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The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1
BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal 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 conseq...
Autores principales: | , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325838/ https://www.ncbi.nlm.nih.gov/pubmed/30621600 http://dx.doi.org/10.1186/s12876-018-0917-5 |
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author | Imhann, Floris Van der Velde, K. J. Barbieri, R. Alberts, R. Voskuil, M. D. Vich Vila, A. Collij, V. Spekhorst, L. M. der Sloot KWJ, Van Peters, V. Van Dullemen, H. M. Visschedijk, M. C. EAM, Festen Swertz, M. A. Dijkstra, G. Weersma, R. K. |
author_facet | Imhann, Floris Van der Velde, K. J. Barbieri, R. Alberts, R. Voskuil, M. D. Vich Vila, A. Collij, V. Spekhorst, L. M. der Sloot KWJ, Van Peters, V. Van Dullemen, H. M. Visschedijk, M. C. EAM, Festen Swertz, M. A. Dijkstra, G. Weersma, R. K. |
author_sort | Imhann, Floris |
collection | PubMed |
description | BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal 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 generated from the same IBD patients. CONSTRUCTION AND CONTENT: We initiated the 1000IBD project (https://1000ibd.org) 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, 1215 participants have been enrolled in the project and enrolment is on-going. 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. UTILITY AND DISCUSSION: All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org, accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. 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. CONCLUSIONS: We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12876-018-0917-5) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6325838 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-63258382019-01-11 The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 Imhann, Floris Van der Velde, K. J. Barbieri, R. Alberts, R. Voskuil, M. D. Vich Vila, A. Collij, V. Spekhorst, L. M. der Sloot KWJ, Van Peters, V. Van Dullemen, H. M. Visschedijk, M. C. EAM, Festen Swertz, M. A. Dijkstra, G. Weersma, R. K. BMC Gastroenterol Database BACKGROUND: Inflammatory bowel disease (IBD) is a chronic complex disease of the gastrointestinal 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 generated from the same IBD patients. CONSTRUCTION AND CONTENT: We initiated the 1000IBD project (https://1000ibd.org) 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, 1215 participants have been enrolled in the project and enrolment is on-going. 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. UTILITY AND DISCUSSION: All molecular data generated within the 1000IBD project will be shared on the European Genome-Phenome Archive (https://ega-archive.org, accession no: EGAS00001002702). The first data release, detailed in this announcement and released simultaneously with this publication, will contain basic phenotypes for 1215 participants, genotypes of 314 participants and gut microbiome data from stool samples (315 participants) and biopsies (107 participants) generated by tag sequencing the 16S gene. 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. CONCLUSIONS: We report on the establishment and future development of the 1000IBD project: the first comprehensive multi-omics dataset aimed at discovering IBD biomarker profiles and treatment targets. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12876-018-0917-5) contains supplementary material, which is available to authorized users. BioMed Central 2019-01-08 /pmc/articles/PMC6325838/ /pubmed/30621600 http://dx.doi.org/10.1186/s12876-018-0917-5 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Database Imhann, Floris Van der Velde, K. J. Barbieri, R. Alberts, R. Voskuil, M. D. Vich Vila, A. Collij, V. Spekhorst, L. M. der Sloot KWJ, Van Peters, V. Van Dullemen, H. M. Visschedijk, M. C. EAM, Festen Swertz, M. A. Dijkstra, G. Weersma, R. K. The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 |
title | The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 |
title_full | The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 |
title_fullStr | The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 |
title_full_unstemmed | The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 |
title_short | The 1000IBD project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 |
title_sort | 1000ibd project: multi-omics data of 1000 inflammatory bowel disease patients; data release 1 |
topic | Database |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6325838/ https://www.ncbi.nlm.nih.gov/pubmed/30621600 http://dx.doi.org/10.1186/s12876-018-0917-5 |
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