COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics

Xi-Guo Yuan; Yuan Zhao; Yang Guo; Lin-Mei Ge; Wei Liu; Shi-Yu Wen; Qi Li; Zhang-Bo Wan; Pei-Na Zheng; Tao Guo; Zhi-Da Li; Martin Peifer; Yu-Peng Cun

doi:10.24272/j.issn.2095-8137.2021.250

Volume 43 Issue 1

Jan. 2022

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Article Navigation > Zoological Research > 2022 > 43(1): 75-77

Xi-Guo Yuan, Yuan Zhao, Yang Guo, Lin-Mei Ge, Wei Liu, Shi-Yu Wen, Qi Li, Zhang-Bo Wan, Pei-Na Zheng, Tao Guo, Zhi-Da Li, Martin Peifer, Yu-Peng Cun. COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics. Zoological Research, 2022, 43(1): 75-77. doi: 10.24272/j.issn.2095-8137.2021.250

Citation:

Xi-Guo Yuan, Yuan Zhao, Yang Guo, Lin-Mei Ge, Wei Liu, Shi-Yu Wen, Qi Li, Zhang-Bo Wan, Pei-Na Zheng, Tao Guo, Zhi-Da Li, Martin Peifer, Yu-Peng Cun. COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics. Zoological Research, 2022, 43(1): 75-77. doi: 10.24272/j.issn.2095-8137.2021.250

Citation:

Xi-Guo Yuan, Yuan Zhao, Yang Guo, Lin-Mei Ge, Wei Liu, Shi-Yu Wen, Qi Li, Zhang-Bo Wan, Pei-Na Zheng, Tao Guo, Zhi-Da Li, Martin Peifer, Yu-Peng Cun. COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics. Zoological Research, 2022, 43(1): 75-77. doi: 10.24272/j.issn.2095-8137.2021.250

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COSINE: A web server for clonal and subclonal structure inference and evolution in cancer genomics

doi: 10.24272/j.issn.2095-8137.2021.250

1.
School of Computer Science and Technology, Xidian University, Xi'an, Shaanxi 710071, China
2.
iFlora Bioinformatics Center, Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunan 650201, China
3.
Yuxi Rongjian Information Technology Co., Ltd., Yuxi, Yunan 653100, China
4.
Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne 50931, Germany
5.
Pediatric Research Institute, Ministry of Education Key Laboratory of Child Development and Disorders, National Clinical Research Center for Child Health and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, Chongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory Disorders, Children’s Hospital of Chongqing Medical University, Chongqing 400014, China

Funds: This work was supported by the CAS Pioneer Hundred Talents Program and National Natural Science Foundation of China (32070683) to Y.P.C.; the Science and Technology Planning Project of XI'AN (GXYD6.2) and National Natural Science Foundation of China (61771369) to X.G.Y.

More Information

Corresponding author: E-mail: cunyp@cqmu.edu.cn
Received Date: 2021-09-25
Accepted Date: 2021-11-19

Published Online: 2021-11-26

Publish Date: 2022-01-18

Abstract

Abstract

Cancer cell genomes originate from single-cell mutation with sequential clonal and subclonal expansion of somatic mutation acquisition during pathogenesis, thus exhibiting a Darwinian evolutionary process (Gerstung et al., 2020; Nik-Zainal et al., 2012). Through next-generation sequencing of tumor tissue, this evolutionary process can be characterized by statistical modelling, which can identify the clonal state, somatic mutation order, and evolutionary process (Gerstung et al., 2020; Mcgranahan & Swanton, 2017). Inference of clonal and subclonal structure from bulk or single-cell tumor genomic sequencing data has a huge impact on studying cancer evolution. Clonal state and mutation order can provide detailed insight into tumor origin and future development. In the past decade, various methods for subclonal reconstruction using bulk tumor sequencing data have been developed. However, these methods had different programming languages and data input formats, which limited their use and comparison. Therefore, we established a web server for Clonal and Subclonal Structure Inference and Evolution (COSINE) of cancer genomic data, which incorporated twelve popular subclonal reconstruction methods. We deconstructed each method to provide a detailed workflow of single processing steps with a user-friendly interface. To the best of our knowledge, this is the first web server providing online subclonal inference based on the integration of most popular subclonal reconstruction methods. COSINE is freely accessible at www.clab-cosine.net.

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References(11)

References

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