Next-Generation Sequencing-Based Panel Testing for Myeloid Neoplasms

Current Hematologic Malignancy Reports

Volumn 10, Issue 2, 2015, Pages 104-111

  Kuo, Frank C ^a   Dong, Fei ^a  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

Acute myeloid leukemia; Myelodysplastic syndromes; Myeloid neoplasm; Next generation sequencing

Indexed keywords

COHESIN; ETNK1 PROTEIN; GUANINE NUCLEOTIDE BINDING PROTEIN BETA SUBUNIT; PHOSPHOTRANSFERASE; TRANSCRIPTION FACTOR ETV6; TRANSCRIPTION FACTOR GATA 1; TRANSCRIPTION FACTOR GATA 2; TRANSCRIPTION FACTOR RUNX1; UNCLASSIFIED DRUG;

CANCER GENETICS; CANCER PROGNOSIS; CANCER SCREENING; DNA METHYLATION; EPIGENETICS; EXON SKIPPING; GENETIC SCREENING; GENOMIC INSTABILITY; HEALTH CARE COST; HEMATOLOGIC MALIGNANCY; HUMAN; KARYOTYPE; LOSS OF FUNCTION MUTATION; MISSENSE MUTATION; MYELOID NEOPLASM; NEXT GENERATION SEQUENCING; ONCOGENE; REVIEW; SOMATIC MUTATION; SPLICEOSOME; TUMOR SUPPRESSOR GENE; TURNAROUND TIME; DNA SEQUENCE; GENETICS; HEMATOLOGIC NEOPLASMS; HIGH THROUGHPUT SEQUENCING; MYELOPROLIFERATIVE DISORDERS; PROCEDURES;

HEMATOLOGIC NEOPLASMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MYELOPROLIFERATIVE DISORDERS; SEQUENCE ANALYSIS, DNA;

EID: 84929959394     PISSN: 15588211     EISSN: 1558822X     Source Type: Journal    
DOI: 10.1007/s11899-015-0256-3     Document Type: Review

References (85)

