Multiple primary tumors (MPT) is a special and rare cancer type, defined as more than two primary tumors presenting at the diagnosis in a single patient. The molecular characteristics and tumorigenesis of MPT remain unclear due to insufficient approaches.
Here, we present MPTevol, a practical computational framework for
comprehensively exploring the MPT from multiregional sequencing
(MRS) experiments. MPTevol facilitates comparison genomic profiles
across multiple primary tumor samples, detection of clonal evolutionary
history and metastatic routines in MPT, and quantification of metastatic
history. This package incorporates multiple cancer evolution analyses,
for a one-stop solution of MPT analysis.The goal of MPTevol is to
provide a practical computation framework for dissecting the evolution
of multiple primary tumors (MPT), reducing analysis complexity with
modular design.
If you are using the MPTevol in academic research, please cite our paper:
Chen, Q., Wu, Q.-N., Rong, Y.-M., Wang, S., Zuo, Z., Bai, L., . . . Zhao, Q. (2022). Deciphering clonal dynamics and metastatic routines in a rare patient of synchronous triple-primary tumors and multiple metastases with MPTevol. Briefings in Bioinformatics. doi:10.1093/bib/bbac175
You can install the development version of MPTevol from GitHub with:
# install.packages("remotes")
remotes::install_github("qingjian1991/MPTevol")The overview of usage could be found at MPTevol online vignette.
This software is developed by:
- Qingjian Chen, [email protected], Sun Yat-Sen Univerity Cancer Center.
- Shixiang Wang, [email protected], Sun Yat-Sen Univerity Cancer Center.
- Qi Zhao from Bioinformatic Center of Sun Yat-sen University Cancer Center.