Applicability of next-generation sequencing to decalcified formalin-fixed and paraffin-embedded chronic myelomonocytic leukaemia samples

International Journal of Clinical and Experimental Pathology

Volumn 7, Issue 4, 2014, Pages 1667-1676

  Bernard, Veronica ^a   Gebauer, Niklas ^a   Dinh, Thomas ^a   Stegemann, Judith ^a   Feller, Alfred C ^a   Merz, Hartmut ^a  

^a UNIVERSITY HOSPITAL SCHLESWIG HOLSTEIN   (Germany)

Author keywords

Chronic myelomonocytic leukaemia; Decalcified; Formalin fixed; Next generation sequencing; Paraffin embedded samples

Indexed keywords

CBL PROTEIN; CBL PROTEIN, HUMAN; DNA; DNA BINDING PROTEIN; FORMALDEHYDE; KRAS PROTEIN, HUMAN; ONCOPROTEIN; PARAFFIN; RAS PROTEIN; TET2 PROTEIN, HUMAN;

AGED; BONE MARROW CELL; CHEMISTRY; CHRONIC MYELOMONOCYTIC LEUKEMIA; COMPARATIVE STUDY; DNA SEQUENCE; FEMALE; GENETICS; HUMAN; MALE; MIDDLE AGED; MONONUCLEAR CELL; MUTATION; PATHOLOGY; PROCEDURES; VERY ELDERLY;

AGED; AGED, 80 AND OVER; BONE MARROW CELLS; DNA, NEOPLASM; DNA-BINDING PROTEINS; FEMALE; FORMALDEHYDE; HUMANS; LEUKEMIA, MYELOMONOCYTIC, CHRONIC; LEUKOCYTES, MONONUCLEAR; MALE; MIDDLE AGED; MUTATION; PARAFFIN EMBEDDING; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS C-CBL; RAS PROTEINS; SEQUENCE ANALYSIS, DNA;

EID: 84899537169     PISSN: None     EISSN: 19362625     Source Type: Journal    
DOI: None     Document Type: Article

References (31)

