This repository contains 91 datasets developed by the ADSP Functional Genomics Consortium.
Published at: https://statfungen.github.io/xqtl-resources/
- Knight-ADRC study info: The Memory and Aging Project at the Charles F. And Joanne Knight Alzheimer's Disease Research Center (Knight-ADRC at Washington University in St. Louis) collects collects plasma, CSF, fibroblast, neuroimaging clinical and cognition data longitudinally and autopsied brain samples. This clinical information combined with deep molecular phenotyping (i.e. genetic, proteomics, transcriptomics and others) will lead to the identification of novel genetic modifiers, protective variants, molecular biomarkers and the novel targets. Participants were recruited by the Knight-ADRC at Washington University in St. Louis (MO). Knight-ADRC participants have to be at least 65 years old and have no memory problems or mild dementia at the time of enrollment.
- MAGENTA study info: Multi-Ancestry Genomics, Epigenomics, and Transcriptomics of Alzheimer’s (MAGENTA) Project: Participants include 465 individuals (AA – 113 with AD, 118 cognitively intact controls; NHW – 116 with AD, 118 controls) ascertained by the John P. Hussman Institute for Human Genomics (HIHG) at the University of Miami Miller School of Medicine (Miami, FL), North Carolina A&T State University (Greensboro, NC), and Case Western Reserve University (Cleveland, OH). Participants were ascertained as part of the ADSP Follow-up Study and included both cases (>65 years of age of onset) and controls (>65 years of age at age of exam). All participants were adjudicated by a clinical panel with expertise in AD related disorders and classified as AD according to standard criteria developed by the National Institute of Aging and the Alzheimer’s Association.
- MiGA study info: 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.
- ROSMAP study info: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) study: ROS is a longitudinal clinical-pathologic cohort study of aging and Alzheimer's disease (AD) run from Rush University that enrolled individuals from religious communities for longitudinal clinical analysis and brain donation. Participants were enrolled from more than 40 groups of religious orders (nuns, priests, brothers) across the United States. MAP is a longitudinal, epidemiologic clinical-pathologic cohort study of common chronic conditions of aging with an emphasis on decline in cognitive and motor function and risk of Alzheimer’s disease that began in 1997 and is run from Rush University.
- STARNET: 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.
- The Mount Sinai Brain Bank (MSBB) study info: This cohort study generated large-scale matched multi-Omics data in AD and control brains for exploring novel molecular underpinnings of AD.
- ADGC GWAS imputation protocol: Adapted from ADGC GWAS Data QC Protocol to generate imputed genotype data for xQTL analysis in some cohorts.
- Alzheimer's Disease GWAS Summary Data (Bellenguez): The SNP-level association testing summary statistics for Alzheimer's disease from Bellenguez et al 2022 Nature Genetics. This study uses UK Biobank (UKBB) proxy AD samples.
- Alzheimer's Disease GWAS Summary Data (Jansen): The SNP-level association testing summary statistics for Alzheimer's disease from Jansen et al 2021 Nature Genetics. This study uses proxy AD individuals from UK Biobank.
- Alzheimer's Disease GWAS Summary Data (Kunkle): The SNP-level association testing summary statistics for Alzheimer's disease from Kunkle et al 2019 Nature Genetics. Position values were converted from hg19 to hg38 using liftOver.
- Alzheimer's Disease GWAS Summary Data (Wightman): The SNP-level association testing summary statistics for Alzheimer's disease from Wightman et al 2021 Nature Genetics. This file contains the meta-analyzed summary statistics of three cohorts: all individuals, all individuals excluding 23andMe, all individuals excluding 23andMe and UKBB.
- DIAN blood derived methylation: TBD, Alan Renton and Carlos Cruchaga.
- EFIGA CSF proteomics: Zining Qi.
- EFIGA genotype: Zining Qi.
- EFIGA genotype: Zining Qi.
- EFIGA plasma metabolomics: Zining Qi.
