Tumor evolution: Linear, branching, neutral or punctuated?

Intratumor heterogeneity has been widely reported in human cancers, but our knowledge of how this genetic diversity emerges over time remains limited. A central challenge in studying tumor evolution is the difficulty in collecting longitudinal samples from cancer patients. Consequently, most studies have inferred tumor evolution from single time-point samples, providing very indirect information. These data have led to several competing models of tumor evolution: linear, branching, neutral and punctuated. Each model makes different assumptions regarding the timing of mutations and selection of clones, and therefore has different implications for the diagnosis and therapeutic treatment of cancer patients. Furthermore, emerging evidence suggests that models may change during tumor progression or operate concurrently for different classes of mutations. Finally, we discuss data that supports the theory that most human tumors evolve from a single cell in the normal tissue. This article is part of a Special Issue entitled: Evolutionary principles - heterogeneity in cancer?, edited by Dr. Robert A. Gatenby.

[1]  C. Maley,et al.  Cancer is a disease of clonal evolution within the body1–3. This has profound clinical implications for neoplastic progression, cancer prevention and cancer therapy. Although the idea of cancer as an evolutionary problem , 2006 .

[2]  Xuemei Lu,et al.  Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution , 2015, Proceedings of the National Academy of Sciences.

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

[4]  A multitype infinite-allele branching process with applications to cancer evolution , 2015, Journal of Applied Probability.

[5]  Martin A. Nowak,et al.  A spatial model predicts that dispersal and cell turnover limit intratumour heterogeneity , 2015, Nature.

[6]  P. Fialkow.  The origin and development of human tumors studied with cell markers. , 1974, The New England journal of medicine.

[7]  D. Santini,et al.  Clone heterogeneity in diploid and aneuploid breast carcinomas as detected by FISH. , 2001, Cytometry.

[8]  C. Swanton,et al.  Can oncology recapitulate paleontology? Lessons from species extinctions , 2015, Nature Reviews Clinical Oncology.

[9]  Marek Kimmel,et al.  Branching processes in biology , 2002 .

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

[11]  A. Børresen-Dale,et al.  The Life History of 21 Breast Cancers , 2012, Cell.

[12]  S. Kopetz,et al.  The Promise of Patient-Derived Xenografts: The Best Laid Plans of Mice and Men , 2012, Clinical Cancer Research.

[13]  B. Kermani,et al.  Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA , 2015, PloS one.

[14]  Robert J Gillies,et al.  Glycolysis in cancer: a potential target for therapy. , 2007, The international journal of biochemistry & cell biology.

[15]  Irmtraud M. Meyer,et al.  The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.

[16]  Kenny Q. Ye,et al.  Novel patterns of genome rearrangement and their association with survival in breast cancer. , 2006, Genome research.

[17]  N. Navin,et al.  Advances and applications of single-cell sequencing technologies. , 2015, Molecular cell.

[18]  Sridhar Ramaswamy,et al.  Circulating Tumor Cell Clusters Are Oligoclonal Precursors of Breast Cancer Metastasis , 2014, Cell.

[19]  Nilgun Donmez,et al.  Clonality inference in multiple tumor samples using phylogeny , 2015, Bioinform..

[20]  Xiaohong Li,et al.  A Comprehensive Survey of Clonal Diversity Measures in Barrett's Esophagus as Biomarkers of Progression to Esophageal Adenocarcinoma , 2010, Cancer Prevention Research.

[21]  W. Koh,et al.  Dissecting the clonal origins of childhood acute lymphoblastic leukemia by single-cell genomics , 2014, Proceedings of the National Academy of Sciences.

[22]  Funda Meric-Bernstam,et al.  Punctuated Copy Number Evolution and Clonal Stasis in Triple-Negative Breast Cancer , 2016, Nature Genetics.

[23]  M. Jimenez-Linan,et al.  Intra-tumour genetic heterogeneity and poor chemoradiotherapy response in cervical cancer , 2010, British Journal of Cancer.

[24]  N. Eldredge,et al.  Punctuated equilibrium comes of age , 1993, Nature.

[25]  M. Kimura.  The number of heterozygous nucleotide sites maintained in a finite population due to steady flux of mutations. , 1969, Genetics.

[26]  R. Solé,et al.  Metapopulation dynamics and spatial heterogeneity in cancer , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[27]  P. Fialkow.  Human genetic markers as tracers of tumour histogenesis , 1974, Journal of clinical pathology. Supplement.

[28]  X. Xie,et al.  Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients , 2013, Proceedings of the National Academy of Sciences.