1. Nangalia J, Massie CE, Baxter EJ, Nice FL, Gundem G, Wedge DC, Avezov E, Li J, Kollmann K, Kent DG, Aziz A, Godfrey AL, Hinton J, Martincorena I, Van Loo P, Jones AV, Guglielmelli P, Tarpey P, Harding HP, Fitzpatrick JD, Goudie CT, Ortmann CA, Loughran SJ, Raine K, Jones DR, Butler AP, Teague JW, O'Meara S, McLaren S, Bianchi M, Silber Y, Dimitropoulou D, Bloxham D, Mudie L, Maddison M, Robinson B, Keohane C, Maclean C, Hill K, Orchard K, Tauro S, Du MQ, Greaves M, Bowen D, Huntly BJ, Harrison CN, Cross NC, Ron D, Vannucchi AM, Papaemmanuil E, Campbell PJ and Green AR. Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2. N Engl J Med 2013; 369: 2391-2405.
2. Klampfl T, Gisslinger H, Harutyunyan AS, Nivarthi H, Rumi E, Milosevic JD, Them NC, Berg T, Gisslinger B, Pietra D, Chen D, Vladimer GI, Bagienski K, Milanesi C, Casetti IC, Sant'An-tonio E, Ferretti V, Elena C, Schischlik F, Cleary C, Six M, Schalling M, Schonegger A, Bock C, Malcovati L, Pascutto C, Superti-Furga G, Cazzola M and Kralovics R. Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med 2013; 369: 2379-2390.
3. Swerdlow SH. WHO Classification of Tumors of Haematopoetic and Lymphoid Tissues. WHO, 2008.
4. Anon C. Chronic myelomonocytic leukemia: single entity or heterogeneous disorder?. A prospective multicenter study of 100 patients. Groupe Francais de Cytogenetique Hematologique. Cancer Genet Cytogenet 1991; 55: 57-65.
5. Cortes J. CMML: a biologically distinct myeloproliferative disease. Curr Hematol Rep 2003; 2: 202-208.
6. Germing U, Strupp C, Knipp S, Kuendgen A, Giagounidis A, Hildebrandt B, Aul C, Haas R, Gattermann N and Bennett JM. Chronic myelomonocytic leukemia in the light of the WHO proposals. Haematologica 2007; 92: 974-977.
7. Beran M, Wen S, Shen Y, Onida F, Jelinek J, Cortes J, Giles F and Kantarjian H. Prognostic factors and risk assessment in chronic myelomonocytic leukemia: validation study of the M.D. Anderson Prognostic Scoring System. Leuk Lymphoma 2007; 48: 1150-1160.
8. Onida F, Kantarjian HM, Smith TL, Ball G, Keating MJ, Estey EH, Glassman AB, Albitar M, Kwari MI and Beran M. Prognostic factors and scoring systems in chronic myelomonocytic leukemia: a retrospective analysis of 213 patients. Blood 2002; 99: 840-849.
9. Beran M, Shen Y, Onida F, Wen S, Kantarjian H and Estey E. Prognostic significance of monocytosis in patients with myeloproliferative disorders. Leuk Lymphoma 2006; 47: 417-423.
10. Fenaux P, Jouet JP, Zandecki M, Lai JL, Simon M, Pollet JP and Bauters F. Chronic and subacute myelomonocytic leukaemia in the adult: a report of 60 cases with special reference to prognostic factors. Br J Haematol 1987; 65: 101-106.
11. Kohlmann A, Grossmann V, Klein HU, Schindela S, Weiss T, Kazak B, Dicker F, Schnittger S, Dugas M, Kern W, Haferlach C and Haferlach T. 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.
12. Kohlmann A, Klein HU, Weissmann S, Bresolin S, Chaplin T, Cuppens H, Haschke-Becher E, Garicochea B, Grossmann V, Hanczaruk B, Hebestreit K, Gabriel C, Iacobucci I, Jansen JH, te Kronnie G, van de Locht L, Martinelli G, McGowan K, Schweiger MR, Timmermann B, Vandenberghe P, Young BD, Dugas M and Haferlach T. 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 2011; 25: 1840-1848.
13. Li Z, Cai X, Cai CL, Wang J, Zhang W, Petersen BE, Yang FC and Xu M. Deletion of Tet2 in mice leads to dysregulated hematopoietic stem cells and subsequent development of myeloid malignancies. Blood 2011; 118: 4509-4518.
14. Grand FH, Hidalgo-Curtis CE, Ernst T, Zoi K, Zoi C, McGuire C, Kreil S, Jones A, Score J, Metzgeroth G, Oscier D, Hall A, Brandts C, Serve H, Reiter A, Chase AJ and Cross NC. Frequent CBL mutations associated with 11q acquired uniparental disomy in myeloproliferative neoplasms. Blood 2009; 113: 6182-6192.
15. Bos JL. Ras oncogenes in human cancer: a review. Cancer Res 1989; 49: 4682-4689.
16. Tyner JW, Erickson H, Deininger MW, Willis SG, Eide CA, Levine RL, Heinrich MC, Gattermann N, Gilliland DG, Druker BJ and Loriaux MM. High-throughput sequencing screen reveals novel, transforming RAS mutations in myeloid leukemia patients. Blood 2009; 113: 1749-1755.
17. Gebauer N, Bernard V, Feller AC and Merz H. ID3 Mutations Are Recurrent Events in Double-hit B-Cell Lymphomas. Anticancer Res 2013; 33: 4771-4778.
