Datasets:

OpenMed
/

pgc-mdd

license: cc-by-4.0
task_categories:
  - tabular-regression
  - tabular-classification
tags:
  - gwas
  - summary-statistics
  - psychiatric-genomics
  - pgc
  - mdd
  - mental-health
  - genetics
  - genomics
  - biology
  - health
  - bioinformatics
pretty_name: PGC Major Depressive Disorder GWAS Summary Statistics
size_categories:
  - 1M-10M
configs:
  - config_name: AntiDepResponse2021
    default: true
    data_files:
      - split: train
        path: data/AntiDepResponse2021/*.parquet
  - config_name: mdd2013
    data_files:
      - split: train
        path: data/mdd2013/*.parquet
  - config_name: mdd2018
    data_files:
      - split: train
        path: data/mdd2018/*.parquet
  - config_name: mdd2018_noUKBB
    data_files:
      - split: train
        path: data/mdd2018_noUKBB/*.parquet
  - config_name: mdd2021asi
    data_files:
      - split: train
        path: data/mdd2021asi/*.parquet
  - config_name: mdd2023diverse
    data_files:
      - split: train
        path: data/mdd2023diverse/*.parquet
  - config_name: mdd2024symptoms
    data_files:
      - split: train
        path: mdd2024symptoms/train-*
  - config_name: mdd2025
    data_files:
      - split: train
        path: data/mdd2025/*.parquet
  - config_name: ppd2023
    data_files:
      - split: train
        path: data/ppd2023/*.parquet
language:
  - en
source_datasets:
  - pgc
dataset_info:
  config_name: mdd2024symptoms
  features:
    - name: '##fileFormat=PGCv1.0'
      dtype: string
    - name: _source_file
      dtype: string
  splits:
    - name: train
      num_bytes: 106084
      num_examples: 1104
  download_size: 11546
  dataset_size: 106084

PGC Major Depressive Disorder — GWAS Summary Statistics

Dataset Description

Genome-wide association study (GWAS) summary statistics for Major Depressive Disorder phenotypes from the Psychiatric Genomics Consortium (PGC).

Each publication is available as a separate subset (config) and can be loaded independently.

Usage

from datasets import load_dataset

# Load a specific GWAS
ds = load_dataset("OpenMed/pgc-mdd", "AntiDepResponse2021")
print(ds)

List all available subsets

from datasets import get_dataset_config_names
print(get_dataset_config_names("OpenMed/pgc-mdd"))

Subsets

Config	Phenotype	Journal	Year	PubMed
`AntiDepResponse2021`	Antidepressant Response	Biol Psychiatry: Global Open Science	2021	Pending
`mdd2013`	Major Depression	Molecular Psychiatry	2013	22472876
`mdd2018`	Major Depression	Nature Genetics	2018	29700475
`mdd2018_noUKBB`	Major Depression (no UK Biobank)	Nature Genetics	2018	29700475
`mdd2021asi`	Major Depression (East Asian)	JAMA Psychiatry	2021	34586374
`mdd2023diverse`	Major Depression (Multi-Ancestry)	Nature Genetics	2023	38177345
`mdd2025`	Major Depression	Cell	2025	39814019
`ppd2023`	Peripartum Depression	American Journal of Psychiatry	2023	37849304

Data Format

All data is stored as Apache Parquet shards (10,000 rows each). Common columns:

Column	Description
`SNP` / `ID`	SNP rsID or variant identifier
`CHR`	Chromosome
`BP` / `POS`	Base-pair position (typically GRCh37/hg19)
`A1`	Effect allele
`A2`	Non-effect allele
`OR` / `BETA`	Odds ratio or effect size
`SE`	Standard error
`P`	P-value
`_source_file`	Original source filename

Column names vary between publications. Check each subset's schema.

Citation

Please cite the original publication (see PubMed links above) and acknowledge the PGC:

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

Terms of Use

Released under CC BY 4.0 / CC0 1.0.

Cite the original publication(s)
Do not attempt to re-identify individual participants
Comply with the PGC data use policies

Source

Last updated: April 2026