English

Inferring clonal composition from multiple tumor biopsies

Genomics 2019-11-26 v2
Authors: Matteo Manica , Hyunjae Ryan Kim , Roland Mathis , Philippe Chouvarine , Dorothea Rutishauser , Laura De Vargas Roditi , Bence Szalai , Ulrich Wagner , Kathrin Oehl , Karim Saba , Arati Pati , Julio Saez-Rodriguez , Angshumoy Roy , Donald W. Parsons , Peter J. Wild , María Rodríguez Martínez , Pavel Sumazin
View on arXiv ↗ PDF ↗

Abstract

Explicit accounting for copy number alterations can dramatically improve mutation frequency estimates, leading to more accurate phylogeny reconstructions and subclone characterizations.

Keywords

cancer biology

Cite

@article{arxiv.1701.07940,
  title  = {Inferring clonal composition from multiple tumor biopsies},
  author = {Matteo Manica and Hyunjae Ryan Kim and Roland Mathis and Philippe Chouvarine and Dorothea Rutishauser and Laura De Vargas Roditi and Bence Szalai and Ulrich Wagner and Kathrin Oehl and Karim Saba and Arati Pati and Julio Saez-Rodriguez and Angshumoy Roy and Donald W. Parsons and Peter J. Wild and María Rodríguez Martínez and Pavel Sumazin},
  journal= {arXiv preprint arXiv:1701.07940},
  year   = {2019}
}

Related papers

View all related →
Methodology · Statistics
Bayesian Inference for Tumor Subclones Accounting for Sequencing and Structural Variants
Juhee Lee, Peter Mueller, Subhajit Sengupta, Kamalakar Gulukota +1
2014-09-26
Populations and Evolution · Quantitative Biology
Reconstructing subclonal composition and evolution from whole genome sequencing of tumors
Amit G. Deshwar, Shankar Vembu, Christina K. Yung, Gun Ho Jang +2
2015-01-08
Machine Learning · Computer Science
A Model of Selective Advantage for the Efficient Inference of Cancer Clonal Evolution
Daniele Ramazzotti
2016-02-25
Methodology · Statistics
Reconstructing DNA copy number by joint segmentation of multiple sequences
Zhongyang Zhang, Kenneth Lange, Chiara Sabatti
2012-03-20
Genomics · Quantitative Biology
Joint Inference of Genome Structure and Content in Heterogeneous Tumour Samples
Andrew McPherson, Andrew Roth, Gavin Ha, Sohrab P. Shah +2
2015-04-28
Genomics · Quantitative Biology
HetFHMM: A novel approach to infer tumor heterogeneity using factorial Hidden Markov model
Gholamreza Haffari, Zhaoxiang Cai, Mohammad S. Rahman, Ann E. Nicholson
2015-03-03
Genomics · Quantitative Biology
Evaluation of simulation methods for tumor subclonal reconstruction
Jiaying Lai, Yunzhou Liu, Robert B. Scharpf, Rachel Karchin
2024-02-16
Genomics · Quantitative Biology
Topological Data Analysis of copy number alterations in cancer
Stefan Groha, Caroline Weis, Alexander Gusev, Bastian Rieck
2021-04-23
Applications · Statistics
A phylogenetic latent feature model for clonal deconvolution
Francesco Marass, Florent Mouliere, Ke Yuan, Nitzan Rosenfeld +1
2017-02-07
Molecular Networks · Quantitative Biology
Cancer systems biology in the genome sequencing era: Part 1, dissecting and modeling of tumor clones and their networks
Edwin Wang, Jinfeng Zou, Naif Zaman, Lenore K. Beitel +2
2014-09-09
Applications · Statistics
TreeClone: Reconstruction of Tumor Subclone Phylogeny Based on Mutation Pairs using Next Generation Sequencing Data
Tianjian Zhou, Subhajit Sengupta, Peter Mueller, Yuan Ji
2017-10-26
Genomics · Quantitative Biology
Wave-LSTM: Multi-scale analysis of somatic whole genome copy number profiles
Charles Gadd, Christopher Yau
2024-08-26
Molecular Networks · Quantitative Biology
Cancer systems biology in the genome sequencing era: Part 2, evolutionary dynamics of tumor clonal networks and drug resistance
Edwin Wang, Jinfeng Zou, Naif Zaman, Lenore K. Beitel +2
2014-09-09
Genomics · Quantitative Biology
COSINE: A Web Server for Clonal and Subclonal Structure Inference and Evolution in Cancer Genomics
Xiguo Yuan, Yuan Zhao, Yang Guo, Linmei Ge +9
2021-03-30
Machine Learning · Computer Science
Inferring clonal evolution of tumors from single nucleotide somatic mutations
Wei Jiao, Shankar Vembu, Amit G. Deshwar, Lincoln Stein +1
2013-11-05
Applications · Statistics
Phylogeny-based tumor subclone identification using a Bayesian feature allocation model
Li Zeng, Joshua L. Warren, Hongyu Zhao
2018-03-20
Genomics · Quantitative Biology
Comparing copy-number profiles under multi-copy amplifications and deletions
Garance Cordonnier, Manuel Lafond
2020-02-27
Methodology · Statistics
Estimating Clonality
Yi Liu, Andrew Z. Fire, Scott Boyd, Richard A. Olshen
2014-08-07
Statistics Theory · Mathematics
Consistent Testing for Recurrent Genomic Aberrations
Vonn Walter, Fred A. Wright, Andrew B. Nobel
2014-03-11
Genomics · Quantitative Biology
Effective Sub-clonal Cancer Representation to Predict Tumor Evolution
Adnan Akbar, Geoffroy Dubourg-Felonneau, Andrey Solovyev, John W Cassidy +2
2019-12-02
Applications · Statistics
Using somatic mutation data to test tumors for clonal relatedness
Irina Ostrovnaya, Venkatraman E. Seshan, Colin B. Begg
2015-11-18
Genomics · Quantitative Biology
Understanding genomic alterations in cancer genomes using an integrative network approach
Edwin Wang
2014-09-12
Computer Vision and Pattern Recognition · Computer Science
Towards computational fluorescence microscopy: Machine learning-based integrated prediction of morphological and molecular tumor profiles
Alexander Binder, Michael Bockmayr, Miriam Hägele, Stephan Wienert +14
2018-05-30
Applications · Statistics
BayCount: A Bayesian Decomposition Method for Inferring Tumor Heterogeneity using RNA-Seq Counts
Fangzheng Xie, Mingyuan Zhou, Yanxun Xu
2017-02-28
Quantitative Methods · Quantitative Biology
Moduli Spaces of Phylogenetic Trees Describing Tumor Evolutionary Patterns
Sakellarios Zairis, Hossein Khiabanian, Andrew J. Blumberg, Raul Rabadan
2014-10-07
R2 v1 2026-06-22T18:02:07.466Z