Advances in understanding tumour evolution through single-cell sequencing

被引:83
作者
Kuipers, Jack
Jahn, Katharina
Beerenwinkel, Niko [1 ]
机构
[1] Swiss Fed Inst Technol, Dept Biosyst Sci & Engn, Basel, Switzerland
来源
BIOCHIMICA ET BIOPHYSICA ACTA-REVIEWS ON CANCER | 2017年 / 1867卷 / 02期
基金
欧洲研究理事会;
关键词
Single-cell sequencing; Cancer evolution; Tumour heterogeneity; Phylogenetics; SOMATIC POINT MUTATIONS; COPY NUMBER EVOLUTION; WHOLE-GENOME; CLONAL EVOLUTION; INTRATUMOR HETEROGENEITY; POPULATION-STRUCTURE; CANCER; INFERENCE; MODEL; NUCLEOTIDE;
D O I
10.1016/j.bbcan.2017.02.001
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
The mutational heterogeneity observed within tumours poses additional challenges to the development of effective cancer treatments. A thorough understanding of a tumour's subclonal composition and its mutational history is essential to open up the design of treatments tailored to individual patients. Comparative studies on a large number of tumours permit the identification of mutational patterns which may refine forecasts of cancer progression, response to treatment and metastatic potential. The composition of tumours is shaped by evolutionary processes. Recent advances in next-generation sequencing offer the possibility to analyse the evolutionary history and accompanying heterogeneity of tumours at an unprecedented resolution, by sequencing single cells. New computational challenges arise when moving from bulk to single-cell sequencing data, leading to the development of novel modelling frameworks. In this review, we present the state of the art methods for understanding the phylogeny encoded in bulk or single-cell sequencing data, and highlight future directions for developing more comprehensive and informative pictures of tumour evolution. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby. (C) 2017 The Authors. Published by Elsevier B.V.
引用
收藏
页码:127 / 138
页数:12
相关论文
共 130 条
[1]  
Allison KH, 2014, ONCOLOGY-NY, V28, P772
[2]  
[Anonymous], 2010, ADV NEURAL INFORM PR
[3]  
[Anonymous], 1997, ACM SIGACT NEWS
[4]   Optimizing sparse sequencing of single cells for highly multiplex copy number profiling [J].
Baslan, Timour ;
Kendall, Jude ;
Ward, Brian ;
Cox, Hilary ;
Leotta, Anthony ;
Rodgers, Linda ;
Riggs, Michael ;
D'Italia, Sean ;
Sun, Guoli ;
Yong, Mao ;
Miskimen, Kristy ;
Gilmore, Hannah ;
Saborowski, Michael ;
Dimitrova, Nevenka ;
Krasnitz, Alexander ;
Harris, Lyndsay ;
Wigler, Michael ;
Hicks, James .
GENOME RESEARCH, 2015, 25 (05) :714-724
[5]   Genetic progression and the waiting time to cancer [J].
Beerenwinkel, Niko ;
Antal, Tibor ;
Dingli, David ;
Traulsen, Arne ;
Kinzler, Kenneth W. ;
Velculescu, Victor E. ;
Vogelstein, Bert ;
Nowak, Martin A. .
PLOS COMPUTATIONAL BIOLOGY, 2007, 3 (11) :2239-2246
[6]   Organoid Models of Human and Mouse Ductal Pancreatic Cancer [J].
Boj, Sylvia F. ;
Hwang, Chang-Il ;
Baker, Lindsey A. ;
Chio, Iok In Christine ;
Engle, Dannielle D. ;
Corbo, Vincenzo ;
Jager, Myrthe ;
Ponz-Sarvise, Mariano ;
Tiriac, Herve ;
Spector, Mona S. ;
Gracanin, Ana ;
Oni, Tobiloba ;
Yu, Kenneth H. ;
van Boxtel, Ruben ;
Huch, Meritxell ;
Rivera, Keith D. ;
Wilson, John P. ;
Feigin, Michael E. ;
Oehlund, Daniel ;
Handly-Santana, Abram ;
Ardito-Abraham, Christine M. ;
Ludwig, Michael ;
Elyada, Ela ;
Alagesan, Brinda ;
Biffi, Giulia ;
Yordanov, Georgi N. ;
Delcuze, Bethany ;
Creighton, Brianna ;
Wright, Kevin ;
Park, Youngkyu ;
Morsink, Folkert H. M. ;
Molenaar, I. Quintus ;
Rinkes, Inne H. Borel ;
Cuppen, Edwin ;
Hao, Yuan ;
Jin, Ying ;
Nijman, Isaac J. ;
Iacobuzio-Donahue, Christine ;
Leach, Steven D. ;
Pappin, Darryl J. ;
Hammell, Molly ;
Klimstra, David S. ;
Basturk, Olca ;
Hruban, Ralph H. ;
Offerhaus, George Johan ;
Vries, Robert G. J. ;
Clevers, Hans ;
Tuveson, David A. .
CELL, 2015, 160 (1-2) :324-338
[7]   Heterogeneity Maintenance in Glioblastoma: A Social Network [J].
Bonavia, Rudy ;
Inda, Maria-del-Mar ;
Cavenee, Webster K. ;
Furnari, Frank B. .
CANCER RESEARCH, 2011, 71 (12) :4055-4060
[8]   Accumulation of driver and passenger mutations during tumor progression [J].
Bozic, Ivana ;
Antal, Tibor ;
Ohtsuki, Hisashi ;
Carter, Hannah ;
Kim, Dewey ;
Chen, Sining ;
Karchin, Rachel ;
Kinzler, Kenneth W. ;
Bogelstein, Bert ;
Nowak, Martin A. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (43) :18545-18550
[9]   Re-Evaluating Clonal Dominance in Cancer Evolution [J].
Burrell, Rebecca A. ;
Swanton, Charles .
TRENDS IN CANCER, 2016, 2 (05) :263-276
[10]   Tumour heterogeneity and the evolution of polyclonal drug resistance [J].
Burrell, Rebecca A. ;
Swanton, Charles .
MOLECULAR ONCOLOGY, 2014, 8 (06) :1095-1111