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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SF-010-4 Distant metastasis occurs late during the genetic evolution of pancreatic cancer
TL;DR: A quantitative analysis of the timing of the genetic evolution of pancreatic cancer was performed, indicating at least a decade between the occurrence of the initiating mutation and the birth of the parental, non-metastatic founder cell.
Journal ArticleDOI
Epigenetic plasticity and the hallmarks of cancer
TL;DR: It is proposed that chromatin and epigenetic aberrations have the potential to confer on cells the full range of oncogenic properties represented in the classic “hallmarks” depiction of cancer, and it is suggested that genetic, environmental, and metabolic factors can make chromatin aberrantly permissive or restrictive.
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Eleven grand challenges in single-cell data science
David Lähnemann,David Lähnemann,Johannes Köster,Johannes Köster,Ewa Szczurek,Davis J. McCarthy,Davis J. McCarthy,Stephanie C. Hicks,Mark D. Robinson,Catalina A. Vallejos,Catalina A. Vallejos,Kieran R Campbell,Kieran R Campbell,Niko Beerenwinkel,Niko Beerenwinkel,Ahmed Mahfouz,Ahmed Mahfouz,Luca Pinello,Luca Pinello,Pavel Skums,Alexandros Stamatakis,Alexandros Stamatakis,Camille Stephan Otto Attolini,Samuel Aparicio,Samuel Aparicio,Jasmijn A. Baaijens,Marleen Balvert,Marleen Balvert,Buys de Barbanson,Antonio Cappuccio,Giacomo Corleone,Bas E. Dutilh,Bas E. Dutilh,Maria Florescu,Victor Guryev,Rens Holmer,Katharina Jahn,Katharina Jahn,Thamar Jessurun Lobo,Emma M. Keizer,Indu Khatri,Szymon M. Kielbasa,Jan O. Korbel,Alexey M. Kozlov,Tzu Hao Kuo,Boudewijn P. F. Lelieveldt,Boudewijn P. F. Lelieveldt,Ion I. Mandoiu,John C. Marioni,John C. Marioni,John C. Marioni,Tobias Marschall,Tobias Marschall,Felix Mölder,Amir Niknejad,Lukasz Raczkowski,Marcel J. T. Reinders,Marcel J. T. Reinders,Jeroen de Ridder,Antoine-Emmanuel Saliba,Antonios Somarakis,Oliver Stegle,Oliver Stegle,Fabian J. Theis,Huan Yang,Alexander Zelikovsky,Alexander Zelikovsky,Alice C. McHardy,Benjamin J. Raphael,Sohrab P. Shah,Alexander Schönhuth,Alexander Schönhuth +71 more
TL;DR: This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years in single-cell data science.
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Tumour heterogeneity and metastasis at single-cell resolution.
TL;DR: Recent advances in single-cell technologies are reviewed and discussed in detail how they can be leveraged to understand tumour heterogeneity and metastasis.
Inference of Tumor Evolution during Chemotherapy by Computational Modeling and In Situ Analysis of Genetic and Phenotypic Cellular Diversity
Vanessa Almendro,Yu-Kang Cheng,Amanda Randles,Shalev Itzkovitz,Andriy Marusyk,Elisabet Ametller,Xavier Gonzalez-Farre,Hege G. Russnes,Inga H. Rye,Anne Lise Børresen-Dale,Reo Maruyama,Alexander van Oudenaarden,Mitchell Dowsett,Robin L. Jones,Jorge S. Reis-Filho,Pere Gascón,Franziska Michor,Kornelia Polyak,Montse Muñoz,Åslaug Helland,Mithat Gonen +20 more
TL;DR: The analysis of cellular heterogeneity for genetic and phenotypic features and their spatial distribution in breast tumors pre- and post-neoadjuvant chemotherapy found that intratumor genetic diversity was tumor-subtype specific, and it did not change during treatment in tumors with partial or no response.
References
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Journal ArticleDOI
BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies
Ke Yuan,Thomas Sakoparnig,Thomas Sakoparnig,Thomas Sakoparnig,Florian Markowetz,Niko Beerenwinkel,Niko Beerenwinkel +6 more
TL;DR: BitPhylogeny, a probabilistic framework to reconstruct intra-tumor evolutionary pathways from methylation patterns in colon cancer and from single-cell exomes in myeloproliferative neoplasm is presented.
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Tracing the Tumor Lineage
TL;DR: Comparing data from primary and metastatic copy number profiles to shed light on the final steps of breast cancer progression is compared and how recent technical advances in single cell genomics will herald a new era in understanding the fundamental basis of tumor heterogeneity and progression is discussed.
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Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol
Funda Meric-Bernstam,Lauren Brusco,Molly S. Daniels,Chetna Wathoo,Ann Marie Bailey,Louise C. Strong,Kenna Rael Shaw,Karen H. Lu,Yuan Qi,Hao Zhao,Humberto Lara-Guerra,Jennifer K. Litton,Banu Arun,Agda Karina Eterovic,Ugur Aytac,Mark J. Routbort,Vivek Subbiah,Filip Janku,M.A. Davies,Scott Kopetz,John Mendelsohn,Gordon B. Mills,Ken Chen +22 more
TL;DR: In this series, 2.3% patients had previously unrecognized pathogenic germline mutations in 19 cancer-related genes, suggesting genomic sequencing must be accompanied by a plan for return of germline results, in partnership with genetic counseling.
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Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing
Chang Yu,Jun Yu,Xiaotian Yao,William K.K. Wu,Youyong Lu,Senwei Tang,Xiangchun Li,Li Bao,Xiaoxing Li,Yong Hou,Renhua Wu,Min Jian,Ruoyan Chen,Fan Zhang,Lixia Xu,Fan Fan,Jun He,Qiaoyi Liang,Hongyi Wang,Xueda Hu,Minghui He,Xiang Zhang,Hancheng Zheng,Qibin Li,Hanjie Wu,Yan Chen,Xu Yang,Shida Zhu,Xun Xu,Huanming Yang,Jian Wang,Xiuqing Zhang,Joseph J.Y. Sung,Yingrui Li,Jun Wang +34 more
TL;DR: This study provides the first exome-wide evidence at single-cell level supporting that colon cancer could be of a biclonal origin, and suggests that low-prevalence mutations in a cohort may also play important protumorigenic roles at the individual level.
Journal ArticleDOI
TrAp: a tree approach for fingerprinting subclonal tumor composition
TL;DR: In this article, an evolutionary framework for deconvolving data from a single genome-wide experiment to infer the composition, abundance and evolutionary paths of the underlying cell subpopulations of a tumor was proposed.
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