gNOME

gNOME performs annotation, filtering, and prioritization of whole-genome and whole-exome sequencing (WGS/WES) variants to identify disease-associated genetic variants.

Key Features:

• Annotation and Filtering: Provides a framework for annotation, filtering, and analysis of genetic variants with emphasis on accuracy and reproducibility of annotation results for clinical applications.
• Variant Prioritization: Prioritizes phenotype-associated variants to reduce false-positive candidate variants.
• Comprehensive Result Summaries: Produces detailed summaries at the variant, gene, and genome levels.
• Enrichment Analysis: Compares specific variants, genes, and gene sets between groups or against population-scale WGS datasets to identify significant associations with known disease pathways.
• Scalability and Performance: Implements scalable, high-performance processing suitable for large WGS/WES datasets.
• Annotation Reconciliation: Integrates up-to-date genomic information and employs strategies to reconcile discrepancies among different annotation software tools.

Scientific Applications:

• Oncology studies: Applied to whole-exome datasets from uveal melanoma and bladder cancer to annotate variants and identify enrichment of loss-of-function variants within known cancer pathways.
• Disease variant discovery: Supports identification and prioritization of disease-associated variants in both rare and non-rare diseases.
• Comparative population analyses: Enables comparison of study cohorts against population-scale WGS datasets to contextualize variant and gene-set findings.

Methodology:

The pipeline performs alignment, variant detection, and annotation, and integrates up-to-date genomic information while employing strategies to reconcile discrepancies among different annotation software tools.