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Datasets:
OpenMed
/
pgc-schizophrenia

Tasks:
Tabular Regression
Tabular Classification
Languages:
English
Tags:
gwas
summary-statistics
psychiatric-genomics
pgc
scz
mental-health
License:
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metadata 
license: cc-by-4.0
task_categories:
  - tabular-regression
  - tabular-classification
tags:
  - gwas
  - summary-statistics
  - psychiatric-genomics
  - pgc
  - scz
  - mental-health
  - genetics
  - genomics
  - biology
  - health
  - bioinformatics
pretty_name: PGC Schizophrenia GWAS Summary Statistics
size_categories:
  - 1M-10M
configs:
  - config_name: scz2011
    data_files:
      - split: train
        path: data/scz2011/*.parquet
    default: true
  - config_name: scz2013sweden
    data_files:
      - split: train
        path: data/scz2013sweden/*.parquet
  - config_name: scz2014
    data_files:
      - split: train
        path: data/scz2014/*.parquet
  - config_name: scz2018clozuk
    data_files:
      - split: train
        path: data/scz2018clozuk/*.parquet
  - config_name: scz2019asi
    data_files:
      - split: train
        path: data/scz2019asi/*.parquet
  - config_name: scz2022
    data_files:
      - split: train
        path: data/scz2022/*.parquet
language:
  - en
source_datasets:
  - pgc

PGC Schizophrenia — GWAS Summary Statistics

License: CC BY 4.0

Dataset Description

Genome-wide association study (GWAS) summary statistics for Schizophrenia 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., scz2011)
ds = load_dataset("OpenMed/pgc-schizophrenia", "scz2011")
print(ds)

Available Configs 

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

Subsets (Publications)

Config Phenotype Journal Year PubMed Rows License
scz2011 Schizophrenia Nature Genetics 2011 21926974 — CC BY 4.0
scz2013sweden Schizophrenia (Swedish) Nature Genetics 2013 23974872 — CC BY 4.0
scz2014 Schizophrenia Nature 2014 25056061 10,172,956 CC BY 4.0
scz2018clozuk Schizophrenia (CLOZUK+PGC2) Nature Genetics 2018 29483656 — CC BY 4.0
scz2019asi Schizophrenia (East Asian + European) Nature Genetics 2019 31740837 24,253,547 CC BY 4.0
scz2022 Schizophrenia Nature 2022 35396580 52,560,584 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