Estimated penetrance of identified SNPs for their corresponding phenotype

<p><b>Copyright information:</b></p><p>Taken from "Standard linkage and association methods identify the mechanism of four susceptibility genes for a simulated complex disease"</p><p></p><p>BMC Genetics 2005;6(Suppl 1):S142-S142.</p><p>Published online 30 Dec 2005</p><p>PMCID:PMC1866793.</p><p></p

Description of retained brain samples for the Agilent microarray study.

1<p>PMI: post-mortem interval.</p>2<p>RIN: RNA Integrity Number.</p>3<p>The pH was measured following a previously established protocol <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002794#pgen.1002794-Harrison1" target="_blank">[58]</a>.</p

Top age at onset (AAO) meta-analysis results for the <i>FOXO1</i> region.

1<p>Position for genome build 36.3 (hg18).</p>2<p>Required p-value level for significance p-values = 8.68E-5; <b>bold</b> indicates significant p-value.</p>3<p>Direction of effects are listed in the following order: PROGENI/GenePD, NIA Phase I, NIA Phase II, LEAPS, HIHG, NGRC; a question mark (?) indicates that the marker failed imputation (Rsq<0.30).</p>4<p>Values for imputed (I) or genotyped (G) status.</p>5<p>The meta-analysis included the PROGENI/GenePD, NIA Phase I, NIA Phase II, HIHG, and NGRC studies.</p>6<p>The SNPExpress database <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1002794#pgen.1002794-Heinzen1" target="_blank">[29]</a> was used to look up eSNP relationships between the expression of <i>FOXO1</i> transcripts or exons and the SNPs of interest. The best <i>FOXO1</i> eSNP result is displayed if a p-value<0.05 was observed. The presented eSNP results were obtained in brain tissue. N/A values are used when the SNPs were not available in the database.</p

Top microarray probes.

<p>Probes with FDR-adjusted p-values smaller than 0.05 and with expression differences between PD and control prefrontal cortex BA9 samples greater than 1.5 fold changes. Twenty-one probes (42%) were in genes with FoxO1 transcription factor binding sites. The GENE-E software (<a href="http://www.broadinstitute.org/cancer/software/GENE-E/" target="_blank">http://www.broadinstitute.org/cancer/software/GENE-E/</a>) was used to generate the heatmap.</p

Expression by genotype relationship between the <i>SMOX</i> probe, A_23_P102731, and the <i>GAK</i> SNP, rs11731387.

<p>The box whiskers extend to the most extreme data point, which is at most 1.5 times the interquartile range from the box. The result for the 2-degree of freedom test was p = 8.1E-6, and the eSNP relationship was stronger in PD (p = 7.47E-5, beta = −0.727) than in controls (p = 0.037, beta = −0.494). The minor allele frequency for rs11731387 in the used brain sample was 0.15, and the odds ratio for this SNP in the additive model affection study of the meta-GWAS was 1.35.</p

FoxO1 TFBS genes with evidence of partial mediation for the relationship between <i>FOXO1</i> and PD.

1<p>The direct effect represents the effect of <i>FOXO1</i> expression on PD directly, while the indirect effect represents the effect that is mediated through each FoxO1 TFBS gene.</p

Sample demographics in the TGen cohort.

a<p>CERAD = The Consortium to Establish a Registry for Alzheimer’s Disease.</p

Forest plot of the <i>CHRFAM7A</i> gene.

<p>The plot represents the meta-analysis of the <i>CHRFAM7A</i> gene using results from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) study, the National Institute of Aging-Late Onset AD/National Cell Repository for AD (NIA-LOAD/NCRAD) Family Study and the TGen study. The odds ratio (OR) and 95% confidence interval (CI) for the odds ratio for each study are represented by black squares and horizontal lines. The summary odds ratio is depicted as a black diamond.</p

Meta-analysis of the <i>CHRFAM7A</i> gene.

a<p>CNV = copy number variation.</p

Genes overlapped by copy number variation calls from at least one case and no control samples in the TGen cohort using the candidate gene approach.

a<p>A case sample had copy number variation calls overlapping the <i>AGT</i>, <i>LHCGR</i> and <i>BAT1</i> genes.</p>b,c,d<p>Three different case samples had copy number variation calls overlapping the <i>HLA-DRA</i> and <i>HLA-E</i>, <i>HLA-DRA</i> and <i>HLA-DQB1</i>, and <i>HLA-DRA</i> and <i>NGB</i> genes respectively.</p>e<p>A different case sample had copy number variation calls overlapping the <i>MYH13</i> and <i>MYH8</i> genes.</p