1
Views
0
CrossRef citations to date
0
Altmetric
Review

The impact of next-generation sequencing for diagnosis and disease understanding of myeloid malignancies

, &
Pages 591-600 | Received 15 May 2024, Accepted 18 Jul 2024, Published online: 25 Jul 2024

References

  • Duncavage EJ, Bagg A, Hasserjian RP, et al. Genomic profiling for clinical decision making in myeloid neoplasms and acute leukemia. Blood. 2022;140(21):2228–2247. doi: 10.1182/blood.2022015853
  • Cho YU. The role of next-generation sequencing in hematologic malignancies. Blood Res. 2024;59(1):11. doi:10.1007/s44313-024-00010-0
  • Duployez N, Preudhomme C. Monitoring molecular changes in the management of myelodysplastic syndromes. Br J Haematol. 2024. doi: 10.1111/bjh.19614
  • Scott S, Travis D, Whitby L, et al. Measurement of BCR-ABL1 by RT-qPCR in chronic myeloid leukaemia: findings from an international EQA programme. Br J Haematol. 2017;177(3):414–422. doi:10.1111/bjh.14557
  • Hourigan CS. Achieving MRD negativity in AML: how important is this and how do we get there? Hematology Am Soc Hematol Educ Program. 2022;2022(1):9–14. doi: 10.1182/hematology.2022000323
  • Stahl M, Derkach A, Farnoud N, et al. Molecular predictors of immunophenotypic measurable residual disease clearance in acute myeloid leukemia. Am J Hematol. 2023;98(1):79–89. doi: 10.1002/ajh.26757
  • Uy GL, Duncavage EJ, Chang GS, et al. Dynamic changes in the clonal structure of MDS and AML in response to epigenetic therapy. Leukemia. 2017;31(4):872–881. doi: 10.1038/leu.2016.282
  • Akkari YMN, Baughn LB, Dubuc AM, et al. Guiding the global evolution of cytogenetic testing for hematologic malignancies. Blood. 2022;139(15):2273–2284. doi: 10.1182/blood.2021014309
  • Herlin MK, Yones SA, Kjeldsen E, et al. What is abnormal in normal karyotype acute myeloid leukemia in children? Analysis of the mutational landscape and prognosis of the TARGET-AML cohort. Genes (Basel). 2021;12(6):792. doi: 10.3390/genes12060792
  • Nimer SD. Is it important to decipher the heterogeneity of normal karyotype AML? Best Pract Res Clin Haematol. 2008;21(1):43–52. doi:10.1016/j.beha.2007.11.010
  • Grimwade D, Hills RK, Moorman AV, et al. Refinement of cytogenetic classification in acute myeloid leukemia: determination of prognostic significance of rare recurring chromosomal abnormalities among 5876 younger adult patients treated in the united kingdom medical research council trials. Blood. 2010;116(3):354–365. doi: 10.1182/blood-2009-11-254441
  • Godley L, Sukhanova M, Raca G, et al. Cytogenetics and genetic abnormalities. In: Kaushansky K, Prchal J, and Press O, et al., editors. Williams Hematology. New York, NY: McGraw Hill Education; 2016. p. 173–190.
  • Schanz J, Tüchler H, Solé F, et al. New comprehensive cytogenetic scoring system for primary myelodysplastic syndromes (MDS) and oligoblastic acute myeloid leukemia after MDS derived from an international database merge. J Clin Oncol. 2012;30(8):820–829. doi: 10.1200/JCO.2011.35.6394
  • Cumbo C, Tota G, Anelli L, et al. TP53 in Myelodysplastic syndromes: recent biological and clinical findings. Int J Mol Sci. 2020;21(10):3432. doi: 10.3390/ijms21103432
  • Arber DA, Orazi A, Hasserjian RP, et al. International consensus classification of myeloid neoplasms and acute leukemias: integrating morphologic, clinical, and genomic data. Blood. 2022;140(11):1200–1228. doi: 10.1182/blood.2022015850
  • Khoury JD, Solary E, Abla O, et al. The 5th edition of the world health organization classification of haematolymphoid tumours: myeloid and Histiocytic/Dendritic neoplasms. Leukemia. 2022;36(7):1703–1719. doi: 10.1038/s41375-022-01613-1
  • Sahoo SS, Kozyra EJ, Wlodarski MW. Germline predisposition in myeloid neoplasms: unique genetic and clinical features of GATA2 deficiency and SAMD9/SAMD9L syndromes. Best Pract Res Clin Haematol. 2020;33(3):101197. doi: 10.1016/j.beha.2020.101197
  • Sahoo SS, Pastor VB, Goodings C, et al. Clinical evolution, genetic landscape and trajectories of clonal hematopoiesis in SAMD9/SAMD9L syndromes. Nat Med. 2021;27(10):1806–1817. doi: 10.1038/s41591-021-01511-6
  • Yang H, Garcia-Manero G, Sasaki K, et al. High-resolution structural variant profiling of myelodysplastic syndromes by optical genome mapping uncovers cryptic aberrations of prognostic and therapeutic significance. Leukemia. 2022;36(9):2306–2316. doi: 10.1038/s41375-022-01652-8
  • Levy B, Baughn LB, Akkari Y, et al. Optical genome mapping in acute myeloid leukemia: a multicenter evaluation. Blood Adv. 2023;7(7):1297–1307. doi: 10.1182/bloodadvances.2022007583
  • Kivioja J, Malani D, Kumar A, et al. FLT3-ITD allelic ratio and HLF expression predict FLT3 inhibitor efficacy in adult AML. Sci Rep. 2021;11(1):23565. doi: 10.1038/s41598-021-03010-7
  • Ayala R, Carreño-Tarragona G, Barragán E, et al. Impact of FLT3–ITD mutation status and its ratio in a cohort of 2901 patients undergoing upfront intensive chemotherapy: a PETHEMA registry study. Cancers (Basel). 2022;14(23):5799. doi: 10.3390/cancers14235799
  • Stone RM, Mandrekar SJ, Sanford BL, et al. Midostaurin plus chemotherapy for acute myeloid leukemia with a FLT3 mutation. N Engl J Med. 2017;377(5):454–464. doi: 10.1056/NEJMoa1614359
  • Zhao JC, Agarwal S, Ahmad H, et al. A review of FLT3 inhibitors in acute myeloid leukemia. Blood Rev. 2022;52:100905. doi:10.1016/j.blre.2021.100905
  • Salmoiraghi S, Cavagna R, Zanghì P, et al. High throughput molecular characterization of normal karyotype acute myeloid leukemia in the context of the prospective trial 02/06 of the northern italy leukemia group (NILG). Cancers (Basel). 2020;12(8):2242. doi: 10.3390/cancers12082242
  • Liquori A, Lesende I, Palomo L, et al. A single-run next-generation sequencing (NGS) assay for the simultaneous detection of both gene mutations and large chromosomal abnormalities in patients with Myelodysplastic syndromes (MDS) and related myeloid neoplasms. Cancers (Basel). 2021;13(8):1947. doi: 10.3390/cancers13081947
  • Mareschal S, Palau A, Lindberg J, et al. Challenging conventional karyotyping by next-generation karyotyping in 281 intensively treated patients with AML. Blood Adv. 2021;5(4):1003–1016. doi: 10.1182/bloodadvances.2020002517
  • Bidet A, Quessada J, Cuccuini W, et al. Cytogenetics in the management of acute myeloid leukemia and histiocytic/dendritic cell neoplasms: guidelines from the groupe francophone de cytogénétique Hématologique (GFCH). Curr Res Transl Med. 2023;71(4):103421. doi: 10.1016/j.retram.2023.103421
  • Arber DA, Campo E, Jaffe ES. Advances in the classification of myeloid and lymphoid neoplasms. Virchows Arch. 2023;482(1):1–9. doi:10.1007/s00428-022-03487-1
  • Weinberg OK, Porwit A, Orazi A, et al. The international consensus classification of acute myeloid leukemia. Virchows Arch. 2023;482(1):27–37. doi: 10.1007/s00428-022-03430-4
  • Döhner H, Wei AH, Appelbaum FR, et al. Diagnosis and management of AML in adults: 2022 recommendations from an international expert panel on behalf of the ELN. Blood. 2022;140(12):1345–1377. doi: 10.1182/blood.2022016867
  • Cheng WY, Li JF, Zhu YM, et al. Transcriptome-based molecular subtypes and differentiation hierarchies improve the classification framework of acute myeloid leukemia. Proc Natl Acad Sci USA. 2022;119(49):e2211429119. doi: 10.1073/pnas.2211429119
  • Samorodnitsky E, Jewell BM, Hagopian R, et al. Evaluation of hybridization capture versus amplicon-based methods for whole-exome sequencing. Hum Mutat. 2015;36(9):903–914. doi: 10.1002/humu.22825
