Mutation–selection balance and compensatory mechanisms in tumour evolution

[1]  N. McGranahan,et al.  Clonal Heterogeneity and Tumor Evolution: Past, Present, and the Future , 2017, Cell.

[2]  Winge Zytologische Untersuchungen ber die Natur maligner Tumoren: II. Teerkarzinome bei Musen , 1930 .

[3]  B. Taylor,et al.  Genome doubling shapes the evolution and prognosis of advanced cancers , 2018, Nature Genetics.

[4]  Shamil R. Sunyaev,et al.  Impact of deleterious passenger mutations on cancer progression , 2012, Proceedings of the National Academy of Sciences.

[5]  S. Elledge,et al.  Tumor aneuploidy correlates with markers of immune evasion and with reduced response to immunotherapy , 2017, Science.

[6]  S. Haferkamp,et al.  LDHA-Associated Lactic Acid Production Blunts Tumor Immunosurveillance by T and NK Cells. , 2016, Cell metabolism.

[7]  Stephen J. Tapscott,et al.  CTCF cis-Regulates Trinucleotide Repeat Instability in an Epigenetic Manner: A Novel Basis for Mutational Hot Spot Determination , 2008, PLoS genetics.

[8]  L. Loeb,et al.  Errors in DNA replication as a basis of malignant changes. , 1974, Cancer research.

[9]  Larry J Young,et al.  Microsatellite Instability Generates Diversity in Brain and Sociobehavioral Traits , 2005, Science.

[10]  Y. Kashi,et al.  Simple sequence repeats as advantageous mutators in evolution. , 2006, Trends in genetics : TIG.

[11]  A. Dueñas-González,et al.  The Epigenetic Origin of Aneuploidy , 2008, Current genomics.

[12]  P. Donnelly,et al.  Re-engineering the zinc fingers of PRDM9 reverses hybrid sterility in mice , 2016, Nature.

[13]  L. Cantley,et al.  Understanding the Warburg Effect: The Metabolic Requirements of Cell Proliferation , 2009, Science.

[14]  E. Koonin,et al.  Positive and strongly relaxed purifying selection drive the evolution of repeats in proteins , 2016, Nature Communications.

[15]  Nicolai J. Birkbak,et al.  Relationship of Extreme Chromosomal Instability with Long-term Survival in a Retrospective Analysis of Primary Breast Cancer , 2011, Cancer Epidemiology, Biomarkers & Prevention.

[16]  C. Swanton,et al.  Determinants and clinical implications of chromosomal instability in cancer , 2018, Nature Reviews Clinical Oncology.

[17]  Joel s. Brown,et al.  Of cancer and cave fish , 2011, Nature Reviews Cancer.

[18]  Daniel C. Desrosiers,et al.  The ankyrin repeat as molecular architecture for protein recognition , 2004, Protein science : a publication of the Protein Society.

[19]  R. Gillies,et al.  Neutralization of Tumor Acidity Improves Antitumor Responses to Immunotherapy. , 2016, Cancer research.

[20]  Shamil Sunyaev,et al.  Bayesian inference of negative and positive selection in human cancers , 2017, Nature Genetics.

[21]  S. Elledge,et al.  Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome , 2013, Cell.

[22]  Benjamin H. Good,et al.  Fate of a mutation in a fluctuating environment , 2015, Proceedings of the National Academy of Sciences.

[23]  Carissa A. Sanchez,et al.  Chromosomal Instability and Copy Number Alterations in Barrett's Esophagus and Esophageal Adenocarcinoma , 2009, Clinical Cancer Research.

[24]  James M. McFarland,et al.  WRN Helicase is a Synthetic Lethal Target in Microsatellite Unstable Cancers , 2019, Nature.

[25]  Jay Shendure,et al.  Classification and characterization of microsatellite instability across 18 cancer types , 2016, Nature Medicine.

[26]  Peng Huang,et al.  Targeting cancer cells by ROS-mediated mechanisms: a radical therapeutic approach? , 2009, Nature Reviews Drug Discovery.

