Tumor evolution: Linear, branching, neutral or punctuated?☆
TLDR
Data is discussed that supports the theory that most human tumors evolve from a single cell in the normal tissue, and suggests that models may change during tumor progression or operate concurrently for different classes of mutations.About:
This article is published in Biochimica et Biophysica Acta.The article was published on 2017-04-01 and is currently open access. It has received 255 citations till now. The article focuses on the topics: Tumor progression.read more
Citations
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Comprehensive, integrated and phased whole-genome analysis of the primary ENCODE cell line K562
Bo Zhou,Steve S. Ho,Xiaowei Zhu,Xianglong Zhang,Noah Spies,Seunggyu Byeon,Joseph G. Arthur,Reenal Pattni,Noa Ben-Efraim,Michael S. Haney,Rajini R Haraksingh,Giltae Song,Dimitri Perrin,Wing H. Wong,Alexej Abyzov,Alexander E. Urban +15 more
TL;DR: This comprehensive whole-genome analysis of K562 serves as a resource for future studies that utilize K562 and as the basis of advanced analyses of the rich amounts of the functional genomics data produced by ENCODE for K562.
Posted ContentDOI
Benchmarking Tools for Copy Number Aberration Detection from Single-cell DNA Sequencing Data
TL;DR: This work categorizes the methods for segmenting the genome into regions of different copy numbers into three groups, select a representative method from each group that has been commonly used in this context, and benchmark them on simulated as well as real datasets.
Journal ArticleDOI
Predicting clone genotypes from tumor bulk sequencing of multiple samples.
Sayaka Miura,Karen Gomez,Karen Gomez,Oscar Murillo,Louise A Huuki,Tracy Vu,Tiffany Buturla,Sudhir Kumar,Sudhir Kumar +8 more
TL;DR: CloneFinder, LICHeE, CITUP and cloneHD inferred clone genotypes with low error for a majority of datasets in which the tumor samples contained evolutionarily-related clones, while AncesTree and Canopy did not produce results for a large number of datasets.
Journal ArticleDOI
The Many Facets of Tumor Heterogeneity: Is Metabolism Lagging Behind?
TL;DR: Historical and current views of intratumoral heterogeneity are reviewed, with an emphasis on summarizing the emerging data that begin to illuminate just how vast the spectrum of metabolic strategies a tumor can employ may be, and what this means for how to interpret other tumor characteristics, such as mutational landscape, contribution of microenvironmental influences, and treatment resistance.
Journal ArticleDOI
Evolution and Impact of Subclonal Mutations in Papillary Thyroid Cancer.
Tariq Masoodi,Abdul K. Siraj,Sarah Siraj,Saud Azam,Zeeshan Qadri,Sandeep Kumar Parvathareddy,Saif S. Al-Sobhi,Mohammed Al-Dawish,Fowzan S. Alkuraya,Khawla S. Al-Kuraya +9 more
TL;DR: It is concluded that relapse in PTC does not follow a predictable evolutionary path and that subclonal mutation burden may serve as a prognostic factor, and larger studies utilizing multi-region sequencing in relapsed PTC case subjects with matching primary tissues are needed to confirm these observations.
References
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Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation
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A genetic model for colorectal tumorigenesis
Eric R. Fearon,Bert Vogelstein +1 more
TL;DR: A model for the genetic basis of colorectal neoplasia that includes the following salient features is presented, which may be applicable to other common epithelial neoplasms, in which tumors of varying stage are more difficult to study.
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Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.
Marco Gerlinger,Andrew Rowan,Stuart Horswell,James Larkin,David Endesfelder,Eva Grönroos,Pierre Martinez,Nicholas Matthews,Aengus Stewart,Patrick S. Tarpey,Ignacio Varela,Benjamin Phillimore,Sharmin Begum,Neil Q. McDonald,Adam Butler,David T. Jones,Keiran Raine,Calli Latimer,Claudio R. Santos,Mahrokh Nohadani,Aron Charles Eklund,Bradley Spencer-Dene,Graham Clark,Lisa Pickering,Gordon Stamp,Martin Gore,Zoltan Szallasi,Zoltan Szallasi,Julian Downward,P. Andrew Futreal,Charles Swanton +30 more
TL;DR: Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development.
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The clonal evolution of tumor cell populations
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Journal ArticleDOI
MET Amplification Leads to Gefitinib Resistance in Lung Cancer by Activating ERBB3 Signaling
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