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

Duplications overlapping the candidate genes <i>APP</i> and <i>DOPEY2</i> in samples of the TGen cohort.

<p>Representative UCSC Genome Browser (March 2006 (NCBI36/hg18) assembly) plots of duplications overlapping the candidate genes: (A) <i>APP</i> and (B) <i>DOPEY2</i>, in samples of the TGen cohort. The chromosomal location of the gene and probes on the Affymetrix Genomewide 6.0 array are shown. The region with the duplication for each sample relative to the gene is represented by a blue rectangle.</p