Participation requirements - genetics-of-dna-methylation-consortium/godmc_phase2 GitHub Wiki
GoDMC Phase 2 inclusion criteria
GoDMC Phase 2 mQTL inclusion criteria
GoDMC Phase 2 will build on the DNA methylation quantitative trait loci (mQTLs) catalogue generated in the first phase in three ways.
- We include all DNA methylation sites covered by the EPIC array providing great resolution of the genetic effects.
- We will use variants imputed by the HRC reference panel (build 37) to again give a greater resolution on QTL signals.
- We will use a new methodology, HASE, which means we can save and ultimately meta-analyses the full surface of mQTLs.
- Please note we will include cohorts with DNAm generated with Illumina EPIC arrays with matched GWA data imputed to HRC available for at least 200 individuals.
- We will include participants of European origin. Please email Josine Min if you have datasets from non European ancestry and you want to contribute to a multi-ancestry mQTL analysis in future.
- In our analyses we will include samples with DNAm profiled from blood only. We also include sorted blood cell types to compare to cell type interacting mQTLs. LCLs or cord blood samples will not be included. Please email Josine Min if you have methylation data on sorted cell type data or on other tissues.
GoDMC Phase 2 EWAS and GWAS inclusion criteria
In addition to this enhanced catalogue of mQTLs we will also run parallel analyses on a number of complementary analyses proposed by the community that require either DNA methylation or genotype data and want to take advantage of our existing computational framework.
In light of this we have curated the following inclusion criteria:
- Cohorts with DNAm generated with Illumina EPIC/450k arrays with matched GWA data available for at least 200 individuals.
- Participants of European origin. Please email Josine Min if you have datasets from non European ancestry if you want to contribute to a global DNAm consortium in future.
- Samples with genetic data, which has been imputed with the HRC reference panel or 1000G (build 37).
- We will include samples with DNAm profiled from blood only. LCLs or cord blood samples will not be included.
Case control studies
If you have a case-control design, we recommend to combine cases and controls for the mQTL analysis to have the largest sample size as possible. We do not recommend to analyse cases and controls separately.
Studies with both 450k and EPIC data
If you have different batches of arrays for your dataset, we recommend to analyse these separately eg ALSPAC_450k and ALSPAC_EPIC. Please only include non-overlapping samples if you have multiple batches.
Read the code of conduct
To participate in the next phase of GoDMC, please review the expectations below and complete any required administration to confirm your intention to participate.
Please read the code of conduct here: