Comparative examination of various PCR-based methods for DNMT3A and IDH1/2 mutations identification in acute myeloid leukemia

Journal of Experimental and Clinical Cancer Research

Volumn 33, Issue 1, 2014, Pages

  Berenstein, Rimma ^a   Blau, Igor Wolfgang ^a   Kar, Asiye ^b   Cay, Ruhiye ^b   Sindram, Annette ^a   Seide, Claudia ^a   Blau, Olga ^a  

^a CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^b BEUTH UNIVERSITY OF APPLIED SCIENCES   (Germany)

Author keywords

AML; ARMS PCR; DNA sequencing; DNMT3A; Endonuclease restriction; HRM analysis; IDH1 2 mutations

Indexed keywords

DNA METHYLTRANSFERASE 3A; ISOCITRATE DEHYDROGENASE 1; ISOCITRATE DEHYDROGENASE 2; NUCLEOPHOSMIN; RESTRICTION ENDONUCLEASE;

ACUTE GRANULOCYTIC LEUKEMIA; ADOLESCENT; ADULT; AGED; AMPLIFICATION REFRACTORY MUTATION SYSTEM; ARTICLE; CONTROLLED STUDY; COST EFFECTIVENESS ANALYSIS; DNA SEQUENCE; EXON; FALSE NEGATIVE RESULT; FEMALE; HIGH RESOLUTION MELTING ANALYSIS; HUMAN; HUMAN TISSUE; LABORATORY TEST; MAJOR CLINICAL STUDY; MALE; MELTING POINT; PATIENT CARE; POINT MUTATION; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; REAL TIME POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; SANGER SEQUENCING; SCREENING TEST; SENSITIVITY ANALYSIS;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; DNA (CYTOSINE-5-)-METHYLTRANSFERASE; DNA MUTATIONAL ANALYSIS; FEMALE; HUMANS; ISOCITRATE DEHYDROGENASE; LEUKEMIA, MYELOID, ACUTE; MALE; MIDDLE AGED; MOLECULAR DIAGNOSTIC TECHNIQUES; POINT MUTATION; POLYMERASE CHAIN REACTION; RESTRICTION MAPPING; SENSITIVITY AND SPECIFICITY; YOUNG ADULT;

EID: 84902120217     PISSN: None     EISSN: 17569966     Source Type: Journal    
DOI: 10.1186/1756-9966-33-44     Document Type: Article

References (39)