1. Bonnet D, Dick JE. Human acute myeloid leukemia is organized as a hierarchy that originates from a primitive hematopoietic cell. Nat Med. 1997;3:730–7.
2. Wilson A, Trumpp A. Bone-marrow haematopoietic-stem-cell niches. Nat Rev Immunol. 2006;6:93–106.
3. Shlush LI, Zandi S, Mitchell A, Chen WC, Brandwein JM, Gupta V, et al. Identification of pre-leukaemic haematopoietic stem cells in acute leukaemia. Nature. 2014;506:328–33.
4. Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368:2059–74.
5. Steensma DP. The beginning of the end of the beginning in cancer genomics. N Engl J Med. 2013;368:2138–40.
6. Duncavage EJ, Abel HJ, Szankasi P, Kelley TW, Pfeifer JD. Targeted next generation sequencing of clinically significant gene mutations and translocations in leukemia. Mod Pathol. 2012;25:795–804.
7. OncoPlex [Internet]. Available from: http://tests.labmed.washington.edu/UW-OncoPlex.
8. FoundationOne [Internet]. Available from: http://foundationone.com/docs/FM_TechnicalOverview_HEM-I-001-20150105.pdf.
9. RHP URL [Internet]. Available from: http://bwhpathology.partners.org/rhp - camd.aspx.
10. Neogenomics [Internet]. Available from: http://www.neogenomics.com/neotype-Myeloid-Disorders-profile.htm.
11. Quest myeloid panel [Internet]. Available from: http://education.questdiagnostics.com/faq/FAQ160.
12. ARUP myeloid [Internet]. Available from: http://ltd.aruplab.com/Tests/Pub/2011117.
13. Knight myeloid [Internet]. Available from: http://www.knightdxlabs.com/home/test-details?id=GeneTrails+AML+MDS+Genotyping+Panel.
14. U penn CPD. Available from: http://www.pennmedicine.org/personalized-diagnostics/services.html.
15. BCW [Internet]. Available from: https://www.bcw.edu/cs/groups/public/documents/document/dgvz/df9k/∼edisp/ngs_hemeonc_test_desc.pdf.
16. Agilent [Internet]. Available from: http://www.chem.agilent.com/Library/datasheets/Public/AML DataSheet 5991-5058EN.pdf?cid=g011488.
17. Fulgent [Internet]. Available from: http://fulgentdiagnostics.com/test/cancer-2800/.
18. ResponseGenetics [Internet]. Available from: http://www.responsegenetics.com/wp-content/uploads/2014/04/NGS-Panels-Sheet-V3_JM-Rev.-5.23.14.pdf.
19. Genoptix [Internet]. Available from: http://www.genoptix.com/uploads/files/genoptix-biopharma-dos.pdf.
20. Rainedance [Internet]. Available from: http://raindancetech.com/thunderbolts-myeloid-panel/.
21. Trusight Myeloid [Internet]. Available from: http://www.illumina.com/products/trusight-myeloid.html.
22. Döhner K, Schlenk RF, Habdank M, Scholl C, Rücker FG, Corbacioglu A, et al. Mutant nucleophosmin (NPM1) predicts favorable prognosis in younger adults with acute myeloid leukemia and normal cytogenetics: interaction with other gene mutations. Blood. 2005;106:3740–6.
23. Thiede C, Koch S, Creutzig E, Steudel C, Illmer T, Schaich M, et al. Prevalence and prognostic impact of NPM1 mutations in 1485 adult patients with acute myeloid leukemia (AML). Blood. 2006;107:4011–20.
24. Falini B, Mecucci C, Tiacci E, Alcalay M, Rosati R, Pasqualucci L, et al. Cytoplasmic nucleophosmin in acute myelogenous leukemia with a normal karyotype. N Engl J Med. 2005;352:254–66.
25. Nakao M, Yokota S, Iwai T, Kaneko H, Horiike S, Kashima K, et al. Internal tandem duplication of the flt3 gene found in acute myeloid leukemia. Leukemia. 1996;10:1911–8.
26. Kottaridis PD, Gale RE, Frew ME, Harrison G, Langabeer SE, Belton AA, et al. The presence of a FLT3 internal tandem duplication in patients with acute myeloid leukemia (AML) adds important prognostic information to cytogenetic risk group and response to the first cycle of chemotherapy: analysis of 854 patients from the United Kingdom Medical Research Council AML 10 and 12 trials. Blood. 2001;98:1752–9.
27. Paschka P, Marcucci G, Ruppert AS, Mrózek K, Chen H, Kittles RA, et al. Adverse prognostic significance of KIT mutations in adult acute myeloid leukemia with inv(16) and t(8;21): a Cancer and Leukemia Group B study. J Clin Oncol. 2006;24:3904–11.
28. Care RS, Valk PJM, Goodeve AC, Abu-Duhier FM, Geertsma-Kleinekoort WMC, Wilson GA, et al. Incidence and prognosis of c-KIT and FLT3 mutations in core binding factor (CBF) acute myeloid leukaemias. Br J Haematol. 2003;121:775–7.
