. Author manuscript; available in PMC: 2022 Jun 22.

Published in final edited form as: Nat Rev Gastroenterol Hepatol. 2022 Mar 17;19(6):399–409. doi: 10.1038/s41575-022-00593-y

Table 1 |.

A summary of prospective birth, at risk and pre-diagnostic cohorts to study IBD and related outcomes

Name of cohort, year	Number of enrolled participants	Cohort and/or study description	primary goal	Types and timing of biological samples collected	Types of omics analyses conducted/planned	Major published findings
Harvard Health Study cohorts, USA
Nurses’ Health Study, 1976	121,000	Pre-diagnostic; prospective cohorts of health-care providers	The non-genetic causes of IBD and other diseases	Blood (two separate collections), cheek cell swabs	Genomics, metabolomics, proteomics	Established the importance of various environmental risk factors in the development of Crohn’s disease and ulcerative colitis^110–112; reported on the association between plasma levels of perfluoroalkyl substances and IBD⁴⁰
Nurses’ Health Study 2, 1989	117,000
Health Professionals Follow-Up Study, 1986	52,000
Preclinical cohorts, Sweden
Malmö Diet and Cancer cohort, 1991	28,000	Birth, FDRs of individuals with IBD, pre-diagnostic; prospective cohorts	The causes and multiomics signatures of IBD onset and course	Blood	Metabolomics, proteomics	Proteomic signatures in serum samples predictive of ulcerative colitis onset⁵⁸
Swedish Newborn Dry Blood Spots cohort, 1975	Population-based			Dried blood spots
Swedish IBD Twin cohort, 2003	>100 twin pairs			Blood, intestinal biopsies, saliva and stool
Northern Sweden Health and Disease Study, 2011	135,000			Blood
Other cohorts
The Crohn’s and Colitis Canada Genetics, Environmental, Microbial (GEM) Project, 2008	5,122	FDRs; prospective cohort of FDRs of individuals with Crohn’s disease	The multiomics signatures of Crohn’s disease	Blood, stool and urine	Genomics, metabolomics, proteomics, and microbiome analysis	Genetic risk profile of FDRs of individuals with Crohn’s disease, interaction between genomic and microbiome signatures, faecal biomarkers preceding ulcerative colitis diagnosis, and antimicrobial antibody signatures predictive of Crohn’s disease onset^{16,92,113,114}
Mechanisms of Disease Transmission In Utero Through the Microbiome (MECONIUM) cohort, USA, 2014	133 mothers with IBD and their offspring; 299 mothers without IBD and their offspring	Early life, FDRs; prospective cohort of pregnant women with and without IBD and their offspring	The link between maternal and offspring multiomics signatures of IBD and transmission of the microbiota	Stool, saliva, vaginal swab, blood, placenta, cord blood, breast milk (mother), meconium, stool and buccal swab (offspring)	Metabolomics, proteomics, microbiome analysis	Microbiome signatures and elevated faecal calprotectin in offspring of women with versus without IBD^59,89
Road to Prevention: A Mount Sinai Initiative, USA, 2016	667 individuals from multiplex families^a; 94 individuals from control families	Birth, FDRs; cross-sectional study design of multiplex fami1ies^a with IBD with longitudinal follow-up and biospecimen collections from unaffected high-risk individuals	The multiomics signatures of IBD onset	Blood, stool, deciduous teeth, hair, saliva	Genomics, exposome analysis, transcriptomics, proteomics, immunophenomics, microbiome analysis	Clustering of IBD in multiplex families^a(REF.¹⁴)
Twin cohort for the study of (pre) clinical IBD in the Netherlands (TWIN), 2017	124	Pre-diagnostic, FDRs; a prospective cohort of twin pairs >16 years of age discordant or concordant for IBD	The causes of IBD and the early multiomics signatures of IBD	Blood, urine, stool, oropharyngeal swabs, rectal biopsies	Proteomics, immunophenomics, microbiome and mycobiome analysis, IgA coating of bacteria	Microbiome signatures in twin pairs discordant for IBD⁹⁰
Proteomic Evaluation and Discovery in an IBD Cohort ofTri-service Subjects (PREDICTS), USA, 2019	1,000 patients each with Crohn’s disease or ulcerative colitis, and 500 healthy individuals as controls	Pre-diagnostic; a nested case-control study of subjects with incident IBD and healthy controls from a cohort of US military personnel	The multiomics signatures of IBD onset and course	Serum	Genomics, metabolomics, proteomics, glycomics, metagenomics, epigenetics	Proteomics signatures in serum samples predictive of Crohn’s disease onset⁵⁷
IBD Tooth Fairy Study, Portugal, 2019	65 patients with IBD, 102 healthy individuals	Birth, FDRs; collection and analysis of deciduous teeth of adults and children with and without IBD	The effect of early life exposures and the timing of exposures on subsequent IBD risk	Deciduous teeth	Exposome analysis, including metals and organic compounds	Differences in the levels of metals in teeth from children with and without IBD⁴⁴
Mother-to-Infant Transfer of Bacteriome, Virome, Fungome and Metabolome in Health and Crohn’s Disease (Mommy-CD), Hong Kong, 2019	1,000 healthy mothers and 620 infants; 15 pregnant mothers with IBD and 5 infants	Birth; prospective cohort of pregnant women with and without IBD and their offspring	The link between maternal and offspring multiomics signatures of IBD and transmission of the microbiome	Stool, saliva, vaginal swab, blood, placenta, cord blood, breast milk (mother); stool and saliva (father); meconium, stool and buccal swab (offspring)	Metabolomics, proteomics, microbiome analysis	NA
Center for Molecular Prediction of IBD (PREDICT), Denmark, 2021	10,000 IBD; 10,000 healthy individuals	Birth, pre-diagnostic; national population-based prospective cohort of individuals with and without IBD	The causes and multiomics signatures of IBD onset and course by combining omics data with nationwide longitudinal health register data on treatment, comorbidities and outcomes	Neonatal blood spots, pre-diagnostic and post-diagnostic serum samples, and on a subset stool	Genomics, geographic information system, metabolomics, proteomics, epigenetics, metagenomics, exposome	NA

FDR, first-degree relative; IBD, inflammatory bowel disease; NA, not applicable.

Families with two or more members with IBD.