Characterization of gene mutations and copy number changes in acute myeloid leukemia using a rapid target enrichment protocol

Haematologica

Volumn 100, Issue 2, 2015, Pages 214-222

  Bolli, Niccolò ^a,b,c   Manes, Nicla ^a,c   McKerrell, Thomas ^a   Chi, Jianxiang ^d   Park, Naomi ^a   Gundem, Gunes ^a   Quail, Michael A ^a   Sathiaseelan, Vijitha ^a   Herman, Bram ^e   Crawley, Charles ^c   Craig, Jenny I O ^c   Conte, Natalie ^a,f   Grove, Carolyn ^a   Papaemmanuil, Elli ^a   Campbell, Peter J ^a   Varela, Ignacio ^g   Costeas, Paul ^d,h   Vassiliou, George S ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^c ADDENBROOKE S HOSPITAL   (United Kingdom)

^d The Center for the Study of Haematological Malignancies   (Cyprus)

^e AGILENT TECHNOLOGIES   (United Kingdom)

^f EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^g UNIVERSITY OF CANTABRIA   (Spain)

^h Karaiskakio Foundation   (Cyprus)

Author keywords

[No Author keywords available]

Indexed keywords

ACUTE GRANULOCYTIC LEUKEMIA; ARTICLE; BCOR GENE; BONE MARROW BIOPSY; CLINICAL ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNMT3A GENE; FLT3 GENE; GENE; GENE DUPLICATION; GENE MUTATION; GENE SEQUENCE; GENETIC ANALYSIS; HUMAN; IDH1 GENE; IDH2 GENE; KARYOTYPING; MULTIPLEX POLYMERASE CHAIN REACTION; NPM1 GENE; PROGNOSIS; TET2 GENE; ACUTE MYELOBLASTIC LEUKEMIA; ALGORITHM; CANCER STAGING; CASE CONTROL STUDY; COMPARATIVE STUDY; FOLLOW UP; GENETICS; HIGH THROUGHPUT SEQUENCING; MUTATION; PATHOLOGY; PROCEDURES;

TUMOR PROTEIN;

ALGORITHMS; CASE-CONTROL STUDIES; DNA COPY NUMBER VARIATIONS; FOLLOW-UP STUDIES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LEUKEMIA, MYELOID, ACUTE; MUTATION; NEOPLASM PROTEINS; NEOPLASM STAGING; PROGNOSIS;

EID: 84922129218     PISSN: 03906078     EISSN: 15928721     Source Type: Journal    
DOI: 10.3324/haematol.2014.113381     Document Type: Article

References (35)

