Participation requirements

DEEP Inclusion criteria

DEEP mQTL inclusion criteria

The DEEP mQTLs will build on the DNA methylation quantitative trait loci (mQTLs) catalogue generated by the Genetics of DNA Methylation Consortium.

1. We include all DNA methylation sites covered by the EPIC v1, EPIC v2 or 450k array.
2. We include samples with genetic data. We will use variants imputed by the TopMed reference or any other appropriate reference panel [GRCh37/hg19 or GRCh38/hg38 (recommended)].
3. 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/450k arrays with matched imputed GWA or sequence data available for at least 100 individuals.
• We will include participants of mainly non-European origin (non-migrant in first phase).
• In our analyses, we will include samples with DNAm profiled from whole blood, cord blood, peripheral blood mononuclear cells (PBMC), peripheral blood leukocytes(PBL), buccal or saliva tissue. We also include sorted blood cell types to compare to cell-type interacting mQTLs. LCLs will not be included. Please email Josine Min and Hannah Eliott if you have methylation data on sorted cell type data or on other tissues.
• Our scripts work on cohorts with different study designs including cohorts with related and unrelated participants and cohorts with participants that are the same age or sex.

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 analyzing cases and controls separately.

DEEP EWAS inclusion criteria

We have curated the following inclusion criteria for EWAS analyses:

1. Cohorts with DNAm generated with Illumina EPIC/450k arrays for at least 100 individuals.
2. Participants of non-European origin (non-migrant). Please email Hannah Elliott if you have datasets from non-European ancestry with phenotype data, if you want to contribute in the future.
3. We will include samples with DNAm profiled from blood, cord blood, saliva or buccal samples only. LCLs will not be included.

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.

Code of conduct

To participate in DEEP, please review the expectations in the collaboration agreement and complete any required administration to confirm your intention to participate. Please note that in DEEP we promote the principles articulated by the ASHG.