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SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution

Christopher A. Miller, Brian S. White, Nathan D. Dees, Malachi Griffith, John S. Welch, Obi L. Griffith, Ravi Vij, Michael H. Tomasson, Timothy A. Graubert, Matthew J. Walter, Matthew J. Ellis, William Schierding (+6 others)
2014 PLoS Computational Biology  
By doing so, we can track tumor evolution and identify the spatial origins of cells resisting therapy.  ...  A fine resolution view of this clonal architecture provides insight into tumor heterogeneity, evolution, and treatment response, all of which may have clinical implications.  ...  Acknowledgments We thank Joshua McMichael for help with figure preparation and David Spencer and Michael Wendl for critical review of the manuscript. Author Contributions  ... 
doi:10.1371/journal.pcbi.1003665 pmid:25102416 pmcid:PMC4125065 fatcat:sodimfirdbbrrgvc3us7bvedke

Longitudinal copy number, whole exome and targeted deep sequencing of 'good risk' IGHV-mutated CLL patients with progressive disease

M J J Rose-Zerilli, J Gibson, J Wang, W Tapper, Z Davis, H Parker, M Larrayoz, H McCarthy, R Walewska, J Forster, A Gardiner, A J Steele (+6 others)
2016 Leukemia  
We thank the patients for supplying tissue and the infrastructure support from a CR-UK centre grant (C34999/A18087), Leukaemia and Lymphoma Research grant (12021) and ECMC grant (C24563/A15581).  ...  Authorship Contributions Disclosure of Conflicts of Interest The authors declare no competing financial interests. Supplementary information is available at Leukemia's website  ...  SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. W, Vembu S, Deshwar AG, Stein L, Morris Q.  ... 
doi:10.1038/leu.2016.10 pmid:26847028 pmcid:PMC4861248 fatcat:oi7qsx6ktjcitaglwjnggdjgha

Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST

Subhayan Chattopadhyay, Jenny Karlsson, Anders Valind, Natalie Andersson, David Gisselsson
2021 Briefings in Bioinformatics  
Two limiting factors for clonal deconvolution that have remained unresolved are variation in purity and chromosomal copy number across different samples of the same tumor.  ...  Clonal deconvolution of mutational landscapes is crucial to understand the evolutionary dynamics of cancer.  ...  Acknowledgments The authors acknowledge technical support from the Science for Life Laboratory, the Knut and Alice Wallenberg Foundation, the National Genomics Infrastructure founded by the Swedish Research  ... 
doi:10.1093/bib/bbab292 pmid:34343239 pmcid:PMC8981300 fatcat:vgjspskpu5aj3and6dr4ynsboe

Assessing intratumor heterogeneity and tracking longitudinal and spatial clonal evolutionary history by next-generation sequencing

Yuchao Jiang, Yu Qiu, Andy J. Minn, Nancy R. Zhang
2016 Proceedings of the National Academy of Sciences of the United States of America  
Here, we propose Canopy, a method for inferring the evolutionary phylogeny of a tumor using both somatic copy number alterations and single-nucleotide alterations from one or more samples derived from  ...  Canopy is an open-source R package available at intratumor heterogeneity | cancer evolution | clonal deconvolution | cancer genomics | phylogeny inference  ...  temporal and spatial order during tumor evolution.  ... 
doi:10.1073/pnas.1522203113 pmid:27573852 pmcid:PMC5027458 fatcat:wge7d574pnazvcwnhcoyrxxipe

MesKit: a tool kit for dissecting cancer evolution of multi-region tumor biopsies through somatic alterations

Mengni Liu, Jianyu Chen, Xin Wang, Chengwei Wang, Xiaolong Zhang, Yubin Xie, Zhixiang Zuo, Jian Ren, Qi Zhao
2021 GigaScience  
The application of MesKit for 2 reported MRS datasets of hepatocellular carcinoma and colorectal cancer identified known heterogeneous features and evolutionary patterns, together with potential driver  ...  Multi-region sequencing (MRS) has been widely used to analyze intra-tumor heterogeneity (ITH) and cancer evolution.  ...  Such spatial-mutation categories largely correspond to the temporal order of mutation genesis during tumor evolution: most public mutations occur early in tumor-initiating cells and are inherited by their  ... 
doi:10.1093/gigascience/giab036 pmid:34018555 pmcid:PMC8138830 fatcat:tbpc657tovb2blrmzuj326lqiu

