FunGen-xQTL Resources

Knight ADRC genotype data

Cohort
Knight-ADRCKnight Alzheimer Disease Research Center
Data type
Genotype / WGSOmics data
Tissue or cell type
blood
Sample size
Not recorded on this page
Release status
Stagednot yet verified
Access
ControlledData use certificate
Lead analysts
Zining QiSelect a name to email them

Access

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

Contact

Zining Qi

Data Descriptions

Raw genotype files

MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.bed, MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.bim (N= 10,641,345), MAP_Brain-xQTL_Gwas_geno_0.1_maf_0.0005.fam (N= 441)were the plink set created by extracting the Washu samples using geno = 0.1 and Maf = 0.0005 filters, Which then was checked for the array duplication. If there are duplicate samples (by array) in the data they will be filtered basing on their missingness and array frequency information.

Data provided is on GRCH38 genome build. We used TOPMED reference panel for imputation. The IDs in the fam were in the PA_DB_UID format . Bim file follows Chr:SNP:Ref:Alt format for snp name and the Ref is set to A2 allele in the plink file. Array information of all the samples was enclosed in the file: ID_Array_info.txt

Detailed QC steps used to process the data can be viewed in file: Imputation QC protocol.pdf

  • Data Location on CU cluster:

  • Data Location on FTP:

Genotype processed via xQTL pipeline:

For details how the phenotype data is processed please check genotype_preprocessing