106 Materials and Methods Lead contact Further information and requests for resources should be directed to the Lead Contact, professor Rinse K. Weersma (r.k.weersma@umcg.nl) Material availability A full list of antibody-bound peptides that were enriched in patients with IBD is publicly available on bioRxiv via the following link: https://doi.org/10.1101/2021.12.07.471581. Data and code availability The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request. The data for the Groningen IBD cohort can be requested with the accession number EGAS00001002702. The raw metagenomics sequencing data used for this study are available from the European Genome-phenome Archive data repository: 1000IBD cohort (https://www.ebi.ac.uk/ega/datasets/EGAD00001004194) and LL-DEEP cohort (https:// www.ebi.ac.uk/ega/datasets/EGAD00001001991). Due to patient confidentiality, the datasets are available upon reasonable request to the University Medical Center Groningen (UMCG) and Lifelines, respectively. All code used for analyses in this study can be found at the following link: https://github.com/GRONINGEN-MICROBIOME-CENTRE/Phip-Seq_LLD-IBD. Study cohorts: 1000IBD and Lifelines-DEEP Serum samples were collected from 497 patients with an established diagnosis of IBD who were included at the outpatient clinic of the UMCG upon participation in the 1000IBD project: a large, multi-omics IBD cohort based in Groningen, the Netherlands.20 Detailed phenotypic information and multi-omics data have been generated for these patients, who were enrolled in the period 2007–2019. Phenotypic data that were collected included age, gender, body-mass index (BMI, bodyweight divided by squared height), disease duration, smoking behavior, theMontreal disease classification, medication usage, history of surgery, extra-intestinal manifestations, clinical disease activity and serum C-reactive protein levels, all of which was assessed at time of sampling. Clinical disease activity was recorded as the Harvey-Bradshaw Index for patients with CD and the Simple Clinical Colitis Activity Index for patients with UC. All participants provided written informed consent prior to sample collection. The study was approved by the Institutional Review Board (IRB) of the UMCG, Groningen, the Netherlands (in Dutch: “Medisch Ethische Toetsingscommissie”, METc; IRB no. 2008/338) and was conducted in accordance with the principles of the Declaration of Helsinki (2013). In addition, plasma samples were collected from an independent population- based cohort (Lifelines-DEEP), which is situated in the northern part of the Netherlands.21 In total, 1,326 participants from this cohort were included, after having excluded participants with known irritable bowel syndrome or IBD. The Lifelines-DEEP cohort study was also approved by the IRB of the UMCG (IRB no. M12.113965) and registered at the Lifelines Research Site in Groningen. A detailed description of this cohort can be found elsewhere.22 Chapter 4
RkJQdWJsaXNoZXIy MjY0ODMw