[27]  D. J. Kiviet,et al.  Reciprocal sign epistasis is a necessary condition for multi-peaked fitness landscapes. , 2011, Journal of theoretical biology.

[28]  David Horn,et al.  Systematic Analysis of Compositional Order of Proteins Reveals New Characteristics of Biological Functions and a Universal Correlate of Macroevolution , 2013, PLoS Comput. Biol..

[29]  D. Eisenberg,et al.  A census of protein repeats. , 1999, Journal of molecular biology.

[30]  O. Gascuel,et al.  Deep Conservation of Human Protein Tandem Repeats within the Eukaryotes , 2014, Molecular biology and evolution.

[31]  Joshua F. McMichael,et al.  Systematic Discovery of Complex Indels in Human Cancers , 2015, Nature medicine.

[32]  A. Jackson,et al.  Induction of microsatellite instability by oxidative DNA damage. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[33]  Guilhem Chalancon,et al.  Constraints and consequences of the emergence of amino acid repeats in eukaryotic proteins , 2017, Nature Structural &Molecular Biology.

[34]  S. Salzberg,et al.  Repetitive DNA and next-generation sequencing: computational challenges and solutions , 2011, Nature Reviews Genetics.

[35]  A. Harris,et al.  HIF-1α Induces Genetic Instability by Transcriptionally Downregulating MutSα Expression , 2005 .

[36]  A. Sivachenko,et al.  Punctuated Evolution of Prostate Cancer Genomes , 2013, Cell.

[37]  Alan Ashworth,et al.  PARP inhibitors: Synthetic lethality in the clinic , 2017, Science.

[38]  Michael M. Desai,et al.  Pervasive Genetic Hitchhiking and Clonal Interference in 40 Evolving Yeast Populations , 2013, Nature.

[39]  Joel s. Brown,et al.  Classifying the evolutionary and ecological features of neoplasms , 2017, Nature Reviews Cancer.

[40]  R. Lenski,et al.  Evolution of high mutation rates in experimental populations of E. coli , 1997, Nature.

[41]  Matteo Benelli,et al.  Divergent clonal evolution of castration resistant neuroendocrine prostate cancer , 2016, Nature Medicine.

[42]  David J. Barry,et al.  APC/C Dysfunction Limits Excessive Cancer Chromosomal Instability. , 2017, Cancer discovery.

[43]  David T. W. Jones,et al.  Genome Sequencing of Pediatric Medulloblastoma Links Catastrophic DNA Rearrangements with TP53 Mutations , 2012, Cell.

[44]  Marc J. Williams,et al.  Quantification of subclonal selection in cancer from bulk sequencing data , 2018, Nature Genetics.

[45]  Y. Hérault,et al.  WD40-repeat 47, a microtubule-associated protein, is essential for brain development and autophagy , 2017, Proceedings of the National Academy of Sciences.

[46]  Derek Y. Chiang,et al.  The landscape of somatic copy-number alteration across human cancers , 2010, Nature.

[47]  C. E. Pearson,et al.  Repeat instability: mechanisms of dynamic mutations , 2005, Nature Reviews Genetics.

[48]  Ö. Winge Zytologische Untersuchungen über die Natur maligner Tumoren , 1930, Zeitschrift für Zellforschung und Mikroskopische Anatomie.

[49]  David Pellman,et al.  Causes and consequences of aneuploidy in cancer , 2012, Nature Reviews Genetics.

[50]  J. Haber,et al.  Expansions and Contractions in a Tandem Repeat Induced by Double-Strand Break Repair , 1998, Molecular and Cellular Biology.

[51]  Samuel F. Bakhoum,et al.  Chromosomal instability drives metastasis through a cytosolic DNA response , 2017, Nature.

[52]  R. Hill,et al.  Hypoxia induces DNA overreplication and enhances metastatic potential of murine tumor cells. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A. Ashworth,et al.  Genetic Interactions in Cancer Progression and Treatment , 2011, Cell.

[54]  M. Kimura,et al.  The neutral theory of molecular evolution. , 1983, Scientific American.

