Single-cell genotyping demonstrates complex clonal diversity in acute myeloid leukemia

Science Translational Medicine

Volumn 7, Issue 281, 2015, Pages

  Paguirigan, Amy L ^a   Smith, Jordan ^a   Meshinchi, Soheil ^a   Carroll, Martin ^b   Maley, Carlo ^c,d   Radich, Jerald P ^a  

^a USA   (United States)

^b UNIVERSITY OF PENNSYLVANIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ARTICLE; CANCER RECURRENCE; CELL POPULATION; CLINICAL PROTOCOL; CLONAL EVOLUTION; CONTROLLED STUDY; CONVERGENT EVOLUTION; FLT3 GENE; GENE FREQUENCY; GENE LOCUS; GENETIC VARIABILITY; HETEROZYGOTE; HOMOZYGOTE; NPM1 GENE; ONCOGENE; PRIORITY JOURNAL; PROCEDURES CONCERNING CELLS; SINGLE CELL GENOTYPING; ARTIFACT; GENETICS; GENOTYPING TECHNIQUE; HUMAN; LEUKEMIA, MYELOID, ACUTE; MUTATION; PATHOLOGY; PROCEDURES; RECURRENT DISEASE; REPRODUCIBILITY; SINGLE CELL ANALYSIS;

CD135 ANTIGEN; NUCLEAR PROTEIN; NUCLEOPHOSMIN;

ARTIFACTS; CLONAL EVOLUTION; FMS-LIKE TYROSINE KINASE 3; GENE FREQUENCY; GENOTYPING TECHNIQUES; HUMANS; LEUKEMIA, MYELOID, ACUTE; MUTATION; NUCLEAR PROTEINS; RECURRENCE; REPRODUCIBILITY OF RESULTS; SINGLE-CELL ANALYSIS;

EID: 84926512812     PISSN: 19466234     EISSN: 19466242     Source Type: Journal    
DOI: 10.1126/scitranslmed.aaa0763     Document Type: Article

References (24)

