FinaleDB: New Tool Supports Developing ‘Liquid Biopsies’ Based on Cell-Free DNA Fragmentation
Published December 2020 | Bioinformatics
Researchers have been intrigued for several years by the potential for circulating cell-free DNA (cfDNA) in blood or urine as a potentially sensitive biomarker for diagnosing cancer and other diseases. In theory, having a blood test this powerful could replace the need for repeated invasive biopsies to track disease progression and adjust treatments.
However, the paperwork involved in gaining access to this detailed level of genomic data has made the concept excessively time-consuming. Meanwhile, differing data gathering methods have complicated the effort of consolidating existing public data sets.
Now a team of scientists at Cincinnati Children’s, led by first authors Haizi Zheng, PhD, and Michelle Zhu, and senior author Yaping Liu, PhD, reports developing a database and analytic tool called FinaleDB that hosts thousands of uniformly processed and curated de-identified cfDNA whole-genome sequencing datasets across different pathological conditions.
FinaleDB also includes a sophisticated fragmentation genome browser, which allows users to integrate other ‘omics data in different cell types to gain a comprehensive view of both the gene-regulatory landscape and of cfDNA fragmentation patterns.
Previously, accessing this level of data required special application processes, sometimes including data transfer agreements that can take months for organizations to arrange. This tool replaces that chore with de-identified data from more than 2,500 paired-end cfDNA datasets across 23 different conditions, Liu says. Conditions include breast, liver, kidney, pancreatic, ovarian, colorectal, and gastric cancers as well as lupus, inflammatory bowel disease and cirrhosis.
This work was supported by a Cincinnati Children’s start-up grant and Trustee Award to Liu. Producing the database also involved using the Extreme Science and Engineering Discovery Environment (XSEDE) at the Pittsburgh Supercomputing Center.
