Scientific Methodology and Work Packages

EpiMigrant Methodology and Work Package Flow Chart
The study design is being delivered through 5 work packages organised in interlinked groups:

(1) Coordination, management and scientific management
WP1 will deal with coordination, management and scientific management of the project, including:
  1. Periodic and final reporting to the European Commission
  2. Communication between participants
  3. Creation of the study website
  4. Responsibility for the overall direction and conduct of the research
  5. Dissemination of the research
This website provides a public face for promoting the research and its findings, 
as well as a password-protected ftp site for sharing of protocols, data and results across partners, using approaches similar to those used successfully by the applicants in GWA studies. 

The primary analyses will be complete by month 30; the final 6 months will focus on discussion, reflection, the preparation of final scientific reports for dissemination.

(2) Data generation – measurement of epigenetic markers
WP2 and WP3 will house data generation, through measurement of epigenetic markers amongst non-migrant and migrant South Asian Type 2 Diabetes (T2D) cases and controls. WP2 will use state-of-the-art Illumina 450K Infinium Methylation BeadChips to measure DNA methylation at CpG sites across the whole genome in 4,000 South Asians (2,000 with T2D) from non-migrant (India and Pakistan) and migrant (UK) samples. WP4 will measure the strongest 384 methylation signals (from WP2) in a further sample of 12,000 South Asians (6,000 with T2D) from India, Pakistan, Sri Lanka, Mauritius, Singapore and the UK. Methylation will be measured in DNA from whole blood, an appropriate sample based on: availability in large scale population studies and suitability for use as a biomarker in the clinical arena. Strengths of 450K BeadChip include: high reproducibility, single site resolution, low sample requirements and cost-effectiveness (~€180 per sample). 

(3) Data analysis to identify epigenetic markers associated with T2D
WP4 will house QC and analysis of the DNA methylation measurements, to identify the epigenetic marks associated with T2D. The analytic team includes experts in the analysis of DNA methylation signatures, analysis of whole genome data and the design, conduct and analysis of large-scale population studies. QC measures will include identification of samples that are outliers or have high miscall rates. Quantile normalization of probe-specific intensity and batch-effect adjustment using empirical Bayes methods, will be used to reduce inter-array variation. The association of epigenetic markers (gene specific and individual CpG sites) with T2D will be investigated by regression techniques. Results will identify, for the first time, epigenetic marks associated with T2D in South Asians. 

(4) Risk factors underlying T2D amongst South Asians in different settings 
WP5 will determine the predictive value of the epigenetic markers to incident T2D, and the contribution of epigenetic and risk factors to T2D amongst non-migrant and migrant South Asians. Predictive vale will be ascertained amongst 8,000 migrant South Asians (1,600 with T2D) participating in the LOLIPOP study (UK), who all have extensive characterisation of clinical, metabolic and genomic markers. The contribution of epigenetic and risk factors to T2D amongst non-migrant and migrant South Asians will be determined using results of the control samples studies in India, Mauritius, Pakistan, Singapore, Sri Lanka and the UK, and the OR for incident T2D observed in the LOLIPOP prospective cohort. Population-attributable risks will be calculated to quantify the contribution of lifestyle, environmental, genetic, and epigenetic risk factors to T2D risk among South Asians in different settings worldwide.

(5) Power considerations
For the epigenome-wide association study, the 384 top-ranking markers will be selected for further testing (corresponding to P<1x10-4 under the null hypothesis). This provides 80% power to identify odds ratios of 1.12, 1.25 and 1.6 for a 1.0SD, 0.5SD and 0.25SD change respectively in methylation score. Power is greater in the replication stage, providing an allowance for regression to the mean. The prospective evaluation of incident T2D in LOLIPOP has 80% power to identify odds ratios of 1.15, 1.2 and 1.5 for a 1.0SD, 0.5SD and 0.25SD change respectively in a quantitative risk factor such as methylation score, or an odds ratio of 1.3 for an exposure with a 20% prevalence, at P<0.05. These effect sizes are within the clinically important range.