1. N. C. Turner, J. S. Reis-Filho, Genetic heterogeneity and cancer drug resistance. Lancet Oncol. 13, e178-e185 (2012).
2. M. Greaves, C. C. Maley, Clonal evolution in cancer. Nature 481, 306-313 (2012).
3. L. M. F. Merlo, N. A. Shah, X. Li, P. L. Blount, T. L. Vaughan, B. J. Reid, C. C. Maley, A comprehensive survey of clonal diversity measures in Barrett's esophagus as biomarkers of progression to esophageal adenocarcinoma. Cancer Prev. Res. 3, 1388-1397 (2010).
4. S. Y. Park, M. Gönen, H. J. Kim, F. Michor, K. Polyak, Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. J. Clin. Invest. 120, 636-644.
5. L. Ding, T. J. Ley, D. E. Larson, C. A. Miller, D. C. Koboldt, J. S. Welch, J. K. Ritchey, M. A. Young, T. Lamprecht, M. D. McLellan, J. F. McMichael, J. W. Wallis, C. Lu, D. Shen, C. C. Harris, D. J. Dooling, R. S. Fulton, L. L. Fulton, K. Chen, H. Schmidt, J. Kalicki-Veizer, V. J. Magrini, L. Cook, S. D. McGrath, T. L. Vickery, M. C. Wendl, S. Heath, M. A. Watson, D. C. Link, M. H. Tomasson, W. D. Shannon, J. E. Payton, S. Kulkarni, P. Westervelt, M. J. Walter, T. A. Graubert, E. R. Mardis, R. K. Wilson, J. F. DiPersio, Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 481, 506-510 (2012).
6. M. Jan, T. M. Snyder, M. R. Corces-Zimmerman, P. Vyas, I. L. Weissman, S. R. Quake, R. Majeti, Clonal evolution of pre-leukemic hematopoietic stem cells precedes human acute myeloid leukemia. Sci. Transl. Med. 4, 149ra118 (2012).
7. J. S. Welch, T. J. Ley, D. C. Link, C. A. Miller, D. E. Larson, D. C. Koboldt, L. D. Wartman, T. L. Lamprecht, F. Liu, J. Xia, C. Kandoth, R. S. Fulton, M. D. McLellan, D. J. Dooling, J. W. Wallis, K. Chen, C. C. Harris, H. K. Schmidt, J. M. Kalicki-Veizer, C. Lu, Q. Zhang, L. Lin, M. D. O'Laughlin, J. F. McMichael, K. D. Delehaunty, L. A. Fulton, V. J. Magrini, S. D. McGrath, R. T. Demeter, T. L. Vickery, J. Hundal, L. L. Cook, G. W. Swift, J. P. Reed, P. A. Alldredge, T. N. Wylie, J. R. Walker, M. A. Watson, S. E. Heath, W. D. Shannon, N. Varghese, R. Nagarajan, J. E. Payton, J. D. Baty, S. Kulkarni, J. M. Klco, M. H. Tomasson, P. Westervelt, M. J. Walter, T. A. Graubert, J. F. DiPersio, L. Ding, E. R. Mardis, R. K. Wilson, The origin and evolution of mutations in acute myeloid leukemia. Cell 150, 264-278 (2012).
8. M. J. Walter, D. Shen, L. Ding, J. Shao, D. C. Koboldt, K. Chen, D. E. Larson, M. D. McLellan, D. Dooling, R. Abbott, R. Fulton, V. Magrini, H. Schmidt, J. Kalicki-Veizer, M. O'Laughlin, X. Fan, M. Grillot, S. Witowski, S. Heath, J. L. Frater, W. Eades, M. Tomasson, P. Westervelt, J. F. DiPersio, D. C. Link, E. R. Mardis, T. J. Ley, R. K. Wilson, T. A. Graubert, Clonal architecture of secondary acute myeloid leukemia. N. Engl. J. Med. 366, 1090-1098 (2012).
9. M. Jan, R. Majeti, Clonal evolution of acute leukemia genomes. Oncogene 32, 135-140 (2013).
10. J. J. Keats, M. Chesi, J. B. Egan, V. M. Garbitt, S. E. Palmer, E. Braggio, S. Van Wier, P. R. Blackburn, A. S. Baker, A. Dispenzieri, S. Kumar, S. V. Rajkumar, J. D. Carpten, M. Barrett, R. Fonseca, A. K. Stewart, P. L. Bergsagel, Clonal competition with alternating dominance in multiple myeloma. Blood 120, 1067-1076 (2012).
11. J. M. Klco, D. H. Spencer, C. A. Miller, M. Griffith, T. L. Lamprecht, M. O'Laughlin, C. Fronick, V. Magrini, R. T. Demeter, R. S. Fulton, W. C. Eades, D. C. Link, T. A. Graubert, M. J. Walter, E. R. Mardis, J. F. Dipersio, R. K. Wilson, T. J. Ley, Functional heterogeneity of genetically defined subclones in acute myeloid leukemia. Cancer Cell 25, 379-392 (2014).
12. S. Yachida, S. Jones, I. Bozic, T. Antal, R. Leary, B. Fu, M. Kamiyama, R. H. Hruban, J. R. Eshleman, M. A. Nowak, V. E. Velculescu, K. W. Kinzler, B. Vogelstein, C. A. Iacobuzio-Donahue, Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature 467, 1114-1117 (2010).
