Single-Cell mutational profiling and clonal phylogeny in cancer

Genome Research

Volumn 23, Issue 12, 2013, Pages 2115-2125

  Potter, Nicola E ^a   Ermini, Luca ^a   Papaemmanuil, Elli ^b   Cazzaniga, Giovanni ^c   Vijayaraghavan, Gowri ^a   Titley, Ian ^a   Ford, Anthony ^a   Campbell, Peter ^b   Kearney, Lyndal ^a   Greaves, Mel ^a  

^a INSTITUTE OF CANCER RESEARCH   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY OF MILANO BICOCCA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIN C; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DAXX PROTEIN; TRANSCRIPTION FACTOR ETV6; TRANSCRIPTION FACTOR PAX5; TRANSCRIPTION FACTOR RUNX1;

ACUTE LYMPHOBLASTIC LEUKEMIA; ALLELE; ARTICLE; CELL SELECTION; CHIMERA; COPY NUMBER VARIATION; GENE DOSAGE; GENE EXPRESSION PROFILING; GENE FUSION; GENETIC VARIABILITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN CELL; LEUKEMIA CELL; MICROFLUIDICS; MISSENSE MUTATION; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; PHYLOGENY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; SINGLE CELL ANALYSIS; SINGLE NUCLEOTIDE POLYMORPHISM;

CELL LINE, TUMOR; CLONAL EVOLUTION; DNA COPY NUMBER VARIATIONS; GENETIC VARIATION; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MULTIPLEX POLYMERASE CHAIN REACTION; MUTATION; NEOPLASMS; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SINGLE-CELL ANALYSIS;

EID: 84890485711     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.159913.113     Document Type: Article

References (50)

