Genotype / WGS Data on FunGen-AD Resources

EFIGA genotype

Mon, 01 Jan 0001 00:00:00 +0000

EFIGA genotype#

Contact#

Zining Qi

EFIGA genotype

Mon, 01 Jan 0001 00:00:00 +0000

EFIGA genotype#

Contact#

Zining Qi

Knight ADRC genotype data

Mon, 01 Jan 0001 00:00:00 +0000

Knight ADRC genotype 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

MAGENTA genotype data

Mon, 01 Jan 0001 00:00:00 +0000

MAGENTA genotype data#

Contact#

Makaela Mews

MiGA genotype data

Mon, 01 Jan 0001 00:00:00 +0000

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.

MSBB WGS data

Mon, 01 Jan 0001 00:00:00 +0000

MSBB WGS data#

MSBB whole-genome sequence data.

Contact#

Minghui Wang and Julia TCW

ROSMAP WGS data

Mon, 01 Jan 0001 00:00:00 +0000

ROSMAP WGS data#

Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) whole-genome sequence data

Contact#

Hao Sun and Xuanhe Chen

Data Descriptions#

This data is part of WGS done for three AMP-AD supported studies: The ROSMAP study (the data provided here), the MayoRNAseq study, and the MSBB study. Provided are VCF files, consisting of all samples from that study divided by chromosome, for the following analysis.

STARNET genotype data

Mon, 01 Jan 0001 00:00:00 +0000

STARNET genotype data#

STARNET is an RNA expression study of various disease-relevant tissues obtained from living patients with cardiovascular disease (CVD). The inclusion criterion for patients was eligibility for coronary artery by-pass graft (CABG) surgery.

Contact#

Travyse Edwards

Data Descriptions#

Raw Data#

The pre-imputation genotype data was received in HG19. We used an internal pipeline to carry out the imputation process using the TOPMED imputation server. We used the TOPMED-r2 reference panel (all populations). Pre- and Post-Imputation Quality Control measures (a part of the internal pipeline, detailed below), were carried out before the use of the xQTL pipeline. The output of the TOPMED Imputation server is in HG38, so liftover was handled as a part of the imputation process.