DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Nature

Volumn 456, Issue 7218, 2008, Pages 66-72

  Ley, Timothy J ^a   Mardis, Elaine R ^a   Ding, Li ^a   Fulton, Bob ^a   McLellan, Michael D ^a   Chen, Ken ^a   Dooling, David ^a   Dunford Shore, Brian H ^a   McGrath, Sean ^a   Hickenbotham, Matthew ^a   Cook, Lisa ^a   Abbott, Rachel ^a   Larson, David E ^a   Koboldt, Dan C ^a   Pohl, Craig ^a   Smith, Scott ^a   Hawkins, Amy ^a   Abbott, Scott ^a   Locke, Devin ^a   Hillier, Ladeana W ^a,b   Miner, Tracie ^a   Fulton, Lucinda ^a   Magrini, Vincent ^a   Wylie, Todd ^a   Glasscock, Jarret ^a   Conyers, Joshua ^a   Sander, Nathan ^a   Shi, Xiaoqi ^a   Osborne, John R ^a   Minx, Patrick ^a   Gordon, David ^b   Chinwalla, Asif ^a   Zhao, Yu ^a   Ries, Rhonda E ^a   Payton, Jacqueline E ^a   Westervelt, Peter ^a   Tomasson, Michael H ^a   Watson, Mark ^a   Baty, Jack ^a   Ivanovich, Jennifer ^a   Heath, Sharon ^a   Shannon, William D ^a   Nagarajan, Rakesh ^a   Walter, Matthew J ^a   Link, Daniel C ^a   Graubert, Timothy A ^a   DiPersio, John F ^a   Wilson, Richard K ^a   more..

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BLOOD; CANCER; DISEASE TREATMENT; DNA; GENE EXPRESSION; GENOME; HEALTH EXPENDITURE; MUTATION; PROTEIN; SKIN; TUMOR;

ACUTE GRANULOCYTIC LEUKEMIA; ADULT; ARTICLE; CANCER GROWTH; CASE REPORT; DNA SEQUENCE; FEMALE; GENE DELETION; GENE FREQUENCY; GENE INSERTION; GENOME ANALYSIS; HUMAN; LEUKEMIA CELL; LEUKEMIA RELAPSE; MISSENSE MUTATION; MUTATIONAL ANALYSIS; NONSENSE MUTATION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; SKIN; SOMATIC MUTATION;

EID: 55549101623     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature07485     Document Type: Article

References (29)

1. Jemal, A. et al. Cancer statistics, 2008. CA Cancer J. Clin. 58, 71-96 (2008).
2. Owen, C., Barnett, M. & Fitzgibbon, J. Familial myelodysplasia and acute myeloid leukaemia - a review. Br. J. Haematol. 140, 123-132 (2008).
3. Mrozek, K., Marcucci, G., Paschka, P., Whitman, S. P. & Bloomfield, C. D. Clinical relevance of mutations and gene-expression changes in adult acute myeloid leukemia with normal cytogenetics: are we ready for a prognostically prioritized molecular classification? Blood 109, 431-448 (2007).
4. Loriaux, M. M. et al. High-throughput sequence analysis of the tyrosine kinome in acute myeloid leukemia. Blood 111, 4788-4796 (2008).
5. Tomasson, M. H. et al. Somatic mutations and germline sequence variants in the expressed tyrosine kinase genes of patients with de novo acute myeloid leukemia. Blood 111, 4797-4808 (2008).
6. Schoch, C. et al. Acute myeloid leukemias with reciprocal rearrangements can be distinguished by specific gene expression profiles. Proc. Natl Acad. Sci. USA 99, 10008-10013 (2002).
7. Bullinger, L. et al. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N. Engl. J. Med. 350, 1605-1616 (2004).
8. Valk, P. J. et al. Prognostically useful gene-expression profiles in acute myeloid leukemia. N. Engl. J. Med. 350, 1617-1628 (2004).
9. Mullighan, C. G. et al. Genome-wide analysis of genetic alterations in acute lymphoblastic leukaemia. Nature 446, 758-764 (2007).
10. Mullighan, C. G. et al. BCR-ABL1 lymphoblastic leukaemia is characterized by the deletion of Ikaros. Nature 453, 110-114 (2008).
11. Raghavan, M. et al. Genome-wide single nucleotide polymorphism analysis reveals frequent partial uniparental disomy due to somatic recombination in acute myeloid leukemias. Cancer Res. 65, 375-378 (2005).
12. Paulsson, K. et al. High-resolution genome-wide array-based comparative genome hybridization reveals cryptic chromosome changes in AML and MDS cases with trisomy 8 as the sole cytogenetic aberration. Leukemia 20, 840-846 (2006).
13. Rucker, F. G. et al. Disclosure of candidate genes in acute myeloid leukemia with complex karyotypes using microarray-based molecular characterization. J. Clin. Oncol. 24, 3887-3894 (2006).
14. Hillier, L. W. et al. Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5, 183-188 (2008).
15. Wheeler, D. A. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872-876 (2008).
16. Levy, S. et al. The diploid genome sequence of an individual human. PLoS Biol. 5, e254 (2007).
17. Byrd, J. C. et al. Pretreatment cytogenetic abnormalities are predictive of induction success, cumulative incidence of relapse, and overall survival in adult patients with de novo acute myeloid leukemia: results from Cancer and Leukemia Group B (CALGB 8461). Blood 100, 4325-4336 (2002).
18. Grimwade, D. et al. The importance of diagnostic cytogenetics on outcome in AML: analysis of 1,612 patients entered into the MRC AML 10 trial. The Medical Research Council Adult and Children's Leukaemia Working Parties. Blood 92, 2322-2333 (1998).
19. Mrozek, K., Heerema, N. A. & Bloomfield, C. D. Cytogenetics in acute leukemia. Blood Rev. 18, 115-136 (2004).
20. Wendl, M. C. & Wilson, R. K. Aspects of coverage in medical DNA sequencing. BMC Bioinformatics 9, 239 (2008).
21. Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res doi:10.1101/gr.078212.108 (in the press).
22. Quinlan, J. R. C4.5:Programs for Machine Learning 302 (Morgan Kaufmann Publishers, 1993).
23. Link, D. C. et al. Distinct patterns of mutations occurring in de novo AML versus AML arising in the setting of severe congenital neutropenia. Blood 110, 1648-1655 (2007).
24. Frohling, S. et al. Identification of driver and passenger mutations of FLT3 by highthroughput DNA sequence analysis and functional assessment of candidate alleles. Cancer Cell 12, 501-513 (2007).
25. Levis, M. & Small, D. FLT3: ITDoes matter in leukemia. Leukemia 17, 1738-1752 (2003).
26. Falini, B. et al. Cytoplasmic nucleophosmin in acute myelogenous leukemia with a normal karyotype. N. Engl. J. Med. 352, 254-266 (2005).
27. Thiede, C. et al. Prevalence and prognostic impact of NPM1 mutations in 1485 adult patients with acute myeloid leukemia (AML). Blood 107, 4011-4020 (2006).
28. den Besten, W., Kuo, M. L., Williams, R. T. & Sherr, C. J. Myeloid leukemia-associated nucleophosmin mutants perturb p53-dependent and independent activities of the Arf tumor suppressor protein. Cell Cycle 4, 1593-1598 (2005).
29. Kelly, L. M. et al. PML/RARa and FLT3-ITD induce an APL-like disease in a mouse model. Proc. Natl Acad. Sci. USA 99, 8283-8288 (2002).