README.md

---
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](https://img.shields.io/badge/License-CC_BY_4.0-lightgrey)](https://creativecommons.org/licenses/by/4.0/)

## Dataset Description

Genome-wide association study (GWAS) summary statistics for **Schizophrenia** phenotypes from the [Psychiatric Genomics Consortium (PGC)](https://pgc.unc.edu/).

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

## Usage

```python
from datasets import load_dataset

# Load a specific GWAS (e.g., scz2011)
ds = load_dataset("OpenMed/pgc-schizophrenia", "scz2011")
print(ds)
```

### Available Configs

```python
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](https://pubmed.ncbi.nlm.nih.gov/21926974/) | — | CC BY 4.0 |
| `scz2013sweden` | Schizophrenia (Swedish) | Nature Genetics | 2013 | [23974872](https://pubmed.ncbi.nlm.nih.gov/23974872/) | — | CC BY 4.0 |
| `scz2014` | Schizophrenia | Nature | 2014 | [25056061](https://pubmed.ncbi.nlm.nih.gov/25056061/) | 10,172,956 | CC BY 4.0 |
| `scz2018clozuk` | Schizophrenia (CLOZUK+PGC2) | Nature Genetics | 2018 | [29483656](https://pubmed.ncbi.nlm.nih.gov/29483656/) | — | CC BY 4.0 |
| `scz2019asi` | Schizophrenia (East Asian + European) | Nature Genetics | 2019 | [31740837](https://pubmed.ncbi.nlm.nih.gov/31740837/) | 24,253,547 | CC BY 4.0 |
| `scz2022` | Schizophrenia | Nature | 2022 | [35396580](https://pubmed.ncbi.nlm.nih.gov/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](https://creativecommons.org/licenses/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](https://pgc.unc.edu/for-researchers/data-access/)

## Source

- **Consortium:** [Psychiatric Genomics Consortium (PGC)](https://pgc.unc.edu/)
- **PGC Downloads:** [pgc.unc.edu/for-researchers/download-results/](https://pgc.unc.edu/for-researchers/download-results/)

---

*Last updated: April 2026*