  • Hung SS, Meissner B, Chavez EA, et al. Assessment of capture and amplicon-based approaches for the development of a targeted next-generation sequencing pipeline to personalize lymphoma management. J Mol Diagn. 2018;20(2):203–214. doi: 10.1016/j.jmoldx.2017.11.010
  • Casbon JA, Osborne RJ, Brenner S, et al. A method for counting PCR template molecules with application to next-generation sequencing. Nucleic Acids Res. 2011;39(12):e81. doi:10.1093/nar/gkr217
  • Hiatt JB, Pritchard CC, Salipante SJ, et al. Single molecule molecular inversion probes for targeted, high-accuracy detection of low-frequency variation. Genome Res. 2013;23(5):843–854. doi: 10.1101/gr.147686.112
  • Ye K, Schulz MH, Long Q, et al. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics. 2009;25(21):2865–2871. doi:10.1093/bioinformatics/btp394
  • Chen X, Schulz-Trieglaff O, Shaw R, et al. Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics. 2016;32(8):1220–1222. doi: 10.1093/bioinformatics/btv710
  • Eisfeldt J, Vezzi F, Olason P, et al. TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Res. 2017;6:664. doi:10.12688/f1000research.11168.1
  • Cameron DL, Schröder J, Penington JS, et al. GRIDSS: sensitive and specific genomic rearrangement detection using positional de bruijn graph assembly. Genome Res. 2017;27(12):2050–2060. doi: 10.1101/gr.222109.117
  • Cucchi DGJ, Denys B, Kaspers GJL, et al. RNA-based FLT3-ITD allelic ratio is associated with outcome and ex vivo response to FLT3 inhibitors in pediatric AML. Blood. 2018;131(22):2485–2489. doi: 10.1182/blood-2017-12-819508
  • Pollyea DA, Altman JK, Assi R, et al. Acute myeloid leukemia, version 3.2023, NCCN clinical practice guidelines in oncology. J Natl Compr Canc Netw. 2023;21(5):503–513. doi: 10.6004/jnccn.2023.0025
  • Kim B, Kim E, Lee ST, et al. Detection of recurrent, rare, and novel gene fusions in patients with acute leukemia using next-generation sequencing approaches. Hematol Oncol. 2020;38(1):82–88. doi: 10.1002/hon.2709
  • Qu X, Yeung C, Coleman I, et al. Comparison of four next generation sequencing platforms for fusion detection: oncomine by ThermoFisher, AmpliSeq by illumina, FusionPlex by ArcherDX, and QIAseq by QIAGEN. Cancer Genet. 2020;243:11–18. doi:10.1016/j.cancergen.2020.02.007
  • Arindrarto W, Borràs DM, de Groen RAL, et al. Comprehensive diagnostics of acute myeloid leukemia by whole transcriptome RNA sequencing. Leukemia. 2021;35(1):47–61. doi: 10.1038/s41375-020-0762-8
  • Heydt C, Wölwer CB, Velazquez Camacho O, et al. Detection of gene fusions using targeted next-generation sequencing: a comparative evaluation. BMC Med Genomics. 2021;14(1):62. doi: 10.1186/s12920-021-00909-y
  • Cilloni D, Petiti J, Rosso V, et al. Digital PCR in myeloid malignancies: ready to replace quantitative PCR? Int J Mol Sci. 2019;20(9):2249. doi: 10.3390/ijms20092249
  • Coccaro N, Tota G, Anelli L, et al. Digital PCR: a reliable tool for analyzing and monitoring hematologic malignancies. Int J Mol Sci. 2020;21(9):3141. doi: 10.3390/ijms21093141
  • Brunetti C, Anelli L, Zagaria A, et al. Droplet digital PCR is a reliable tool for monitoring minimal residual disease in acute promyelocytic leukemia. J Mol Diagn. 2017;19(3):437–444. doi: 10.1016/j.jmoldx.2017.01.004
  • Chin L, Wong CYG, Gill H. Targeting and monitoring acute myeloid leukaemia with nucleophosmin-1 (NPM1) mutation. Int J Mol Sci. 2023;24(4):3161. doi: 10.3390/ijms24043161
  • Cabrera K, Gole J, Leatham B, et al. Analytical performance and concordance with next-generation sequencing of a rapid, multiplexed dPCR panel for the detection of DNA and RNA biomarkers in non-small-cell lung cancer. Diagnostics (Basel). 2023;13(21):3299. doi: 10.3390/diagnostics13213299
  • Spencer DH, Tyagi M, Vallania F, et al. Performance of common analysis methods for detecting low-frequency single nucleotide variants in targeted next-generation sequence data. J Mol Diagn. 2014;16(1):75–88. doi: 10.1016/j.jmoldx.2013.09.003
