15 research outputs found

    Location of eQTLs of the 5p13.1 region and the SNPs associated to MS and Crohn diseases.

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    <p>Image from the UCSC browser showing the chr5:39,840,547-40,924,217 (NCBI36/hg18) region. Vertical bars indicate the location of eQTLs and SNPs associated to Crohn or MS in different studies. eQTL PTGER4 are described by Zeller et al.; eQTL PTGER4 CEU are obtained from the correlation of PTGER4 expression in the CEU lymphoblastoid cell lines with the variants of the region; eQTL RPL37 are described by Stranger et al. and Dixon et al.; GWAS Crohn indicate the SNPs associated with the disease in different studies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036140#pone.0036140-The1" target="_blank">[9]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036140#pone.0036140-Libioulle1" target="_blank">[14]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036140#pone.0036140-Anderson1" target="_blank">[15]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0036140#pone.0036140-Franke1" target="_blank">[16]</a>; GWAS MS indicate the SNPs associated with MS. LD plot performed with HapMap data from CEU population.</p

    Manhattan plot and QQ plot of association findings.

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    <p>The figure summarizes the association results obtained on the ImmunoChip and MetaboChip markers (Step 3). The blue dotted line marks the Bonferroni threshold significance levels (1.7×10<sup>−7</sup>), and SNPs in loci exceeding this threshold are highlighted in green. The bottom panel represents the QQ plot, where the red line corresponds to all test statistics, and the blue line to results after excluding statistics at top markers (highlighted in green in the Manhattan Plot). The gray area corresponds to the 90% confidence region from a null distribution of P values (generated from 100 simulations).</p

    Zoom views of the association results in the loci associated with MCP-1 and hsCRP.

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    <p>Each panel shows the association curve around the strongest SNP, which is highlighted with a purple dot. The SNPs are coloured according to their linkage disequilibrium (r<sup>2</sup>) with the top variant in the 1000 Genomes European data set, with symbols that reflect genomic annotation as indicated in the legend. Arrows highlight independent signals, if any, described in the manuscript; while light blue lines indicate the recombination rate, according to the right-hand Y axis. Genomic positions are as in build 37. Gene transcripts are annotated in the lower box. Plots were drawn using the standalone LocusZoom version <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002480#pgen.1002480-Pruim1" target="_blank">[65]</a>.</p

    Zoom views of the association results in the loci associated with IL-6 and ESR.

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    <p>Each panel shows the association curve around the strongest SNP, which is highlighted with a purple dot. The SNPs are coloured according to their linkage disequilibrium (r<sup>2</sup>) with the top variant in the 1000 Genomes European data set, with symbols that reflect genomic annotation as indicated in the legend. Arrows highlight independent signals, if any, described in the manuscript; while light blue lines indicate the recombination rate, according to the right-hand Y axis. Genomic positions are as in build 37. Gene transcripts are annotated in the lower box. Plots were drawn using the standalone LocusZoom version <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002480#pgen.1002480-Pruim1" target="_blank">[65]</a>.</p

    Top association signals for IL-6, ESR, MCP-1, and hsCRP in the ImmunoChip and MetaboChip data-sets.

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    <p>The table summarizes top association signals for IL-6, ESR, MCP-1 and hsCRP phenotypes in the ImmunoChip and MetaboChip data-sets (Step 3). For each marker, frequency and effect estimates are given with respect to the minor allele. We also reported the r<sup>2</sup> with the SNP detected in the GWAS scan (Step 1). Novel signals are indicated in bold.</p>a<p>The effect size is measured in standard deviation units, being estimated as the β coefficient of the regression model when using the normalized trait (e.g. an effect size of 1.0 implies each additional copy of the allele being evaluated increases trait values by 1.0 standard deviations).</p>b<p>I =  ImmunoChip, M =  MetaboChip.</p>c<p>The table reports the pvalue on the primary analysis. On the conditional analysis, the pvalue for the independent SNPs were: rs12378220, 9.43×10<sup>−08</sup>; rs3093077, 9.02×10<sup>−11</sup>; rs2259816, 7.58×10<sup>−10</sup>.</p>d<p>Independent signals.</p

    Top genome-wide association results for IL-6, ESR, MCP-1, and hsCRP.

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    <p>The table summarizes top genome-wide association signals for IL-6, ESR, MCP-1 and hsCRP phenotypes in the HapMap based GWAS (Step 1), as well as results in the replication independent cohort (Step 2) and in the combined data-sets. For each marker, frequency and effect estimates are given with respect to the minor allele. Imputation quality scores (RSQ) are reported for imputed SNPs. Novel signals are indicated in bold.</p>a<p>The effect size is measured in standard deviation units, being estimated as the β coefficient of the regression model when using the normalized trait (e.g. an effect size of 1.0 implies each additional copy of the allele being evaluated increases trait values by 1.0 standard deviations).</p>b<p>Independent signals.</p

    Summary of the differences between HapMap and 1000G imputation for the 29 overlapping loci.

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    <p>Summary of the differences between HapMap and 1000G imputation for the 29 overlapping loci.</p
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