Marks-lab/LOL-EVE-UltraRare

LOL-EVE Ultra Rare Variants Dataset

Dataset Description

This dataset contains ultra rare variants from gnomAD for evaluating variant effect prediction models. The dataset includes variants with minor allele frequency (MAF) < 0.001 in promoter regions across diverse genes.

Dataset Structure

• Total Variants: ~549,000
• Species: Primates (Homo sapiens)
• Variant Types: Insertions, deletions, and substitutions in promoter regions
• Sequence Length: Up to 1,000bp promoter regions
• MAF Range: < 0.001 (ultra rare)

Features

Basic Variant Information

• gene: Gene symbol
• species: Species name
• clade: Evolutionary clade
• chromosome: Chromosome
• position: Genomic position
• ref: Reference allele
• alt: Alternative allele
• variant_type: Type of variant (insertion/deletion/substitution)

Sequences

• wt_sequence: Wild-type sequence
• var_sequence: Variant sequence
• sequence_length: Length of sequence
• wt_sequence_start: Start position of sequence

Variant Annotations

• filter: Variant filtering status
• maf: Minor allele frequency

Usage

from datasets import load_dataset

# Load the dataset
dataset = load_dataset("cshearer/LOL-EVE-UltraRare")

# Access the data
print(f"Dataset size: {len(dataset['train'])}")
print(f"Features: {dataset['train'].features}")

# Example: Get variants by MAF threshold
rare_variants = dataset['train'].filter(lambda x: x['maf'] < 0.0001)
print(f"Ultra rare variants (MAF < 0.0001): {len(rare_variants)}")

# Example: Get variants by type
insertions = dataset['train'].filter(lambda x: x['variant_type'] == 'insertion')
deletions = dataset['train'].filter(lambda x: x['variant_type'] == 'deletion')
substitutions = dataset['train'].filter(lambda x: x['variant_type'] == 'substitution')

Citation

If you use this dataset in your research, please cite:

@article{loleve2024,
  title={LOL-EVE: Language of Life - Evolutionary Variant Effects},
  author={Your Name and Collaborators},
  journal={Nature},
  year={2024}
}

License

This dataset is released under the MIT License.