RT Journal Article
SR Electronic
T1 OncoGEMINI: Software for Investigating Tumor Variants From Multiple Biopsies With Integrated Cancer Annotations
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.03.10.979591
DO 10.1101/2020.03.10.979591
A1 Thomas J. Nicholas
A1 Michael J. Cormier
A1 Xiaomeng Huang
A1 Yi Qiao
A1 Gabor T. Marth
A1 Aaron R. Quinlan
YR 2020
UL http://biorxiv.org/content/early/2020/03/11/2020.03.10.979591.abstract
AB DNA sequencing has unveiled extensive tumor heterogeneity in several different cancer types, with many exhibiting diverse subclonal populations. Identifying and tracing mutations throughout the expansion and progression of a tumor represents a significant challenge. Furthermore, prioritizing the subset of such mutations most likely to contribute to tumor evolution or that could serve as potential therapeutic targets represents an ongoing problem. Here we describe OncoGEMINI, a new tool designed for exploring the complex patterns and trajectory of somatic and inherited variation observed in heterogeneous tumors biopsied over the course of treatment. This is accomplished by creating a searchable database of variants that includes tumor sampling timepoints and allows for filtering methods that reflect specific changes in variant allele frequencies over time. Additionally, by incorporating existing annotations and resources that facilitate the interpretation of cancer mutations (e.g., CIViC, DGIdb), OncoGEMINI enables rapid searches for, and potential identification of, mutations that may be driving subclonal evolution.