[55]  Lauren M. Zasadil,et al.  Chromosome missegregation rate predicts whether aneuploidy will promote or suppress tumors , 2013, Proceedings of the National Academy of Sciences.

[56]  David T. W. Jones,et al.  Signatures of mutational processes in human cancer , 2013, Nature.

[57]  Fran Lewitter,et al.  Intragenic tandem repeats generate functional variability , 2005, Nature Genetics.

[58]  H. Garner,et al.  Molecular origins of rapid and continuous morphological evolution , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[59]  J. Lupski,et al.  Mechanisms underlying structural variant formation in genomic disorders , 2016, Nature Reviews Genetics.

[60]  T. Hubbard,et al.  A census of human cancer genes , 2004, Nature Reviews Cancer.

[61]  J. Haigh The accumulation of deleterious genes in a population--Muller's Ratchet. , 1978, Theoretical population biology.

[62]  E. Koonin,et al.  Common origins and host-dependent diversity of plant and animal viromes. , 2011, Current opinion in virology.

[63]  Yun-chi Tang,et al.  Gene Copy-Number Alterations: A Cost-Benefit Analysis , 2013, Cell.

[64]  Nicholas D. Socci,et al.  Mad2-induced chromosome instability leads to lung tumor relapse after oncogene withdrawal , 2010, Nature.

[65]  Robert J. Gillies,et al.  A microenvironmental model of carcinogenesis , 2008, Nature Reviews Cancer.

[66]  Molly Przeworski,et al.  The Case of the Fickle Fingers: How the PRDM9 Zinc Finger Protein Specifies Meiotic Recombination Hotspots in Humans , 2011, PLoS biology.

[67]  Andrea Sottoriva,et al.  Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine , 2016, Trends in cancer.

[68]  Chuang Tan,et al.  Universal Patterns of Selection in Cancer and Somatic Tissues , 2018, Cell.

[69]  E. Koonin The Logic of Chance: The Nature and Origin of Biological Evolution , 2011 .

[70]  André Hoelz,et al.  The structure of the nuclear pore complex. , 2011, Annual review of biochemistry.

[71]  M. Kimura The Neutral Theory of Molecular Evolution: Introduction , 1983 .

[72]  P. Glazer,et al.  Genetic instability induced by the tumor microenvironment. , 1996, Cancer research.

[73]  H. Muller THE RELATION OF RECOMBINATION TO MUTATIONAL ADVANCE. , 1964, Mutation research.

[74]  M. Glickman,et al.  PCI complexes: Beyond the proteasome, CSN, and eIF3 Troika. , 2009, Molecular cell.

[75]  Robert J Gillies,et al.  Eco-evolutionary causes and consequences of temporal changes in intratumoural blood flow , 2018, Nature Reviews Cancer.

[76]  R. Waterland,et al.  Dnmt1 deficiency promotes CAG repeat expansion in the mouse germline. , 2008, Human molecular genetics.

[77]  Anita Saraf,et al.  Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast , 2010, Nature.

[78]  S. Mirkin,et al.  On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability. , 2020, The Journal of biological chemistry.

[79]  Krutiakov Vm [Eukaryotic error prone DNA polymerases: suggested roles in replication, repair and mutagenesis]. , 2006 .

[80]  Darryl Shibata,et al.  Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis , 1993, Nature.

[81]  R. Houlston,et al.  Systematic review of microsatellite instability and colorectal cancer prognosis. , 2005, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[82]  Raman Nambudripad,et al.  The ancient regulatory-protein family of WD-repeat proteins , 1994, Nature.

[83]  F. Nicolantonio,et al.  Inactivation of DNA repair triggers neoantigen generation and impairs tumour growth , 2017, Nature.

[84]  Hanlee P. Ji,et al.  Pan-cancer analysis of the extent and consequences of intratumor heterogeneity , 2015, Nature Medicine.

[85]  A. Hannan,et al.  Dynamic mutations as digital genetic modulators of brain development, function and dysfunction , 2007, BioEssays : news and reviews in molecular, cellular and developmental biology.

