FunGen-xQTL Resources

MiGA genotype data

Microglia Genomic Atlas from the Netherlands Brain Bank (NBB) and the Neuropathology Brain Bank and Research CoRE at Mount Sinai Hospital. The permission to collect human brain material was obtained from the Ethical Committee of the VU University Medical Center, Amsterdam, The Netherlands, and the Mount Sinai Institutional Review Board. For the Netherlands Brain bank, informed consent for autopsy, the use of brain tissue and accompanied clinical information for research purposes was obtained per donor ante-mortem.
Cohort
MiGAMicroglia Genomic Atlas
Data type
Genotype / WGSOmics data
Sample size
Not recorded on this page
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
Travyse EdwardsSelect a name to email them

Access

Controlled access. Request data access for MiGA on the AD Knowledge Portal; you need a Synapse account. See How to get the data.

Contact

Travyse Edwards

Data Descriptions

Raw Data

The samples were genotyped using the Illumina Infinium Global Screening Array (GSA). Genotype imputation was performed through the Michigan Imputation Server v1.4.1 (Minimac 4) using the 1000 Genomes (Phase 3) v5 (GRCh37) European panel and Eagle v2.4 phasing in quality control and imputation mode with rsq filter set to 0.3. Following imputation, variants were lifted over to the GRCh38 reference to match the RNA-seq data using Picard liftoverVCF and the “b37ToHg38.over.chain.gz” liftover chain file.

Further method information can be found:

I began analysis on the post-imputation/QC VCF file provided by the Towfique lab.

Other Key Files

TBD

  1. EDA: https://github.com/cumc/fungen-xqtl-analysis/tree/main/analysis/Marcora_MSSM/MiGA/data_overview.ipynb
  2. Molecular Phenotype Calling
  3. Genotype Preprocessing
  4. Phenotype Preprocessing
  5. Covariate Preprocessing
  6. Association Scan