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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.

Type: Other
Archive: European Genome-phenome Archive (EGA)

13 Datasets 35 Publications

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	Sequencing of V4 hypervariable region of 16S gene of microbiota present in feces of IBD patients	Illumina MiSeq	315
EGAD00001003936	Sequencing of V4 hypervariable region of 16S gene from microbiota present in intestinal biopsies of IBD patients	Illumina MiSeq	107
EGAD00001003991	Complete clinical phenotypic description of all patients; the number listed represents all the samples linked to the 609 patients present in the dataset. Please consult the key file to visualise the sample-patient relationship		1094
EGAD00001004194	Complete Microbiome Metagenomics from feces of 461 IBD patients; The sequencer used was the Illumina HiSeq 2000 with a paired end reads design, reflected in the 2 FastQ format files per sample.	Illumina HiSeq 2000	355
EGAD00001006789	eQTLsummary&GeneTable from eQTL study in 299 intestinal biopsy samples from IBD		1
EGAD00001006790	intrstinal.eQTLsummary		1
EGAD00001006791	eQTL.study.release.phenotype		1
EGAD00001006792	eQTLsummary&GeneTable		1
EGAD00001006798	eQTL.study.release.inflammation.eQTLsummary		1
EGAD00001008214	This is the RNAseq data from mucosal biopsies.	Illumina HiSeq 2000	440
EGAD00001008215	This is the dataset of 16S data from mucosal biopsies.	Illumina MiSeq	833
EGAD00010001495	Intensity files for Immunochip genotypes from blood	Illumina Immunochip	314
EGAD00010001649	This set features unfiltered, aligned, UMI-based single cell RNA sequencing count data for 5290 Blood, intraepithelial ileum (IEL) and lamina propria ileum (LPL) T cells from Crohn's disease patients as published in Uniken Venema et al, Gastroenterology 2019	Smartseq2_adapted	3

Publications	Citations
The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1. Imhann F, Van der Velde KJ, Barbieri R, Alberts R, Voskuil MD, Vich Vila A, Collij V, Spekhorst LM, Van der Sloot KWJ, Peters V, Van Dullemen HM, Visschedijk MC, Festen EAM, Swertz MA, Dijkstra G, Weersma RK. BMC Gastroenterol 19: 2019 5	83
SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects. Collij V, Imhann F, Vich Vila A, Fu J, Dijkstra G, Festen EAM, Voskuil MD, Daly MJ, Xavier RJ, Wijmenga C, Zhernakova A, Weersma RK. PLoS One 14: 2019 e0211328	12
Microbial genes and pathways in inflammatory bowel disease. Schirmer M, Garner A, Vlamakis H, Xavier RJ. Nat Rev Microbiol 17: 2019 497-511	714
Impact of commonly used drugs on the composition and metabolic function of the gut microbiota. Vich Vila A, Collij V, Sanna S, Sinha T, Imhann F, Bourgonje AR, Mujagic Z, Jonkers DMAE, Masclee AAM, Fu J, Kurilshikov A, Wijmenga C, Zhernakova A, Weersma RK. Nat Commun 11: 2020 362	623
Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK. Gut 70: 2021 285-296	46
Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity. Chen L, Collij V, Jaeger M, van den Munckhof ICL, Vich Vila A, Kurilshikov A, Gacesa R, Sinha T, Oosting M, Joosten LAB, Rutten JHW, Riksen NP, Xavier RJ, Kuipers F, Wijmenga C, Zhernakova A, Netea MG, Weersma RK, Fu J. Nat Commun 11: 2020 4018	139
Genetic Risk Scores Identify Genetic Aetiology of Inflammatory Bowel Disease Phenotypes. Voskuil MD, Spekhorst LM, van der Sloot KWJ, Jansen BH, Dijkstra G, van der Woude CJ, Hoentjen F, Pierik MJ, van der Meulen AE, de Boer NKH, Löwenberg M, Oldenburg B, Festen EAM, Weersma RK. J Crohns Colitis 15: 2021 930-937	9
The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease. Ruigrok RAAA, Collij V, Sureda P, Klaassen MAY, Bolte LA, Jansen BH, Voskuil MD, Fu J, Wijmenga C, Zhernakova A, Weersma RK, Vich Vila A. J Crohns Colitis 15: 2021 1326-1338	34
Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases. Iablokov SN, Klimenko NS, Efimova DA, Shashkova T, Novichkov PS, Rodionov DA, Tyakht AV. Front Mol Biosci 7: 2020 603740	14
Inflammation status modulates the effect of host genetic variation on intestinal gene expression in inflammatory bowel disease. Hu S, Uniken Venema WT, Westra HJ, Vich Vila A, Barbieri R, Voskuil MD, Blokzijl T, Jansen BH, Li Y, Daly MJ, Xavier RJ, Dijkstra G, Festen EA, Weersma RK. Nat Commun 12: 2021 1122	48
Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome. Bolte LA, Vich Vila A, Imhann F, Collij V, Gacesa R, Peters V, Wijmenga C, Kurilshikov A, Campmans-Kuijpers MJE, Fu J, Dijkstra G, Zhernakova A, Weersma RK. Gut 70: 2021 1287-1298	491
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities. Iablokov SN, Novichkov PS, Osterman AL, Rodionov DA. Front Microbiol 12: 2021 653314	12
A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease. Gacesa R, Vich Vila A, Collij V, Mujagic Z, Kurilshikov A, Voskuil MD, Festen EAM, Wijmenga C, Jonkers DMAE, Dijkstra G, Fu J, Zhernakova A, Imhann F, Weersma RK. Gut Microbes 13: 2021 1943288	12
The Effect of Phenotype and Genotype on the Plasma Proteome in Patients with Inflammatory Bowel Disease. Bourgonje AR, Hu S, Spekhorst LM, Zhernakova DV, Vich Vila A, Li Y, Voskuil MD, van Berkel LA, Bley Folly B, Charrout M, Mahfouz A, Reinders MJT, van Heck JIP, Joosten LAB, Visschedijk MC, van Dullemen HM, Faber KN, Samsom JN, Festen EAM, Dijkstra G, Weersma RK. J Crohns Colitis 16: 2022 414-429	36
Polygenetic risk scores do not add predictive power to clinical models for response to anti-TNFα therapy in inflammatory bowel disease. Karmi N, Bangma A, Spekhorst LM, van Dullemen HM, Visschedijk MC, Dijkstra G, Weersma RK, Voskuil MD, Festen EAM. PLoS One 16: 2021 e0256860	7
Inulin-grown <i>Faecalibacterium prausnitzii</i> cross-feeds fructose to the human intestinal epithelium. Fagundes RR, Bourgonje AR, Saeed A, Vich Vila A, Plomp N, Blokzijl T, Sadaghian Sadabad M, von Martels JZH, van Leeuwen SS, Weersma RK, Dijkstra G, Harmsen HJM, Faber KN. Gut Microbes 13: 2021 1993582	38
Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All. Sudhakar P, Alsoud D, Wellens J, Verstockt S, Arnauts K, Verstockt B, Vermeire S. J Crohns Colitis 16: 2022 1306-1320	20
Long-Term Dietary Patterns Are Reflected in the Plasma Inflammatory Proteome of Patients with Inflammatory Bowel Disease. Bourgonje AR, Bolte LA, Vranckx LLC, Spekhorst LM, Gacesa R, Hu S, van Dullemen HM, Visschedijk MC, Festen EAM, Samsom JN, Dijkstra G, Weersma RK, Campmans-Kuijpers MJE. Nutrients 14: 2022 2522	10
HIF1α-Dependent Induction of <i>TFRC</i> by a Combination of Intestinal Inflammation and Systemic Iron Deficiency in Inflammatory Bowel Disease. Fagundes RR, Bourgonje AR, Hu S, Barbieri R, Jansen BH, Sinnema N, Blokzijl T, Taylor CT, Weersma RK, Faber KN, Dijkstra G. Front Physiol 13: 2022 889091	19
Proteomic analyses do not reveal subclinical inflammation in fatigued patients with clinically quiescent inflammatory bowel disease. Bourgonje AR, Wichers SJ, Hu S, van Dullemen HM, Visschedijk MC, Faber KN, Festen EAM, Dijkstra G, Samsom JN, Weersma RK, Spekhorst LM. Sci Rep 12: 2022 14581	7
Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa. Guzzo GL, Mittinty MN, Llamas B, Andrews JM, Weyrich LS. Microorganisms 10: 2022 1910	12
Faecal metabolome and its determinants in inflammatory bowel disease. Vich Vila A, Hu S, Andreu-Sánchez S, Collij V, Jansen BH, Augustijn HE, Bolte LA, Ruigrok RAAA, Abu-Ali G, Giallourakis C, Schneider J, Parkinson J, Al-Garawi A, Zhernakova A, Gacesa R, Fu J, Weersma RK. Gut 72: 2023 1472-1485	137
Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire. Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S, Lifelines Cohort Study, Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A. Immunity 56: 2023 1376-1392.e8	32
Oxidative stress gene expression, DNA methylation, and gut microbiota interaction trigger Crohn's disease: a multi-omics Mendelian randomization study. Xu S, Li X, Zhang S, Qi C, Zhang Z, Ma R, Xiang L, Chen L, Zhu Y, Tang C, Bourgonje AR, Li M, He Y, Zeng Z, Hu S, Feng R, Chen M. BMC Med 21: 2023 179	167
Decreased TMIGD1 aggravates colitis and intestinal barrier dysfunction via the BANF1-NF-κB pathway in Crohn's disease. Zhou L, Zhu L, Wu X, Hu S, Zhang S, Ning M, Yu J, Chen M. BMC Med 21: 2023 287	24
Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts. Ning L, Zhou YL, Sun H, Zhang Y, Shen C, Wang Z, Xuan B, Zhao Y, Ma Y, Yan Y, Tong T, Huang X, Hu M, Zhu X, Ding J, Zhang Y, Cui Z, Fang JY, Chen H, Hong J. Nat Commun 14: 2023 7135	234
<i>Faecalibacterium prausnitzii</i> promotes intestinal epithelial IL-18 production through activation of the HIF1α pathway. Fagundes RR, Bravo-Ruiseco G, Hu S, Kierans SJ, Weersma RK, Taylor CT, Dijkstra G, Harmsen HJM, Faber KN. Front Microbiol 14: 2023 1298304	16
Mucosal host-microbe interactions associate with clinical phenotypes in inflammatory bowel disease. Hu S, Bourgonje AR, Gacesa R, Jansen BH, Björk JR, Bangma A, Hidding IJ, van Dullemen HM, Visschedijk MC, Faber KN, Dijkstra G, Harmsen HJM, Festen EAM, Vich Vila A, Spekhorst LM, Weersma RK. Nat Commun 15: 2024 1470	67
Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota. Carasso S, Zaatry R, Hajjo H, Kadosh-Kariti D, Ben-Assa N, Naddaf R, Mandelbaum N, Pressman S, Chowers Y, Gefen T, Jeffrey KL, Jofre J, Coyne MJ, Comstock LE, Sharon I, Geva-Zatorsky N. Cell Host Microbe 32: 2024 322-334.e9	64
Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study. Al Radi ZMA, Prins FM, Collij V, Vich Vila A, Festen EAM, Dijkstra G, Weersma RK, Klaassen MAY, Gacesa R. Inflamm Bowel Dis 30: 2024 1642-1653	12
Noninvasive, microbiome-based diagnosis of inflammatory bowel disease. Zheng J, Sun Q, Zhang M, Liu C, Su Q, Zhang L, Xu Z, Lu W, Ching J, Tang W, Cheung CP, Hamilton AL, Wilson O'Brien AL, Wei SC, Bernstein CN, Rubin DT, Chang EB, Morrison M, Kamm MA, Chan FKL, Zhang J, Ng SC. Nat Med 30: 2024 3555-3567	125
Butyrate suppresses mucosal inflammation in inflammatory bowel disease primarily through HDAC3 inhibition in monocytes and macrophages. Parada-Venegas D, De la Fuente López M, Dubois-Camacho K, Landskron G, Blokzijl T, Molina H, Casanova MC, Cui Y, Liu M, Da Costa De Pina AM, Simian D, González MJ, Weersma RK, Quera R, Dijkstra G, Faber KN, Hermoso MA. FEBS J 292: 2025 6134-6157	18
Human DNA levels in feces reflect gut inflammation and associate with presence of gut species in IBD patients across the age spectrum. Mazzoni C, Ochana BL, Orlanski-Meyer E, Ben Ya'acov A, Focht G, Harpenas E, Shmorak S, Ledder O, Lev-Tzion R, Shemer R, Shteyer E, Dor Y, Yassour M. Microbiome 14: 2026 104	1
DUOX2-Driven Oxidative Stress Alters the Gut Redox Niche and Promotes Microbial Dysbiosis in Crohn's Disease. Xu S, Li X, Wu X, Zheng K, Yi Y, Lin Y, Tian C, Zhu Y, Tang C, Hu S, Zhang S, He Y, Chen M, Feng R. Antioxidants (Basel) 15: 2026 292	1
Systemic antibody responses against bacterial and viral antigens associate with fatigue in patients with inflammatory bowel disease. Griesbaum MG, Vogl T, Visschedijk MC, Festen EAM, Dijkstra G, Weinberger A, Segal E, Weersma RK, Bourgonje AR. iScience 29: 2026 116828	0