29. Yamamoto Y, Kiyoi H, Nakano Y, Suzuki R, Kodera Y, Miyawaki S, et al. Activating mutation of D835 within the activation loop of FLT3 in human hematologic malignancies. Blood. 2001;97:2434–9.
30. Abu-Duhier FM, Goodeve AC, Wilson GA, Care RS, Peake IR, Reilly JT. Identification of novel FLT-3 Asp835 mutations in adult acute myeloid leukaemia. Br J Haematol. 2001;113:983–8.
31. Maxson JE, Gotlib J, Pollyea DA, Fleischman AG, Agarwal A, Eide CA, et al. Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML. N Engl J Med. 2013;368:1781–90.
32. Kosmider O, Itzykson R, Chesnais V, Lasho T, Laborde R, Knudson R, et al. Mutation of the colony-stimulating factor-3 receptor gene is a rare event with poor prognosis in chronic myelomonocytic leukemia. Leukemia. 2013;27:1946–9.
33. Gits J, van Leeuwen D, Carroll HP, Touw IP, Ward AC. Multiple pathways contribute to the hyperproliferative responses from truncated granulocyte colony-stimulating factor receptors. Leukemia. 2006;20:2111–8.
34. Maxson JE, Luty SB, MacManiman JD, Abel ML, Druker BJ, Tyner JW. Ligand independence of the T618I mutation in the colony-stimulating factor 3 receptor (CSF3R) protein results from loss of O-linked glycosylation and increased receptor dimerization. J Biol Chem. 2014;289:5820–7.
35. Klampfl T, Gisslinger H, Harutyunyan AS, Nivarthi H, Rumi E, Milosevic JD, et al. Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med. 2013;369:2379–90.
36. Nangalia J, Massie CE, Baxter EJ, Nice FL, Gundem G, Wedge DC, et al. Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2. N Engl J Med. 2013;369:2391–405.
37. Tefferi A, Guglielmelli P, Lasho TL, Rotunno G, Finke C, Mannarelli C, et al. CALR and ASXL1 mutations-based molecular prognostication in primary myelofibrosis: an international study of 570 patients. Leukemia. 2014;28:1494–500. This study looked at large numbers of patients with and without CALR mutations with very long follow-up and confirmed the clinical characteristics of the CALR-mutated group and showed the similar outcome between these groups.
38. Ha JS, Kim YK. Calreticulin exon 9 mutations in myeloproliferative neoplasms. Ann Lab Med. 2015;31:22–7.
39. Vannucchi AM, Rotunno G, Bartalucci N, Raugei G, Carrai V, Balliu M, et al. Calreticulin mutation-specific immunostaining in myeloproliferative neoplasms: pathogenetic insight and diagnostic value. Leukemia. 2014;28:1–29.
40. Mardis ER, Ding L, Dooling DJ, Larson DE, McLellan MD, Chen K, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009;361:1058–66.
41. Figueroa ME, Abdel-Wahab O, Lu C, Ward PS, Patel J, Shih A, et al. Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell. 2010;18:553–67.
42. Delhommeau F, Dupont S, Della Valle V, James C, Trannoy S, Massé A, et al. Mutation in TET2 in myeloid cancers. N Engl J Med. 2009;360:2289–301.
43. Metzeler KH, Maharry K, Radmacher MD, Mrózek K, Margeson D, Becker H, et al. TET2 mutations improve the new European LeukemiaNet risk classification of acute myeloid leukemia: a Cancer and Leukemia Group B study. J Clin Oncol. 2011;29:1373–81.
44. Chou WC, Chou SC, Liu CY, Chen CY, Hou HA, Kuo YY, et al. TET2 mutation is an unfavorable prognostic factor in acute myeloid leukemia patients with intermediate-risk cytogenetics. Blood. 2011;118:3803–10.
45. Ley TJ, Ding L, Walter MJ, McLellan MD, Lamprecht T, Larson DE, et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363:2424–33.
46. Thol F, Damm F, Lüdeking A, Winschel C, Wagner K, Morgan M, et al. Incidence and prognostic influence of DNMT3A mutations in acute myeloid leukemia. J Clin Oncol. 2011;29:2889–96.
47. Gelsi-Boyer V, Trouplin V, Adélaïde J, Bonansea J, Cervera N, Carbuccia N, et al. Mutations of polycomb-associated gene ASXL1 in myelodysplastic syndromes and chronic myelomonocytic leukaemia. Br J Haematol. 2009;145:788–800.
48. Metzeler KH, Becker H, Maharry K, Radmacher MD, Kohlschmidt J, Mrózek K, et al. ASXL1 mutations identify a high-risk subgroup of older patients with primary cytogenetically normal AML within the ELN Favorable genetic category. Blood. 2011;118:6920–9.
49. Abdel-Wahab O, Adli M, LaFave LM, Gao J, Hricik T, Shih AH, et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 2012;22:180–93.
