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Datasets:
OpenMed
/
pgc-substance-use

Tasks:
Tabular Regression
Tabular Classification
Modalities:
Tabular
Text
Formats:
parquet
Languages:
English
Size:
100M - 1B
Tags:
gwas
summary-statistics
psychiatric-genomics
pgc
sud
mental-health
Libraries:
Datasets
Dask
Polars
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metadata 
license: cc-by-4.0
task_categories:
  - tabular-regression
  - tabular-classification
tags:
  - gwas
  - summary-statistics
  - psychiatric-genomics
  - pgc
  - sud
  - mental-health
  - genetics
  - genomics
  - biology
  - health
  - bioinformatics
pretty_name: PGC Substance Use Disorders GWAS Summary Statistics
size_categories:
  - 1M-10M
configs:
  - config_name: SUD2023
    default: true
    data_files:
      - split: train
        path: data/SUD2023/*.parquet
  - config_name: sud2018-alc
    data_files:
      - split: train
        path: data/sud2018-alc/*.parquet
  - config_name: sud2019-alcuse
    data_files:
      - split: train
        path: data/sud2019-alcuse/*.parquet
  - config_name: sud2020-cud
    data_files:
      - split: train
        path: data/sud2020-cud/*.parquet
  - config_name: sud2020-op
    data_files:
      - split: train
        path: data/sud2020-op/*.parquet
language:
  - en
source_datasets:
  - pgc

PGC Substance Use Disorders — GWAS Summary Statistics

License: CC BY 4.0

Dataset Description

Genome-wide association study (GWAS) summary statistics for Substance Use Disorders phenotypes from the Psychiatric Genomics Consortium (PGC).

This dataset contains multiple GWAS publications as separate subsets (configs). Each can be loaded independently.

Usage 

from datasets import load_dataset

# Load a specific GWAS (e.g., SUD2023)
ds = load_dataset("OpenMed/pgc-substance-use", "SUD2023")
print(ds)

Available Configs 

from datasets import get_dataset_config_names
configs = get_dataset_config_names("OpenMed/pgc-substance-use")
print(configs)

Subsets (Publications)

Config Phenotype Journal Year PubMed Rows License
SUD2023 Substance Use Disorder Nature Mental Health 2023 37250466 5,736,488 CC BY 4.0
sud2018-alc Alcohol Dependence Nature Neuroscience 2018 30482948 — CC BY 4.0
sud2019-alcuse Alcohol Use / AUDIT American Journal of Psychiatry 2019 30336701 — CC BY 4.0
sud2020-cud Cannabis Use Disorder Lancet Psychiatry 2020 33096046 — CC BY 4.0
sud2020-op Opioid Dependence Molecular Psychiatry 2020 32099098 57,445,238 CC BY 4.0

Data Format

All data has been converted to Apache Parquet format with shards of 10,000 rows. Common columns include:

Column Description
SNP / ID SNP rsID or variant identifier
CHR Chromosome
BP / POS Base-pair position (typically GRCh37/hg19)
A1 / ALT Effect allele
A2 / REF Non-effect (reference) allele
OR / BETA Odds ratio or effect size
SE Standard error
P P-value
INFO Imputation quality score
FRQ / MAF Allele frequency
_source_file Original source filename

Note: Column names vary between publications. The _source_file column tracks the original file each row came from.

Citation

When using any subset, please cite:

  1. The original publication (see PubMed links above)
  2. The data DOI from Figshare (see supplementary metadata)
  3. Acknowledge the PGC:

    "Data were obtained from the Psychiatric Genomics Consortium — https://pgc.unc.edu/"

Terms of Use

This dataset is released under the CC BY 4.0 license.

By using PGC summary statistics you agree to:

  1. Cite the original publication(s)
  2. Not attempt to re-identify individual participants
  3. Comply with the PGC's data use policies

Source

Last updated: April 2026