In vincent-van-hoef/Analysis5204: Analysis for NBIS support project #5204

knitr::opts_chunk$set(
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library("knitr")
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Introduction

The ANCA-associated vasculitides are rare but severe autoimmune disorders. Tools for improved diagnostics and prognostics are needed. In this project, 184 proteins (Olink; CARDIOVASCULAR III and INFLAMMATION panels) and four additional proteins (Luminex data) were measured in serum or plasma samples from patients with ANCA-associated vasculitis and several controls (healthy, remission, disease control), in order to identify biomarkers for active disease, organ involvement and accurate diagnosis.

To accomplish this, following analyses have been agreed upon:

• Quality Control of PEA data
• Unsupervised analysis of data structure using PCA
• Differential expression between selected subgroups:
• Active AAV vs Healthy (for GPA, MPA, MPO and PR3 each)
• Active AAV vs Remission AAV (for GPA, MPA, MPO and PR3 each)
• Active AAV vs RA or SLE Nephritis (for GPA, MPA, MPO and PR3 each)
• Active disease (GPA vs MPA and MPO vs PR3 both)
• Remission (GPA vs MPA and MPO vs PR3 both)
• Serum and plasma Samples will be analyzed separately
• Pathway analysis of differential expressed proteins using KEGG, GO, MsigDB, ... gene set collections
• Correlation of proteins with the inflammation markers and BVAS scores
• Effect of cortisone treatment on protein expression
• Biomarkers/Predictors of GPA vs MPA and MPO-ANCA+ vs PR3-ANCA+ (using appropriate multivariate techniques)

:::note This report describes the performed analyses and a selection of the resulting output for one comparison of the plasma results only. The full results and all plots are found in the accompanying Results folder. :::

vincent-van-hoef/Analysis5204 documentation built on June 24, 2022, 2:41 p.m.