All ENIGMA protocols are now linked on the ENIGMA GitHub page page. Please check here for the latest amendments and updates!
ENIGMA Protocols for Imputation and Genetic Associations
Anyone is welcome to use these protocols for their projects! If you use the protocols on this site for projects outside of ENIGMA, please include a reference to the ENIGMA main page (http://enigma.usc.edu/) so that your readers and reviewers know about it as well. If you are using the 'ENIGMA1' protocols, please cite Stein et al., Nature Genetics, 2012. If you are using the 'ENIGMA2' protocols, please cite Hibar et al., Nature, 2015. If you are using the 'ENIGMA3' protocols, please cite Grasby et al., Nature, 2020.
Current Imputation Protocol
Below is the current imputation protocol for GWAS meta-analysis of Cortical and Subcortical ROIs.
ENIGMA3 - GWAS Meta Analysis of Cortical Thickness and Surface Area
Below are the imputation and association protocols for GWAS meta-analysis of Cortical ROIs, aka the ENIGMA3 project. Note: For ENIGMA3 we will be using the same imputation protocol as used for the ENIGMA2 project.
- Same Protocol as ENIGMA2: Imputation Protocol (PDF) -- Updated (July 27, 2012)
- ENIGMA3 Association Protocols: Now available on ENIGMA-Git - click here!
The protocol can also be downloaded in Word format: ENIGMA3 Protocol
ENIGMA2 - GWAS Meta Analysis of Subcortical Volumes
Below are the imputation and association protocols for GWAS meta-analysis of subcortical volumes, aka the ENIGMA2 project.
- Imputation Protocol (PDF) -- Updated (July 27, 2012)
- ENIGMA2 Association Protocol (PDF) -- Method A for Unrelated Samples w/ Only Healthy Subjects
- ENIGMA2 Association Protocol (PDF) -- Method B for Unrelated Samples w/ Patients and Healthy Subjects
- ENIGMA2 Association Protocol (PDF) -- Method C for Family Designs w/ Only Healthy Subjects
{Legacy Version} ENIGMA1 - GWAS Meta Analysis of Hippocampal, Intracranial and Total Brain Volume
Below are the protocols from the ENIGMA pilot project (Stein et al., 2012, Nature Genetics):
- Imputation to HapMap III
- Association Protocol
- Meta-Analysis Protocol (coming soon!)
- Until the meta-analysis protocol is posted, an example protocol for meta-analysis used in an international GWAS consortium can be found here. We gratefully thank Margie Wright, Beben, and Peter from Queensland Institute for Medical Research, Australia.
ENIGMA-Epigenetics - EWAS Meta Analysis of blood DNA methylation
Below are the DNA Methylation quality control and epigenome-wide association studies protocols from the ENIGMA-Epigenetics Working Group.
- ENIGMA-Epigenetics DNA Methylation QC (Word) -- Updated 4 May, 2016
- Protocol for Brain EWAS (Word) -- Updated April 22, 2016
