MPRA Library

This markdown shows which source each of the 11,805 variants tested in the MPRA come from.

The variants come from the following sources:

  1. All microglia 300-donor eQTL significant variants (FDR <= 0.05) + SNPs in LD (r2 > 0.8) that are found in significant (FDR <= 0.05) microglia ATAC-seq peaks
  2. All microglia 300-donor eQTL significant lead SNPs (FDR <= 0.05) + SNPs in LD (r2 > 0.8) that are found in significant enhancers identified by the Activity-by-Contact Model (ABC Score >= 0.02)
  3. All microglia 300-donor eQTL significant lead SNPs (FDR <= 0.05), regardless of whether they are found in ATAC-seq peaks or not
  4. Results from fine-mapping chromatin accessibility QTLs via eCAVIAR (PP >= 0.5) - Roussos Lab (https://www.medrxiv.org/content/10.1101/2021.10.17.21264910v1.full)
  5. Results from fine-mapping latest EADB GWAS (Bellenguez 2021) using SuSiE (PIP >= 0.01) with pre-computed LD based on the GWAS population
  6. Published results from fine-mapping Schwartzentruber (2020) GWAS meta-analysis (PP >= 0.01) - Jeremy Schwartzentruber (https://www.nature.com/articles/s41588-020-00776-w)
  7. All lead SNPs from the 4 most recent Alzheimer’s Disease GWAS (Bellenguez 2021, Kunkle 2019, Jansen 2018, Schwartzentruber 2020)

Interactive MPRA Library Table

We provide a table to query tested variants in the MPRA based on the prioritization method.

library(readr)

setwd('/Users/ashvinravi/Desktop/AD_MPRA/')
mpra_table <- read_tsv('iMGL_MPRA_consensus_table.tsv', show_col_types=F)
createDT(mpra_table)