[29]  Yoshitaka Narita,et al.  Tumor heterogeneity is an active process maintained by a mutant EGFR-induced cytokine circuit in glioblastoma. , 2010, Genes & development.

[30]  James D. Brenton,et al.  Phylogenetic Quantification of Intra-tumour Heterogeneity , 2013, PLoS Comput. Biol..

[31]  Robin L. Jones,et al.  Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. , 2014, Cell reports.

[32]  Barbara L Parsons,et al.  Many different tumor types have polyclonal tumor origin: evidence and implications. , 2008, Mutation research.

[33]  Charles Swanton,et al.  Intratumor Heterogeneity: Seeing the Wood for the Trees , 2012, Science Translational Medicine.

[34]  Cheng-Zhong Zhang,et al.  Chromothripsis and beyond: rapid genome evolution from complex chromosomal rearrangements , 2013, Genes & development.

[35]  A. Bouchard-Côté,et al.  PyClone: statistical inference of clonal population structure in cancer , 2014, Nature Methods.

[36]  Faraz Hach,et al.  Spatial genomic heterogeneity within localized, multifocal prostate cancer , 2015, Nature Genetics.

[37]  Cheng-Zhong Zhang,et al.  Chromothripsis: A New Mechanism for Rapid Karyotype Evolution. , 2015, Annual review of genetics.

[38]  O. Scharovsky,et al.  Metronomic chemotherapy: changing the paradigm that more is better , 2009, Current oncology.

[39]  K. Polyak,et al.  Non-cell autonomous tumor-growth driving supports sub-clonal heterogeneity , 2014, Nature.

[40]  A. Tward,et al.  High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma , 2013, Cancer.

[41]  Alexandre Bouchard-Côté,et al.  Clonal genotype and population structure inference from single-cell tumor sequencing , 2016, Nature Methods.

[42]  Y. Iwasa,et al.  Evolutionary Dynamics of Intratumor Heterogeneity , 2011, PloS one.

[43]  K. Polyak,et al.  Tumor heterogeneity: causes and consequences. , 2010, Biochimica et biophysica acta.

[44]  Subramanian Venkatesan,et al.  Tumor Evolutionary Principles: How Intratumor Heterogeneity Influences Cancer Treatment and Outcome. , 2016, American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting.

[45]  Benjamin J. Raphael,et al.  Reconstruction of clonal trees and tumor composition from multi-sample sequencing data , 2015, Bioinform..

[46]  F. Waldman,et al.  ERBB-2 (HER2/neu) gene copy number, p185HER-2 overexpression, and intratumor heterogeneity in human breast cancer. , 1995, Cancer research.

[47]  Nicholas J. Wang,et al.  Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease , 2015, PloS one.

[48]  Huanming Yang,et al.  Single-cell sequencing analysis characterizes common and cell-lineage-specific mutations in a muscle-invasive bladder cancer , 2012, GigaScience.

[49]  Ann M. Bailey,et al.  Incidental germline variants in 1000 advanced cancers on a prospective somatic genomic profiling protocol. , 2016, Annals of oncology : official journal of the European Society for Medical Oncology.

[50]  J. Bielas,et al.  Mutator phenotype in cancer: Timing and perspectives , 2005, Environmental and molecular mutagenesis.

[51]  Frida Rosengren,et al.  Multiregion Whole-Exome Sequencing Uncovers the Genetic Evolution and Mutational Heterogeneity of Early-Stage Metastatic Melanoma. , 2016, Cancer research.

[52]  R. Gillies,et al.  Exploiting evolutionary principles to prolong tumor control in preclinical models of breast cancer , 2016, Science Translational Medicine.

[53]  Yu Cao,et al.  Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing , 2014, Science.

[54]  Carlo C. Maley,et al.  Clonal evolution in cancer , 2012, Nature.

[55]  E. Letouzé,et al.  Analysis of the copy number profiles of several tumor samples from the same patient reveals the successive steps in tumorigenesis , 2010, Genome Biology.

[56]  N. André,et al.  Metronomics as Maintenance Treatment in Oncology: Time for Chemo-Switch , 2014, Front. Oncol..

[57]  Carlos Caldas,et al.  Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer , 2015, Nature Communications.

[58]  I. Fidler,et al.  Tumor heterogeneity and the biology of cancer invasion and metastasis. , 1978, Cancer research.

[59]  L. Pusztai,et al.  Cancer heterogeneity: implications for targeted therapeutics , 2013, British Journal of Cancer.