1. Bennett JM, Catovsky D, Daniel MT, et al. Proposals for the classification of the acute leukaemias. French-American-British (FAB) co-operative group. British J Haematol. 1976;33(4):451-458.
2. Jaffe E, Harris N, Stein H, Vardiman J. Pathology and genetics of tumours of hematopoietic and lymphoid tissues. Lyon, France: IARC Press; 2001.
3. Döhner H, Estey EH, Amadori S, et al. Diagnosis and management of acute myeloid leukemia in adults: recommendations from an international expert panel, on behalf of the European LeukemiaNet. Blood. 2010;115(3):453-474.
4. Cancer Genome Atlas Research N. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368(22):2059-2074.
5. Patel JP, Gonen M, Figueroa ME, et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med. 2012;366(12):1079-1089.
6. Vardiman JW, Thiele J, Arber DA, et al. The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes. Blood. 2009;114(5):937-951.
7. Falini B, Martelli MP, Bolli N, et al. Acute myeloid leukemia with mutated nucle- ophosmin (NPM1): is it a distinct entity? Blood. 2011;117(4):1109-1120.
8. Dufour A, Schneider F, Metzeler KH, et al. Acute myeloid leukemia with biallelic CEBPA gene mutations and normal kary-otype represents a distinct genetic entity associated with a favorable clinical outcome. J Clin Oncol. 2010;28(4):570-577.
9. Döhner K, Schlenk RF, Habdank M, et al. Mutant nucleophosmin (NPM1) predicts favorable prognosis in younger adults with acute myeloid leukemia and normal cyto-genetics: interaction with other gene mutations. Blood. 2005;106(12):3740-3746.
10. Renneville A, Boissel N, Gachard N, et al. The favorable impact of CEBPA mutations in patients with acute myeloid leukemia isonly observed in the absence of associated cytogenetic abnormalities and FLT3 internal duplication. Blood. 2009;113(21):5090-5093.
11. Cairoli R, Beghini A, Grillo G, et al. Prognostic impact of c-KIT mutations in core binding factor leukemias: an Italian retrospective study. Blood. 2006;107(9): 3463-3468.
12. Schlenk RF, Döhner K, Krauter J, et al. Mutations and treatment outcome in cyto-genetically normal acute myeloid leukemia. N Engl J Med. 2008; 358(18):1909-1918.
13. Wang YY, Zhao LJ, Wu C F, et al. C-KIT mutation cooperates with full-length AML1-ETO to induce acute myeloid leukemia in mice. Proc Natl Acad Sci USA. 2011;108(6):2450-2455.
14. Chevalier N, Solari ML, Becker H, et al. Robust in vivo differentiation of t(8;21)-positive acute myeloid leukemia blasts to neutrophilic granulocytes induced by treatment with dasatinib. Leukemia. 2010; 24(10):1779-1781.
15. Leung AY, Man CH, Kwong YL. FLT3 inhibition: a moving and evolving target in acute myeloid leukaemia. Leukemia. 2013; 27(2):260-268.
16. Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53-59.
17. Ley TJ, Mardis ER, Ding L, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008;456(7218):66-72.
18. Conte N, Varela I, Grove C, et al. Detailed molecular characterisation of acute myeloid leukaemia with a normal kary-otype using targeted DNA capture. Leukemia. 2013;27(9):1820-1825.
19. Papaemmanuil E, Gerstung M, Malcovati L, et al. Clinical and biological implications of driver mutations in myelodysplastic syndromes. Blood. 2013;122(22):3616-3622.
20. Haferlach T, Nagata Y, Grossmann V, et al. Landscape of genetic lesions in 944 patients with myelodysplastic syndromes. Leukemia. 2014;28(2):241-247.
21. Berglund EC, Lindqvist CM, Hayat S, et al. Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment. BMC Genomics. 2013;14:856.
22. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26(5):589-595.
23. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26(6):841-842.
24. R Core Team. A language and environment for statistical computing: R Foundation for Statistical Computing; 2014.
25. Bolli N, Avet-Loiseau H, Wedge DC, et al. Heterogeneity of genomic evolution and mutational profiles in multiple myeloma. Nat Commun. 2014;5:2997.
26. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009; 25(21):2865-2871.
27. Genomes Project C, Abecasis GR, Auton A, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012;491(7422):56-65.
28. Shlush LI, Zandi S, Mitchell A, et al. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature. 2014;506(7488):328-333.
29. Spencer DH, Abel HJ, Lockwood CM, et al. Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data. J Mol Diagn. 2013;15(1):81-93.
30. Ding L, Ley TJ, Larson DE, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature. 2012;481(7382):506-510.
31. Lawrence MS, Stojanov P, Mermel CH, et al. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature. 2014;505(7484):495-501.
32. Luthra R, Patel KP, Reddy NG, et al. Next-generation sequencing-based multigene mutational screening for acute myeloid leukemia using MiSeq: applicability for diagnostics and disease monitoring. Haematologica. 2014;99(3):465-473.
33. Klco JM, Spencer DH, Miller CA, Griffith M. Functional Heterogeneity of Genetically Defined Subclones in Acute Myeloid Leukemia. Cancer Cell. 2014;25(3):379-392.
34. Schaub FX, Looser R, Li S, et al. Clonal analysis of TET2 and JAK2 mutations suggests that TET2 can be a late event in the progression of myeloproliferative neoplasms. Blood. 2010;115(10):2003-2007.
35. Busque L, Patel JP, Figueroa ME, et al. Recurrent somatic TET2 mutations in normal elderly individuals with clonal hematopoiesis. Nat Genet. 2012; 44(11): 1179-1181.