1. Acute myeloid leukemia: 2013 update on risk-stratification and management. Estey EH, Am J Hematol 2013 88 4 318 327 23526416
2. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. Cancer Genome Atlas Research, N, N Engl J Med 2013 368 22 2059 2074 23634996
3. DNMT3A and IDH mutations in acute myeloid leukemia and other myeloid malignancies: associations with prognosis and potential treatment strategies. Im AP, Sehgal AR, Carroll MP, Smith BD, Tefferi A, Johnson DE, Boyiadzis M, Leukemia 2014 Epub ahead of print, doi:10.1038/leu.2014.124
4. DNA methyltransferases in hematologic malignancies. Li KK, Luo LF, Shen Y, Xu J, Chen Z, Chen SJ, Semin Hematol 2013 50 1 48 60 10.1053/j.seminhematol. 2013.01.005 23507483
5. DNMT3A mutations in acute myeloid leukemia. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, Kandoth C, Payton JE, Baty J, Welch J, Harris CC, Lichti CF, Townsend RR, Fulton RS, Dooling DJ, Koboldt DC, Schmidt H, Zhang Q, Osborne JR, Lin L, O'Laughlin M, McMichael JF, Delehaunty KD, McGrath SD, Fulton LA, Magrini VJ, Vickery TL, Hundal J, Cook LL, Conyers JJ, et al. N Engl J Med 2010 363 25 2424 2433 10.1056/NEJMoa1005143 21067377
6. Age-related prognostic impact of different types of DNMT3A mutations in adults with primary cytogenetically normal acute myeloid leukemia. Marcucci G, Metzeler KH, Schwind S, Becker H, Maharry K, Mrozek K, Radmacher MD, Kohlschmidt J, Nicolet D, Whitman SP, Wu YZ, Powell BL, Carter TH, Kolitz JE, Wetzler M, Carroll AJ, Baer MR, Moore JO, Caligiuri MA, Larson RA, Bloomfield CD, J Clin Oncol 2012 30 7 742 750 10.1200/JCO.2011.39.2092 22291079
7. Array-based genomic resequencing of human leukemia. Yamashita Y, Yuan J, Suetake I, Suzuki H, Ishikawa Y, Choi YL, Ueno T, Soda M, Hamada T, Haruta H, Takada S, Miyazaki Y, Kiyoi H, Ito E, Naoe T, Tomonaga M, Toyota M, Tajima S, Iwama A, Mano H, Oncogene 2010 29 25 3723 3731 10.1038/onc.2010.117 20400977
8. The role of mutations in epigenetic regulators in myeloid malignancies. Shih AH, Abdel-Wahab O, Patel JP, Levine RL, Nat Rev Cancer 2012 12 9 599 612 10.1038/nrc3343 22898539
9. Lack of association of IDH1, IDH2 and DNMT3A mutations with outcome in older patients with acute myeloid leukemia treated with hypomethylating agents. Dinardo CD, Patel KP, Garcia-Manero G, Luthra R, Pierce S, Borthakur G, Jabbour E, Kadia T, Pemmaraju N, Konopleva M, Faderl S, Cortes J, Kantarjian HM, Ravandi F, Leuk Lymphoma 2014 Epub ahead of print
10. Prognostic significance of IDH1 mutations in acute myeloid leukemia: a meta-analysis. Feng JH, Guo XP, Chen YY, Wang ZJ, Cheng YP, Tang YM, Am J Blood Res 2012 2 4 254 264 23226625
11. Clinical implications of novel mutations in epigenetic modifiers in AML. Abdel-Wahab O, Patel J, Levine RL, Hematol Oncol Clin North Am 2011 25 6 1119 1133 10.1016/j.hoc.2011.09.013 22093580
12. IDH mutations in glioma and acute myeloid leukemia. Dang L, Jin S, Su SM, Trends Mol Med 2010 16 9 387 397 10.1016/j.molmed.2010.07.002 20692206
13. What a difference a hydroxyl makes: mutant IDH, (R)-2-hydroxyglutarate, and cancer. Losman JA, Kaelin WG Jr, Genes Dev 2013 27 8 836 852 10.1101/gad.217406.113 23630074
14. Effects of DNMT1 silencing on malignant phenotype and methylated gene expression in cervical cancer cells. Zhang Y, Chen FQ, Sun YH, Zhou SY, Li TY, Chen R, J Exp Clin Cancer Res 2011 30 98 10.1186/1756-9966-30-98 21999220
15. DNMT3A mutations and clinical features in Chinese patients with acute myeloid leukemia. Lu Q, Chen Y, Wang H, Li Z, Cancer Cell Int 2013 13 1 1 10.1186/1475-2867-13-1 23305405
