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 ( so that your readers and reviewers know about it as well. Please also reference the ENIGMA publication if you are using the ENIGMA1 protocols (Stein et al., 2012, Nature Genetics).

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.

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.

{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.


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