% CI from two-sample MR analyses was based on GERA, DIAGRAM, and UK Biobank (UKB), indicated with blue diamonds an... More
Images
Mapping of IGT10 and identification of a causative novel splice mutation. ...
Published: 11 February 2016
Figure 1 Mapping of IGT10 and identification of a causative novel splice mutation. A: Mapping of minimal candidate region on chromosome 6. B: Confirmation of intronic ENU-induced mutation in Itm2b by Sanger sequencing and diagram of intron/exon structure. C: Confirmation of intronic ENU-induced mutation in Ppp2r2a by Sanger sequencing and diagram of intron/exon structure. D: Reduction in relative expression levels of Ppp2r2a. E: Relative expression levels of Itm2b. Quantitative RT-PCR data are representative of mean ± SD, N = 8 biological replicates. Het, heterozygous; Sk., skeletal; SNP, single nucleotide polymorphism. ***P < 0.001, two-way ANOVA. Figure 1. Mapping of IGT10 and identification of a causative novel splice mutation. A: Mapping of minimal candidate region on chromosome 6. B: Confirmation of intronic ENU-induced mutation in Itm2b by Sanger sequencing and diagram of intron/exon structure. C: Confirmation of intronic ENU-induced mutation in Ppp2r2a by Sanger sequencing and diagram of intron/exon structure. D: Reduction in relative expression levels of Ppp2r2a. E: Relative expression levels of Itm2b. Quantitative RT-PCR data are representative of mean ± SD, N = 8 biological replicates. Het, heterozygous; Sk., skeletal; SNP, single nucleotide polymorphism. ***P < 0.001, two-way ANOVA. More
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<span class="search-highlight">Single</span>-cell epigenetic techniques and landscape of incretin receptor DVC ce...
Published: 27 June 2021
Figure 2 Single-cell epigenetic techniques and landscape of incretin receptor DVC cells. A: Graphical illustration of the epigenetic features regulating enhancer activity. Enhancers typically reside in DNA stretches found in open chromatin, with high levels of active histone marks, devoid of cytosine methylation and in physical proximity to gene promoter regions. These features can be measured at single-cell resolution using the indicated assays. B: Graphical illustration of how single-cell epigenetic profiling can predict cell type–specific enhancers mediating genetic risk to human obesity. Colocalization of a BMI-associated genetic variant with the active enhancer in cell type A suggests that the genetic variant exerts its effect on obesity risk by modifying expression of the associated effector gene X in cell type A (and not cell type B). C: UMAP plots of 22,545 cells and 11,651 neurons from the snATAC-seq atlas provided by Ludwig et al. ( 16 ). The top four most enriched motifs in incretin receptor–expressing cells are shown by their position weight matrices; at each position of a given motif, the relative distribution of a given nucleotide is depicted. SNP, single nucleotide polymorphism; TF, transcription factor. Figure 2. Single-cell epigenetic techniques and landscape of incretin receptor DVC cells. A: Graphical illustration of the epigenetic features regulating enhancer activity. Enhancers typically reside in DNA stretches found in open chromatin, with high levels of active histone marks, devoid of cytosine methylation and in physical proximity to gene promoter regions. These features can be measured at single-cell resolution using the indicated assays. B: Graphical illustration of how single-cell epigenetic profiling can predict cell type–specific enhancers mediating genetic risk to human obesity. Colocalization of a BMI-associated genetic variant with the active enhancer in cell type A suggests that the genetic variant exerts its effect on obesity risk by modifying expression of the associated effector gene X in cell type A (and not cell type B). C: UMAP plots of 22,545 cells and 11,651 neurons from the snATAC-seq atlas provided by Ludwig et al. (16). The top four most enriched motifs in incretin receptor–expressing cells are shown by their position weight matrices; at each position of a given motif, the relative distribution of a given nucleotide is depicted. SNP, single nucleotide polymorphism; TF, transcription factor. More
Images
Impact of Val94Met transversion at LEP rs17151919 on leptin secretion rate ...
