PSiTE: a Phylogeny guided Simulator for Tumor Evolution

Hechuan Yang; Bingxin Lu; Lan Huong Lai; Abner Herbert Lim; Jacob Josiah Santiago Alvarez; Weiwei Zhai

doi:10.1093/bioinformatics/btz028

PSiTE: a Phylogeny guided Simulator for Tumor Evolution

Bioinformatics. 2019 Sep 1;35(17):3148-3150. doi: 10.1093/bioinformatics/btz028.

Authors

Hechuan Yang^{1

2}, Bingxin Lu², Lan Huong Lai², Abner Herbert Lim², Jacob Josiah Santiago Alvarez², Weiwei Zhai^{1

2

3

4

5}

Affiliations

¹ Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, P.R.China.
² Human Genetics, Genome Institute of Singapore, A*STAR, Singapore, Singapore.
³ National Cancer Centre Singapore, Singapore, Singapore.
⁴ School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
⁵ Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, P.R.China.

PMID: 30649258
DOI: 10.1093/bioinformatics/btz028

Abstract

Summary: Simulating realistic clonal dynamics of tumors is an important topic in cancer genomics. Here, we present Phylogeny guided Simulator for Tumor Evolution, a tool that can simulate different types of tumor samples including single sector, multi-sector bulk tumor as well as single-cell tumor data under a wide range of evolutionary trajectories. Phylogeny guided Simulator for Tumor Evolution provides an efficient tool for understanding clonal evolution of cancer.

Availability and implementation: PSiTE is implemented in Python and is available at https://github.com/hchyang/PSiTE.

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Clonal Evolution
Genomics
Humans
Neoplasms*
Phylogeny
Software*