[60]  M. Nowak,et al.  Distant Metastasis Occurs Late during the Genetic Evolution of Pancreatic Cancer , 2010, Nature.

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

[62]  Joshua F. McMichael,et al.  Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft , 2010, Nature.

[63]  C. Thompson,et al.  Therapeutic targets in cancer cell metabolism and autophagy , 2012, Nature Biotechnology.

[64]  Manuel Hidalgo,et al.  Patient-derived xenograft models: an emerging platform for translational cancer research. , 2014, Cancer discovery.

[65]  X. Xie,et al.  Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell , 2012, Science.

[66]  M. Choti,et al.  Detection of Circulating Tumor DNA in Early- and Late-Stage Human Malignancies , 2014, Science Translational Medicine.

[67]  Markus J. van Roosmalen,et al.  Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer , 2011, Genome Biology.

[68]  S. Gestl,et al.  Tumor cell heterogeneity maintained by cooperating subclones in Wnt-driven mammary cancers , 2014, Nature.

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

[70]  Eric S. Lander,et al.  The genomic complexity of primary human prostate cancer , 2010, Nature.

[71]  Francesco Falciani,et al.  DNA Microarrays: a Powerful Genomic Tool for Biomedical and Clinical Research , 2007, Molecular medicine.

[72]  D. Pellman.  Cell biology: Aneuploidy and cancer , 2007, Nature.

[73]  A. Sidow,et al.  Concepts in solid tumor evolution. , 2015, Trends in genetics : TIG.

[74]  Rick Durrett.  Cancer modelling: a personal perspective , 2013 .

[75]  Robert E. Brown,et al.  Field effect in cancer-an update. , 2009, Annals of clinical and laboratory science.

[76]  M. Kimura.  Rare variant alleles in the light of the neutral theory. , 1983, Molecular biology and evolution.

[77]  V. P. Collins,et al.  Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics , 2013, Proceedings of the National Academy of Sciences.

[78]  N. Navin,et al.  Clonal Evolution in Breast Cancer Revealed by Single Nucleus Genome Sequencing , 2014, Nature.

[79]  Le Zhang,et al.  Simulating brain tumor heterogeneity with a multiscale agent-based model: Linking molecular signatures, phenotypes and expansion rate , 2006, Math. Comput. Model..

[80]  Aviv Regev,et al.  Whole exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer , 2014, Nature Biotechnology.

[81]  R. DePinho,et al.  Cancer chromosomes in crisis , 2004, Nature Genetics.

[82]  M Kimmel,et al.  Mathematical models of gene amplification with applications to cellular drug resistance and tumorigenicity. , 1990, Genetics.

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

[84]  J. Troge,et al.  Tumour evolution inferred by single-cell sequencing , 2011, Nature.

[85]  J. Troge,et al.  Inferring tumor progression from genomic heterogeneity. , 2010, Genome research.

[86]  Edward T. Bullmore,et al.  The Multilayer Connectome of Caenorhabditis elegans , 2016, PLoS Comput. Biol..

[87]  G. Bepler,et al.  Combination of p53 Cancer Vaccine with Chemotherapy in Patients with Extensive Stage Small Cell Lung Cancer , 2006, Clinical Cancer Research.

[88]  Ash A. Alizadeh,et al.  Toward understanding and exploiting tumor heterogeneity , 2015, Nature Medicine.

[89]  Ash A. Alizadeh,et al.  An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage , 2013, Nature Medicine.

[90]  Florian Markowetz,et al.  OncoNEM: inferring tumor evolution from single-cell sequencing data , 2016, Genome Biology.

[91]  Joel s. Brown,et al.  Evolutionary dynamics in cancer therapy. , 2011, Molecular pharmaceutics.

[92]  S. Noguchi,et al.  Clonal analysis of human gynecologic cancers by means of the polymerase chain reaction , 1994, International journal of cancer.

[93]  Huanming Yang,et al.  Single-Cell Exome Sequencing Reveals Single-Nucleotide Mutation Characteristics of a Kidney Tumor , 2012, Cell.

[94]  Serafim Batzoglou,et al.  Genome evolution during progression to breast cancer , 2013, Genome research.

[95]  David A Kessler,et al.  Resistance to chemotherapy: patient variability and cellular heterogeneity. , 2014, Cancer research.

[96]  Niko Beerenwinkel,et al.  BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies , 2015, Genome Biology.

[97]  Matthew Meyerson,et al.  CHROMOTHRIPSIS FROM DNA DAMAGE IN MICRONUCLEI , 2015, Nature.

