Detecting known neoepitopes, gene fusions, transposable elements, and circular RNAs in cell-free RNA.

ABSTRACT:

Motivation

Cancer is the second leading cause of death worldwide, and although there have been advances in treatments, including immunotherapies, these often require biopsies which can be costly and invasive to obtain. Due to lack of pre-emptive cancer detection methods, many cases of cancer are detected at a late stage when the definitive symptoms appear. Plasma samples are relatively easy to obtain, and they can be used to monitor the molecular signatures of ongoing processes in the body. Profiling cell-free DNA is a popular method for monitoring cancer, but only a few studies have explored the use of cell-free RNA (cfRNA), which shows the recent footprint of systemic transcription.

Results

Here, we developed FastNeo, a computational method for detecting known neoepitopes

SUBMITTER: Mahajan M 

PROVIDER: S-EPMC12057812 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature