MiGA multi-brain region gene expression QTL

MiGA multi-brain region gene expression QTL #

A genetic and transcriptomic resource comprised of 255 primary human microglia samples isolated ex vivo from four different brain regions of 100 human subjects with neurodegenerative, neurological, or neuropsychiatric disorders, as well as unaffected controls. 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.

Contact #

Travyse Edwards

Study Overview #

  • Sample information: MiGA/MiGA_brain_expression_sample_attributes.csv.
  • Lab protocol: MiGA/MiGA_brain_expression_lab_protocol.csv.
  • Computational protocol: MiGA/MiGA_brain_expression_computational_protocol.csv.
  • Medial Frontal Gyrus QTL summary statistics output:
  • Path on Minerva: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/GFM/TensorQTL/5N/.
  • Superior Temporal Gyrus QTL summary statistics output:
  • Path on Minerva: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/GTS/TensorQTL/5N/.
  • Thalamus QTL summary statistics output:
  • Path on Minerva: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/THA/TensorQTL/5N/.
  • Subventricular Zone QTL summary statistics output:
  • Path on Minerva: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/SVZ/TensorQTL/5N/.
  • Fine-mapping results individual level data model: TBD.
  • Fine-mapping results summary statistics model: TBD.

Analysis Status #

TransQTL association: Need to be performed.

Dataset Details #

Path(s) to genotype matrix #

  • Path to genotype list: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.final.plink_files_list.txt
  • Path to genotype directory: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr10.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.10.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr11.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.11.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr12.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.12.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr13.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.13.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr14.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.14.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr15.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.15.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr16.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.16.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr17.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.17.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr18.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.18.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr19.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.19.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr1.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.1.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr20.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.20.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr21.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.21.bed
lrwxrwxrwx 1 edwart10 LOAD 207 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr22.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.22.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr2.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.2.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr3.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.3.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr4.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.4.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr5.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.5.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr6.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.6.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr7.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.7.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr8.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.8.bed
lrwxrwxrwx 1 edwart10 LOAD 206 Oct 14 21:05 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.genotype.chr9.bed -> /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/genotype_per_chrom/raj_microglia_anno.MAF.leftnorm.snp.filtered.filtered.for_pca.filtered.no_outlier.filtered.9.bed

Path(s) to omics-data matrix #

  • Medial Frontal Gyrus
  • Path to Phenotype List File: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.GFM.final.recipe
  • Path to Phenotype Directory: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/
  • Superior Temporal Gyrus
  • Path to Phenotype List File: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.GTS.final.recipe
  • Path to Phenotype Directory: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/
  • Thalamus
  • Path to Phenotype List File: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.THA.final.recipe
  • Path to Phenotype Directory: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/
  • Subventricular Zone
  • Path to Phenotype List File: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.SVZ.final.recipe
  • Path to Phenotype Directory: /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/
-rw-r--r-- 1 edwart10 LOAD 217K Sep 30 11:47 /sc/arion/projects/load/users/edwart10/projects/09-07-2022-MiGA-Analysis/output/10-14-2022/association_scan/finalized-input-files/miga.phenotype.GFM.chr10.bed.gz
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Path(s) to covariate data matrix #

  • Medial Frontal Gyrus
  • Path to Covariate File: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/finalized-input-files/miga.GFM.final.PEER.5N.cov.gz
  • Superior Temporal Gyrus
  • Path to Covariate File: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/finalized-input-files/miga.GTS.final.PEER.5N.cov.gz
  • Thalamus
  • Path to Covariate File: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/finalized-input-files/miga.THA.final.PEER.5N.cov.gz
  • Subventricular Zone
  • Path to Covariate File: /sc/arion/projects/load/users/edwart10/projects/12-19-2022-MiGA-Replication/output/age_sex/12-19-2022/association_scan/finalized-input-files/miga.SVZ.final.PEER.5N.cov.gz
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Path(s) to QTL results #

Path(s) to fine-mapping with SuSiE model #

Path(s) to fine-mapping with SuSiE RSS model #

Path(s) to colocalization with SuSiE-coloc #

FIXME: Also maybe let’s include the within MiGA integrative analysis here (MASH and mvSuSiE) instead of a separate resource? The data-set is small enough to not warrant being complicated with other notebooks …