Mutational dynamics of early and late relapsed childhood ALL: rapid clonal expansion and long-term dormancy

Jean-François Spinella, Chantal Richer, Pauline Cassart, Manon Ouimet, Jasmine Healy, Daniel Sinnett
2018 Blood Advances  
by a putative defect of DNA repair processes, illustrating the quick emergence of fitter clones, and on the other hand, a quasi-inert evolution pattern, suggesting the escape from dormancy of leukemia  ...  ) to assess the fitness of somatic mutations and infer their ancestral relationships.  ...  Acknowledgments The authors thank the patients and their parents for participating in this study. Patient tissue samples were provided by the CHU Sainte-Justine Pediatric Cancer biobank.  ... 
doi:10.1182/bloodadvances.2017011510 pmid:29365312 pmcid:PMC5812325 fatcat:ipbuojjp2rfyjnp7itlfnkhjda

Optimizing Cancer Genome Sequencing and Analysis

Malachi Griffith, Christopher A. Miller, Obi L. Griffith, Kilannin Krysiak, Zachary L. Skidmore, Avinash Ramu, Jason R. Walker, Ha X. Dang, Lee Trani, David E. Larson, Ryan T. Demeter, Michael C. Wendl (+15 others)
2015 Cell Systems  
We evaluated the effects of different library generation approaches, depth of sequencing, and analysis strategies on the ability to effectively characterize a complex tumor.  ...  We demonstrate that current sequencing paradigms are inadequate for tumors that are impure, aneuploid or clonally heterogeneous.  ...  Acknowledgements We thank the McDonnell Genome Institute's LIMS, Analysis Pipeline, and Systems groups for developing and maintaining the automated sequence analysis pipelines.  ... 
doi:10.1016/j.cels.2015.08.015 pmid:26645048 pmcid:PMC4669575 fatcat:3sm5sn4tfncjrhmzdjrmucvqxi

Deciphering Genetic Intratumor Heterogeneity and Its Impact on Cancer Evolution

Rachel Rosenthal, Nicholas McGranahan, Javier Herrero, Charles Swanton
2017 Annual Review of Cancer Biology  
patterns of somatic evolution observed in normal tissues.  ...  Cancer is a disease reliant on the generation of mutations and the subsequent selection of those subpopulations endowed with the greatest fitness advantage.  ...  clonal architecture has on tumor evolution.  ... 
doi:10.1146/annurev-cancerbio-042516-011348 fatcat:zmivjuqvenh3rkyi6mjs3hw7da

Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations

V. Ljungstrom, D. Cortese, E. Young, T. Pandzic, L. Mansouri, K. Plevova, S. Ntoufa, P. Baliakas, R. Clifford, L.-A. Sutton, S. J. Blakemore, N. Stavroyianni (+22 others)
2015 Blood  
of the 40S ribosomal subunit.  ...  We confirmed the recently postulated direct interaction between RPS15 and MDM2/MDMX and transient expression of mutant RPS15 revealed defective regulation of endogenous p53 compared with wild-type RPS15  ...  All authors contributed to the preparation of the manuscript and approved the submission in its current form.  ... 
doi:10.1182/blood-2015-10-674572 pmid:26675346 pmcid:PMC4768426 fatcat:v5isjtvs3jan5egn7cov6iuspm

A phylogenetic latent feature model for clonal deconvolution

Francesco Marass, Florent Mouliere, Ke Yuan, Nitzan Rosenfeld, Florian Markowetz
2016 Annals of Applied Statistics  
The resulting model can capture both the acquisition and the loss of mutations, as well as episodes of convergent evolution.  ...  We establish the validity of Cloe on synthetic data and assess its performance on controlled biological data, comparing our reconstructions to those of several published state-of-the-art methods.  ...  We would like to acknowledge the support of The University of Cambridge, Cancer Research UK and Hutchison Whampoa Limited.  ... 
doi:10.1214/16-aoas986 fatcat:v5fszig6ezbrrm5eppnyhwbogq

