The relative utilities of genome-wide, gene panel, and individual gene sequencing in clinical practice

Blood

Volumn 130, Issue 4, 2017, Pages 433-439

  Kuo, Frank C ^a,b,c   Mar, Brenton G ^b,c,d   Lindsley, R Coleman ^b,c   Lindeman, Neal I ^a,b,c  

^a BRIGHAM AND WOMEN S HOSPITAL   (United States)

^b DANA FARBER CANCER INSTITUTE   (United States)

^c HARVARD MEDICAL SCHOOL   (United States)

^d BOSTON CHILDREN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CLINICAL PRACTICE; EXOME; GENE SEQUENCE; GENOME ANALYSIS; GENOME-WIDE ASSOCIATION STUDY; GENOMICS; HEMATOLOGIC MALIGNANCY; HUMAN; LYMPHOMA; MOLECULAR DIAGNOSTICS; PRIORITY JOURNAL; REVIEW; WHOLE EXOME SEQUENCING; GENETICS; HEMATOLOGIC DISEASE; HIGH THROUGHPUT SEQUENCING; PROCEDURES;

EXOME; GENOME-WIDE ASSOCIATION STUDY; HEMATOLOGIC NEOPLASMS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS;

EID: 85026294405     PISSN: 00064971     EISSN: 15280020     Source Type: Journal    
DOI: 10.1182/blood-2017-03-734533     Document Type: Review

References (85)