- HIHG African American blood alternative splicing: Makaela Mews.
- HIHG genotype data: Makaela Mews.
- Knight ADRC brain gene expression: Chunming Liu.
- Knight ADRC brain metabolomics: Zining Qi.
- Knight ADRC brain methylation: Alexandre Pelletier.
- Knight ADRC brain proteomics: Charles F And Joanne Knight Alzheimer's Disease Research Center (Knight-ADRC).
- Knight ADRC brain splicing: Xuanhe Chen.
- Knight ADRC CSF metabolomics: Zining Qi.
- Knight ADRC CSF proteomics: Zining Qi.
- Knight ADRC genotype data: Zining Qi.
- MAGENTA African American blood gene expression
- MAGENTA Non-Hispanic White blood alternative splicing: Makaela Mews.
- MAGENTA Non-Hispanic White blood gene expression
- 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.
- MiGA multi-brain region gene expression: 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.
- MSBB brain alternative splicing: Minghui Wang.
- MSBB brain gene expression: Minghui Wang.
- MSBB brain methylation: Alexandre Pelletier.
- MSBB brain proteomics: Minghui Wang.
- MSBB WGS data: MSBB whole-genome sequence data.
- PART working group brain methylation: Alexandre Pelletier, Corey McMillan.
- ROSMAP AC alternative splicing: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing.
- ROSMAP AC gene expression: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC gene expression.
- ROSMAP Covariates data: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) covariates data.
- ROSMAP DLPFC alternative splicing: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC alternative splicing.
- ROSMAP DLPFC gene expression: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC gene expression.
- ROSMAP DLPFC H3K9ac: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) h3k9ac data-set.
- ROSMAP DLPFC methylation: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC methylation data-set.
- ROSMAP DLPFC protein expression: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression.
- ROSMAP PCC alternative splicing: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
- ROSMAP PCC gene expression: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
- ROSMAP RNA-seq microglia gene expression: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) microglia data-set.
- ROSMAP RNA-seq monocyte gene expression: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) monocyte data-set.
- ROSMAP snRNA-seq pseudo-bulk gene expression: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) snRNA-seq from different cells in Dorsolateral Prefrontal Cortex (DLPFC).
- ROSMAP WGS data: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) whole-genome sequence data.
- 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.
- STARNET macrophage gene expression QTL: 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.
- WHICAP (pilot) plasma metabolomics: Zining Qi.
- DIAN blood derived methylation QTL: TBD, Alan Renton and Carlos Cruchaga.
- EFIGA CSF proteomics QTL: Zining Qi.
- EFIGA plasma metabolomics QTL: Zining Qi.
- FunGen-xQTL protocol data: A toy data-set consisting of 49 de-identified samples from ROSMAP project, used to illustrates the computational protocols we developed for the detection and analysis of molecular QTLs (xQTLs).
- HIHG Non-Hispanic White blood alternative splicing QTL: Makaela Mews.
- Knight ADRC brain gene expression QTL: Chunming Liu.
- Knight ADRC brain metabolomics QTL: Zining Qi.
- Knight ADRC brain methylation QTL: Alexandre Pelletier.
- Knight ADRC brain proteomics QTL: Charles F. And Joanne Knight Alzheimer's Disease Research Center (Knight-ADRC).
- Knight ADRC brain splicing QTL: Xuanhe Chen.
- Knight ADRC CSF metabolomics QTL: Zining Qi.
- Knight ADRC CSF proteomics QTL: Zining Qi.
- MAGENTA African American blood alternative splicing QTL: Makaela Mews.