13. M. Gerlinger, A. J. Rowan, S. Horswell, J. Larkin, D. Endesfelder, E. Gronroos, P. Martinez, N. Matthews, A. Stewart, P. Tarpey, I. Varela, B. Phillimore, S. Begum, N. Q. McDonald, A. Butler, D. Jones, K. Raine, C. Latimer, C. R. Santos, M. Nohadani, A. C. Eklund, B. Spencer-Dene, G. Clark, L. Pickering, G. Stamp, M. Gore, Z. Szallasi, J. Downward, P. A. Futreal, C. Swanton, Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883-892 (2012).
14. X. Wu, P. A. Northcott, A. Dubuc, A. J. Dupuy, D. J. H. Shih, H. Witt, S. Croul, E. Bouffet, D. W. Fults, C. G. Eberhart, L. Garzia, T. Van Meter, D. Zagzag, N. Jabado, J. Schwartzentruber, J. Majewski, T. E. Scheetz, S. M. Pfister, A. Korshunov, X.-N. Li, S. W. Scherer, Y.-J. Cho, K. Akagi, T. J. MacDonald, J. Koster, M. G. McCabe, A. L. Sarver, V. P. Collins, W. A. Weiss, D. A. Largaespada, L. S. Collier, M. D. Taylor, Clonal selection drives genetic divergence of metastatic medulloblastoma. Nature 482, 529-533 (2012).
15. A. E. O. Hughes, V. Magrini, R. Demeter, C. A. Miller, R. Fulton, L. L. Fulton, W. C. Eades, K. Elliott, S. Heath, P. Westervelt, L. Ding, D. F. Conrad, B. S. White, J. Shao, D. C. Link, J. F. DiPersio, E. R. Mardis, R. K. Wilson, T. J. Ley, M. J. Walter, T. A. Graubert, Clonal architecture of secondary acute myeloid leukemia defined by single-cell sequencing. PLOS Genet. 10, e1004462 (2014).
16. S. Meshinchi, F. R. Appelbaum, Structural and functional alterations of FLT3 in acute myeloid leukemia. Clin. Cancer Res. 15, 4263-4269 (2009).
17. J. P. Patel, M. Gönen, M. E. Figueroa, H. Fernandez, Z. Sun, J. Racevskis, P. Van Vlierberghe, I. Dolgalev, S. Thomas, O. Aminova, K. Huberman, J. Cheng, A. Viale, N. D. Socci, A. Heguy, A. Cherry, G. Vance, R. R. Higgins, R. P. Ketterling, R. E. Gallagher, M. Litzow, M. R. van den Brink, H. M. Lazarus, J. M. Rowe, S. Luger, A. Ferrando, E. Paietta, M. S. Tallman, A. Melnick, O. Abdel-Wahab, R. L. Levine, Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N. Engl. J. Med. 366, 1079-1089 (2012).
18. R. Rau, P. Brown, Nucleophosmin (NPM1) mutations in adult and childhood acute myeloid leukaemia: Towards definition of a new leukaemia entity. Hematol. Oncol. 27, 171-181 (2009).
19. C. Thiede, C. Steudel, B. Mohr, M. Schaich, U. Schäkel, U. Platzbecker, M. Wermke, M. Bornhäuser, M. Ritter, A. Neubauer, G. Ehninger, T. Illmer, Analysis of FLT3-activating mutations in 979 patients with acute myelogenous leukemia: Association with FAB subtypes and identification of subgroups with poor prognosis. Blood 99, 4326-4335 (2002).
20. S. Meshinchi, D. L. Stirewalt, T. A. Alonzo, T. J. Boggon, R. B. Gerbing, J. L. Rocnik, B. J. Lange, D. G. Gilliland, J. P. Radich, Structural and numerical variation of FLT3/ITD in pediatric AML. Blood 111, 4930-4933 (2008).
21. C. Thiede, S. Koch, E. Creutzig, C. Steudel, T. Illmer, M. Schaich, G. Ehninger, for the Deutsche Studieninitiative Leukämie (DSIL), Prevalence and prognostic impact of NPM1 mutations in 1485 adult patients with acute myeloid leukemia (AML). Blood 107, 4011-4020 (2006).
22. R. E. Gale, C. Green, C. Allen, A. J. Mead, A. K. Burnett, R. K. Hills, D. C. Linch; Medical Research Council Adult Leukaemia Working Party, The impact of FLT3 internal tandem duplication mutant level, number, size, and interaction with NPM1 mutations in a large cohort of young adult patients with acute myeloid leukemia. Blood 111, 2776-2784 (2008).
23. L. Li, E. Bailey, S. Greenblatt, D. Huso, D. Small, Loss of the wild-type allele contributes to myeloid expansion and disease aggressiveness in FLT3/ITD knockin mice. Blood 118, 4935-4945 (2011).
24. W. Qu, Z. Shen, D. Zhao, Y. Yang, C. Zhang, MFEprimer: Multiple factor evaluation of the specificity of PCR primers. Bioinformatics 25, 276-278 (2009).