1. Cleary ML, Chao J, Warnke R, Sklar J. Immunoglobulin gene rearrangement as a diagnostic criterion of B-cell lymphoma. Proc Natl Acad Sci USA. 1984;81(2):593-597.
2. Saiki RK, Scharf S, Faloona F, et al. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985;230(4732):1350-1354.
3. Sheikine Y, Kuo FC, Lindeman NI. Clinical and technical aspects of genomic diagnostics for precision oncology. J Clin Oncol. 2017;35(9): 929-933.
4. Li MM, Datto M, Duncavage EJ, et al. Standards and guidelines for the interpretation and reporting of sequence variants in cancer: a joint consensus recommendation of the Association for Molecular Pathology, American Society of Clinical Oncology, and College of American Pathologists. J Mol Diagn. 2017;19(1):4-23.
5. Bentley DR, Balasubramanian S, Swerdlow HP, et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 2008;456(7218):53-59.
6. Metzker ML. Sequencing technologies - the next generation. Nat Rev Genet. 2010;11(1):31-46.
7. Dong Z, Zhang J, Hu P, et al. Low-pass whole-genome sequencing in clinical cytogenetics: a validated approach. Genet Med. 2016;18(9): 940-948.
8. Arber DA, Orazi A, Hasserjian R, et al. The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 2016;127(20):2391-2406.
9. Kralovics R, Passamonti F, Buser AS, et al. A gain-of-function mutation of JAK2 in myeloproliferative disorders. N Engl J Med. 2005;352(17):1779-1790.
10. Bejar R, Stevenson K, Abdel-Wahab O, et al. Clinical effect of point mutations in myelodysplastic syndromes. N Engl J Med. 2011;364(26):2496-2506.
11. Mardis ER, Ding L, Dooling DJ, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. N Engl J Med. 2009;361(11): 1058-1066.
12. Kuo FC, Dong F. Next-generation sequencing-based panel testing for myeloid neoplasms. Curr Hematol Malig Rep. 2015;10(2):104-111.
13. Döhner H, Estey E, Grimwade D, et al. Diagnosis and management of AML in adults: 2017 ELN recommendations from an international expert panel. Blood. 2017;129(4):424-447.
14. Pabst T, Eyholzer M, Fos J, Mueller BU. Heterogeneity within AML with CEBPA mutations; only CEBPA double mutations, but not single CEBPA mutations are associated with favourable prognosis. Br J Cancer. 2009;100(8):1343-1346.
15. Devillier R, Mansat-De Mas V, Gelsi-Boyer V, et al. Role of ASXL1 and TP53 mutations in the molecular classification and prognosis of acute myeloid leukemias with myelodysplasia-related changes. Oncotarget. 2015;6(10):8388-8396.
16. Care RS, Valk PJM, Goodeve AC, et al. Incidence and prognosis of c-KIT and FLT3 mutations in core binding factor (CBF) acute myeloid leukaemias. Br J Haematol. 2003;121(5):775-777.
17. Tang JL, Hou HA, Chen CY, 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(26):5352-5361.
18. Schneider F, Hoster E, Unterhalt M, et al. The FLT3ITD mRNA level has a high prognostic impact in NPM1 mutated, but not in NPM1 unmutated, AML with a normal karyotype. Blood. 2012;119(19):4383-4386.
19. Liersch R, Müller-Tidow C, Berdel WE, Krug U. Prognostic factors for acute myeloid leukaemia in adults–biological significance and clinical use. Br J Haematol. 2014;165(1):17-38.
20. Bejar R, Stevenson KE, Caughey BA, et al. Validation of a prognostic model and the impact of mutations in patients with lower-risk myelodysplastic syndromes. J Clin Oncol. 2012;30(27):3376-3382.
21. Bejar R, Stevenson KE, Caughey B, et al. Somatic mutations predict poor outcome in patients with myelodysplastic syndrome after hematopoietic stem-cell transplantation. J Clin Oncol. 2014;32(25):2691-2698.
22. Klampfl T, Gisslinger H, Harutyunyan AS, et al. Somatic mutations of calreticulin in myeloproliferative neoplasms. N Engl J Med. 2013;369(25):2379-2390.
23. Nangalia J, Massie CE, Baxter EJ, et al. Somatic CALR mutations in myeloproliferative neoplasms with nonmutated JAK2. N Engl J Med. 2013; 369(25):2391-2405.
24. Pardanani AD, Levine RL, Lasho T, et al. MPL515 mutations in myeloproliferative and other myeloid disorders: a study of 1182 patients. Blood. 2006; 108(10):3472-3476.
25. Maxson JE, Gotlib J, Pollyea DA, et al. Oncogenic CSF3R mutations in chronic neutrophilic leukemia and atypical CML. N Engl J Med. 2013;368(19): 1781-1790.
26. Cui Y, Li B, Gale RP, et al. CSF3R, SETBP1 and CALR mutations in chronic neutrophilic leukemia. J Hematol Oncol. 20147:77.
27. Yaqub F. Inhibition of mutant IDH1 in acute myeloid leukaemia. Lancet Oncol. 2015;16(1):e9.
28. Wang F, Travins J, DeLaBarre B, et al. Targeted inhibition of mutant IDH2 in leukemia cells induces cellular differentiation. Science. 2013;340(6132): 622-626.
29. Inoue S, Li WY, Tseng A, Nolan GP, Cairns RA, Mak TW. Mutant IDH1 downregulates ATM and alters DNA repair and sensitivity to DNA damage independent of TET2. Cancer Cell. 2016:30(2): 337-348.
30. Jaiswal S, Fontanillas P, Flannick J, et al. Age-related clonal hematopoiesis associated with adverse outcomes. N Engl J Med. 2014;371(26): 2488-2498.
