Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history

Yanshuo Chu; Ling Wang; Rongjie Wang; Mingxiang Teng; Yadong Wang

doi:10.1109/BIBM.2017.8217998

Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history

Yanshuo Chu
, Ling Wang
, Rongjie Wang
, Mingxiang Teng
, Yadong Wang^*

^*Corresponding author for this work

School of Computer Science and Technology, Harbin Institute of Technology

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

6 Scopus citations

Abstract

Next-generation sequencing (NGS) and the third generation sequencing (TGS) have recently allowed us to develop algorithms to quantitatively dissect the extent of heterogeneity within a tumour, resolve cancer evolution history and identify the somatic variations and aneuploidy events. Simulation of tumor NGS and TGS data serves as a powerful and cost-effective approach for benchmarking these algorithms, however, there is no available tool that could simulate all the distinct subclonal genomes with diverse aneuploidy events and somatic variations according to the given tumor evolution history. We provide a simulation package, Pysubsim-tree, which could simulate the tumor genomes according to their evolution history defined by the somatic variations and aneuploidy events.

Original language	English
Title of host publication	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Editors	Illhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	2195-2197
Number of pages	3
ISBN (Electronic)	9781509030491
DOIs	https://doi.org/10.1109/BIBM.2017.8217998
State	Published - 15 Dec 2017
Externally published	Yes
Event	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States Duration: 13 Nov 2017 → 16 Nov 2017

Publication series

Name	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume	2017-January

Conference

Conference	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/Territory	United States
City	Kansas City
Period	13/11/17 → 16/11/17

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Keywords

Tumor subclonal population
tumor genome simulation

Access to Document

10.1109/BIBM.2017.8217998

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Chu, Y., Wang, L., Wang, R., Teng, M., & Wang, Y. (2017). Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C.-R. Shyu, Y. Bromberg, J. Gao, & D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 2195-2197). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217998

Chu, Yanshuo ; Wang, Ling ; Wang, Rongjie et al. / Pysubsim-tree : A package for simulating tumor genomes according to tumor evolution history. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 2195-2197 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).

@inproceedings{5e2dabe83f524c99accc7c4fee250cf0,

title = "Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history",

abstract = "Next-generation sequencing (NGS) and the third generation sequencing (TGS) have recently allowed us to develop algorithms to quantitatively dissect the extent of heterogeneity within a tumour, resolve cancer evolution history and identify the somatic variations and aneuploidy events. Simulation of tumor NGS and TGS data serves as a powerful and cost-effective approach for benchmarking these algorithms, however, there is no available tool that could simulate all the distinct subclonal genomes with diverse aneuploidy events and somatic variations according to the given tumor evolution history. We provide a simulation package, Pysubsim-tree, which could simulate the tumor genomes according to their evolution history defined by the somatic variations and aneuploidy events.",

keywords = "Tumor subclonal population, tumor genome simulation",

author = "Yanshuo Chu and Ling Wang and Rongjie Wang and Mingxiang Teng and Yadong Wang",

note = "Publisher Copyright: {\textcopyright} 2017 IEEE.; 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 ; Conference date: 13-11-2017 Through 16-11-2017",

year = "2017",

month = dec,

day = "15",

doi = "10.1109/BIBM.2017.8217998",

language = "英语",

series = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "2195--2197",

editor = "Illhoi Yoo and Zheng, \{Jane Huiru\} and Yang Gong and Hu, \{Xiaohua Tony\} and Chi-Ren Shyu and Yana Bromberg and Jean Gao and Dmitry Korkin",

booktitle = "Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017",

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Chu, Y , Wang, L, Wang, R, Teng, M & Wang, Y 2017, Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 2195-2197, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 13/11/17. https://doi.org/10.1109/BIBM.2017.8217998

Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history. / Chu, Yanshuo ; Wang, Ling; Wang, Rongjie et al.
Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 2195-2197 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution › peer-review

TY - GEN

T1 - Pysubsim-tree

T2 - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

AU - Chu, Yanshuo

AU - Wang, Ling

AU - Wang, Rongjie

AU - Teng, Mingxiang

AU - Wang, Yadong

PY - 2017/12/15

Y1 - 2017/12/15

N2 - Next-generation sequencing (NGS) and the third generation sequencing (TGS) have recently allowed us to develop algorithms to quantitatively dissect the extent of heterogeneity within a tumour, resolve cancer evolution history and identify the somatic variations and aneuploidy events. Simulation of tumor NGS and TGS data serves as a powerful and cost-effective approach for benchmarking these algorithms, however, there is no available tool that could simulate all the distinct subclonal genomes with diverse aneuploidy events and somatic variations according to the given tumor evolution history. We provide a simulation package, Pysubsim-tree, which could simulate the tumor genomes according to their evolution history defined by the somatic variations and aneuploidy events.

AB - Next-generation sequencing (NGS) and the third generation sequencing (TGS) have recently allowed us to develop algorithms to quantitatively dissect the extent of heterogeneity within a tumour, resolve cancer evolution history and identify the somatic variations and aneuploidy events. Simulation of tumor NGS and TGS data serves as a powerful and cost-effective approach for benchmarking these algorithms, however, there is no available tool that could simulate all the distinct subclonal genomes with diverse aneuploidy events and somatic variations according to the given tumor evolution history. We provide a simulation package, Pysubsim-tree, which could simulate the tumor genomes according to their evolution history defined by the somatic variations and aneuploidy events.

KW - Tumor subclonal population

KW - tumor genome simulation

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M3 - 会议稿件

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SP - 2195

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BT - Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017

A2 - Yoo, Illhoi

A2 - Zheng, Jane Huiru

A2 - Gong, Yang

A2 - Hu, Xiaohua Tony

A2 - Shyu, Chi-Ren

A2 - Bromberg, Yana

A2 - Gao, Jean

A2 - Korkin, Dmitry

PB - Institute of Electrical and Electronics Engineers Inc.

Y2 - 13 November 2017 through 16 November 2017

ER -

Chu Y , Wang L, Wang R, Teng M, Wang Y. Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu CR, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 2195-2197. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). doi: 10.1109/BIBM.2017.8217998

Pysubsim-tree: A package for simulating tumor genomes according to tumor evolution history

Abstract

Publication series

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UN SDGs

Keywords

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