| --- |
| 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 |
|
|
| [](https://creativecommons.org/licenses/by/4.0/) |
|
|
| ## Dataset Description |
|
|
| Genome-wide association study (GWAS) summary statistics for **Substance Use Disorders** 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., SUD2023) |
| ds = load_dataset("OpenMed/pgc-substance-use", "SUD2023") |
| print(ds) |
| ``` |
|
|
| ### Available Configs |
|
|
| ```python |
| 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](https://pubmed.ncbi.nlm.nih.gov/37250466/) | 5,736,488 | CC BY 4.0 | |
| | `sud2018-alc` | Alcohol Dependence | Nature Neuroscience | 2018 | [30482948](https://pubmed.ncbi.nlm.nih.gov/30482948/) | — | CC BY 4.0 | |
| | `sud2019-alcuse` | Alcohol Use / AUDIT | American Journal of Psychiatry | 2019 | [30336701](https://pubmed.ncbi.nlm.nih.gov/30336701/) | — | CC BY 4.0 | |
| | `sud2020-cud` | Cannabis Use Disorder | Lancet Psychiatry | 2020 | [33096046](https://pubmed.ncbi.nlm.nih.gov/33096046/) | — | CC BY 4.0 | |
| | `sud2020-op` | Opioid Dependence | Molecular Psychiatry | 2020 | [32099098](https://pubmed.ncbi.nlm.nih.gov/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](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* |
|
|