31. Kwok B, Hall JM, Witte JS, et al. MDS-associated somatic mutations and clonal hematopoiesis are common in idiopathic cytopenias of undetermined significance. Blood. 2015;126(21):2355-2361.
32. Delhommeau F, Dupont S, Della Valle V, et al. Mutation in TET2 in myeloid cancers. N Engl J Med. 2009;360(22):2289-2301.
33. Malcovati L, Papaemmanuil E, Ambaglio I, et al. Driver somatic mutations identify distinct disease entities within myeloid neoplasms with myelodysplasia. Blood. 2014;124(9):1513-1521.
34. Duncavage EJ, Tandon B. The utility of next-generation sequencing in diagnosis and monitoring of acute myeloid leukemia and myelodysplastic syndromes. Int J Lab Hematol. 2015;37(Suppl 1):115-121.
35. Wen XM, Hu JB, Yang J, et al. CEBPA methylation and mutation in myelodysplastic syndrome. Med Oncol. 2015;32(7):192.
36. Lindsley RC, Mar BG, Mazzola E, et al. Acute myeloid leukemia ontogeny is defined by distinct somatic mutations. Blood. 2015;125(9): 1367-1376.
37. Papaemmanuil E, Gerstung M, Bullinger L, et al. Genomic classification and prognosis in acute myeloid leukemia. N Engl J Med. 2016;374(23): 2209-2221.
38. Ivey A, Hills RK, Simpson MA, et al. Assessment of minimal residual disease in standard-risk AML. N Engl J Med. 2016;374:422-433.
39. Debarri H, Lebon D, Roumier C, et al. IDH1/2 but not DNMT3A mutations are suitable targets for minimal residual disease monitoring in acute myeloid leukemia patients: a study by the Acute Leukemia French Association. Oncotarget. 2015; 6(39):42345-42353.
40. Arock M, Sotlar K, Akin C, et al. KIT mutation analysis in mast cell neoplasms: recommendations of the European Competence Network on Mastocytosis. Leukemia. 2015;29(6):1223-1232.
41. De Matteis G, Zanotti R, Colarossi S, et al. The impact of sensitive KIT D816V detection on recognition of indolent Systemic Mastocytosis. Leuk Res. 2015;39(3):273-278.
42. Mochizuki H, Thomas R, Moroff S, Breen M. Genomic profiling of canine mast cell tumors identifies DNA copy number aberrations associated with KIT mutations and high histological grade. Chromosome Res. 2017;25(2): 129-143.
43. Nakao M, Yokota S, Iwai T, et al. Internal tandem duplication of the flt3 gene found in acute myeloid leukemia. Leukemia. 1996;10(12):1911-1918.
44. Patel JP, Gönen M, Figueroa ME, et al. Prognostic relevance of integrated genetic profiling in acute myeloid leukemia. N Engl J Med. 2012;366(12):1079-1089.
45. Gale RE, Green C, Allen C, et al; Medical Research Council Adult Leukaemia Working Party. The impact of FLT3 internal tandem duplication mutant level, number, size, and interaction with NPM1 mutations in a large cohort of young adult patients with acute myeloid leukemia. Blood. 2008;111(5):2776-2784.
46. Spencer DH, Abel HJ, Lockwood CM, et al. Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data. J Mol Diagn. 2013;15(1):81-93.
47. Rustagi N, Hampton OA, Li J, et al. ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. BMC Bioinformatics. 2016;17(1):188.
48. McKerrell T, Moreno T, Ponstingl H, et al. Development and validation of a comprehensive genomic diagnostic tool for myeloid malignancies. Blood. 2016;128(1):e1-e9.
49. Behdad A, Weigelin HC, Elenitoba-Johnson KSJ, Betz BL. A clinical grade sequencing-based assay for CEBPA mutation testing: report of a large series of myeloid neoplasms [published correction appears in J Mol Diagn. 2015;17(2):206]. J Mol Diagn. 2015;17(1):76-84.
50. Cheng DT, Cheng J, Mitchell TN, et al. Detection of mutations in myeloid malignancies through paired-sample analysis of microdroplet-PCR deep sequencing data. J Mol Diagn. 2014;16(5): 504-518.
51. Zhen C, Wang YL. Molecular monitoring of chronic myeloid leukemia: international standardization of BCR-ABL1 quantitation. J Mol Diagn. 2013;15(5):556-564.
52. Kalmanti L, Saussele S, Lauseker M, et al. Safety and efficacy of imatinib in CML over a period of 10 years: data from the randomized CML-study IV. Leukemia. 2015;29(5):1123-1132.
53. Soverini S, Colarossi S, Gnani A, et al; GIMEMA Working Party on Chronic Myeloid Leukemia. Contribution of ABL kinase domain mutations to imatinib resistance in different subsets of Philadelphia-positive patients: by the GIMEMA Working Party on Chronic Myeloid Leukemia. Clin Cancer Res. 2006;12(24):7374-7379.
54. Nicolini FE, Corm S, Lê Q-H, et al. Mutation status and clinical outcome of 89 imatinib mesylate-resistant chronic myelogenous leukemia patients: a retrospective analysis from the French intergroup of CML (Fi(phi)-LMC GROUP). Leukemia. 2006;20(6):1061-1066.
55. Swerdlow SH, Campo E, Pileri SA, et al. The 2016 revision of the World Health Organization classification of lymphoid neoplasms. 2016;127(20):2375-2391.
56. van Dongen JJM, Langerak AW, Brüggemann M, et al. Design and standardization of PCR primers and protocols for detection of clonal immunoglobulin and T-cell receptor gene recombinations in suspect lymphoproliferations: report of the BIOMED-2 Concerted Action BMH4-CT98-3936. Leukemia. 2003;17(12):2257-2317.
