| Literature DB >> 26319774 |
Ettje F Tigchelaar1, Alexandra Zhernakova1, Jackie A M Dekens1, Gerben Hermes2, Agnieszka Baranska3, Zlatan Mujagic4, Morris A Swertz5, Angélica M Muñoz6, Patrick Deelen7, Maria C Cénit8, Lude Franke8, Salome Scholtens9, Ronald P Stolk9, Cisca Wijmenga1, Edith J M Feskens10.
Abstract
PURPOSE: There is a critical need for population-based prospective cohort studies because they follow individuals before the onset of disease, allowing for studies that can identify biomarkers and disease-modifying effects, and thereby contributing to systems epidemiology. PARTICIPANTS: This paper describes the design and baseline characteristics of an intensively examined subpopulation of the LifeLines cohort in the Netherlands. In this unique subcohort, LifeLines DEEP, we included 1539 participants aged 18 years and older. FINDINGS TO DATE: We collected additional blood (n = 1387), exhaled air (n = 1425) and faecal samples (n = 1248), and elicited responses to gastrointestinal health questionnaires (n = 1176) for analysis of the genome, epigenome, transcriptome, microbiome, metabolome and other biological levels. Here, we provide an overview of the different data layers in LifeLines DEEP and present baseline characteristics of the study population including food intake and quality of life. We also describe how the LifeLines DEEP cohort allows for the detailed investigation of genetic, genomic and metabolic variation for a wide range of phenotypic outcomes. Finally, we examine the determinants of gastrointestinal health, an area of particular interest to us that can be addressed by LifeLines DEEP. FUTURE PLANS: We have established a cohort of which multiple data levels allow for the integrative analysis of populations for translation of this information into biomarkers for disease, and which will offer new insights into disease mechanisms and prevention. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.Entities:
Keywords: EPIDEMIOLOGY; GENETICS; PUBLIC HEALTH
Mesh:
Substances:
Year: 2015 PMID: 26319774 PMCID: PMC4554905 DOI: 10.1136/bmjopen-2014-006772
Source DB: PubMed Journal: BMJ Open ISSN: 2044-6055 Impact factor: 2.692
Overview of additional data collected in LifeLines DEEP, including the number of samples, the source biomaterial it originates from and the method of analysis used
| LifeLines DEEP data | n | Source | Methods |
|---|---|---|---|
| Biological ageing | 1387 | Cells from whole blood | FlowFish |
| Biological ageing | 1387 | DNA from whole blood | qPCR and sjTRECs |
| Biomarkers (citrulline, cytokines) | 1387 | Plasma | HPLC, ECLIA |
| Biomarkers (calprotectin, HBD-2, chromogranin A, SCFA) | 1248 | Faeces | ELISA, ELISA, RIA, GC-MS |
| CVD risk score | 1448 | Biochemical measures and questionnaire | Scoring algorithm Framingham Heart Study |
| Functional studies | 1387 | PBMC from whole blood | Various methods |
| Gastrointestinal symptoms | 1176 | Questionnaire | Rome III criteria and Bristol Stool Form Scale |
| Genetics | 1387 | DNA from whole blood | CytoSNP and ImmunoChip, GoNL as imputation reference |
| Metabolomics | 1425 | Exhaled air | GC-tof-MS |
| Metabolomics | 1387 | Plasma | NMR |
| Methylation | 761+ | DNA from whole blood | 450 K chip |
| Microbiome | 1248 | Faeces | 16S rRNA based sequencing |
| Transcriptomics | 1387 | Whole blood (PAXgene) | RNA sequencing |
CVD, cardiovascular disease; ECLIA, electro-chemiluminescence immunoassay; GC-(tof-)MS, gas chromatography-(time of flight-)mass spectrometry; HBD-2, human β defensin 2; HPLC, high-performance liquid chromatography; NMR, nuclear MR; qPCR, quantitative PCR; RIA, radioimmunoassay; SCFA, short chain fatty acids; sjTRECs, signal joint T cell receptor excision circles.
Baseline characteristics of LifeLines DEEP by gender, including smoking, age, BMI, cholesterol level, glucose level, blood pressure and Framingham risk score for cardiovascular disease
| Characteristic | Men | Women | ||
|---|---|---|---|---|
| n | 636 | 903 | ||
| Smoking status | Current | % | 19.5 | 18.3 |
| Former | % | 29.9 | 28.5 | |
| Never | % | 47.0 | 48.0 | |
| Age | mean (SD) | 44.0 (13.9) | 43.3 (13.8) | |
| BMI | mean (SD) | 25.4 (3.5) | 25.0 (4.7) | |
| Total cholesterol (mmol/L) | mean (SD) | 5.0 (1.0) | 5.0 (1.0) | |
| HDL cholesterol (mmol/L) | mean (SD) | 1.3 (0.3) | 1.7 (0.4) | |
| Glucose level (mmol/L) | mean (SD) | 5.1 (0.7) | 4.9 (0.7) | |
| Systolic blood pressure (mm Hg) | mean (SD) | 123.5 (12.4) | 115.6 (13.4) | |
| Diastolic blood pressure (mm Hg) | mean (SD) | 73.6 (9.6) | 68.4 (8.3) | |
| CVD risk score | mean (SD) | 8.6 (8.9) | 5.7 (7.0) | |
BMI, body mass index; CVD, cardiovascular disease; HDL, high-density lipoprotein.
Figure 1Mean and SD of crude and adjusted quality of life scores, 2 component scores and 8 group scores in the LifeLines DEEP population (n=1539) compared to a national sample of the Dutch population.34 42 Adjusted score is adjusted for gender and age. PCS, physical component score; MCS, mental component score; PF, physical functioning; RP, role-physical; BP, bodily pain; GH, general health; VT, vitality; SF, social functioning; RE, role-emotional; MH, mental health.
Figure 2Functional bowel disorders in the LifeLines DEEP cohort based on Rome III criteria (n=1176). IBS (Irritable Bowel Syndrome): pain or discomfort at least 2–3 days/month, IBS_strict: pain or discomfort more than 1 day/week, FBD, functional bowel disorder, healthy gut, lowest possible score on Rome III questionnaire.
Figure 3Qualitative intake of (A) bread, (B) coffee, (C) meat and poultry, (D) vegetables, (E) fruit, (F) fish, (G) milk and buttermilk and (H) alcoholic beverages, in LifeLines DEEP (n=1539). Bars represent: ‘not this month’, ‘1 day/month’, ‘2–3 days/month’, ‘1 day/week’, ‘2–3 days/week’, ‘4–5 days/week’ and ‘6–7 days/week’.
Figure 4Change in abundance of Actinobacteria on ageing.