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Ethics statement Destination: subsubsection..1.2.1.1 Item: Title: 2.1.2 | Plasma and CSF cohorts Destination: subsubsection..1.2.1.2 Item: Title: 2.1.3 | AD genome-wide association study (GWAS) risk summary statistics Destination: subsubsection..1.2.1.3 Item: Title: 2.2 | Proteins Destination: subsection..1.2.2 Children: Item: Title: 2.2.1 | Protein-level data generation and quality control Destination: subsubsection..1.2.2.1 Item: Title: 2.2.2 | Normalization of protein concentration measurements Destination: subsubsection..1.2.2.2 Item: Title: 2.2.3 | Quality control of protein concentration measurements Destination: subsubsection..1.2.2.3 Item: Title: 2.3 | Analyses Destination: subsection..1.2.3 Children: Item: Title: 2.3.1 | Genetic quality control Destination: subsubsection..1.2.3.1 Item: Title: 2.3.2 | Protein level GWAS Destination: subsubsection..1.2.3.2 Item: Title: 2.3.3 | In silico functional annotation Destination: subsubsection..1.2.3.3 Item: Title: 2.3.4 | Protein level correlations between tissues Destination: subsubsection..1.2.3.4 Item: Title: 2.3.5 | Predicting AD status from protein levels Destination: subsubsection..1.2.3.5 Item: Title: 2.3.6 | Genetic co-localization Destination: subsubsection..1.2.3.6 Item: Title: 3 | RESULTS Destination: section..1.3 Children: Item: Title: 3.1 | Study design Destination: subsection..1.3.1 Item: Title: 3.2 | CSF and plasma pQTL findings Destination: subsection..1.3.2 Children: Item: Title: 3.2.1 | Plasma GWASs Destination: subsubsection..1.3.2.1 Item: Title: 3.2.2 | CSF GWAS Destination: subsubsection..1.3.2.2 Item: Title: 3.3 | Comparison of plasma and CSF Destination: subsection..1.3.3 Children: Item: Title: 3.3.1 | Across tissue pQTL effect size correlations are weak Destination: subsubsection..1.3.3.1 Item: Title: 3.3.2 | CSF and plasma protein levels are weakly correlated Destination: subsubsection..1.3.3.2 Item: Title: 3.3.3 | CSF and plasma pQTLs are shared except in the APOE region Destination: subsubsection..1.3.3.3 Item: Title: 3.4 | Plasma and CSF biomarkers as quantitative traits for genetics studies for AD Destination: subsection..1.3.4 Children: Item: Title: 3.4.1 | AD top hits co-localize with CSF sentinel variants more frequently than plasma sentinel variants Destination: subsubsection..1.3.4.1 Item: Title: 3.4.2 | CSF protein levels predict AD status more accurately than plasma protein levels Destination: subsubsection..1.3.4.2 Item: Title: 3.4.3 | AD PRS correlates weakly with both plasma and CSF protein levels Destination: subsubsection..1.3.4.3 Item: Title: 4 | DISCUSSION Destination: section..1.4 Item: Title: ACKNOWLEDGMENTS Destination: section*.16 Item: Title: CONFLICT OF INTEREST STATEMENT Destination: section*.18 Item: Title: CONSENT STATEMENT Destination: section*.20 Item: Title: ORCID Destination: section*.22 Item: Title: REFERENCES Destination: section*.24 Item: Title: SUPPORTING INFORMATION Destination: section*.26 Info: Title: A genetic and proteomic 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