57. Ladetto M, Brüggemann M, Monitillo L, et al. Next-generation sequencing and real-time quantitative PCR for minimal residual disease detection in B-cell disorders. Leukemia. 2014;28(6):1299-1307.
58. Pulsipher MA, Carlson C, Langholz B, et al. IgH-V(D)J NGS-MRD measurement pre- and early post-allotransplant defines very low- and very high-risk ALL patients. Blood. 2015;125(22): 3501-3508.
59. Meyer C, Kowarz E, Hofmann J, et al. New insights to the MLL recombinome of acute leukemias. Leukemia. 2009;23(8):1490-1499.
60. Roberts KG, Mullighan CG. Genomics in acute lymphoblastic leukaemia: insights and treatment implications. Nat Rev Clin Oncol. 2015;12(6): 344-357.
61. Roberts KG, Li Y, Payne-Turner D, et al. Targetable kinase-activating lesions in Ph-like acute lymphoblastic leukemia. N Engl J Med. 2014;371(11):1005-1015.
62. Iacobucci I, Li Y, Roberts KG, et al. Truncating erythropoietin receptor rearrangements in acute lymphoblastic leukemia. Cancer Cell. 2016;29(2): 186-200.
63. Clappier E, Grardel N, Bakkus M, et al. IKZF1 deletion is an independent prognostic marker in childhood B-cell precursor acute lymphoblastic leukemia, and distinguishes patients benefiting from pulses during maintenance therapy: results of the EORTC Children’s Leukemia Group study 58951. Leukemia. 2015;29(11):2154-2161.
64. Kuiper RP, Waanders E, van der Velden VHJ, et al. IKZF1 deletions predict relapse in uniformly treated pediatric precursor B-ALL. Leukemia. 2010;24(7):1258-1264.
65. van der Veer A, Waanders E, Pieters R, et al. Independent prognostic value of BCR-ABL1-like signature and IKZF1 deletion, but not high CRLF2 expression, in children with B-cell precursor ALL. Blood. 2013;122(15):2622-2629.
66. Treon SP, Xu L, Yang G, et al. MYD88 L265P somatic mutation in Waldenström’s macroglobulinemia. N Engl J Med. 2012;367(9): 826-833.
67. Treon SP, Tripsas CK, Meid K, et al. Ibrutinib in previously treated Waldenström’s macroglobulinemia. N Engl J Med. 2015; 372(15):1430-1440.
68. Xu L, Hunter ZR, Tsakmaklis N, et al. Clonal architecture of CXCR4 WHIM-like mutations in Waldenström Macroglobulinaemia. Br J Haematol. 2016;172(5):735-744.
69. Xu L, Tsakmaklis N, Yang G, et al. Acquired mutations associated with ibrutinib resistance in Waldenstrom macroglobulinemia. Blood. 2017; 129(18):2519-2525.
70. Falini B, Martelli MP, Tiacci E. BRAF V600E mutation in hairy cell leukemia: from bench to bedside. Blood. 2016;128(15):1918-1927.
71. Badalian-Very G, Vergilio J-A, Degar BA, et al. Recurrent BRAF mutations in Langerhans cell histiocytosis. Blood. 2010;116(11):1919-1923.
72. Hervier B, Haroche J, Arnaud L, et al; French Histiocytoses Study Group. Association of both Langerhans cell histiocytosis and Erdheim-Chester disease linked to the BRAFV600E mutation. Blood. 2014;124(7):1119-1126.
73. Waterfall JJ, Arons E, Walker RL, et al. High prevalence of MAP2K1 mutations in variant and IGHV4-34-expressing hairy-cell leukemias. Nat Genet. 2014;46(1):8-10.
74. Mason EF, Brown RD, Szeto DP, et al. Detection of activating MAP2K1 mutations in atypical hairy cell leukemia and hairy cell leukemia variant. Leuk Lymphoma. 2017;58(1):233-236.
75. Richter J, Schlesner M, Hoffmann S, et al; ICGC MMML-Seq Project. Recurrent mutation of the ID3 gene in Burkitt lymphoma identified by integrated genome, exome and transcriptome sequencing. Nat Genet. 2012;44(12):1316-1320.
76. Love C, Sun Z, Jima D, et al. The genetic landscape of mutations in Burkitt lymphoma. Nat Genet. 2012;44(12):1321-1325.
77. Yoo HY, Sung MK, Lee SH, et al. A recurrent inactivating mutation in RHOA GTPase in angioimmunoblastic T cell lymphoma. Nat Genet. 2014;46(4):371-375.
78. Sakata-Yanagimoto M, Enami T, Yoshida K, et al. Somatic RHOA mutation in angioimmunoblastic T cell lymphoma. Nat Genet. 2014;46(2):171-175.
79. Palomero T, Couronné L, Khiabanian H, et al. Recurrent mutations in epigenetic regulators, RHOA and FYN kinase in peripheral T cell lymphomas. Nat Genet. 2014;46(2):166-170.
80. Puente XS, Pinyol M, Quesada V, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature. 2011; 475(7354):101-105.
81. Rossi D, Rasi S, Fabbri G, et al. Mutations of NOTCH1 are an independent predictor of survival in chronic lymphocytic leukemia. Blood. 2012; 119(2):521-529.
82. Quesada V, Conde L, Villamor N, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet. 2011;44(1):47-52.
83. Nadeu F, Delgado J, Royo C, et al. Clinical impact of clonal and subclonal TP53, SF3B1, BIRC3, NOTCH1, and ATM mutations in chronic lymphocytic leukemia. Blood. 2016;127(17): 2122-2130.
84. Pastore A, Jurinovic V, Kridel R, et al. Integration of gene mutations in risk prognostication for patients receiving first-line immunochemotherapy for follicular lymphoma: a retrospective analysis of a prospective clinical trial and validation in a population-based registry. Lancet Oncol. 2015;16(9):1111-1122.
85. Lamy T, Moignet A, Loughran TP Jr. LGL leukemia: from pathogenesis to treatment. Blood. 2017;129(9):1082-1094.