Ventajas de la secuenciación de próxima generación sobre la hibridación fluorescente in situ para detectar la codeleción 1p/19q en oligodendrogliomas
Barra lateral del artículo
Descargas
Esta obra está bajo una licencia internacional Creative Commons Atribución-NoComercial-SinDerivadas 4.0.
Contenido principal del artículo
Resumen
El perfil molecular de los gliomas permite garantizar la precisión del diagnóstico, informar el pronóstico e identificar opciones de tratamiento. Esta revisión tiene como objetivo exponer que con la secuenciación de próxima generación (NSG) el diagnóstico de los pacientes con oligodendrogliomas puede ser más exacto. Además, con un dispositivo de diagnóstico in vitro, basado en la NSG (F1CDx), en el que se utilizan los bloques de parafina de gliomas para analizar hasta 395 genes relacionados con cáncer (incluido IDH 1 y 2), se puede también informar la pérdida de la totalidad del brazo corto del cromosoma 1 y del brazo largo del cromosoma 19 (codeleción 1p/19q), a diferencia de la hibridación fluorescente in situ (FISH) que detecta desde la más mínima deleción, lo cual los hace sensibles pero no específicos ya que el FISH es incapaz de distinguir entre la pérdida de la totalidad del brazo del cromosoma y una deleción focal. Esta distinción es importante ya que la sobrevida es inferior en tumores con deleción parcial en relación con los oligodendrogliomas, que tienen por definición la pérdida total de ambos cromosomas. Se hace también alusión a otras plataformas genómicas como GlioSeq y GLIO-DNA panel, que pueden cumplir la misma función. En conclusión, la F1CDx puede determinar con precisión 1p/19q con una concordancia del 96.7% frente a FISH. Los casos en que el FISH dio positivo y no concordaban con F1CDx, era porque no se trataba de oligodendrogliomas. F1CDx también analiza todos los genes que permiten la aproximación más exacta al diagnóstico de oligodendroglioma.
Citas
Pérez A, Huse JT. The evolving classification of diffuse gliomas: World Health Organization Updates for 2021. Curr Neurol Neurosci Rep. 2021;21(12):67.
Louis DN, Wesseling P, Aldape K, Brat DJ, Capper D, Cree IA, et al. cIMPACT-NOW update 6: New entity and diagnostic principle recommendations of the cIMPACT-Utrecht meeting on future CNS tumor classification and grading. Brain Pathol. 2020;30(4):844–56.
Ball MK, Kollmeyer TM, Praska CE, McKenna ML, Giannini C, Raghunathan A, et al. Frequency of false-positive FISH 1p/19q codeletion in adult diffuse astrocytic gliomas. Neuro-Oncol Adv. 2020;2(1):vdaa109.
De Biase D, Acquaviva G, Visani M, Marucci G, De Leo A, Maloberti T, et al. Next-generation sequencing panel for 1p/19q codeletion and IDH1-IDH2 mutational analysis uncovers mistaken overdiagnoses of 1p/19q codeletion by FISH. J Mol Diagn. 2021;23(9):1185–94.
Cairncross G, Wang M, Shaw E, Jenkins R, Brachman D, Buckner J, et al. Phase III trial of chemoradiotherapy for anaplastic oligodendroglioma: Long-term results of RTOG 9402. J Clin Oncol. 2013;31(3):337–43.
Van den Bent MJ, Brandes AA, Taphoorn MJB, Kros JM, Kouwenhoven MCM, Delattre JY, et al. Adjuvant procarbazine, lomustine, and vincristine chemotherapy in newly diagnosed anaplastic oligodendroglioma: Long-term follow-up of EORTC Brain Tumor Group Study 26951. J Clin Oncol. 2013;31(3):344–50.
Jamshidi P, Brat DJ. The 2021 WHO classification of central nervous system tumors: what neurologists need to know. Curr Opin Neurol. 2022 (in press).
Massaad E, Tabbarah A, Barmada M, Rbeiz J, Nasser S, Farra C. FISH analyses for 1p and 19q status on gliomas: Reporting an 8 years’ experience from a tertiary care center in the Middle East. Ann Diagn Pathol. 2022;57:151899.
