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Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia

Leukemia volume 25, pages 1908–1910 (2011)Cite this article

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The pathogenesis of chronic lymphocytic leukemia (CLL) remains incompletely understood.1 Although acquired chromosomal aberrations have been demonstrated to influence CLL biology and clinical behavior, it remains unclear what single gene defects other than p53 or ATM mutations cause or contribute to the CLL phenotype.2 In particular, recurrent gene mutations that are increasingly found in other hematological malignancies have not yet been identified in CLL. One recent CLL gene re-sequencing study reported the analysis of selected exons of 70 tyrosine kinase genes in 95 CLL patients and reported no somatically acquired mutations.3 Given the frequent identification of stereotypical immunoglobulin receptor genes in CLL, it has been suggested that antigen engagement of the B-cell receptor on CLL cells serves a critical role in CLL cell survival and CLL disease etiology. Further, the reduced expression of del(13q)(14)-resident microRNAs has been implicated in early CLL pathogenesis in a subset of cases.4 It is unknown whether CLL is driven by high-frequency recurrent gene mutations in one or a few genes.

To address this question for phosphokinases, we sequenced the coding regions of 515 kinases (for a listing of kinase genes sequenced and kinase family classification see Supplementary Table S1) in DNA from CD19+ sorted cells from 23 CLL cases.5 This research was approved by the University of Michigan Institutional Review Board (IRBMED #2004-0962), and written informed consent was obtained from all patients before enrollment. CD19+ and CD3+ cells were purified from CLL samples using FACS as described.6 Clinical and molecular characteristics of the CLL cases studied are summarized in Supplementary Table S2. Primers used for sequence analysis of 8308 distinct coding exons from 515 kinase genes were derived from prior sequencing projects.7 A summary of kinase gene reference sequences, primer sequences and exon coverage can be found in Supplementary Table S3. Amplicons were sequenced unidirectionally. All mutations were confirmed in independently generated amplicons. A total of 9003 amplicons were considered to be of high enough quality to be scored for mutations. To be considered eligible for scoring at least 50% of the bases in 50% of the samples for a given amplicon had to have a Phred score of 20 and it further had to be judged to be of good quality by visual inspection. A total of 8798 (97.7%) amplicons of the 9003 reported in this study had 20 or more samples that were scored for mutations. Mutations were scored in all 24 samples for 6763 (75%) of the amplicons, and only 12 amplicons had as few as 12 samples that were scored. The average Phred score for all of the bases in all of samples in all of amplicons reported in this study was 54.3.

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References

  1. Chiorazzi N, Rai KR, Ferrarini M . Chronic lymphocytic leukemia. N Engl J Med 2005; 352: 804–815.

    Article  CAS  Google Scholar 

  2. Dohner H, Stilgenbauer S, Benner A, Leupolt E, Krober A, Bullinger L et al. Genomic aberrations and survival in chronic lymphocytic leukemia. N Engl J Med 2000; 343: 1910–1916.

    Article  CAS  PubMed  Google Scholar 

  3. Brown JR, Levine RL, Thompson C, Basile G, Gilliland DG, Freedman AS . Systematic genomic screen for tyrosine kinase mutations in CLL. Leukemia 2008; 22: 1966–1969.

    Article  CAS  PubMed  Google Scholar 

  4. Calin GA, Dumitru CD, Shimizu M, Bichi R, Zupo S, Noch E et al. Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 2002; 99: 15524–15529.

    Article  CAS  PubMed  Google Scholar 

  5. Manning G, Whyte DB, Martinez R, Hunter T, Sudarsanam S . The protein kinase complement of the human genome. Science (New York, NY) 2002; 298: 1912–1934.

    Article  CAS  Google Scholar 

  6. Kujawski L, Ouillette P, Erba H, Saddler C, Jakubowiak A, Kaminski M et al. Genomic complexity identifies patients with aggressive chronic lymphocytic leukemia. Blood 2008; 112: 1993–2003.

