FinaleDB: a browser and database of cell-free DNA fragmentation patterns

Haizi Zheng; Michelle S Zhu; Yaping Liu

doi:10.1093/bioinformatics/btaa999

FinaleDB: a browser and database of cell-free DNA fragmentation patterns

Bioinformatics. 2021 Aug 25;37(16):2502-2503. doi: 10.1093/bioinformatics/btaa999.

Authors

Haizi Zheng¹, Michelle S Zhu², Yaping Liu^{1

3

4

5}

Affiliations

¹ Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
² Department of Computer Science, University of Texas at Austin, Austin, TX 78712, USA.
³ Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
⁴ Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 45229, USA.
⁵ Department of Electrical Engineering and Computing Sciences, University of Cincinnati College of Engineering and Applied Science, Cincinnati, OH 45229, USA.

Abstract

Summary: Circulating cell-free DNA (cfDNA) is a promising biomarker for the diagnosis and prognosis of many diseases, including cancer. The genome-wide non-random fragmentation patterns of cfDNA are associated with the nucleosomal protection, epigenetic environment and gene expression in the cell types that contributed to cfDNA. However, current progress on the development of computational methods and understanding of molecular mechanisms behind cfDNA fragmentation patterns is significantly limited by the controlled-access of cfDNA whole-genome sequencing (WGS) dataset. Here, we present FinaleDB (FragmentatIoN AnaLysis of cEll-free DNA DataBase), a comprehensive database to host thousands of uniformly processed and curated de-identified cfDNA WGS datasets across different pathological conditions. Furthermore, FinaleDB comes with a fragmentation genome browser, from which users can seamlessly integrate thousands of other omics data in different cell types to experience a comprehensive view of both gene-regulatory landscape and cfDNA fragmentation patterns.

Availability and implementation: FinaleDB service: http://finaledb.research.cchmc.org/. FinaleDB source code: https://github.com/epifluidlab/finaledb_portal, https://github.com/epifluidlab/finaledb_workflow.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Cell-Free Nucleic Acids*
DNA Fragmentation
Genome
Software
Whole Genome Sequencing

Substances

Cell-Free Nucleic Acids