16. Prognostic impact of DNMT3A mutations in patients with intermediate cytogenetic risk profile acute myeloid leukemia. Markova J, Michkova P, Burckova K, Brezinova J, Michalova K, Dohnalova A, Maaloufova JS, Soukup P, Vitek A, Cetkovsky P, Schwarz J, Eur J Haematol 2012 88 2 128 135 10.1111/j.1600-0609. 2011.01716.x 21967546
17. Mutant DNMT3A: a marker of poor prognosis in acute myeloid leukemia. Ribeiro AF, Pratcorona M, Erpelinck-Verschueren C, Rockova V, Sanders M, Abbas S, Figueroa ME, Zeilemaker A, Melnick A, Lowenberg B, Valk PJ, Delwel R, Blood 2012 119 24 5824 5831 10.1182/blood-2011-07-367961 22490330
18. DNMT3A mutations in AML: a new prognostic factor? Schwarz J, Markova J, Leuk Res 2013 37 11 1432 1433 10.1016/j.leukres.2013.08.012 24045027
19. Incidence and prognostic influence of DNMT3A mutations in acute myeloid leukemia. Thol F, Damm F, Ludeking A, Winschel C, Wagner K, Morgan M, Yun H, Gohring G, Schlegelberger B, Hoelzer D, Lubbert M, Kanz L, Fiedler W, Kirchner H, Heil G, Krauter J, Ganser A, Heuser M, J Clin Oncol 2011 29 21 2889 2896 10.1200/JCO.2011.35.4894 21670448
20. Isocitrate dehydrogenase 1 (IDH1) mutation-specific microRNA signature predicts favorable prognosis in glioblastoma patients with IDH1 wild type. Wang Z, Bao Z, Yan W, You G, Wang Y, Li X, Zhang W, J Exp Clin Cancer Res 2013 32 1 59 10.1186/1756-9966-32-59 23988086
21. Type and location of isocitrate dehydrogenase mutations influence clinical characteristics and disease outcome of acute myeloid leukemia. Koszarska M, Bors A, Feczko A, Meggyesi N, Batai A, Csomor J, Adam E, Kozma A, Orban TI, Lovas N, Sipos A, Karaszi E, Dolgos J, Fekete S, Reichardt J, Lehoczky E, Masszi T, Tordai A, Andrikovics H, Leuk Lymphoma 2013 54 5 1028 1035 10.3109/10428194.2012.736981 23039322
22. Adverse impact of IDH1 and IDH2 mutations in primary AML: experience of the Spanish CETLAM group. Nomdedeu J, Hoyos M, Carricondo M, Esteve J, Bussaglia E, Estivill C, Ribera JM, Duarte R, Salamero O, Gallardo D, Pedro C, Aventin A, Brunet S, Sierra J, Leuk Res 2012 36 8 990 997 10.1016/j.leukres.2012.03.019 22520341
23. IDH1 and IDH2 mutations are frequent genetic alterations in acute myeloid leukemia and confer adverse prognosis in cytogenetically normal acute myeloid leukemia with NPM1 mutation without FLT3 internal tandem duplication. Paschka P, Schlenk RF, Gaidzik VI, Habdank M, Kronke J, Bullinger L, Spath D, Kayser S, Zucknick M, Gotze K, Horst HA, Germing U, Dohner H, Dohner K, J Clin Oncol 2010 28 22 3636 3643 10.1200/JCO.2010.28.3762 20567020
24. Therapy with demethylating agents significantly improves overall- and AML-free survival in patients with MDS classified as high-risk by IPSS or very high risk by IPSS-R and partial or total monosomy 7-results from a German Multicenter Study. Julie Schanz M, Friederike Braulke P, Katayoon Shirneshan M, Kathrin Nachtkamp M, Ulrich Germing M, Stephan Schmitz M, Peter Haas M, Michael Lübbert M, Müller-Thomas C, Katharina G, Uwe Platzbecker M, Florian Nolte M, Wolf-Karsten Hofmann M, Detlef Haase M, Blood 2013 122 21 2784 24009232
25. DNA demethylating agents and epigenetic therapy of cancer. Mani S, Herceg Z, Adv Genet 2010 70 327 340 20920754
26. The 2008 revision of the World Health Organization (WHO) classification of the myeloid neoplasms and leukemia: rationale and important changes. Vardiman JW, Thiele J, Arber DA, Brunning RD, Borovitz MJ, Porwit A, Harris NL, Le Beau MM, Hellström-Lindberg E, Tefferi A, Bloomfield CD, Blood 2009 114 5 937 951 10.1182/blood-2009-03-209262 19357394
