The Interlaboratory RObustness of Next-generation sequencing (IRON) study: A deep sequencing investigation of TET2, CBL and KRAS mutations by an international consortium involving 10 laboratories

Leukemia

Volumn 25, Issue 12, 2011, Pages 1840-1848

  Kohlmann, A ^a   Klein, H U ^b   Weissmann, S ^a   Bresolin, S ^c   Chaplin, T ^d   Cuppens, H ^e   Haschke Becher, E ^f   Garicochea, B ^g   Grossmann, V ^a   Hanczaruk, B ^h   Hebestreit, K ^b   Gabriel, C ⁱ   Iacobucci, I ^j   Jansen, J H ^k   Te Kronnie, G ^c   Van De Locht, L ^k   Martinelli, G ^j   McGowan, K ^h   Schweiger, M R ^l   Timmermann, B ^l   Vandenberghe, P ^e   Young, B D ^d   Dugas, M ^b   Haferlach, T ^a   more..

^a MLL MUNICH LEUKEMIA LABORATORY   (Germany)

^b UNIVERSITY OF MÜNSTER   (Germany)

^c UNIVERSITY OF PADOVA   (Italy)

^d QUEEN MARY UNIVERSITY OF LONDON   (United Kingdom)

^e UNIVERSITY HOSPITALS LEUVEN   (Belgium)

^f KH Elisabethinen Linz GmbH   (Austria)

^g PONTIFICAL CATHOLIC UNIVERSITY OF RIO GRANDE DO SUL   (Brazil)

^h R and D Molecular Biology   (United States)

ⁱ sterreichisches Rotes Kreuz   (Austria)

^j UNIVERSITY OF BOLOGNA   (Italy)

^k RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^l MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

more..

Author keywords

454; amplicon; coverage; deep sequencing; mutation analysis; next generation sequencing

Indexed keywords

ACCURACY; ADULT; AGED; AMPLICON; ARTICLE; CBL GENE; CHRONIC MYELOMONOCYTIC LEUKEMIA; CLINICAL ARTICLE; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; FEMALE; GENE; GENE MUTATION; GENE SEQUENCE; HUMAN; HUMAN CELL; LABORATORY DIAGNOSIS; MALE; NEXT GENERATION SEQUENCING; ONCOGENE K RAS; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PYROSEQUENCING; REPRODUCIBILITY; TET2 GENE;

EID: 83555166249     PISSN: 08876924     EISSN: 14765551     Source Type: Journal    
DOI: 10.1038/leu.2011.155     Document Type: Article

References (25)