Nigro JM, Takahashi MA, Ginzinger DG, Law M, Passe S, Jenkins RB, et al. Detection of 1p and 19q loss in oligodendroglioma by quantitative microsatellite analysis, a real-time quantitative polymerase chain reaction assay. Am J Pathol. 2001;158(4):1253–62.
Natté R, Eijk R, Eilers P, Cleton-Jansen AM, Oosting J, Kouwenhove M, et al. Multiplex ligation-dependent probe amplification for the detection of 1p and 19q chromosomal loss in oligodendroglial tumors. Brain Pathol. 20065;15(3):192–7.
Harada S, Henderson LB, Eshleman JR, Gocke CD, Burger P, Griffin CA, et al. Genomic changes in gliomas detected using single nucleotide polymorphism array in formalin-fixed, paraffin-embedded tissue. J Mol Diagn. 2011;13(5):541–8.
Woehrer A, Hainfellner JA. Molecular diagnostics: Techniques and recommendations for 1p/19q assessment. CNS Oncol. 2015;4(5):295–306.
Burger PC, Minn AY, Smith JS, Borell TJ, Jedlicka AE, Huntley BK, et al. Losses of chromosomal arms 1p and 19q in the diagnosis of oligodendroglioma. A study of paraffin-embedded sections. Mod Pathol. 2001;14(9):842–53.
Jenkins RB, Blair H, Ballman KV, Giannini C, Arusell RM, Law M, et al. A t(1;19)(q10;p10) mediates the combined deletions of 1p and 19q and predicts a better prognosis of patients with oligodendroglioma. Cancer Res. 200615;66(20):9852–61.
Fernández AF, Assenov Y, Martin-Subero JI, Balint B, Siebert R, Taniguchi H, et al. A DNA methylation fingerprint of 1628 human samples. Genome Res. 2012;22(2):407–19.
Reifenberger G, Wirsching HG, Knobbe-Thomsen CB, Weller M. Advances in the molecular genetics of gliomas —implications for classification and therapy. Nat Rev Clin Oncol. 2017;14(7):434–52.
Zacher A, Kaulich K, Stepanow S, Wolter M, Köhrer K, Felsberg J, et al. Molecular diagnostics of gliomas using next generation sequencing of a glioma-tailored gene panel: Next generation molecular diagnostics of gliomas. Brain Pathol. 2017;27(2):146–59.
Sharaf R, Pavlick DC, Frampton GM, Cooper M, Jenkins J, Danziger N, et al. FoundationOne CDx testing accurately determines whole arm 1p19q codeletion status in gliomas. Neuro-Oncol Adv. 2021;3(1):vdab017.
Tirrò E, Massimino M, Broggi G, Romano C, Minasi S, Gianno F, et al. A Custom DNA-based NGS panel for the molecular characterization of patients with diffuse gliomas: Diagnostic and therapeutic applications. Front Oncol. 2022;12:861078.
Low JT, Ostrom QT, Cioffi G, Neff C, Waite KA, Kruchko C, et al. Primary brain and other central nervous system tumors in the United States (2014-2018): A summary of the CBTRUS statistical report for clinicians. Neuro-Oncol Pract. 2022;9(3):165–82.
Wong D, Lee TH, Lum A, Tao VL, Yip S. Integrated proteomic analysis of low-grade gliomas reveals contributions of 1p-19q co-deletion to oligodendroglioma. Acta Neuropathol Commun. 2022;10(1):70.
Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D, et al. The 2021 WHO Classification of Tumors of the Central Nervous System: A summary. Neuro-Oncol. 2020;23(8):1231–51.
Wykes V, Zisakis A, Irimia M, Ughratdar I, Sawlani V, Watts C. Importance and evidence of extent of resection in glioblastoma. J Neurol Surg Part Cent Eur Neurosurg. 2021;82(01):075–86.
Stupp R, Mason WP, van den Bent MJ, Weller M, Fisher B, Taphoorn MJB, et al. Radiotherapy plus concomitant and adjuvant temozolomide for glioblastoma. N Engl J Med. 2005;352(10):987–96.