1. Anderson K, Lutz C, van Delft FW, Bateman CM, Guo Y, Colman SM, Kempski H, Moorman AV, Titley I, Swansbury J, et al. 2011. Genetic variegation of clonal architecture and propagating cells in leukaemia. Nature 469: 356-361
2. Baslan T, Kendall J, Rodgers L, Cox H, Riggs M, Stepansky A, Troge J, Ravi K, Esposito D, Lakshmi B, et al. 2012. Genome-wide copy number analysis of single cells. Nat Protoc 7: 1024-1041
3. Bateman CM, Colman SM, Chaplin T, Young BD, Eden TO, Bhakta M, Gratias EJ, van Wering ER, Cazzaniga G, Harrison CJ, et al. 2010. Acquisition of genome-wide copy number alterations in monozygotic twins with acute lymphoblastic leukemia. Blood 115: 3553-3558
4. Chin L, Andersen JN, Futreal PA. 2011. Cancer genomics: From discovery science to personalized medicine. Nat Med 17: 297-303
5. Citri A, Pang ZP, Sudhof TC,Wernig M, Malenka RC. 2012. Comprehensive qPCR profiling of gene expression in single neuronal cells. Nat Protoc 7: 118-127
6. Clark J, Attard G, Jhavar S, Flohr P, Reid A, De-Bono J, Eeles R, Scardino P, Cuzick J, Fisher G, et al. 2008. Complex patterns of ETS gene alteration arise during cancer development in the human prostate. Oncogene 27: 1993-2003
7. Diaz LA Jr, Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, et al. 2012. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 486: 537-540
8. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpet P, et al. 2012. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366: 883-892
9. Greaves M. 2013. Cancer stem cells as 'units of selection.' Evol Appl 6: 102-108
10. Greaves M, Maley CC. 2012. Clonal evolution in cancer. Nature 481: 306-313
11. Horsley SW, Colman S, McKinley M, Bateman CM, Jenney M, Chaplin T, Young BD, Greaves M, Kearney L. 2008. Genetic lesions in a preleukemic aplasia phase in a child with acute lymphoblastic leukemia. Genes Chromosomes Cancer 47: 333-340
12. Huson DH, Scornavacca C. 2012. Dendroscope 3: An interactive tool for rooted phylogenetic trees and networks. Syst Biol 61: 1061-1067
13. Kitagawa Y, Inoue K, Sasaki S, Hayashi Y, Matsuo Y, Lieber MR,Mizoguchi H, Yokota J, Kohno T. 2002. Prevalent involvement of illegitimate V(D)J recombination in chromosome 9p21 deletions in lymphoid leukemia. J Biol Chem 277: 46289-46297
14. Klein CA, Stoecklein NH. 2009. Lessons from an aggressive cancer: Evolutionary dynamics in esophageal carcinoma. Cancer Res 69: 5285-5288
15. Klemm L, Duy C, Iacobucci I, Kuchen S, von Levetzow G, Feldhahn N, Henke N, Li Z, Hoffmann TK, Kim YM, et al. 2009. The B cell mutator AID promotes B lymphoid blast crises and drug resistance in chronic myeloid leukemia. Cancer Cell 16: 232-245
16. Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows- Wheeler transform. Bioinformatics 26: 589-595
17. LiuW, Laitinen S, Khan S, VihinenM, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, et al. 2009. Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer. Nat Med 15: 559-565
18. Longerich S, Basu U, Alt F, Storb U. 2006. AID in somatic hypermutation and class switch recombination. Curr Opin Immunol 18: 164-174
19. Maley CC, Galipeau PC, Finley JC, Wongsurawat VJ, Li X, Sanchez CA, Paulson TG, Blount PL, Risques RA, Rabinovitch PS, et al. 2006. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat Genet 38: 468-473
20. Margush T, McMorris FR. 1981. Consensus n-trees. Bull Math Biol 43: 239-244
21. Marusyk A, Almendro V, Polyak K. 2012. Intra-tumour heterogeneity: A looking glass for cancer? Nat Rev Cancer 12: 323-334
22. Merlo LMF, Pepper JW, Reid BJ, Maley CC. 2006. Cancer as an evolutionary and ecological process. Nat Rev Cancer 6: 924-935
23. Merlo LM, Shah NA, Li X, Blount PL, Vaughan TL, Reid BJ, Maley CC. 2010. A comprehensive survey of clonal diversity measures in Barrett's esophagus as biomarkers of progression to esophageal adenocarcinoma. Cancer Prev Res (Phila) 3: 1388-1397
24. Mroz EA, Tward AD, Pickering CR, Myers JN, Ferris RL, Rocco JW. 2013. High intratumor genetic heterogeneity is related to worse outcome in patients with head and neck squamous cell carcinoma. Cancer 119: 3034-3042
25. Mullighan CG, Goorha S, Radtke I, Miller CB, Coustan-Smith E, Dalton JD, Girtman K, Mathew S, Ma J, Pounds SB, et al. 2007. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446: 758-764
26. Mullighan CG, Phillips LA, Su X, Ma J, Miller CB, Shurtleff SA, Downing Jr. 2008. Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia. Science 322: 1377-1380
27. Mullighan CG, Collins-Underwood JR, Phillips LA, Loudin MG, Liu W, Zhang J, Ma J, Coustan-Smith E, Harvey RC, Willman CL, et al. 2009. Rearrangement of CRLF2 in B-progenitor- and Down syndromeassociated acute lymphoblastic leukemia. Nat Genet 41: 1243-1246
28. Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, et al. 2010. Inferring tumor progression from genomic heterogeneity. Genome Res 20: 68-80
29. Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, et al. 2011. Tumour evolution inferred by single-cell sequencing. Nature 472: 90-94
30. Nik-Zainal S, Van Loo P,Wedge DC, Alexandrov LB, Greenman CD, LauKW, Raine K, Jones D, Marshall J, Ramakrishna M, et al. 2012. The life history of 21 breast cancers. Cell 149: 994-1007
31. Notta F, Mullighan CG, Wang JC, Poeppl A, Doulatov S, Phillips LA, Ma J, Minden MD, Downing JR, Dick JE. 2011. Evolution of human BCR-ABL1 lymphoblastic leukaemia-initiating cells. Nature 469: 362-367
32. Nowell PC. 1976. The clonal evolution of tumor cell populations. Science 194: 23-28
33. Page RMD, Holmes EC. 1998. Molecular evolution: A phylogenetic approach. Wiley-Blackwell, New York
34. Park SY, Gönen M, Kim HJ, Michor F, Polyak K. 2010. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J Clin Invest 120: 636-644
35. Pina C, Fugazza C, Tipping AJ, Brown J, Soneji S, Teles J, Peterson C, Enver T. 2012. Inferring rules of lineage commitment in haematopoiesis. Nat Cell Biol 14: 287-294
36. R Core Team. 2013. R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. http://www.Rproject.org/
37. Stephens PJ, McBride DJ, Lin M-L, Varela I, Pleasance ED, Simpson JT, Stebbings LA, Leroy C, Edkins S, Mudie LJ, et al. 2009. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature 462: 1005-1010
38. Swanton C. 2012. Intratumor heterogeneity: Evolution through space and time. Cancer Res 72: 4875-4882
39. Swofford D. 2005. PAUP*: Phylogenetic analysis using parsimony (and other methods), Version 4.0, Beta 10. Sinauer, Sunderland, MA
40. Van Loo P, Nordgard SH, Lingjaerde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, et al. 2010. Allelespecific copy number analysis of tumors. Proc Natl Acad Sci 107: 16910-16915
41. Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, et al. 2011. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 469: 539-542
42. Vogelstein B, Papadopoulos N, Velculescu V, Zhou S, Diaz L, Kinzler K. 2013. Cancer genome landscapes. Science 339: 1546-1558
43. Waanders E, Scheijen B, van der Meer LT, van Reijmersdal SV, van Emst L, Kroeze Y, Sonneveld E, Hoogerbrugge PM, van Kessel AG, Van Leeuwen FN, et al. 2012. The origin and nature of tightly clustered BTG1 deletions in precursor B-cell acute lymphoblastic leukemia support a model of multiclonal evolution. PLoS Genet 8: e1002533
44. Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang W-Y, Hayes R, Chanock S, et al. 2009. High-throughput single nucleotide polymorphism genotyping using nanofluidic dynamic arrays. BMC Genomics 10: 561
45. Weaver S, Dube S, Mir A, Qin J, Sun G, Ramakrishnan R, Jones RC, Livak KJ. 2010. Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution. Methods 50: 271-276
46. Wiemels JL, Greaves M. 1999. Structure and possible mechanisms of TELAML1 gene fusions in childhood acute lymphoblastic leukemia. Cancer Res 59: 4075-4082
47. Wolman SR. 1986. Cytogenetic heterogeneity: Its role in tumor evolution. Cancer Genet Cytogenet 19: 129-140
48. Yates LR, Campbell PJ. 2012. Evolution of the cancer genome. Nat Rev Genet 13: 795-806
49. Ye K, SchulzMH, Long Q, Apweiler R, Ning Z. 2009. Pindel: A pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25: 2865- 2871
50. Zong C, Lu S, Chapman AR, Xie XS. 2012. Genome-wide detection of singlenucleotide and copy-number variations of a single human cell. Science 338: 1622-1626