27. Isolation of mononuclear cells from human cord blood by Ficoll-Paque density gradient. Jaatinen T, Laine J, Curr Protoc Stem Cell Biol 2007 Chapter 2 nit 2A.1 18785173
28. Recurrent DNMT3A R882 mutations in Chinese patients with acute myeloid leukemia and myelodysplastic syndrome. Lin J, Yao DM, Qian J, Chen Q, Qian W, Li Y, Yang J, Wang CZ, Chai HY, Qian Z, Xiao GF, Xu WR, PLoS One 2011 6 10 26906 10.1371/journal.pone.0026906 22066015
29. Molecular alterations of isocitrate dehydrogenase 1 and 2 (IDH1 and IDH2) metabolic genes and additional genetic mutations in newly diagnosed acute myeloid leukemia patients. Chotirat S, Thongnoppakhun W, Promsuwicha O, Boonthimat C, Auewarakul CU, J Hematol Oncol 2012 5 5 10.1186/1756-8722-5-5 22397365
30. Diagnostic testing for IDH1 and IDH2 variants in acute myeloid leukemia an algorithmic approach using high-resolution melting curve analysis. Patel KP, Barkoh BA, Chen Z, Ma D, Reddy N, Medeiros LJ, Luthra R, J Mol Diagn 2011 13 6 678 686 10.1016/j.jmoldx.2011.06.004 21889610
31. A comparison of Direct sequencing, Pyrosequencing, High resolution melting analysis, TheraScreen DxS, and the K-ras StripAssay for detecting KRAS mutations in non small cell lung carcinomas. Jancik S, Drabek J, Berkovcova J, Xu YZ, Stankova M, Klein J, Kolek V, Skarda J, Tichy T, Grygarkova I, Radzioch D, Hajduch M, J Exp Clin Cancer Res 2012 31 79 10.1186/1756-9966-31-79 22995035
32. DNMT3A mutation is a poor prognosis biomarker in AML: results of a meta-analysis of 4500 AML patients. Shivarov V, Gueorguieva R, Stoimenov A, Tiu R, Leuk Res 2013 37 11 1445 1450 10.1016/j.leukres.2013.07.032 23962568
33. Detection of t(14;18), P53 and RAS gene mutations and quantification of residual disease in patients with B-cell non-Hodgkin's lymphoma. Cikota BM, Tukic LJ, Tarabar OT, Magic ZM, J Exp Clin Cancer Res 2007 26 4 535 542 18365550 (Pubitemid 351157872)
34. Evaluation of high-resolution melting analysis as a diagnostic tool to detect the BRAF V600E mutation in colorectal tumors. Pichler M, Balic M, Stadelmeyer E, Ausch C, Wild M, Guelly C, Bauernhofer T, Samonigg H, Hoefler G, Dandachi N, J Mol Diagn 2009 11 2 140 147 10.2353/jmoldx.2009.080100 19213871
35. High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer. Krypuy M, Newnham GM, Thomas DM, Conron M, Dobrovic A, BMC Cancer 2006 6 295 10.1186/1471-2407-6-295 17184525 (Pubitemid 46178886)
36. A comparison of ARMS and DNA sequencing for mutation analysis in clinical biopsy samples. Ellison G, Donald E, McWalter G, Knight L, Fletcher L, Sherwood J, Cantarini M, Orr M, Speake G, J Exp Clin Cancer Res 2010 29 132 10.1186/1756-9966-29-132 20925915
37. Restriction digestion and real-time PCR (qAMP). Oakes CC, La Salle S, Trasler JM, Robaire B, Methods Mol Biol 2009 507 271 280 10.1007/978-1-59745- 522-0-20 18987821
38. 454 next generation-sequencing outperforms allele-specific PCR, Sanger sequencing, and pyrosequencing for routine KRAS mutation analysis of formalin-fixed, paraffin-embedded samples. Altimari A, de Biase D, De Maglio G, Gruppioni E, Capizzi E, Degiovanni A, D'Errico A, Pession A, Pizzolitto S, Fiorentino M, Tallini G, Onco Targets Ther 2013 6 1057 1064 23950653
39. Comparison of high resolution melting analysis, pyrosequencing, next generation sequencing and immunohistochemistry to conventional Sanger sequencing for the detection of p.V600E and non-p.V600E BRAF mutations. Ihle MA, Fassunke J, Konig K, Grunewald I, Schlaak M, Kreuzberg N, Tietze L, Schildhaus HU, Buttner R, Merkelbach-Bruse S, BMC Cancer 2014 14 13 10.1186/1471-2407-14-13 24410877