[98]  Modeling neutral evolution using an infinite-allele Markov branching process , 2013 .

[99]  Franziska Michor,et al.  Intratumor Heterogeneity in Evolutionary Models of Tumor Progression , 2011, Genetics.

[100]  Obi L. Griffith,et al.  SciClone: Inferring Clonal Architecture and Tracking the Spatial and Temporal Patterns of Tumor Evolution , 2014, PLoS Comput. Biol..

[101]  C. Swanton,et al.  Re-Evaluating Clonal Dominance in Cancer Evolution. , 2016, Trends in cancer.

[102]  Tae-Min Kim,et al.  Subclonal Genomic Architectures of Primary and Metastatic Colorectal Cancer Based on Intratumoral Genetic Heterogeneity , 2015, Clinical Cancer Research.

[103]  Huanming Yang,et al.  Single-Cell Exome Sequencing and Monoclonal Evolution of a JAK2-Negative Myeloproliferative Neoplasm , 2012, Cell.

[104]  K. Korolev,et al.  Genetic demixing and evolution in linear stepping stone models. , 2010, Reviews of modern physics.

[105]  S. Nelson,et al.  Melanomas acquire resistance to B-RAF(V600E) inhibition by RTK or N-RAS upregulation , 2010, Nature.

[106]  N. McGranahan,et al.  Biological and therapeutic impact of intratumor heterogeneity in cancer evolution. , 2015, Cancer cell.

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

[108]  J. Troge,et al.  High-resolution ROMA CGH and FISH analysis of aneuploid and diploid breast tumors. , 2005, Cold Spring Harbor symposia on quantitative biology.

[109]  J. Mosser,et al.  ‘From the core to beyond the margin’: a genomic picture of glioblastoma intratumor heterogeneity , 2014, Oncotarget.

[110]  Carlos Caldas,et al.  Analysis of circulating tumor DNA to monitor metastatic breast cancer. , 2013, The New England journal of medicine.

[111]  Sohrab P. Shah,et al.  Dynamics of genomic clones in breast cancer patient xenografts at single-cell resolution , 2014, Nature.

[112]  F. Michor,et al.  Stochastic dynamics of cancer initiation , 2011, Physical biology.

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

[114]  Y. Kluger,et al.  TrAp: a tree approach for fingerprinting subclonal tumor composition , 2013, Nucleic acids research.

[115]  P. A. P. Moran,et al.  Random processes in genetics , 1958, Mathematical Proceedings of the Cambridge Philosophical Society.

[116]  Robert S. Kerbel,et al.  The anti-angiogenic basis of metronomic chemotherapy , 2004, Nature Reviews Cancer.

[117]  M. Loda,et al.  Establishment and genomic characterization of mouse xenografts of human primary prostate tumors. , 2010, The American journal of pathology.

[118]  Martin A. Nowak,et al.  Quantifying Clonal and Subclonal Passenger Mutations in Cancer Evolution , 2016, PLoS Comput. Biol..

[119]  Ali Bashashati,et al.  Divergent modes of clonal spread and intraperitoneal mixing in high-grade serous ovarian cancer , 2016, Nature Genetics.

[120]  Ali Bashashati,et al.  Distinct evolutionary trajectories of primary high-grade serous ovarian cancers revealed through spatial mutational profiling , 2013, The Journal of pathology.

[121]  H. Koyama,et al.  Clonal analysis of human breast cancer by means of the polymerase chain reaction. , 1992, Cancer research.

[122]  Jian Wang,et al.  Discovery of biclonal origin and a novel oncogene SLC12A5 in colon cancer by single-cell sequencing , 2014, Cell Research.

[123]  Franziska Michor,et al.  The Origins and Implications of Intratumor Heterogeneity , 2010, Cancer Prevention Research.

[124]  S. Corey,et al.  Stochastic Hypothesis of Transition from Inborn Neutropenia to AML: Interactions of Cell Population Dynamics and Population Genetics , 2013, Front. Oncol..

[125]  M. Kimmel,et al.  New explicit expressions for relative frequencies of single-nucleotide polymorphisms with application to statistical inference on population growth. , 2003, Genetics.

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

[127]  Shankar Vembu,et al.  PhyloWGS: Reconstructing subclonal composition and evolution from whole-genome sequencing of tumors , 2015, Genome Biology.

[128]  L. Loeb,et al.  Human cancers express mutator phenotypes: origin, consequences and targeting , 2011, Nature Reviews Cancer.