Published: 11 September 2020
Figure 2 Impact of Val94Met transversion at LEP rs17151919 on leptin secretion rate in HEK293 cells. The rs17151919 variant changes valine to methionine in position 73 of the mature leptin protein. A: The 3D illustration of leptin structure derived from RSCB Protein Data Bank (PDB) and modified with UCSF Chimera1.13.1. The prediction of protein stability is derived from the SDM server ( 30 ). B: Leptin secretion rates for Val94 and Met94 expressed as the amount of leptin secreted (ng) during a 1-h incubation (72–73 h posttransfection) (LEPs/h) normalized by the respective cellular leptin content (LEPc) in untreated control cells at the end of incubation. Individual data points from four separate experiments (each with two to three technical replicates) are plotted. The normality of data distribution was examined using D’Agostino and Pearson normality test (P = 0.65 and 0.54 for LEPV94 (Val94) and LEPM94 (Met94), respectively), and repeated-measures one-way ANOVA was performed to assess the difference in secretion rate between the genotypes. Mean ± SD and AVOVA results (F and P values) are reported in the table below the graph. C: Intracellular leptin turnover rates for Val94 and Met94 alleles, obtained by measuring the relative cellular leptin contents in the untreated control cells (defined as 1 for the respective LEP variant) and in samples treated with the protein synthesis inhibitor CHX (20 μg/mL) for 0.5 and 1.0 h. Mean ± SD at each time point from four separate experiments (each with two to three technical replicates) is plotted. Paired t test was used to assess the genotype effect on the fractions of cellular LEP that remained after 0.5 h and 1.0 h of CHX treatment (P values are reported in the table below the graph). The average hourly turnover rates for Val94 and Met94 were 61 ± 2% and 60 ± 3%, respectively, calculated by subtraction of the percent cellular LEP that remained after 1 h of CHX treatment from those of the respective untreated controls (defined as 100%). hr, hour(s); ID, identifier; M94, Met94; pseudo ΔΔG, predicted stability difference score; SNP, single nucleotide polymorphism; V94, Val94; WT, wild type. Figure 2. Impact of Val94Met transversion at LEP rs17151919 on leptin secretion rate in HEK293 cells. The rs17151919 variant changes valine to methionine in position 73 of the mature leptin protein. A: The 3D illustration of leptin structure derived from RSCB Protein Data Bank (PDB) and modified with UCSF Chimera1.13.1. The prediction of protein stability is derived from the SDM server (30). B: Leptin secretion rates for Val94 and Met94 expressed as the amount of leptin secreted (ng) during a 1-h incubation (72–73 h posttransfection) (LEPs/h) normalized by the respective cellular leptin content (LEPc) in untreated control cells at the end of incubation. Individual data points from four separate experiments (each with two to three technical replicates) are plotted. The normality of data distribution was examined using D’Agostino and Pearson normality test (P = 0.65 and 0.54 for LEPV94 (Val94) and LEPM94 (Met94), respectively), and repeated-measures one-way ANOVA was performed to assess the difference in secretion rate between the genotypes. Mean ± SD and AVOVA results (F and P values) are reported in the table below the graph. C: Intracellular leptin turnover rates for Val94 and Met94 alleles, obtained by measuring the relative cellular leptin contents in the untreated control cells (defined as 1 for the respective LEP variant) and in samples treated with the protein synthesis inhibitor CHX (20 μg/mL) for 0.5 and 1.0 h. Mean ± SD at each time point from four separate experiments (each with two to three technical replicates) is plotted. Paired t test was used to assess the genotype effect on the fractions of cellular LEP that remained after 0.5 h and 1.0 h of CHX treatment (P values are reported in the table below the graph). The average hourly turnover rates for Val94 and Met94 were 61 ± 2% and 60 ± 3%, respectively, calculated by subtraction of the percent cellular LEP that remained after 1 h of CHX treatment from those of the respective untreated controls (defined as 100%). hr, hour(s); ID, identifier; M94, Met94; pseudo ΔΔG, predicted stability difference score; SNP, single nucleotide polymorphism; V94, Val94; WT, wild type. More
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Genotype analysis by MALDI-TOF spectrometry. <em>A</em>: PROBE reac...
Published: 01 April 2001
FIG. 1. Genotype analysis by MALDI-TOF spectrometry. A: PROBE reaction. The region containing the PPARγ2 Pro12Ala (CCA->GCA) variant is amplified with a biotinylated primer to enable purification of the single-stranded template. Next, the PROBE primer anneals to the template and is extended. When the single nucleotide polymorphism (SNP) is C, the probe is extended by one nucleotide, dideoxy-CTP. When the SNP is G, the probe is extended by two nucleotides, deoxy-GTP, and dideoxy-CTP. B: Mass spectrometry profiles of primer extension products. Peaks at 6,989.6 and 7,318.8 Da correspond to the mass of the probe primer extended by one or two nucleotides, respectively. Genotypes of the spectra are 1) CC, 2) CG, and 3) GG. The mass of the unextended PROBE primer is indicated at 6,716.4 Da, but in these examples, none is detected. FIG. 1. Genotype analysis by MALDI-TOF spectrometry. A: PROBE reaction. The region containing the PPARγ2 Pro12Ala (CCA->GCA) variant is amplified with a biotinylated primer to enable purification of the single-stranded template. Next, the PROBE primer anneals to the template and is extended. When the single nucleotide polymorphism (SNP) is C, the probe is extended by one nucleotide, dideoxy-CTP. When the SNP is G, the probe is extended by two nucleotides, deoxy-GTP, and dideoxy-CTP. B: Mass spectrometry profiles of primer extension products. Peaks at 6,989.6 and 7,318.8 Da correspond to the mass of the probe primer extended by one or two nucleotides, respectively. Genotypes of the spectra are 1) CC, 2) CG, and 3) GG. The mass of the unextended PROBE primer is indicated at 6,716.4 Da, but in these examples, none is detected. More
Journal Articles
Journal: Diabetes
Diabetes 2007;56(4):1174–1176
Published: 01 April 2007
... the association of IL2RA with type 1 diabetes and to attempt further mapping of the genetic effect with a new set of 12 single nucleotide polymorphisms (SNPs). We genotyped 949 nuclear family trios with one type 1 diabetes–affected offspring and two parents (2,847 individuals). Two of the 12...