  • Peng Q, Xu C, Kim D, et al. Targeted single primer enrichment sequencing with single end duplex-UMI. Sci Rep. 2019;9(1):4810. doi:10.1038/s41598-019-41215-z
  • Patkar N, Kakirde C, Shaikh AF, et al. Clinical impact of panel-based error-corrected next generation sequencing versus flow cytometry to detect measurable residual disease (MRD) in acute myeloid leukemia (AML). Leukemia. 2021;35(5):1392–1404. doi: 10.1038/s41375-021-01131-6
  • Li Y, Solis-Ruiz J, Yang F, et al. NGS-defined measurable residual disease (MRD) after initial chemotherapy as a prognostic biomarker for acute myeloid leukemia. Blood Cancer J. 2023;13(1):59. doi: 10.1038/s41408-023-00833-7
  • Gurbuxani S, Hochman MJ, DeZern AE, et al. The times, they are A-Changing: the impact of next-generation sequencing on diagnosis, classification, and prognostication of myeloid malignancies with focus on myelodysplastic syndrome, AML, and germline predisposition. Am Soc Clin Oncol Educ Book. 2023;43(43):e390026. doi: 10.1200/EDBK_390026
  • Gurnari C, Robin M, Godley LA, et al. Germline predisposition traits in allogeneic hematopoietic stem-cell transplantation for myelodysplastic syndromes: a survey-based study and position paper on behalf of the chronic malignancies working party of the EBMT. Lancet Haematol. 2023;10(12):e994–e1005. doi: 10.1016/S2352-3026(23)00265-X
  • Kanagal-Shamanna R, Schafernak KT, Calvo KR. Diagnostic work-up of hematological malignancies with underlying germline predisposition disorders (GPD). Semin Diagn Pathol. 2023;40(6):443–456. doi:10.1053/j.semdp.2023.11.004
  • Obiorah IE, Upadhyaya KD, Calvo KR. Germline predisposition to myeloid neoplasms: diagnostic concepts and classifications. Clin Lab Med. 2023;43(4):615–638. doi: 10.1016/j.cll.2023.06.004
  • Drazer MW, Kadri S, Sukhanova M, et al. Prognostic tumor sequencing panels frequently identify germ line variants associated with hereditary hematopoietic malignancies. Blood Adv. 2018;2(2):146–150. doi: 10.1182/bloodadvances.2017013037
  • Kraft IL, Basdag H, Koppayi A, et al. Sequential tumor molecular profiling identifies likely germline variants. Genet Med. 2024;26(3):101037. doi: 10.1016/j.gim.2023.101037
  • Williams LS, Williams KM, Gillis N, et al. Donor-derived malignancy and transplantation morbidity: risks of patient and donor genetics in allogeneic hematopoietic stem cell transplantation. Transpl Cell Ther. 2024;30(3):255–267. doi: 10.1016/j.jtct.2023.10.018
  • Cai SF, Levine RL. Genetic and epigenetic determinants of AML pathogenesis. Semin Hematol. 2019;56(2):84–89. doi:10.1053/j.seminhematol.2018.08.001
  • DeRoin L, Cavalcante de Andrade Silva M, Petras K, et al. Feasibility and limitations of cultured skin fibroblasts for germline genetic testing in hematologic disorders. Hum Mutat. 2022;43(7):950–962. doi: 10.1002/humu.24374
  • Makishima H, Saiki R, Nannya Y, et al. Germ line DDX41 mutations define a unique subtype of myeloid neoplasms. Blood. 2023;141(5):534–549. doi: 10.1182/blood.2022018221
  • Makishima H, Bowman TV, Godley LA. DDX41-associated susceptibility to myeloid neoplasms. Blood. 2023;141(13):1544–1552. doi: 10.1182/blood.2022017715
  • Duncavage EJ, Schroeder MC, O’Laughlin M, et al. Genome sequencing as an alternative to cytogenetic analysis in myeloid cancers. N Engl J Med. 2021;384(10):924–935. doi: 10.1056/NEJMoa2024534
  • Euskirchen P, Bielle F, Labreche K, et al. Same-day genomic and epigenomic diagnosis of brain tumors using real-time nanopore sequencing. Acta Neuropathol. 2017;134(5):691–703. doi: 10.1007/s00401-017-1743-5
  • Nattestad M, Goodwin S, Ng K, et al. Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line. Genome Res. 2018;28(8):1126–1135. doi: 10.1101/gr.231100.117