1. Metzker ML. Sequencing technologiesFthe next generation. Nat Rev Genet 2010; 11: 31-46.
2. Voelkerding KV, Dames S, Durtschi JD. Next generation sequencing for clinical diagnostics-principles and application to targeted resequencing for hypertrophic cardiomyopathy: a paper from the 2009 William Beaumont Hospital Symposium on Molecular Pathology. J Mol Diagn 2010; 12: 539-551.
3. Thomas RK, Greulich H, Yuza Y, Lee JC, Tengs T, Feng W et al. Detection of oncogenic mutations in the EGFR gene in lung adenocarcinoma with differential sensitivity to EGFR tyrosine kinase inhibitors. Cold Spring Harb Symp Quant Biol 2005; 70: 73-81. (Pubitemid 44124858)
4. Grossmann V, Kohlmann A, Zenger M, Schindela S, Eder C, Weissmann S et al. A deep-sequencing study of chronic myeloid leukemia patients in blast crisis (BC-CML) detects mutations in 76.9% of cases. Leukemia 2011; 25: 557-560.
5. Grossmann V, Kohlmann A, Eder C, Haferlach C, Kern W, Cross NC et al. Molecular profiling of chronic myelomonocytic leukemia reveals diverse mutations in480% of patients with TET2 and EZH2 being of high prognostic relevance. Leukemia 2011; 25: 877-879.
6. Kohlmann A, Grossmann V, Klein HU, Schindela S, Weiss T, Kazak B et al. Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8% of chronic myelomonocytic leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1. J Clin Oncol 2010; 28: 3858-3865.
7. Smith AE, Mohamedali AM, Kulasekararaj A, Lim Z, Gaken J, Lea NC et al. Next-generation sequencing of the TET2 gene in 355 MDS and CMML patients reveals low-abundance mutant clones with early origins, but indicates no definite prognostic value. Blood 2010; 116: 3923-3932.
8. Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009; 74: 393-403.
9. Holcomb CL, Hoglund B, Anderson MW, Blake LA, Bohme I, Egholm M et al. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 2011; 77: 206-217.
10. Delhommeau F, Dupont S, Della Valle V, James C, Trannoy S, Masse A et al. Mutation in TET2 in myeloid cancers. N Engl J Med 2009; 360: 2289-2301.
11. Bowen DT, Frew ME, Hills R, Gale RE, Wheatley K, Groves MJ et al. RAS mutation in acute myeloid leukemia is associated with distinct cytogenetic subgroups but does not influence outcome in patients younger than 60 years. Blood 2005; 106: 2113-2119. (Pubitemid 41291728)
12. Dunbar AJ, Gondek LP, O'Keefe CL, Makishima H, Rataul MS, Szpurka H et al. 250 K single nucleotide polymorphism array karyotyping identifies acquired uniparental disomy and homozygous mutations, including novel missense substitutions of c-Cbl, in myeloid malignancies. Cancer Res 2008; 68: 10349-10357.
13. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437: 376-380. (Pubitemid 41613494)
14. Thomas RK, Nickerson E, Simons JF, Janne PA, Tengs T, Yuza Y et al. Sensitive mutation detection in heterogeneous cancer specimens by massively parallel picoliter reactor sequencing. Nat Med 2006; 12: 852-855. (Pubitemid 44050078)
15. Klein HU, Bartenhagen C, Kohlmann A, Grossmann V, Ruckert C, Haferlach T et al. R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data. Bioinformatics 2011; 27: 1162-1163.
16. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2011; 39: D38-D51.
17. Noether GE. Introduction to Statistics: The Nonparametric Way. Springer: New York, 1991.
18. Wellek S. Testing Statistical Hypotheses of Equivalence. Chapman & Hall/CRC: Boca Raton, 2003.
19. Bland JM, Altman DG. Measuring agreement in method comparison studies. Stat Methods Med Res 1999; 8: 135-160. (Pubitemid 29425900)
20. Baccarani M, Pane F, Saglio G. Monitoring treatment of chronic myeloid leukemia. Haematologica 2008; 93: 161-169.
21. Ernst T, Erben P, Muller MC, Paschka P, Schenk T, Hoffmann J et al. Dynamics of BCR-ABL mutated clones prior to hematologic or cytogenetic resistance to imatinib. Haematologica 2008; 93: 186-192. (Pubitemid 351397706)
22. Zenz T, Eichhorst B, Busch R, Denzel T, Habe S, Winkler D et al. TP53 mutation and survival in chronic lymphocytic leukemia. J Clin Oncol 2010; 28: 4473-4479.
23. Kohlmann A, Grossmann V, Schindela S, Kern W, Haferlach C, Haferlach T et al. Ultra-deep next-generation sequencing detects RUNX1 mutations with unprecedented sensitivity and allows to monitor minimal residual disease in 116 samples from MDS and AML patients. Blood 2010; 116: 1691a.
24. Simen BB, Simons JF, Hullsiek KH, Novak RM, Macarthur RD, Baxter JD et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009; 199: 693-701.
25. Grossmann V, Schnittger S, Schindela S, Klein HU, Eder C, Dugas M et al. Strategy for robust detection of insertions, deletions, and point mutations in CEBPA, a GC-rich content gene, using 454 next-generation deep-sequencing technology. J Mol Diagn 2011; 13: 129-136.