Journal Articles
Journal: Diabetes
Diabetes 2002;51(1):247–250
Published: 01 January 2002
... and in at least three Northern European populations. Studies in nondiabetic Pima Indians showed that one of the at-risk DNA polymorphisms, single-nucleotide polymorphism (SNP)-43, in CAPN10 was associated with insulin resistance, and individuals with the G/G-genotype had significantly higher fasting...
Includes: Supplementary data
Journal Articles
Journal: Diabetes
Diabetes 2005;54(10):3040–3042
Published: 01 October 2005
... metabolism. The USF1 gene is located at chromosome 1q22-q23, within the most consistently replicated type 2 diabetes susceptibility locus in the human genome. In this study, we have examined the contribution of eight common USF1 single nucleotide polymorphisms (SNPs) to type 2 diabetes susceptibility...
Journal Articles
Journal: Diabetes
Diabetes 2006;55(9):2626–2630
Published: 01 September 2006
... ENPP1 polymorphisms influencing these phenotypes has received little attention. Our aim was to examine the associations of tagging single nucleotide polymorphisms (SNPs) and haplotypes of the linkage disequilibrium (LD) block containing K121Q polymorphism with type 2 diabetes in a Polish population...
Journal Articles
Journal: Diabetes
Diabetes 2004;53(9):2483–2486
Published: 01 September 2004
...Emmanuelle Durand; Philippe Boutin; David Meyre; M. Aline Charles; Karine Clement; Christian Dina; Philippe Froguel Positional candidate gene analysis of the obesity-linked chromosome Xq24 locus identified two obesity-associated single nucleotide polymorphisms (SNPs) in the membrane amino acid...
Journal Articles
Journal: Diabetes
Diabetes 2004;53(3):865–869
Published: 01 March 2004
... hypothesized that GFPT1, which encodes for GFAT, may confer genetic susceptibility to this complication among Caucasians. Screening of all known functional regions of GFPT1 revealed six single nucleotide polymorphisms (SNPs) that were located in the promoter, introns, and 3′ untranslated...
Includes: Supplementary data
Journal Articles
Journal: Diabetes
Diabetes 2006;55(5):1270–1275
Published: 01 May 2006
..., or 2,190, respectively). Furthermore, type 2 diabetes (n = 342 of 2,434) was analyzed as an outcome. FFA concentrations were significantly associated with several single nucleotide polymorphisms (SNPs) of ATGL (P values from 0.015 to 0.00003), consistent with additive inheritance...
Includes: Supplementary data
Journal Articles
Journal: Diabetes
Diabetes 2008;57(3):777–782
Published: 01 March 2008
... NRF1 genetic polymorphisms and development of type 2 diabetes. RESEARCH DESIGN AND METHODS— Using a variation screening approach, 6 novel and 10 known single nucleotide polymorphisms (SNPs) in the NRF1 gene were identified. Nine SNPs were then selected using pairwise tagging...
Journal Articles
Journal: Diabetes
Diabetes 2004;53(4):1162–1165
Published: 01 April 2004
... region upstream of the gene for variation using denaturing high-performance liquid chromatography technology. An A>G single nucleotide polymorphism (SNP) at position −579 in the promoter region was associated with nephropathy in a case-control study using 393 type 1 diabetic patients from Northern...
Journal Articles
Journal: Diabetes
Diabetes 2007;56(2):513–517
Published: 01 February 2007
... with type 2 diabetes and related traits in several populations suggesting the involvement of this transcription factor in diabetes pathogenesis. Single nucleotide polymorphisms (SNPs) within a large haplotype block surrounding the alternate P2 promoter, located ∼45 kb upstream from the coding region, have...
Journal Articles
Journal: Diabetes
Diabetes 2005;54(5):1588–1591
Published: 01 May 2005
...′-oligoadenylate synthetase RNaseL, latent RNase SNP, single nucleotide polymorphism VNTR, variable number tandem repeat Type 1 diabetes is caused by some combination of multiple genetic and environmental factors that precipitate autoimmune destruction of the insulin-producing β-cells of the pancreas...
Journal Articles
Journal: Diabetes
Diabetes 2004;53(7):1900–1904
Published: 01 July 2004
... highly significant associations of single nucleotide polymorphisms (SNPs) and haplotypes of INPPL1 with hypertension as well as with other components of the metabolic syndrome. In a cohort of 905 French type 2 diabetic patients, we found evidence of association of INPPL1 SNPs...
Includes: Supplementary data