Van Den Bent MJ, Bromberg JEC, Buckner J. Low-grade and anaplastic oligodendroglioma. In: Handbook of Clinical Neurology [Internet]. Elsevier; 2016 [cited 2022 Oct 15]. p. 361–80. Available from: https://linkinghub.elsevier.com/retrieve/pii/B9780128029978000220
Otani R, Mukasa A, Uzuka T, Higuchi F, Matsuda H, Nomura M, et al. Gene expression profiling of 19q-loss astrocytomas suggest a specific pattern associated with the better prognosis. J Neurooncol. 2021;154(2):221–8.
Garton ALA, Kinslow CJ, Rae AI, Mehta A, Pannullo SC, Magge RS, et al. Extent of resection, molecular signature, and survival in 1p19q-codeleted gliomas. J Neurosurg. 2021;134(5):1357–67.
Ryckman JM, Surkar SM, Haque W, Butler EB, Teh BS, Verma V. Sequencing of chemotherapy and radiotherapy for newly diagnosed anaplastic oligodendroglioma and oligoastrocytoma. Am J Clin Oncol. 2019;42(3):258–64.
Berger TR, Wen PY, Lang-Orsini M, Chukwueke UN. World Health Organization 2021 Classification of Central Nervous System Tumors and Implications for Therapy for Adult-Type Gliomas: A review. JAMA Oncol. 2022;8(10):1493-501.
Luchi T, Sugiyama T, Ohira M, Kageyama H, Yokoi S, Sakaida T, et al. Clinical significance of the 2016 WHO classification in Japanese patients with gliomas. Brain Tumor Pathol. 2018;35(2):71–80.
Brandner S. Molecular diagnostics of adult gliomas in neuropathological practice. Acta Medica Acad. 2021;50(1):29.
Gritsch S, Batchelor TT, Gonzalez LN. Diagnostic, therapeutic, and prognostic implications of the 2021 World Health Organization classification of tumors of the central nervous system. Cancer. 2022;128(1):47–58.
Komori T. Grading of adult diffuse gliomas according to the 2021 WHO Classification of Tumors of the Central Nervous System. Lab Invest. 2022;102(2):126–33.
Takeda M, Takahama T, Sakai K, Shimizu S, Watanabe S, Kawakami H, et al. Clinical application of the FoundationOne CDx Assay to Therapeutic decision-making for patients with advanced solid tumors. The Oncologist. 2021;26(4):e588–96.
Li Y, Sun T, Chen Z, Shao Y, Huang Y, Zhou Y. Characterization of a new human astrocytoma cell line SHG140: Cell proliferation, cell phenotype, karyotype, STR markers and tumorigenicity analysis. J Cancer. 2021;12(2):371–8.
Schröck E, Veldman T, Padilla-Nash H, Ning Y, Spurbeck J, Jalal S, et al. Spectral karyotyping refines cytogenetic diagnostics of constitutional chromosomal abnormalities. Hum Genet. 1997;101(3):255–62.
Junker K, Fritsch T, Hartmann A, Schulze W, Schubert J. Multicolor fluorescence in situ hybridization (M-FISH) on cells from urine for the detection of bladder cancer. Cytogenet Genome Res. 2006;114(3–4):279–83.
Brown J, Byatt S, Khan T, St Heaps L, Dexter M, Nahar N, et al. FISH analysis of brain smears obtained at intraoperative diagnosis –An accurate and fast method to detect 1p/19q-codeletion in gliomas. J Clin Neurosci. 2021;92:115–9.
Jha P, Sarkar C, Pathak P, Sharma MC, Kale SS, Gupta D, et al. Detection of allelic status of 1p and 19q by microsatellite-based PCR versus FISH: Limitations and advantages in application to patient management. Diagn Mol Pathol Am J Surg Pathol Part B. 2011;20(1):40–7.
Idbaih A, Ducray F, Dehais C, Courdy C, Carpentier C, de Bernard S, et al. SNP array analysis reveals novel genomic abnormalities including copy neutral loss of heterozygosity in anaplastic oligodendrogliomas. Plos One. 201210;7(10):e45950.
Pinkham MB, Telford N, Whitfield GA, Colaco RJ, O’Neill F, McBain CA. FISHing Tips: What every clinician should know about 1p19q analysis in gliomas using fluorescence in situ hybridisation. Clin Oncol. 2015;27(8):445–53.