Reconstructing metastatic seeding patterns of human cancers

Johannes G. Reiter, Alvin P. Makohon-Moore, Jeffrey M. Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine A. Iacobuzio-Donahue, Bert Vogelstein, Martin A. Nowak
2017 Nature Communications  
SciClone: Inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput. Biol. 10, e1003665 (2014). 36. Deshwar, A. G. et al.  ...  Moreover, the temporal, spatial and evolutionary rules governing the seeding of metastases at spatially-distinct sites distant from the primary tumor have mostly remained undetermined 6, 10, 11 .  ...  False-negatives: Calculate the probability to observe fewer than k s min variant reads of a clonal variant in a sample s with purity f pur assuming diploid cancer cells: 4.  ... 
doi:10.1038/ncomms14114 pmid:28139641 pmcid:PMC5290319 fatcat:25avxzcat5ddro6tysdkknom2u

Cancer Evolution: Mathematical Models and Computational Inference

Niko Beerenwinkel, Roland F. Schwarz, Moritz Gerstung, Florian Markowetz
2014 Systematic Biology  
Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data.  ...  We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between  ...  However, in most studies, the samples used are a mixture of cancer cells and stromal cells. In the following, we discuss how to analyze clonal architecture from genomic profiles of mixed samples.  ... 
doi:10.1093/sysbio/syu081 pmid:25293804 pmcid:PMC4265145 fatcat:7wzq6td2mvdqzbmurwnspweh4e

UVB-Induced Tumor Heterogeneity Diminishes Immune Response in Melanoma

Yochai Wolf, Osnat Bartok, Sushant Patkar, Gitit Bar Eli, Sapir Cohen, Kevin Litchfield, Ronen Levy, Alejandro Jiménez-Sánchez, Sophie Trabish, Joo Sang Lee, Hiren Karathia, Eilon Barnea (+17 others)
2019 Cell  
Using phylogenetic analyses and mixing experiments of single-cell clones, we dissect two characteristics of ITH: the number of clones forming the tumor and their clonal diversity.  ...  These findings highlight the importance of clonal mutations in robust immune surveillance and the need to quantify patient ITH to determine the response to checkpoint blockade.  ...  SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput. Biol. 10, e1003665.Milner, E., Gutter-Kapon, L., Bassani-Strenberg, M.  ... 
doi:10.1016/j.cell.2019.08.032 pmid:31522890 pmcid:PMC6863386 fatcat:zzlzitocdbewvpccftofnw3a3a

Dynamic evolution of cervical cancer mutations during chemoradiation using novel sampling approach [article]

Bhavana V. Chapman, Tatiana Karpinets, Travis T. Sims, Greyson Biegert, Xiaogang Wu, Andrea Y. Delgado Medrano, Patricia J. Eifel, Anuja Jhingran, Lilie L. Lin, Lois M. Ramondetta, Andrew M. Futreal, Amir A. Jazaeri (+11 others)
2019 bioRxiv   pre-print
Tumor purity from collected swabs correlated with MRI tumor volumes during the course of treatment (R2=0.969).  ...  CDK4/CDK6/cyclin D1-related gene mutations involved in the ERK1/2, p16INK4, and p53 pathway and G1/S checkpoint most commonly persisted at the end of CRT.ConclusionThis non-invasive swab technique to serially  ...  SciClone: inferring clonal architecture and tracking the spatial and 391 temporal patterns of tumor evolution. PLoS Comput. Biol. 10, e1003665 (2014). 392 25. Xia, P. et al.  ... 
doi:10.1101/850388 fatcat:5l572723o5erxc6bndqaoiuypa

Reconstructing tumor evolutionary histories and clone trees in polynomial-time with SubMARine [article]

Linda K Sundermann, Jeff Wintersinger, Gunnar Rätsch, Jens Stoye, Quaid Morris
2020 bioRxiv   pre-print
Subclonal reconstruction methods cluster mutations into groups that co-occur within the same subpopulations, estimate the frequency of cells belonging to each subpopulation, and infer the ancestral relationships  ...  Tumors contain multiple subpopulations of genetically distinct cancer cells. Reconstructing their evolutionary history can improve our understanding of how cancers develop and respond to treatment.  ...  Author contributions All authors devised the conceptional ideas of this work. LKS, JW and QM developed the algorithms. JW simulated the data. LKS wrote the code and performed the experiments.  ... 
doi:10.1101/2020.06.11.146100 fatcat:yvljwhkwz5f4jjzeoh2x6xeliu
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