50. Piazza R, Valletta S, Winkelmann N, Redaelli S, Spinelli R, Pirola A, et al. Recurrent SETBP1 mutations in atypical chronic myeloid leukemia. 2013;45(1):18–24.
51. Makishima H, Yoshida K, Nguyen N, Przychodzen B, Sanada M, Okuno Y, et al. Somatic SETBP1 mutations in myeloid malignancies. Nat Genet. 2013;45:942–6.
52. Sakaguchi H, Okuno Y, Muramatsu H, Yoshida K, Shiraishi Y, Takahashi M, et al. Exome sequencing identifies secondary mutations of SETBP1 and JAK3 in juvenile myelomonocytic leukemia. Nat Genet. 2013;45:937–41.
53. Meggendorfer M, Bacher U, Alpermann T, Haferlach C, Kern W, Gambacorti-Passerini C, et al. SETBP1 mutations occur in 9% of MDS/MPN and in 4% of MPN cases and are strongly associated with atypical CML, monosomy 7, isochromosome i(17)(q10), ASXL1 and CBL mutations. Leukemia. 2013;27:1852–60.
54. Thol F, Suchanek KJ, Koenecke C, Stadler M, Platzbecker U, Thiede C, et al. SETBP1 mutation analysis in 944 patients with MDS and AML. Leukemia. 2013;27:2072–5.
55. Damm F, Itzykson R, Kosmider O, Droin N, Renneville A, Chesnais V, et al. SETBP1 mutations in 658 patients with myelodysplastic syndromes, chronic myelomonocytic leukemia and secondary acute myeloid leukemias. Leukemia. 2013;27:1401–3.
56. Schichman SA, Caligiuri MA, Gu Y, Strout MP, Canaani E, Bloomfield CD, et al. ALL-1 partial duplication in acute leukemia. Proc Natl Acad Sci U S A. 1994;91:6236–9.
57. Grossmann V, Tiacci E, Holmes AB, Kohlmann A, Martelli MP, Kern W, et al. Whole-exome sequencing identifies somatic mutations of BCOR in acute myeloid leukemia with normal karyotype. Blood. 2011;118:6153–63.
58. Damm F, Chesnais V, Nagata Y, Yoshida K, Scourzic L, Okuno Y, et al. BCOR and BCORL1 mutations in myelodysplastic syndromes and related disorders. Blood. 2013;122:3169–77.
59. Jankowska AM, Makishima H, Tiu RV, Szpurka H, Huang Y, Traina F, et al. Mutational spectrum analysis of chronic myelomonocytic leukemia includes genes associated with epigenetic regulation: UTX, EZH2, and DNMT3A. Blood. 2011;118:3932–41.
60. Van Haaften G, Dalgliesh GL, Davies H, Chen L, Bignell G, Greenman C, et al. Somatic mutations of the histone H3K27 demethylase gene UTX in human cancer. Nat Genet. 2009;41:521–3.
61. Haferlach C, Dicker F, Herholz H, Schnittger S, Kern W, Haferlach T. Mutations of the TP53 gene in acute myeloid leukemia are strongly associated with a complex aberrant karyotype. Leukemia. 2008;22:1539–41.
62. Krauth M, Alpermann T, Bacher U, Eder C, Dicker F, Ulke M, et al. WT1 mutations are secondary events in AML, show varying frequencies and impact on prognosis between genetic subgroups. Leukemia. 2014. doi: 10.1038/leu.2014.243. This large study examined more than 3000 cases of AML and found WT1 mutations in 5 % of patients with independent adverse effect of EFS besides age and FLT3-ITD status.
63. Van Vlierberghe P, Patel J, Abdel-Wahab O, Lobry C, Hedvat CV, Balbin M, et al. PHF6 mutations in adult acute myeloid leukemia. Leukemia. 2011;25:130–4.
64. Preudhomme C, Sagot C, Boissel N, Cayuela J-M, Tigaud I, de Botton S, et al. Favorable prognostic significance of CEBPA mutations in patients with de novo acute myeloid leukemia: a study from the Acute Leukemia French Association (ALFA). Blood. 2002;100:2717–23.
65. Fröhling S, Schlenk RF, Stolze I, Bihlmayr J, Benner A, Kreitmeier S, et al. CEBPA mutations in younger adults with acute myeloid leukemia and normal cytogenetics: prognostic relevance and analysis of cooperating mutations. J Clin Oncol. 2004;22:624–33.
66. Tang JL, Hou HA, Chen CY, Liu CY, Chou WC, Tseng MH, et al. AML1/RUNX1 mutations in 470 adult patients with de novo acute myeloid leukemia: prognostic implication and interaction with other gene alterations. Blood. 2009;114:5352–61.
67. Gaidzik VI, Bullinger L, Schlenk RF, Zimmermann AS, Rock J, Paschka P, et al. RUNX1 mutations in acute myeloid leukemia: results from a comprehensive genetic and clinical analysis from the AML study group. J Clin Oncol. 2011;29:1364–72.
68. Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, et al. Frequent pathway mutations of splicing machinery in myelodysplasia. Nature. 2011;478:64–9.
