FunGen-xQTL Resources

Non-Hispanic White Linkage Disequilibrium Reference Panel

LD matrices calculated from whole genome sequencing data from 16571 non-Hispanic white individuals obtained from the Genome Center for Alzheimer’s Disease (GCAD). Correlation matrices were calculated between SNPs within 1361 LD blocks which were obtained from this Github page (generated from 1000 Genomes EUR samples).
Cohort
ADSP
Modality
LD panelReference
Sample size
16,571 samples
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
Oluwatosin OlayinkaSelect a name to email them
Open syn53171227 in Synapse ↗

Access

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

WhereIDAccessWhat you get
Synapsesyn53171227ControlledFiles described below

Other Synapse IDs on this page syn69670651 syn69670652

shell
pip install synapseclient
synapse login
synapse get -r syn53171227

Contact

Oluwatosin Olayinka

Output Format

Each LD block contains two files of interest:

  • an xz-compressed file containing the correlation values, suffixed by .cor.xz
    • this file is a compressed file where the matrix is encoded in a space-separated format
    • the data is stored in the upper triangle of the matrix
  • a Plink .bim file suffixed by .cor.xz.bim containing unique IDs for each variant
r
ld_block_ref_file = "/path/to/matrix.cor.xz"
var_names = read.table(paste0(ld_block_ref_file, ".bim"), header = F)$V2
ld <- scan(xzfile(ld_block_ref_file))
ld <- matrix(ld, ncol = sqrt(length(ld)), byrow = TRUE)
ld <- ld + t(ld)
diag(ld) = 1
rownames(ld) = var_names
colnames(ld) = var_names

Data Availability

The generated files can be found on Synapse.

  1. Generating LD Reference Panel: https://github.com/cumc/xqtl-pipeline/blob/main/code/reference_data/ld_reference_generation.ipynb

ADSP Whole Genome Sequencing LD Reference Panel

The FunGen-xQTL flagship paper used a large LD reference panel derived from the Alzheimer’s Disease Sequencing Project (ADSP) whole genome sequencing data for fine-mapping analyses.

  • Samples: 16,571 individuals of European ancestry
  • Variant call: WGS, high-quality SNPs and indels
  • Use: LD reference for SuSiE-RSS fine-mapping of xQTL and AD GWAS loci
ResourceSynapse ID
ADSP WGS LD reference (genotype data)syn69670651
ADSP WGS LD reference (LD matrices)syn69670652