    Article  CAS  PubMed  Google Scholar 

  7. Wood LD, Parsons DW, Jones S, Lin J, Sjoblom T, Leary RJ et al. The genomic landscapes of human breast and colorectal cancers. Science (New York, NY) 2007; 318: 1108–1113.

    Article  CAS  Google Scholar 

  8. Davies H, Bignell GR, Cox C, Stephens P, Edkins S, Clegg S et al. Mutations of the BRAF gene in human cancer. Nature 2002; 417: 949–954.

    Article  CAS  Google Scholar 

  9. Carter H, Chen S, Isik L, Tyekucheva S, Velculescu VE, Kinzler KW et al. Cancer-specific high-throughput annotation of somatic mutations: computational prediction of driver missense mutations. Cancer Res 2009; 69: 6660–6667.

    Article  CAS  PubMed  Google Scholar 

  10. Carter H, Samayoa J, Hruban RH, Karchin R . Prioritization of driver mutations in pancreatic cancer using cancer-specific high-throughput annotation of somatic mutations (CHASM). Cancer biol ther 2010; 10: 582–587.

    Article  CAS  PubMed  Google Scholar 

  11. Amit YaG D . Shape quantization and recognition with random trees. Neural Comput 1997; 9: 1545–1588.

    Article  Google Scholar 

  12. Breiman L . Random Forest. Machine Learning 2001; 45: 5–32.

    Article  Google Scholar 

  13. Forbes SA, Tang G, Bindal N, Bamford S, Dawson E, Cole C et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res 2010; 38 (Database issue): D652–D657.

    Article  CAS  PubMed  Google Scholar 

  14. Backert S, Gelos M, Kobalz U, Hanski ML, Bohm C, Mann B et al. Differential gene expression in colon carcinoma cells and tissues detected with a cDNA array. Int J Cancer 1999; 82: 868–874.

    Article  CAS  PubMed  Google Scholar 

  15. Rajagopalan H, Bardelli A, Lengauer C, Kinzler KW, Vogelstein B, Velculescu VE . Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status. Nature 2002; 418: 934.

    Article  CAS  PubMed  Google Scholar 

  16. Ding L, Getz G, Wheeler DA, Mardis ER, McLellan MD, Cibulskis K et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 2008; 455: 1069–1075.

    Article  CAS  PubMed  Google Scholar 

  17. Garnett MJ, Rana S, Paterson H, Barford D, Marais R . Wild-type and mutant B-RAF activate C-RAF through distinct mechanisms involving heterodimerization. Mol cell 2005; 20: 963–969.

    Article  CAS  PubMed  Google Scholar 

  18. Wan PT, Garnett MJ, Roe SM, Lee S, Niculescu-Duvaz D, Good VM et al. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell 2004; 116: 855–867.

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

This study was supported by the Virginia and DK Ludwig Fund for Cancer Research, National Institutes of Health Grants CA136537 (SNM), CA135877 (RK), CA 43460 (BV), the Translational Research Program of the Leukemia and Lymphoma Society of America (SM), NSF Grant DBI 0845275 (RK), DOD NDSEG fellowship 32 CFR 168a (HC) and the University of Michigan′s Cancer Center Support Grant (5 P30 CA46592). We are grateful for services provided by the microarray core of the University of Michigan Comprehensive Cancer Center.

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  1. X Zhang and M Reis: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Medicine, Massachusetts General Hospital, Boston, MA, USA

    X Zhang

  2. The Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins, Baltimore, MD, USA

    M Reis, M Li, L A Diaz Jr, V E Velculescu, N Papadopoulos, K W Kinzler & B Vogelstein

  3. Departments of Internal Medicine, Division of Hematology and Oncology University of Michigan, Ann Arbor, MI, USA

    R Khoriaty, Y Li, P Ouillette & S N Malek

  4. Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA

    J Samayoa, H Carter & R Karchin

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  1. X Zhang
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Correspondence to S N Malek.

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Zhang, X., Reis, M., Khoriaty, R. et al. Sequence analysis of 515 kinase genes in chronic lymphocytic leukemia. Leukemia 25, 1908–1910 (2011). https://doi.org/10.1038/leu.2011.163

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