| Literature DB >> 32840675 |
Paul W Franks1,2, Hugo Pomares-Millan3.
Abstract
Epidemiologists have for many decades reported on the patterns and distributions of diabetes within and between populations and have helped to elucidate the aetiology of the disease. This has helped raise awareness of the tremendous burden the disease places on individuals and societies; it has also identified key risk factors that have become the focus of diabetes prevention trials and helped shape public health recommendations. Recent developments in affordable high-throughput genetic and molecular phenotyping technologies have driven the emergence of a new type of epidemiology with a more mechanistic focus than ever before. Studies employing these technologies have identified gene variants or causal loci, and linked these to other omics data that help define the molecular processes mediating the effects of genetic variation in the expression of clinical phenotypes. The scale of these epidemiological studies is rapidly growing; a trend that is set to continue as the public and private sectors invest heavily in omics data generation. Many are banking on this massive volume of diverse molecular data for breakthroughs in drug discovery and predicting sensitivity to risk factors, response to therapies and susceptibility to diabetes complications, as well as the development of disease-monitoring tools and surrogate outcomes. To realise these possibilities, it is essential that omics technologies are applied to well-designed epidemiological studies and that the emerging data are carefully analysed and interpreted. One might view this as next-generation epidemiology, where complex high-dimensionality data analysis approaches will need to be blended with many of the core principles of epidemiological research. In this article, we review the literature on omics in diabetes epidemiology and discuss how this field is evolving. Graphical abstract.Entities:
Keywords: Bioinformatics; Biomarkers; Diabetes; Epidemiology; Genetics; Omics; Review
Year: 2020 PMID: 32840675 PMCID: PMC7641957 DOI: 10.1007/s00125-020-05246-w
Source DB: PubMed Journal: Diabetologia ISSN: 0012-186X Impact factor: 10.122
Overview of omics technologies
| Technology | Term coined by, year | Concept | Objective | Platform(s) | Reference |
|---|---|---|---|---|---|
| Genomics | Thomas H. Roderick, 1986 | Genes, their mapping and functions | Identify genetic functionality | Next-generation sequencing; arrays; bioinformatics | [ |
| Genetics | William Bateson, 1905 | Genes and their variations | Identify genetic makeup, heredity and functionality | Next-generation sequencing; arrays; bioinformatics | [ |
| Metagenomics | Jo Handelsman, 1998 | Analysis of the interacting population of organisms in the body | Identify genetic functionality from environmental sources (e.g. gut, oral microbiome) | Microbial genome sequencing (16S rRNA/“Shotgun”); bioinformatics | [ |
| Nutrigenomics | Nancy Fogg-Johnson and Alex Merolli, 1996 | The relationship between nutritional physiology and genetic makeup | Measure dietary effects on the transcriptome or metabolome | RNA-Seq; Microarray; Chromatography; MS; NMR | [ |
| Proteomics | Marc Wilkins, 1995 | Proteins | Identify structure and activity of proteins expressed | MS; protein arrays | [ |
| Metabolomics/ Metabonomics | Steven Oliver, 1998 /Jeremy Nicholson, 1999 | Metabolites | Identify and quantify molecules associated with physiological and pathological effects | Chromatography; MS; NMR | [ |
| Epigenetics | Conrad Waddington, 1940 | DNA methylation and histone modifications | Study processes that regulate how and when certain genes are turned on and turned off | Next-generation sequencing; arrays; bioinformatics | [ |
| Epigenomics | NA, 2006 | DNA methylation, chromatin and histone modifications in the genome | Analyse epigenetic changes across many genes in a cell or entire organism | Next-generation sequencing; RNA-Seq; arrays; bioinformatics; ChIP-Seq; ATAC-Seq | [ |
| Glycomics | Raymond Dwek, 1982 | Cellular carbohydrates | Identify and quantify glycomic molecules | Chromatography; MS; NMR | [ |
| Lipidomics | NA, 2003 | Cellular lipids | Identify and quantify lipids | Chromatography; MS; NMR | [ |
| Transcriptomics | Charles Auffray, 1996 | mRNA | Identify genetic transcription and activity intensity | RNA-Seq; arrays | [ |
ATAC-Seq, assay for transposase-accessible chromatin using sequencing; ChIP-Seq analysis, chromatin immunoprecipitation followed by sequencing; NA, not attributed; RNA-Seq, RNA sequencing
Fig. 1Omics studies workflow. Initial stages of omic studies involve the ethical approval of the study protocol (research ethics) and written consent (participant recruitment) provided by the participants where biological samples are drawn for further analyses. Downstream stages include critical steps, i.e. sample storage and processing, data generation, and data analysis (integration, interpretation and dissemination). This figure is available as a downloadable slide
Examples of IMI public–private initiatives in diabetes
| Acronym/Study name | Objective | Diabetes context | Total cost (€) | Ref. | Status | Website |
|---|---|---|---|---|---|---|
| IMI-SUMMIT: Surrogate markers for micro- and macrovascular hard endpoints for innovative diabetes tools | Assess biomarkers for diabetes complications | Diabetic complications in T2D | 34,812,081 | [ | Final report | www.imi-summit.eu/ |
| IMI-RHAPSODY: Risk Assessment and Progression of Diabetes | Assess glycaemic deterioration before and after the onset of type 2 diabetes | Prediabetes/T2D | 18,488,749 | - | Ongoing | https://imi-rhapsody.eu/ |
| IMI-INNODIA: Translational Approaches to Disease Modifying Therapy of Type 1 Diabetes: An Innovative Approach Towards Understanding and Arresting Type 1 Diabetes | Advance the understanding of type 1 diabetes | T1D | 36,563,723 | - | Ongoing | www.innodia.eu/ |
| IMI-BEAT-DKD: Biomarker Enterprise to Attack DKD | Assess diabetic kidney disease | Diabetic complications in T2D | 30,163,037 | [ | Ongoing | www.beat-dkd.eu/ |
| IMI-CARDIATEAMa: Cardiomyopathy in Type 2 Diabetes Mellitus | Assess diabetic cardiomyopathy | T2D | 12,882,500 | – | Ongoing | https://cardiateam.eu/ |
| IMI-Hypo-RESOLVE: Hypoglycaemia – Redefining Solutions for Better Lives | Assess diabetic hypoglycaemia | Diabetic complications in T1D | 26,774,583 | – | Ongoing | https://hypo-resolve.eu/ |
| IMI-DIRECTa: Diabetes Research on Patient Stratification | Identify diabetes subtypes and determine the most appropriate treatments | Prediabetes/T2D | 46,484,127 | [ | Final report | www.direct-diabetes.org/ |
aInvolves new cohort generation
DKD, diabetic ketoacidosis; IMI, Innovative Medicines Initiative; T1D, type 1 diabetes; T2D, type 2 diabetes