[86]  S. Karlin,et al.  Amino acid runs in eukaryotic proteomes and disease associations , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[87]  A. Tannapfel,et al.  A Distinct Oncogenerative Multinucleated Cancer Cell Serves as a Source of Stemness and Tumor Heterogeneity. , 2018, Cancer research.

[88]  Lilach Hadany,et al.  THE EVOLUTION OF STRESS‐INDUCED HYPERMUTATION IN ASEXUAL POPULATIONS , 2012, Evolution; international journal of organic evolution.

[89]  Yunfu Lin,et al.  Environmental stress induces trinucleotide repeat mutagenesis in human cells , 2015, Proceedings of the National Academy of Sciences.

[90]  Benjamin G. Bitler,et al.  Synthetic lethality by targeting EZH2 methyltransferase activity in ARID1A-mutated cancers , 2015, Nature Medicine.

[91]  Cristina Montagna,et al.  Aneuploidy acts both oncogenically and as a tumor suppressor. , 2007, Cancer cell.

[92]  D. Hanahan,et al.  Hallmarks of Cancer: The Next Generation , 2011, Cell.

[93]  Jiri Bartek,et al.  Replication stress links structural and numerical cancer chromosomal instability , 2013, Nature.

[94]  J. Grimsby,et al.  RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues , 2019, Science.

[95]  A. Duval,et al.  Mutations at coding repeat sequences in mismatch repair-deficient human cancers: toward a new concept of target genes for instability. , 2002, Cancer research.

[96]  M. Stratton,et al.  Instability of short tandem repeats (microsatellites) in human cancers , 1994, Nature Genetics.

[97]  S. Mirkin Expandable DNA repeats and human disease , 2007, Nature.

[98]  Robert J. Gillies,et al.  Causes and Consequences of Increased Glucose Metabolism of Cancers , 2008, Journal of Nuclear Medicine.

[99]  Davide Prandi,et al.  Clonal evolution of chemotherapy-resistant urothelial carcinoma , 2016, Nature Genetics.

[100]  M. Kimura,et al.  On the probability of fixation of mutant genes in a population. , 1962, Genetics.

[101]  Matthieu Legendre,et al.  Variable tandem repeats accelerate evolution of coding and regulatory sequences. , 2010, Annual review of genetics.

[102]  Lucas Lochovsky,et al.  Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences , 2020, Cell.

[103]  O. Feron,et al.  Tumour acidosis: from the passenger to the driver's seat , 2017, Nature Reviews Cancer.

[104]  S. Tapscott,et al.  CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus , 2001, Nature Genetics.

[105]  Jason M. Sheltzer,et al.  Systematic identification of mutations and copy number alterations associated with cancer patient prognosis , 2018, eLife.

[106]  Replication stress links structural and numerical cancer chromosomal instability (vol 494, pg 492, 2013) , 2013 .

[107]  D. Beebe,et al.  High rates of chromosome missegregation suppress tumor progression but do not inhibit tumor initiation , 2016, Molecular biology of the cell.

[108]  Aaron Klug,et al.  ‘Zinc fingers’: a novel protein motif for nucleic acid recognition , 1987 .

[109]  E. Koonin,et al.  Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability , 2020, Nature Communications.

[110]  P. Nowell The clonal evolution of tumor cell populations. , 1976, Science.

[111]  Jukka Corander,et al.  Parallel independent evolution of pathogenicity within the genus Yersinia , 2014, Proceedings of the National Academy of Sciences.

[112]  E. Jaffee,et al.  Targeting neoantigens to augment antitumour immunity , 2017, Nature Reviews Cancer.

[113]  N. Takebe,et al.  Targeting signalling pathways and the immune microenvironment of cancer stem cells — a clinical update , 2019, Nature Reviews Clinical Oncology.

[114]  E. Koonin,et al.  Proteomic and genomic signatures of repeat instability in cancer and adjacent normal tissues , 2019, Proceedings of the National Academy of Sciences.

