22 research outputs found

    Conditional FDR; SCZ loci given BD (SCZ|BD).

    No full text
    <p>Independent complex or single gene loci (r<sup>2</sup><0.2) with SNP(s) with a conditional FDR (condFDR)<0.05 in schizophrenia (SCZ) given the association in bipolar disorder (BD). We defined the most significant SCZ SNP in each LD block based on the minimum condFDR for BD. The most significant SNPs in each LD block are listed. All loci with SNPs with condFDR<0.05 were used to define the number of the loci. Chromosome location (Chr). SCZ FDR values<0.05 are in bold.</p>†<p>Same locus identified in previous SCZ genome-wide association studies. All data were first corrected for genomic inflation.</p

    Gene expression data of the Allen Human Brain Atlas were mapped onto the 12 genetically based cortical regions in the MR space.

    No full text
    <p>A) Resulting volume registration between FreeSurfer surface (fsaverage) and Allen brain MNI coordinates displayed as a point cloud, with a slice of the MRI imaging at the bottom (colin27). B) After the volume registration, gene expression data points are mapped to FreeSurfer surface vertices by assigning each surface vertex the gene expression of the closest (Euclidean distance) Allen brain data point using nearest neighbor interpolation. If two vertices have the same closest Allen brain data point, they belong to the same patch and the patch id is displayed as color. Thus, the color patches illustrate the local density of data points. The color patches with similar sizes across the cortex represent an even distribution of Allen brain data points and their surface correspondences. Colors of the dots in both (A) and (B) panels represent cortical regions to which they were assigned, corresponding to the color schemes in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006143#pgen.1006143.g001" target="_blank">Fig 1B</a>.</p

    Conditional FDR; BD loci given SCZ (BD|SCZ).

    No full text
    <p>For the independent complex or single gene loci (r<sup>2</sup><0.2) with SNP(s) with a conditional FDR (condFDR)<0.05 in bipolar disorder (BD) given association with schizophrenia (SCZ). All independent loci are listed consecutively. Chromosome location (Chr). All data were first corrected for genomic inflation. BD FDR values<0.05 are in bold.</p>†<p>Same locus identified in previous BD genome-wide association studies.</p

    ‚ÄúConditional Manhattan plot‚ÄĚ of conditional ‚ąílog<sub>10</sub> (FDR) values for schizophrenia (SCZ) alone (black) and SCZ given bipolar disorder (BD; SCZ|BD, red).

    No full text
    <p>SNPs with conditional ‚ąílog<sub>10</sub> FDR>1.3 (i.e. FDR<0.05) are shown with large points. A black line around the large points indicates the most significant SNP in each LD block and this SNP was annotated with the closest gene, which is listed above the symbols in each locus. The figure shows the localization of significant loci. Details about the loci are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003455#pgen-1003455-t001" target="_blank">Table 1</a>.</p

    Conjunction FDR; pleiotropic loci in SCZ and BD (SCZ&BD).

    No full text
    <p>Independent complex or single gene loci (r<sup>2</sup><0.2) with SNP(s) with a conjunctional FDR (conjFDR)<0.05 in schizophrenia (SCZ) <i>and</i> bipolar disorder (BD). All SNPs with a conjFDR value<0.05 (bidirectional association, i.e. association with SCZ given association with BD (condFDR<0.05) and association with BD given association with SCZ (condFDR<0.05)) are listed and sorted in each LD block. We defined the most significant SNP in each LD block based on the minimum conjFDR. All independent loci are listed consecutively, and the same locus number are used as in the condFDR<0.05 results (<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003455#pgen-1003455-t001" target="_blank">Table 1</a>). Chromosome (Chr). Z-scores for each pleiotropic locus are provided, with minor allele (A1) and major allele (A2). All data were first corrected for genomic inflation.</p>†<p>Same locus identified in previous BD or SCZ genome-wide association studies.</p

    ‚ÄúConditional Manhattan plot‚ÄĚ of conditional ‚ąílog<sub>10</sub> (FDR) values for Bipolar disorder (BD) alone (black) and BD given schizophrenia (SCZ; BD|SCZ, blue).

    No full text
    <p>SNPs with conditional ‚ąílog<sub>10</sub> FDR>1.3 (i.e. FDR<0.05) are shown with large points. A black line around the large points indicates the most significant SNP in each LD block and this SNP was annotated with the closest gene, which is listed above the symbols in each locus. The figure shows the localization of significant loci. Details about the loci are provided in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003455#pgen-1003455-t002" target="_blank">Table 2</a>.</p

    Kaplan‚ÄďMeier estimates and Cox proportional hazard model fits from the ADGC Phase 1 case‚Äďcontrol dataset, excluding NIA ADC and ADNI samples.

    No full text
    <p>The proportional hazard assumptions were checked based on graphical comparisons between Kaplan‚ÄďMeier estimations (dashed lines) and Cox proportional hazard models (solid lines). The 95% confidence intervals of Kaplan‚ÄďMeier estimations are also demonstrated (shaded with corresponding colors). The baseline hazard (gray line) in this model is based on the mean of ADGC data. ADGC, Alzheimer‚Äôs Disease Genetics Consortium; ADNI, Alzheimer‚Äôs Disease Neuroimaging Initiative; NIA ADC, National Institute on Aging Alzheimer‚Äôs Disease Center; PHS, polygenic hazard score.</p

    Mean replication z-scores stratified by genomic annotation, pleiotropy and heterozygosity.

    No full text
    <p>The conditional mean z-scores in replication sample (y axis) were plotted against the z-scores in the discovery sample (x axis). The shrinkage of replication z-score is differentiated by A.) genomic annotation categories (All SNPs; Intergenic; 5‚Äô untranslated region,5‚Äô UTR; Intron; Exon; and 3‚Äô untranslated region, 3‚Äô UTR), B.) by heterozygosity (H) intervals, C.) by associations with bipolar disorder (BIP; All SNPs; -log<sub>10</sub> p ‚Č• 1.0; -log<sub>10</sub> p ‚Č• 2.0; and log<sub>10</sub> p ‚Č• 3.0) and D.) by total LD (TLD) intervals. All plots were generated by randomly assigning 26 of the PGC Schizophrenia sub-studies as discovery sample and 26 as replication sample (split half). The average value over 500 iterations is shown.</p
    corecore