69. Graubert TA, Shen D, Ding L, Okeyo-Owuor T, Lunn CL, Shao J, et al. Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes. Nat Genet. 2011;44:53–7.
70. Adamia S, Bar-Natan M, Haibe-Kains B, Pilarski PM, Bach C, Pevzner S, et al. NOTCH2 and FLT3 gene mis-splicings are common events in patients with acute myeloid leukemia (AML): new potential targets in AML. Blood. 2014;123:2816–25.
71. Brooks AN, Choi PS, De Waal L, Sharifnia T, Imielinski M, Saksena G, et al. A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PLoS One. 2014;9(1)9-23.
72. Chen L, Kostadima M, Martens JHA, Canu G, Garcia SP, Turro E, et al. Transcriptional diversity during lineage commitment of human blood progenitors. Science. 2014;345(6204):1251033.
73. Papaemmanuil E, Cazzola M, Boultwood J, Malcovati L, Vyas P, Bowen D, et al. Somatic SF3B1 mutation in myelodysplasia with ring sideroblasts. N Engl J Med. 2011;365(15):1384–95.
74. Kon A, Shih L-Y, Minamino M, Sanada M, Shiraishi Y, Nagata Y, et al. Recurrent mutations in multiple components of the cohesin complex in myeloid neoplasms. Nat Genet. 2013;45:1232–7.
75. Thol F, Bollin R, Gehlhaar M, Walter C, Dugas M, Suchanek KJ, et al. Mutations in the cohesin complex in acute myeloid leukemia: clinical and prognostic implications. Blood. 2014;123:914–20.
76. Lindsley RC, Mar BG, Mazzola E, Grauman PV, Shareef S, Allen SL, et al. Acute myeloid leukemia ontogeny is defined by distinct somatic mutations. Blood. 2014;2014-11-610543. The classification of AML into de novo, secondary and therapy-related depends on the availability of detailed clinical history and is sometimes subject. This study looks for genetic classifiers and identify SF3B1, U2AF1, ZRSR2, STAG2, ASXL1, EZH2, BCOR and SRSF2 as marker for secondary AML which included some AML previously thought to be de novo or therapy-related.
77. Rahul K, Borhane G, Jung Bok L, Claudia I, Hopkins MB. Pleiotropic roles of Notch signaling in normal, malignant, and developmental hematopoiesis in the human. EMBO Rep. 2014;15:1128–38.
78. Wouters BJ, Jordà MA, Keeshan K, Louwers I, Erpelinck-Verschueren CAJ, Tielemans D, et al. Distinct gene expression profiles of acute myeloid/T-lymphoid leukemia with silenced CEBPA and mutations in NOTCH1. Blood. 2007;110:3706–14.
79. Gambacorti-Passerini C, Donadoni C, Parmiani A, Pirola A, Redaelli S, Signore G, et al. Recurrent ETNK1 mutations in atypical chronic myeloid leukemia. Blood. 2015;125:499–503.
80. Yoda A, Adelmant G, Tamburini J, Chapuy B, Shindoh N, Yoda Y, et al. Mutations in G protein β subunits promote transformation and kinase inhibitor resistance. Nat Med. 2015;21:71–5.
81. Genovese G, Kähler AK, Handsaker RE, Lindberg J, Rose SA, Bakhoum SF, et al. Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N Engl J Med. 2014;371:2477–87. This and the previous studies looked at large cohort of individuals with no known hematologic abnormalities and found variants in genes known to be associated with myeloid neoplasm. The frequency and allele fractions of these alterations increase with age. It remains to be seen whether these alterations are “pre-neoplastic” or not.
82. Jaiswal S, Fontanillas P, Flannick J, Manning A, Grauman PV, Mar BG, et al. Age-related clonal hematopoiesis associated with adverse outcomes. N Engl J Med. 2014;371:2488–98. This and the previous studies looked at large cohort of individuals with no known hematologic abnormalities and found variants in genes known to be associated with myeloid neoplasm. The frequency and allele fractions of these alterations increase with age. It remains to be seen whether these alterations are “pre-neoplastic” or not.
83. Sakai H, Fujigaki H, Mazur SJ, Appella E. Wild-type p53-induced phosphatase 1 (Wip1) forestalls cellular premature senescence at physiological oxygen levels by regulating DNA damage response signaling during DNA replication. Cell Cycle. 2014;13:14.
84. Zhang L, Chen LH, Wan H, Yang R, Wang Z, Feng J, et al. Exome sequencing identifies somatic gain-of-function PPM1D mutations in brainstem gliomas. Nat Genet. 2014;46:726–30.
85. Ruark E, Snape K, Humburg P, Loveday C, Bajrami I, Brough R, et al. Mosaic PPM1D mutations are associated with predisposition to breast and ovarian cancer. Nature. 2013;493:406–10.