[115]  Maitreya J. Dunham,et al.  Effects of Aneuploidy on Cellular Physiology and Cell Division in Haploid Yeast , 2007, Science.

[116]  N. McGranahan,et al.  The causes and consequences of genetic heterogeneity in cancer evolution , 2013, Nature.

[117]  Neil Vasan,et al.  A view on drug resistance in cancer , 2019, Nature.

[118]  P. A. Futreal,et al.  Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. , 2012, The New England journal of medicine.

[119]  E. Koonin,et al.  Selection in the evolution of gene duplications , 2002, Genome Biology.

[120]  Rong Li,et al.  Hsp90 Stress Potentiates Rapid Cellular Adaptation through Induction of Aneuploidy , 2012, Nature.

[121]  Zoltan Szallasi,et al.  Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. , 2014, Cancer discovery.

[122]  S. Mirkin,et al.  On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability , 2020, The Journal of Biological Chemistry.

[123]  K. Kinzler,et al.  Glucose Deprivation Contributes to the Development of KRAS Pathway Mutations in Tumor Cells , 2009, Science.

[124]  Jun S. Liu,et al.  Landscape of tumor-infiltrating T cell repertoire of human cancers , 2016, Nature Genetics.

[125]  H. Ohtsuki,et al.  Accumulation of driver and passenger mutations during tumor progression , 2009, Proceedings of the National Academy of Sciences.

[126]  M. Stratton,et al.  High burden and pervasive positive selection of somatic mutations in normal human skin , 2015, Science.

[127]  Jacob G. Scott,et al.  The Damaging Effect of Passenger Mutations on Cancer Progression. , 2017, Cancer research.

[128]  R. Gatenby,et al.  Evolutionary triage governs fitness in driver and passenger mutations and suggests targeting never mutations , 2014, Nature Communications.

[129]  Virginia Espina,et al.  What is the malignant nature of human ductal carcinoma in situ? , 2011, Nature Reviews Cancer.

[130]  Sara El-Metwally,et al.  Next-Generation Sequence Assembly: Four Stages of Data Processing and Computational Challenges , 2013, PLoS Comput. Biol..

[131]  O. Warburg [Origin of cancer cells]. , 1956, Oncologia.

[132]  E. Jaffee,et al.  Tumor Mutational Burden and Response Rate to PD-1 Inhibition. , 2017, The New England journal of medicine.

[133]  Y. Barde,et al.  Neurotrophins: key regulators of cell fate and cell shape in the vertebrate nervous system. , 2000, Genes & development.

[134]  M. Novelli,et al.  Revisiting tumour aneuploidy — the place of ploidy assessment in the molecular era , 2016, Nature Reviews Clinical Oncology.

[135]  C. E. Pearson,et al.  Repeat instability as the basis for human diseases and as a potential target for therapy , 2010, Nature Reviews Molecular Cell Biology.

[136]  Andrés Aguilera,et al.  R loops: new modulators of genome dynamics and function , 2015, Nature Reviews Genetics.

[137]  J. Plotkin,et al.  The Population Genetics of dN/dS , 2008, PLoS genetics.

[138]  F. Kondrashov,et al.  The evolution of gene duplications: classifying and distinguishing between models , 2010, Nature Reviews Genetics.

[139]  Bruce L. Miller,et al.  Expanded GGGGCC Hexanucleotide Repeat in Noncoding Region of C9ORF72 Causes Chromosome 9p-Linked FTD and ALS , 2011, Neuron.

[140]  K. Cole,et al.  Comprehensive Analysis of Hypermutation in Human Cancer , 2017, Cell.

[141]  M. Matzke,et al.  Rapid structural and epigenetic changes in polyploid and aneuploid genomes , 1999, BioEssays : news and reviews in molecular, cellular and developmental biology.

[142]  D. Davies,et al.  Leucine-rich repeats and pathogen recognition in Toll-like receptors. , 2003, Trends in immunology.

[143]  B. Vogelstein,et al.  Stem cell divisions, somatic mutations, cancer etiology, and cancer prevention , 2017, Science.