18. Langemeijer SM, Kuiper RP, Berends M, Knops R, Aslanyan MG, Massop M, Stevens-Linders E, van Hoogen P, van Kessel AG, Raymakers RA, Kamping EJ, Verhoef GE, Verburgh E, Hagemeijer A, Vandenberghe P, de Witte T, van der Reijden BA and Jansen JH. Acquired mutations in TET2 are common in myelodysplastic syndromes. Nat Genet 2009; 41: 838-842.
19. Kosmider O, Gelsi-Boyer V, Cheok M, Grabar S, Della-Valle V, Picard F, Viguie F, Quesnel B, Beyne-Rauzy O, Solary E, Vey N, Hunault-Berger M, Fenaux P, Mansat-De Mas V, Delabesse E, Guardiola P, Lacombe C, Vainchenker W, Preudhomme C, Dreyfus F, Bernard OA, Birnbaum D and Fontenay M. TET2 mutation is an independent favorable prognostic factor in myelodysplastic syndromes (MDSs). Blood 2009; 114: 3285-3291.
20. Bacher U, Weissmann S, Kohlmann A, Schindela S, Alpermann T, Schnittger S, Kern W, Haferlach T and Haferlach C. TET2 deletions are a recurrent but rare phenomenon in myeloid malignancies and are frequently accompanied by TET2 mutations on the remaining allele. Br J Haematol 2012; 156: 67-75.
21. Grossmann V, Kohlmann A, Eder C, Haferlach C, Kern W, Cross NC, Haferlach T and Schnittger S. Molecular profiling of chronic myelomonocytic leukemia reveals diverse mutations in >80% of patients with TET2 and EZH2 being of high prognostic relevance. Leukemia 2011; 25: 877-879.
22. Kosmider O, Gelsi-Boyer V, Ciudad M, Racoeur C, Jooste V, Vey N, Quesnel B, Fenaux P, Bastie JN, Beyne-Rauzy O, Stamatoulas A, Dreyfus F, Ifrah N, de Botton S, Vainchenker W, Bernard OA, Birnbaum D, Fontenay M and Solary E. TET2 gene mutation is a frequent and adverse event in chronic myelomonocytic leukemia. Haematologica 2009; 94: 1676-1681.
23. Smith AE, Mohamedali AM, Kulasekararaj A, Lim Z, Gaken J, Lea NC, Przychodzen B, Mian SA, Nasser EE, Shooter C, Westwood NB, Strupp C, Gattermann N, Maciejewski JP, Germing U and Mufti GJ. 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.
24. Tefferi A, Levine RL, Lim KH, Abdel-Wahab O, Lasho TL, Patel J, Finke CM, Mullally A, Li CY, Pardanani A and Gilliland DG. Frequent TET2 mutations in systemic mastocytosis: clinical, KITD816V and FIP1L1-PDGFRA correlates. Leukemia 2009; 23: 900-904.
25. Tefferi A, Pardanani A, Lim KH, Abdel-Wahab O, Lasho TL, Patel J, Gangat N, Finke CM, Schwager S, Mullally A, Li CY, Hanson CA, Mesa R, Bernard O, Delhommeau F, Vainchenker W, Gilliland DG and Levine RL. TET2 mutations and their clinical correlates in polycythemia vera, essential thrombocythemia and myelofibrosis. Leukemia 2009; 23: 905-911.
26. Weissmann S, Alpermann T, Grossmann V, Kowarsch A, Nadarajah N, Eder C, Dicker F, Fasan A, Haferlach C, Haferlach T, Kern W, Schnittger S and Kohlmann A. Landscape of TET2 mutations in acute myeloid leukemia. Leukemia 2012; 26: 934-942.
27. Metzeler KH, Maharry K, Radmacher MD, Mrozek K, Margeson D, Becker H, Curfman J, Holland KB, Schwind S, Whitman SP, Wu YZ, Blum W, Powell BL, Carter TH, Wetzler M, Moore JO, Kolitz JE, Baer MR, Carroll AJ, Larson RA, Caligiuri MA, Marcucci G and Bloomfield CD. TET2 mutations improve the new European LeukemiaNet risk classification of acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol 2011; 29: 1373-1381.
28. Abdel-Wahab O, Mullally A, Hedvat C, Garcia-Manero G, Patel J, Wadleigh M, Malinge S, Yao J, Kilpivaara O, Bhat R, Huberman K, Thomas S, Dolgalev I, Heguy A, Paietta E, Le Beau MM, Beran M, Tallman MS, Ebert BL, Kantarjian HM, Stone RM, Gilliland DG, Crispino JD and Levine RL. Genetic characterization of TET1, TET2, and TET3 alterations in myeloid malignancies. Blood 2009; 114: 144-147.
29. Hoefig KP, Thorns C, Roehle A, Kaehler C, Wesche KO, Repsilber D, Branke B, Thiere M, Feller AC and Merz H. Unlocking pathology archives for microRNA-profiling. Anticancer Res 2008; 28: 119-123.
30. Hosein AN, Song S, McCart Reed AE, Jayanthan J, Reid LE, Kutasovic JR, Cummings MC, Waddell N, Lakhani SR, Chenevix-Trench G and Simpson PT. Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis. Lab Invest 2013; 93: 701-10.
31. Bennett JM, Catovsky D, Daniel MT, Flandrin G, Galton DA, Gralnick H, Sultan C and Cox C. The chronic myeloid leukaemias: guidelines for distinguishing chronic granulocytic, atypical chr-onic myeloid, and chronic myelomonocytic leukaemia. Proposals by the French-American-British Cooperative Leukaemia Group. Br J Haematol 1994; 87: 746-754.