  • Oehler JB, Wright H, Stark Z, et al. The application of long-read sequencing in clinical settings. Hum Genomics. 2023;17(1):73. doi:10.1186/s40246-023-00522-3
  • Cumbo C, Minervini CF, Orsini P, et al. Nanopore targeted sequencing for rapid gene mutations detection in acute myeloid leukemia. Genes (Basel). 2019;10(12):1026. doi: 10.3390/genes10121026
  • Jeck WR, Lee J, Robinson H, et al. A nanopore sequencing-based assay for rapid detection of gene fusions. J Mol Diagn. 2019;21(1):58–69. doi: 10.1016/j.jmoldx.2018.08.003
  • Sala-Torra O, Reddy S, Hung LH, et al. Rapid detection of myeloid neoplasm fusions using single-molecule long-read sequencing. PloS Glob Public Health. 2023;3(9):e0002267. doi: 10.1371/journal.pgph.0002267
  • Norris AL, Workman RE, Fan Y, et al. Nanopore sequencing detects structural variants in cancer. Cancer Biol Ther. 2016;17(3):246–253. doi:10.1080/15384047.2016.1139236
  • Tse OYO, Jiang P, Cheng SH, et al. Genome-wide detection of cytosine methylation by single molecule real-time sequencing. Proc Natl Acad Sci U S A. 2021;118(5). doi: 10.1073/pnas.2019768118
  • Zhang J, Xie S, Xu J, et al. Cancer biomarkers discovery of methylation modification with direct high-throughput nanopore sequencing. Front Genet. 2021;12:672804. doi:10.3389/fgene.2021.672804
  • Karst SM, Ziels RM, Kirkegaard RH, et al. High-accuracy long-read amplicon sequences using unique molecular identifiers with nanopore or PacBio sequencing. Nat Methods. 2021;18(2):165–169. doi: 10.1038/s41592-020-01041-y
  • Ediriwickrema A, Gentles AJ, Majeti R. Single-cell genomics in AML: extending the frontiers of AML research. Blood. 2023;141(4):345–355. doi:10.1182/blood.2021014670
  • O’Sullivan JM, Mead AJ, Psaila B. Single-cell methods in myeloproliferative neoplasms: old questions, new technologies. Blood. 2023;141(4):380–390. doi:10.1182/blood.2021014668
  • Ediriwickrema A, Aleshin A, Reiter JG, et al. Single-cell mutational profiling enhances the clinical evaluation of AML MRD. Blood Adv. 2020;4(5):943–952. doi: 10.1182/bloodadvances.2019001181
  • Rutella S, Vadakekolathu J, Mazziotta F, et al. Immune dysfunction signatures predict outcomes and define checkpoint blockade-unresponsive microenvironments in acute myeloid leukemia. J Clin Invest. 2022;132(21). doi: 10.1172/JCI159579
  • Li Z, Liu X, Wang L, et al. Integrated analysis of single-cell RNA-seq and bulk RNA-seq reveals RNA N6-methyladenosine modification associated with prognosis and drug resistance in acute myeloid leukemia. Front Immunol. 2023;14:1281687. doi: 10.3389/fimmu.2023.1281687
  • Gao X. Integrated analysis of single-cell RNA-Seq and bulk RNA-Seq unravels the molecular feature of tumor-associated macrophage of acute myeloid leukemia. Genet Res (Camb). 2024;2024:5539065. doi: 10.1155/2024/5539065
  • Guijarro F, Garrote M, Villamor N, et al. Novel tools for diagnosis and monitoring of AML. Curr Oncol. 2023;30(6):5201–5213. doi:10.3390/curroncol30060395
  • Selim AG, Moore AS. Molecular minimal residual disease monitoring in acute myeloid leukemia: challenges and future directions. J Mol Diagn. 2018;20(4):389–397. doi:10.1016/j.jmoldx.2018.03.005
  • Shimony S, Stahl M, Stone RM. Acute myeloid leukemia: 2023 update on diagnosis, risk-stratification, and management. Am J Hematol. 2023;98(3):502–526. doi:10.1002/ajh.26822
  • Alhajahjeh A, Nazha A. Unlocking the potential of artificial intelligence in acute myeloid leukemia and myelodysplastic syndromes. Curr Hematol Malig Rep. 2024;19(1):9–17. doi:10.1007/s11899-023-00716-5
  • Bernardi S, Vallati M, Gatta R. Artificial intelligence-based management of adult chronic myeloid leukemia: where are we and where are we going? Cancers (Basel). 2024;16(5):848. doi: 10.3390/cancers16050848

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.