README.md

metadata

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.

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.

Note: For any commercial use of dbNSFP data, please review the dbNSFP commercial license requirements.

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.

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.

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
• Gene based precomputed score viewer: P-KNN-Viewer
• Manuscript: P-KNN: Maximizing variant classification evidence through joint calibration of multiple pathogenicity prediction tools
• dbNSFP License: dbNSFP Commercial Use Requirements