Giannini C, Scheithauer BW, Weaver AL, Burger PC, Kros JM, Mork S, et al. Oligodendrogliomas: Reproducibility and prognostic value of histologic diagnosis and grading. J Neuropathol Exp Neurol. 2001;60(3):248–62.
Figarella-Branger D, Mokhtari K, Dehais C, Jouvet A, Uro-Coste E, Colin C, et al. Mitotic index, microvascular proliferation, and necrosis define 3 groups of 1p/19q codeleted anaplastic oligodendrogliomas associated with different genomic alterations. Neuro-Oncol. 2014;16(9):1244–54.
Appay R, Dehais C, Maurage CA, Alentorn A, Carpentier C, Colin C, et al. CDKN2A homozygous deletion is a strong adverse prognosis factor in diffuse malignant IDH-mutant gliomas. Neuro- Oncol. 2019;noz124.
Laghari AA, Khalid MU, Qadeer N, Shamim MS. Prognostic value of 1p/19q chromosomal codeletion in patients with oligodendroglioma. JPMA J Pak Med Assoc. 2019;69(1):132–4.
Louis DN, Perry A, Wesseling P, Brat DJ, Cree IA, Figarella-Branger D, et al. The 2021 WHO Classification of Tumors of the Central Nervous System: A summary. Neuro-Oncol. 2021;23(8):1231–51.
van den Bent MJ, Smits M, Kros JM, Chang SM. Diffuse infiltrating oligodendroglioma and astrocytoma. J Clin Oncol. 2017;35(21):2394–401.
Weller M, Stupp R, Hegi ME, van den Bent M, Tonn JC, Sanson M, et al. Personalized care in neuro-oncology coming of age: why we need MGMT and 1p/19q testing for malignant glioma patients in clinical practice. Neuro-Oncol. 2012;14(suppl 4):iv100–8.
Burger PC, Minn AY, Smith JS, Borell TJ, Jedlicka AE, Huntley BK, et al. Losses of chromosomal arms 1p and 19q in the diagnosis of oligodendroglioma. A study of paraffin-embedded sections. Mod Pathol. 2001;14(9):842–53.
Reuss DE, Sahm F, Schrimpf D, Wiestler B, Capper D, Koelsche C, et al. ATRX and IDH1-R132H immunohistochemistry with subsequent copy number analysis and IDH sequencing as a basis for an “integrated” diagnostic approach for adult astrocytoma, oligodendroglioma and glioblastoma. Acta Neuropathol (Berl). 2015;129(1):133–46.
Dao LTM, Galindo-Albarrán AO, Castro-Mondragon JA, Andrieu-Soler C, Medina-Rivera A, Souaid C, et al. Genome-wide characterization of mammalian promoters with distal enhancer functions. Nat Genet. 2017;49(7):1073–81.
Ziegenhain C, Vieth B, Parekh S, Reinius B, Guillaumet-Adkins A, Smets M, et al. Comparative analysis of single-cell RNA sequencing methods. Mol Cell. 2017;65(4):631-643.e4.
Armand EJ, Li J, Xie F, Luo C, Mukamel EA. Single-cell sequencing of brain cell transcriptomes and epigenomes. Neuron. 2021;109(1):11–26.
Favello A, Hillier L, Wilson RK. Chapter 23. Genomic DNA Sequencing Methods. In: Methods in Cell Biology [Internet]. Elsevier; 1995 [cited 2022 Oct 17]. p. 551–69. Available from: https:// linkinghub.elsevier.com/retrieve/pii/S0091679X0861403X
Meyer M, Kircher M. Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. 2010;2010(6):pdb.prot5448.
Koboldt DC. Best practices for variant calling in clinical sequencing. Genome Med. 2020;12(1):91.
Xu C, Zhang R, Shen H, Deng HW. Medium-coverage DNA sequencing in the design of the genetic association study. Eur J Hum Genet. 2020;28(10):1459–66.
McKinzie PB, Bishop ME. A Streamlined and high-throughput error-corrected next-generation sequencing method for low variant allele frequency quantitation. Toxicol Sci. 2019;kfz221.
