Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution. However, comprehensive analysis of mutational data from MRS is still challenging, which requires complicated integration of a plethora of computational and statistical approaches. Here, we present MesKit, an R/Bioconductor package, that can assist in characterizing genetic ITH and tracing the evolutionary history of tumors based on somatic alterations detected by MRS. MesKit provides a wide range of analysis and visualization modules, including ITH evaluation, metastatic route inference, and mutational signature identification. In addition, MesKit implements an auto-layout algorithm to generate phylogenetic trees based on somatic mutations. The application of MesKit for two reported MRS datasets of hepatocellular carcinoma (HCC) and colorectal cancer (CRC) identified known heterogeneous features and evolutionary patterns, together with potential driver events during cancer evolution.

Keywords:

• multi-region sequencing
• somatic alterations
• intra-tumor heterogeneity
• metastatic routes
• phylogenetic tree

Read the peer-reviewed publication(s):

(PubMed: 34018555)

Additional information:

http://doi.org/10.18129/B9.bioc.MesKit

http://meskit.renlab.org/

Github links:

https://github.com/Niinleslie/MesKit

Accessions (data referenced by this study):

BioProject: PRJNA325415
EGA: EGAS00001003573