[129]  Joon-Oh Park,et al.  MET Amplification Leads to Gefitinib Resistance in Lung Cancer by Activating ERBB3 Signaling , 2007, Science.

[130]  S. Gartler,et al.  Glucose-6-Phosphate Dehydrogenase Mosaicism: Utilization as a Cell Marker in the Study of Leiomyomas , 1965, Science.

[131]  O. Hallatschek,et al.  Interfering Waves of Adaptation Promote Spatial Mixing , 2011, Genetics.

[132]  Joshy George,et al.  Whole–genome characterization of chemoresistant ovarian cancer , 2015, Nature.

[133]  Iman Hajirasouliha,et al.  A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data , 2014, Bioinform..

[134]  M. Stratton,et al.  Subclonal phylogenetic structures in cancer revealed by ultra-deep sequencing , 2008, Proceedings of the National Academy of Sciences.

[135]  Elaine R. Mardis,et al.  A decade’s perspective on DNA sequencing technology , 2011, Nature.

[136]  Martin A. Nowak,et al.  Genetic Progression and the Waiting Time to Cancer , 2007, PLoS Comput. Biol..

[137]  David M. Thomas,et al.  Next-Generation Sequence Analysis of Cancer Xenograft Models , 2013, PloS one.

[138]  C. Curtis,et al.  Many private mutations originate from the first few divisions of a human colorectal adenoma , 2015, The Journal of pathology.

[139]  B. Fingleton,et al.  Matrix Metalloproteinase Inhibitors and Cancer—Trials and Tribulations , 2002, Science.

[140]  Andrew Menzies,et al.  Subclonal diversification of primary breast cancer revealed by multiregion sequencing , 2015, Nature Medicine.

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

[142]  Robert A Gatenby,et al.  Application of Evolutionary Principles to Cancer Therapy. , 2015, Cancer research.

[143]  Arun K. Ramani,et al.  Spatial genomic heterogeneity in diffuse intrinsic pontine and midline high-grade glioma: implications for diagnostic biopsy and targeted therapeutics , 2016, Acta Neuropathologica Communications.

[144]  Z. Szallasi,et al.  Spatial and temporal diversity in genomic instability processes defines lung cancer evolution , 2014, Science.

[145]  S. Rosenberg.  Evolving responsively: adaptive mutation , 2001, Nature Reviews Genetics.

[146]  Iman Hajirasouliha,et al.  Fast and scalable inference of multi-sample cancer lineages , 2014, Genome Biology.

[147]  Rick Durrett,et al.  POPULATION GENETICS OF NEUTRAL MUTATIONS IN EXPONENTIALLY GROWING CANCER CELL POPULATIONS. , 2013, The annals of applied probability : an official journal of the Institute of Mathematical Statistics.

[148]  David Allard,et al.  Inhibition of Hedgehog Signaling Enhances Delivery of Chemotherapy in a Mouse Model of Pancreatic Cancer , 2009, Science.

[149]  Alex M. Fichtenholtz,et al.  Integrated genomic DNA/RNA profiling of hematologic malignancies in the clinical setting. , 2016, Blood.

[150]  R. Orecchia,et al.  Intratumor heterogeneity of chromosome 1, 7, 17, and 18 aneusomies obtained by FISH and association with flow cytometric DNA index in human colorectal adenocarcinomas. , 1999, Cytometry.

[151]  S. Gabriel,et al.  Advances in understanding cancer genomes through second-generation sequencing , 2010, Nature Reviews Genetics.

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

[153]  James Hicks,et al.  Tracing the tumor lineage , 2010, Molecular oncology.

[154]  Robert A Gatenby,et al.  Evolutionary Strategy for Systemic Therapy of Metastatic Breast Cancer: Balancing Response with Suppression of Resistance , 2014, Women's health.

[155]  Gabor T. Marth,et al.  SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization , 2014, Genome Biology.

[156]  E. Freese.  On the evolution of the base composition of DNA , 1962 .

[157]  B. Vogelstein,et al.  A genetic model for colorectal tumorigenesis , 1990, Cell.

[158]  C. Curtis,et al.  A Big Bang model of human colorectal tumor growth , 2015, Nature Genetics.

[159]  N. Navin.  Cancer genomics: one cell at a time , 2014, Genome Biology.

[160]  P. A. Futreal,et al.  Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing , 2014, Nature Genetics.

[161]  Shankar Vembu,et al.  Inferring clonal evolution of tumors from single nucleotide somatic mutations , 2012, BMC Bioinformatics.

[162]  Mark Cobbold,et al.  Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study , 2014, PLoS biology.