Guo Y, Wang S, Yuan X. HBOS-CNV: A new approach to detect copy number variations from next-generation sequencing data. Front Genet. 2021;12:642473.
Vicedomini R, Vezzi F, Scalabrin S, Arvestad L, Policriti A. GAM-NGS: genomic assemblies merger for next generation sequencing. BMC Bioinformatics. 2013;14(S7):S6.
Morganti S, Tarantino P, Ferraro E, D’Amico P, Viale G, Trapani D, et al. Complexity of genome sequencing and reporting: Next generation sequencing (NGS) technologies and implementation of precision medicine in real life. Crit Rev Oncol Hematol. 2019;133:171–82.
Le Gallo M, Lozy F, Bell DW. Next-generation sequencing. In: Hedrick Ellenson L, editor. Molecular genetics of endometrial carcinoma. Springer International Publishing; 2017. p. 119–48.
Wardell CP, Ashby C, Bauer MA. FiNGS: High quality somatic mutations using filters for next generation sequencing. BMC Bioinformatics. 2021;22(1):77.
Susswein LR, Marshall ML, Nusbaum R, Vogel KJ, Weissman SM, Yackowski L, et al. Pathogenic and likely pathogenic variant prevalence among the first 10 000 patients referred for next-generation cancer panel testing. Genet Med. 2016;18(8):823–32.
Takano S, Tian W, Matsuda M, Yamamoto T, Ishikawa E, Kaneko MK, et al. Detection of IDH1 mutation in human gliomas: comparison of immunohistochemistry and sequencing. Brain Tumor Pathol. 2011;28(2):115–23.
Cormen TH. Introduction to algorithms. 3rd ed. Cambridge, Mass: MIT Press; 2009. 1292 p.
Abel HJ, Duncavage EJ. Detection of structural DNA variation from next generation sequencing data: a review of informatic approaches. Cancer Genet. 2013;206(12):432–40.
Zolotovskaia MA, Kovalenko MA, Tkachev VS, Simonov AM, Sorokin MI, Kim E, et al. Next-generation grade and survival expression biomarkers of human gliomas based on algorithmically reconstructed molecular pathways. Int J Mol Sci. 2022;23(13):7330.
Sun JX, He Y, Sanford E, Montesion M, Frampton GM, Vignot S, et al. A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal. Plos Comput Biol. 2018;14(2):e1005965.
Nikiforova MN, Wald AI, Melan MA, Roy S, Zhong S, Hamilton RL, et al. Targeted next-generation sequencing panel (GlioSeq) provides comprehensive genetic profiling of central nervous system tumors. Neuro-Oncol. 2016;18(3):379–87.
Pallavajjala A, Haley L, Stinnett V, Adams E, Pallavajjala R, Huang J, et al. Utility of targeted next-generation sequencing assay to detect 1p/19q co-deletion in formalin-fixed paraffin-embedded glioma specimens. Hum Pathol. 2022;126:63–76.
Dubbink HJ, Atmodimedjo PN, van Marion R, Krol NMG, Riegman PHJ, Kros JM, et al. Diagnostic detection of allelic losses and imbalances by next-generation sequencing. J Mol Diagn. 2016;18(5):775–86.
McAleenan A, Kelly C, Spiga F, Kernohan A, Cheng HY, Dawson S, et al. Prognostic value of test(s) for O6-methylguanine-DNA methyltransferase (MGMT) promoter methylation for predicting overall survival in people with glioblastoma treated with temozolomide. Cochrane Database Syst Rev. 2021;CD013316.pub2
Castel D, Philippe C, Calmon R, Le Dret L, Truffaux N, Boddaert N, et al. Histone H3F3A and HIST1H3B K27M mutations define two subgroups of diffuse intrinsic pontine gliomas with different prognosis and phenotypes. Acta Neuropathol (Berl). 2015;130(6):815–27.
Dubbink HJ, Atmodimedjo PN, Kros JM, French PJ, Sanson M, Idbaih A, et al. Molecular classification of anaplastic oligodendroglioma using next-generation sequencing: A report of the prospective randomized EORTC Brain Tumor Group 26951 phase III trial. Neuro-Oncol. 2016;18(3):388–400.