- MAGENTA African American Blood Gene Expression QTL: Multi-Ancestry Genomics, Epigenomics, and Transcriptomics of Alzheimer’s (MAGENTA) Project: Participants include 465 individuals (AA – 113 with AD, 118 cognitively intact controls; NHW – 116 with AD, 118 controls) ascertained by the John P. Hussman Institute for Human Genomics (HIHG) at the University of Miami Miller School of Medicine (Miami, FL), North Carolina A&T State University (Greensboro, NC), and Case Western Reserve University (Cleveland, OH). Participants were ascertained as part of the ADSP Follow-up Study and included both cases (>65 years of age of onset) and controls (>65 years of age at age of exam). All participants were adjudicated by a clinical panel with expertise in AD related disorders and classified as AD according to standard criteria developed by the National Institute of Aging and the Alzheimer’s Association.
- MAGENTA Non-Hispanic White Blood Gene Expression QTL: Multi-Ancestry Genomics, Epigenomics, and Transcriptomics of Alzheimer’s (MAGENTA) Project: Participants include 465 individuals (AA – 113 with AD, 118 cognitively intact controls; NHW – 116 with AD, 118 controls) ascertained by the John P. Hussman Institute for Human Genomics (HIHG) at the University of Miami Miller School of Medicine (Miami, FL), North Carolina A&T State University (Greensboro, NC), and Case Western Reserve University (Cleveland, OH). Participants were ascertained as part of the ADSP Follow-up Study and included both cases (>65 years of age of onset) and controls (>65 years of age at age of exam). All participants were adjudicated by a clinical panel with expertise in AD related disorders and classified as AD according to standard criteria developed by the National Institute of Aging and the Alzheimer’s Association.
- 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.
- MSBB brain alternative splicing QTL: Minghui Wang.
- MSBB brain gene expression QTL: Minghui Wang.
- MSBB brain methylation QTL: Alexandre Pelletier.
- MSBB brain proteomics QTL: Minghui Wang.
- PART working group brain methylation QTL: Alexandre Pelletier, Corey McMillan.
- ROSMAP AC alternative splicing QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC alternative splicing.
- ROSMAP AC gene expression QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) AC gene expression.
- ROSMAP DLPFC alternative splicing QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC alternative splicing.
- ROSMAP DLPFC gene expression QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC gene expression.
- ROSMAP DLPFC H3K9ac QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) h3k9ac QTL analysis using the FGC xQTL pipeline.
- ROSMAP DLPFC methylation QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC methylation data-set.
- ROSMAP DLPFC protein expression QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression.
- ROSMAP DLPFC protein expression QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) DLPFC protein expression.
- ROSMAP PCC alternative splicing QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
- ROSMAP PCC Expression QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) PCC alternative splicing.
- ROSMAP RNA-seq microglia gene expression QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) microglia data-set.
- ROSMAP RNA-seq monocyte QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) monocyte data-set.
- ROSMAP snRNA-seq pseudo-bulk gene expression QTL: Religious Orders Study (ROS) or the Rush Memory and Aging Project (MAP) snRNA-seq from different cells in Dorsolateral Prefrontal Cortex (DLPFC).
- STARNET macrophage gene expression QTL: 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.
- WHICAP (pilot) plasma metabolomics QTL: Zining Qi.
- 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).
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├── content/ # Source markdown files
│ ├── xqtl-data/ # xQTL datasets
│ │ ├── study_info/ # Study descriptions
│ │ ├── gwas/ # GWAS summary statistics
│ │ ├── omics/ # Omics data
│ │ ├── qtl/ # QTL results
│ │ └── reference_data/ # Reference panels
│ └── *.md # Documentation pages
├── scripts/ # Processing scripts
│ └── hugo_generator.py
└── website/ # Generated Hugo site (git-ignored)
To add or update content:
- Edit markdown files in
content/directory - Run
makeorpython scripts/hugo_generator.py --serveto preview locally - Submit a pull request
The website/ directory is automatically generated and should not be edited directly.
# Install Hugo (https://gohugo.io/getting-started/installing/)
# Then run:
# Generate and serve locally
python scripts/hugo_generator.py --serve
# Build for production
python scripts/hugo_generator.py --build --minify