| | --- |
| | license: mit |
| | tags: |
| | - biology |
| | - genomics |
| | - variant-classification |
| | --- |
| | |
| | # P-KNN Precomputed Scores Dataset |
| | This dataset provides **precomputed pathogenicity prediction scores** generated by the P-KNN method using **dbNSFP v5.2** (academic or commercial version) with joint calibration. |
| | It contains pathogenicity assessments for **all missense variants**, organized into multiple subfolders. |
| | ## Dataset Structure |
| | ### 1. `precomputed_score_academic_chromosome` |
| | Includes precomputed scores derived from the **academic version** of dbNSFP v5.2a, organized by genomic coordinates. |
| | ### 2. `precomputed_score_academic_gene` |
| | Includes precomputed scores derived from the **academic version** of dbNSFP v5.2a, organized by MANE Ensembl transcripts. You can explore these scores using the [P-KNN-Viewer](https://huggingface.co/spaces/brandeslab/P-KNN-Viewer). |
| | ### 3. `precomputed_score_commercial_chromosome` |
| | Includes precomputed scores derived from the **commercial version** of dbNSFP v5.2c, organized by genomic coordinates. |
| | ### 4. `precomputed_score_commercial_gene` |
| | Includes precomputed scores derived from the **commercial version** of dbNSFP v5.2a, organized by MANE Ensembl transcripts. You can explore these scores using the [P-KNN-Viewer](https://huggingface.co/spaces/brandeslab/P-KNN-Viewer). |
| |
|
| | > **Note:** For any **commercial use** of dbNSFP data, please review the [dbNSFP commercial license requirements](https://www.dbnsfp.org/license). |
| |
|
| | Both folders share the same file structure and columns. Files are typically named by genome build, variant type, database version, and chromosome, e.g.: P_KNN_hg38_missense_dbNSFP_chrY.csv |
| | ## Column Descriptions |
| | ### files in `_chromosome` folder: |
| | Each CSV file contains the following **8 columns**: |
| | | Column | Description | |
| | |--------|-------------| |
| | | `#Chr` | Chromosome number or identifier (e.g., 1–22, X, Y). | |
| | | `Start` | 1-based genomic start position of the variant. | |
| | | `End` | 1-based genomic end position of the variant. For SNVs, this is typically the same as `Start`. | |
| | | `Ref` | Reference allele observed in the reference genome. | |
| | | `Alt` | Alternate allele observed in the variant call. | |
| | | `P_KNN_posterior_probability(pathogenic)` | Posterior probability that the variant is **pathogenic**. | |
| | | `P_KNN_posterior_probability(benign)` | Posterior probability that the variant is **benign**. | |
| | | `P_KNN_log_likelihood_ratio(evidence_strength)` | Log-likelihood ratio corresponding to the **ACMG guideline evidence strength**. | |
| | ### files in `_gene` folder: |
| | | Column | Description | |
| | |--------|-------------| |
| | | `genename` | Official gene symbol where the variant is located. | |
| | | `Ensembl_transcriptid` | Ensembl transcript identifier associated with the variant. | |
| | | `Pos(cDNA)` | Position of the variant in the complementary DNA (cDNA) sequence of the transcript. | |
| | | `#Chr` | Chromosome number or identifier (e.g., 1–22, X, Y). | |
| | | `Pos(hg38)` | 1-based genomic start position of the variant in the human genome build hg38. | |
| | | `Ref` | Reference allele observed in the reference genome. | |
| | | `Alt` | Alternate allele observed in the variant call. | |
| | | `Pos(protein)` | Position of the variant in the protein sequence. | |
| | | `aaref` | Reference amino acid at the given protein position. | |
| | | `aaalt` | Alternate amino acid resulting from the variant. | |
| | | `P_KNN_posterior_probability(pathogenic)` | Posterior probability that the variant is **pathogenic**. | |
| | | `P_KNN_posterior_probability(benign)` | Posterior probability that the variant is **benign**. | |
| | | `P_KNN_log_likelihood_ratio(evidence_strength)` | Log-likelihood ratio corresponding to the **ACMG guideline evidence strength**. | |
| |
|
| | ## Other Folders |
| | ### 3. `dataset4commandline` |
| | Contains the **default calibration** and **regularization** datasets used by the P-KNN command-line tool. |
| | For more details, see the [P-KNN GitHub repository](https://github.com/Brandes-Lab/P-KNN). |
| | ### 4. `manuscript_dataset` |
| | Contains additional datasets used in the study: |
| | > *P-KNN: Maximizing variant classification evidence through joint calibration of multiple pathogenicity prediction tools.* |
| | ### 5. `dataset4viewer` |
| | Contains the re-organized data used in [P-KNN precomputed score viewer](https://huggingface.co/spaces/brandeslab/P-KNN-Viewer). |
| | ## Citation |
| | If you use this dataset, please cite the relevant publication (when available) and the P-KNN tool. |
| | ## Related Resources |
| | - **Tool & Source Code**: [Brandes-Lab/P-KNN on GitHub](https://github.com/Brandes-Lab/P-KNN) |
| | - **Gene based precomputed score viewer**: [P-KNN-Viewer](https://huggingface.co/spaces/brandeslab/P-KNN-Viewer) |
| | - **Manuscript**: [P-KNN: Maximizing variant classification evidence through joint calibration of multiple pathogenicity prediction tools](https://doi.org/10.1101/2025.09.24.678417) |
| | - **dbNSFP License**: [dbNSFP Commercial Use Requirements](https://www.dbnsfp.org/license) |