[144]  M. Greaves,et al.  Fetal origins of the TEL-AML1 fusion gene in identical twins with leukemia. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[145]  Karl J. Dykema,et al.  Chromosome instability drives phenotypic switching to metastasis , 2016, Proceedings of the National Academy of Sciences.

[146]  C. Curtis,et al.  Quantitative evidence for early metastatic seeding in colorectal cancer , 2019, Nature Genetics.

[147]  Joel s. Brown,et al.  Darwinian Dynamics of Intratumoral Heterogeneity: Not Solely Random Mutations but Also Variable Environmental Selection Forces. , 2016, Cancer research.

[148]  Jan O. Korbel,et al.  Negative Selection and Chromosome Instability Induced by Mad2 Overexpression Delay Breast Cancer but Facilitate Oncogene-Independent Outgrowth , 2016, Cell reports.

[149]  P. Hieter,et al.  Synthetic lethality and cancer , 2017, Nature Reviews Genetics.

[150]  P. A. Futreal,et al.  Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal , 2018, Cell.

[151]  R. Gillies,et al.  Causes and Consequences of Variable Tumor Cell Metabolism on Heritable Modifications and Tumor Evolution , 2020, Frontiers in Oncology.

[152]  R. Vale,et al.  RNA Phase Transitions in Repeat Expansion Disorders , 2017, Nature.

[153]  Z. Trajanoski,et al.  Integrative Analyses of Colorectal Cancer Show Immunoscore Is a Stronger Predictor of Patient Survival Than Microsatellite Instability. , 2016, Immunity.

[154]  G. Gutman,et al.  Slipped-strand mispairing: a major mechanism for DNA sequence evolution. , 1987, Molecular biology and evolution.

[155]  Joel s. Brown,et al.  Poly‐aneuploid cancer cells promote evolvability, generating lethal cancer , 2020, Evolutionary applications.

[156]  Wolfgang Stephan,et al.  The evolutionary dynamics of repetitive DNA in eukaryotes , 1994, Nature.

[157]  Joshua F. McMichael,et al.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.

[158]  Navdeep S. Chandel,et al.  Fundamentals of cancer metabolism , 2016, Science Advances.

[159]  Michael M. Desai,et al.  Dynamic Mutation–Selection Balance as an Evolutionary Attractor , 2012, Genetics.

[160]  Ashton C. Berger,et al.  Genomic and Functional Approaches to Understanding Cancer Aneuploidy. , 2018, Cancer cell.

[161]  Derek LeRoith,et al.  Obesity and Diabetes: The Increased Risk of Cancer and Cancer-Related Mortality. , 2015, Physiological reviews.

[162]  Peter J. Campbell,et al.  Somatic mutant clones colonize the human esophagus with age , 2018, Science.

[163]  J. Taylor,et al.  Repeat expansion disease: progress and puzzles in disease pathogenesis , 2010, Nature Reviews Genetics.

[164]  Andrew P. Feinberg,et al.  Epigenetic modulators, modifiers and mediators in cancer aetiology and progression , 2016, Nature Reviews Genetics.

[165]  Marc J. Williams,et al.  Identification of neutral tumor evolution across cancer types , 2016, Nature Genetics.

[166]  Nicolai J. Birkbak,et al.  Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution , 2020, Nature Genetics.

[167]  B. Vogelstein,et al.  Variation in cancer risk among tissues can be explained by the number of stem cell divisions , 2015, Science.

[168]  A. Hoffmann,et al.  Environmental Stress as an Evolutionary Force , 2000 .

[169]  Michael R. Speicher,et al.  The tumor microenvironment and Immunoscore are critical determinants of dissemination to distant metastasis , 2016, Science Translational Medicine.

[170]  A. Amon,et al.  Context is everything: aneuploidy in cancer , 2019, Nature Reviews Genetics.

[171]  P. Phillips Epistasis — the essential role of gene interactions in the structure and evolution of genetic systems , 2008, Nature Reviews Genetics.

[172]  S. Leibler,et al.  Phenotypic Diversity, Population Growth, and Information in Fluctuating Environments , 2005, Science.

