FinaleDB

FinaleDB catalogs uniformly processed, quality-controlled paired-end whole-genome sequencing (WGS) datasets of de-identified cell-free DNA (cfDNA) and provides fragmentation profiles and visualization to analyze nucleosomal protection, epigenetic modifications, and gene expression signals for biomarker and disease-mechanism research.

Key Features:

• Comprehensive Dataset Collection: Hosts thousands of uniformly processed, quality-controlled paired-end WGS cfDNA datasets derived from de-identified samples across diverse pathological conditions.
• Fragmentation Genome Browser: Visualizes and enables analysis of non-random cfDNA fragmentation patterns influenced by nucleosomal protection, epigenetic modifications, and contributing cell-type gene expression profiles.
• Integration with Omics Data: Links cfDNA fragmentation profiles with thousands of other omics datasets across different cell types to support integrative analyses of gene-regulatory landscapes.

Scientific Applications:

• Biomarker discovery and prognostic modeling: Uses cfDNA fragmentation features to support development of diagnostic and prognostic models in oncology and other diseases.
• Tissue-of-origin and gene-regulatory inference: Enables inference of contributing cell types and epigenetic/gene-expression states by relating fragmentation patterns to nucleosomal and epigenetic signals.
• Comparative and mechanistic studies: Facilitates comparative analyses of fragmentation landscapes across pathological conditions to investigate disease mechanisms.

Methodology:

Uniform processing and quality control of paired-end WGS cfDNA datasets, generation of fragmentation profiles, visualization via a fragmentation genome browser, and integration with other omics datasets.