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Multi-omics data of 1000 Inflammatory Bowel Disease patients

Portal available at https://1000ibd.org Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal (GI) tract. Patients with IBD can experience a wide range of symptoms, but the pathophysiological mechanisms that cause these individual differences in clinical presentation remain largely unknown. In consequence, IBD is currently classified into subtypes using clinical characteristics. If we are to develop a more targeted treatment approach, molecular subtypes of IBD need to be discovered that can be used as new drug targets. To achieve this, we need multiple layers of molecular data are generated from the same IBD patients.We initiated the 1000IBD project to prospectively follow more than 1000 IBD patients from the Northern provinces of the Netherlands. For these patients, we have collected a uniquely large number of phenotypes and generated multi-omics profiles. To date, 1,215 participants have been enrolled in the project and enrolment is on-going, with 609 patients being present in the first data release. Phenotype data collected for these participants includes information on dietary and environmental factors, drug responses, and adverse drug events. Genome information has been generated using genotyping (ImmunoChip, Global Screening Array and HumanExomeChip) and sequencing (whole exome sequencing and targeted resequencing of IBD susceptibility loci), transcriptome information generated using RNA-sequencing of intestinal biopsies and microbiome information generated using both sequencing of the 16S rRNA gene and whole genome shotgun metagenomic sequencing.All molecular data generated within the 1000IBD project will be shared in multiple data on the European Genome-Phenome Archive (www.ega-archive.org). The first data release, will contain basic phenotypes for 609 participants, genotypes of 314 participants, gut microbiome data generated by tag sequencing the 16S gene of feces from 315 participants and intestinal biopsies from 107 participants, and gut microbiome metagenomic sequencing of feces of 355 participants . Future releases will comprise many more additional phenotypes and -omics data layers. 1000IBD data can be used by other researchers as a replication cohort, a dataset to test new software tools, or a dataset for applying new statistical models.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001003935 315
EGAD00001003936 107
EGAD00001003991 1094
EGAD00001004194 Illumina HiSeq 2000 355
EGAD00001006789 1
EGAD00001006790 1
EGAD00001006791 1
EGAD00001006792 1
EGAD00001006798 1
EGAD00001008214 Illumina HiSeq 2000 440
EGAD00001008215 Illumina MiSeq 833
EGAD00010001495 Illumina Immunochip 314
EGAD00010001649 Smartseq2_adapted 3
Publications Citations
The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1.
BMC Gastroenterol 19: 2019 5
44
SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects.
PLoS One 14: 2019 e0211328
10
Microbial genes and pathways in inflammatory bowel disease.
Nat Rev Microbiol 17: 2019 497-511
293
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota.
Nat Commun 11: 2020 362
276
Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD.
Gut 70: 2021 285-296
26
Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity.
Nat Commun 11: 2020 4018
67
Genetic Risk Scores Identify Genetic Aetiology of Inflammatory Bowel Disease Phenotypes.
J Crohns Colitis 15: 2021 930-937
5
The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease.
J Crohns Colitis 15: 2021 1326-1338
13
Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases.
Front Mol Biosci 7: 2020 603740
7
Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease.
Nat Commun 12: 2021 1122
18
Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome.
Gut 70: 2021 1287-1298
197
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities.
Front Microbiol 12: 2021 653314
5
A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease.
Gut Microbes 13: 2021 1943288
3
The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease.
J Crohns Colitis 16: 2022 414-429
17
Polygenetic risk scores do not add predictive power to clinical models for response to anti-TNFα therapy in inflammatory bowel disease.
PLoS One 16: 2021 e0256860
2
Inulin-grown <i>Faecalibacterium prausnitzii</i> cross-feeds fructose to the human intestinal epithelium.
Gut Microbes 13: 2021 1993582
11
Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All.
J Crohns Colitis 16: 2022 1306-1320
9
Long-Term Dietary Patterns Are Reflected in the Plasma Inflammatory Proteome of Patients with Inflammatory Bowel Disease.
Nutrients 14: 2022 2522
5
HIF1α-Dependent Induction of <i>TFRC</i> by a Combination of Intestinal Inflammation and Systemic Iron Deficiency in Inflammatory Bowel Disease.
Front Physiol 13: 2022 889091
5
Proteomic analyses do not reveal subclinical inflammation in fatigued patients with clinically quiescent inflammatory bowel disease.
Sci Rep 12: 2022 14581
3
Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa.
Microorganisms 10: 2022 1910
2
Faecal metabolome and its determinants in inflammatory bowel disease.
Gut 72: 2023 1472-1485
29
Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study.
BMC Med 21: 2023 179
36
Decreased TMIGD1 aggravates colitis and intestinal barrier dysfunction via the BANF1-NF-κB pathway in Crohn's disease.
BMC Med 21: 2023 287
1
Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts.
Nat Commun 14: 2023 7135
11
<i>Faecalibacterium prausnitzii</i> promotes intestinal epithelial IL-18 production through activation of the HIF1α pathway.
Front Microbiol 14: 2023 1298304
1
Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease.
Nat Commun 15: 2024 1470
1