[173]  Huda Y. Zoghbi,et al.  Diseases of Unstable Repeat Expansion: Mechanisms and Common Principles , 2005, Nature Reviews Genetics.

[174]  R. Gillies,et al.  Evolutionary dynamics of carcinogenesis and why targeted therapy does not work , 2012, Nature Reviews Cancer.

[175]  M. Lynch,et al.  The evolutionary fate and consequences of duplicate genes. , 2000, Science.

[176]  M. Babu,et al.  Amino acid homorepeats in proteins , 2020, Nature Reviews Chemistry.

[177]  Peter L Lee,et al.  The SOS response regulates adaptive mutation. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[178]  A. Hannan,et al.  Tandem repeats mediating genetic plasticity in health and disease , 2018, Nature Reviews Genetics.

[179]  Koji Abe,et al.  Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy , 2018, Nature Genetics.

[180]  I. Shih,et al.  Targeting EZH2 methyltransferase activity in ARID1A mutated cancer cells is synthetic lethal , 2015, Nature medicine.

[181]  Yaniv Erlich,et al.  Abundant contribution of short tandem repeats to gene expression variation in humans , 2015, Nature Genetics.

[182]  D. Cox Regression Models and Life-Tables , 1972 .

[183]  S. Maciver Asexual Amoebae Escape Muller's Ratchet through Polyploidy. , 2016, Trends in parasitology.

[184]  N. Carter,et al.  Massive Genomic Rearrangement Acquired in a Single Catastrophic Event during Cancer Development , 2011, Cell.

[185]  Y. Pilpel,et al.  Chromosomal duplication is a transient evolutionary solution to stress , 2012, Proceedings of the National Academy of Sciences.

[186]  J. Strathern,et al.  Error-prone DNA polymerases: when making a mistake is the only way to get ahead. , 2003, Annual review of genetics.

[187]  P. Martinez,et al.  Evolution of Barrett’s esophagus through space and time at single-crypt and whole-biopsy levels , 2018, Nature Communications.

[188]  P. Edwards,et al.  Spectral karyotyping suggests additional subsets of colorectal cancers characterized by pattern of chromosome rearrangement , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[189]  A. Regev,et al.  Acquired HER2 mutations in ER+ metastatic breast cancer confer resistance to estrogen receptor–directed therapies , 2018, Nature Genetics.

[190]  Leonid A. Mirny,et al.  Tug-of-war between driver and passenger mutations in cancer and other adaptive processes , 2014, Proceedings of the National Academy of Sciences.

[191]  Zoltan Szallasi,et al.  Paradoxical relationship between chromosomal instability and survival outcome in cancer. , 2011, Cancer research.

[192]  Steven A. Roberts,et al.  Mutational heterogeneity in cancer and the search for new cancer genes , 2014 .

[193]  A. Ashworth,et al.  Synthetic lethality as an engine for cancer drug target discovery , 2019, Nature Reviews Drug Discovery.

[194]  M. Lynch,et al.  The Origins of Genome Complexity , 2003, Science.

[195]  L. A. Sawyer,et al.  Natural variation in a Drosophila clock gene and temperature compensation. , 1997, Science.

[196]  Mark D. M. Leiserson,et al.  Criticality in tumor evolution and clinical outcome , 2018, Proceedings of the National Academy of Sciences.

[197]  John Cairns,et al.  Mutation selection and the natural history of cancer , 1975, Nature.

[198]  Matthew P. Jacobson,et al.  Dysregulated pH: a perfect storm for cancer progression , 2011, Nature Reviews Cancer.

[199]  K. Wellen,et al.  Metabolic control of epigenetics in cancer , 2016, Nature Reviews Cancer.

[200]  S. Rosenberg,et al.  Stress-Induced Mutagenesis: Implications in Cancer and Drug Resistance. , 2017, Annual review of cancer biology.

[201]  E. Ruppin,et al.  Systems analysis of intracellular pH vulnerabilities for cancer therapy , 2018, Nature Communications.