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Original Articles

Clinical utility of targeted NGS panel with comprehensive bioinformatics analysis for patients with acute lymphoblastic leukemia

, , , , &
Pages 3138-3145 | Received 10 Feb 2019, Accepted 26 May 2019, Published online: 17 Jun 2019

References

  • Inaba H, Greaves M, Mullighan CG. Acute lymphoblastic leukaemia. Lancet. 2013;381:1943–1955.
  • Taylor J, Xiao W, Abdel-Wahab O. Diagnosis and classification of hematologic malignancies on the basis of genetics. Blood. 2017;130:410–423.
  • Hunger SP, Mullighan CG. Redefining ALL classification: toward detecting high-risk ALL and implementing precision medicine. Blood. 2015;125:3977–3987.
  • 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;29:2154–2161.
  • Jia M, Wang ZJ, Li JY, et al. The impact of IKZF1 deletion on the prognosis of acute lymphoblastic leukemia: an updated meta-analysis. Cancer Biomark. 2014;14:493–503.
  • Mullighan CG, Su X, Zhang J, et al. Deletion of IKZF1 and prognosis in acute lymphoblastic leukemia. N Engl J Med. 2009;360:470–480.
  • Olsson L, Castor A, Behrendtz M, et al. Deletions of IKZF1 and SPRED1 are associated with poor prognosis in a population-based series of pediatric B-cell precursor acute lymphoblastic leukemia diagnosed between 1992 and 2011. Leukemia. 2014;28:302–310.
  • van der Veer A, Zaliova M, Mottadelli F, et al. IKZF1 status as a prognostic feature in BCR-ABL1-positive childhood ALL. Blood. 2014;123:1691–1698.
  • Agarwal M, Bakhshi S, Dwivedi SN, et al. Cyclin dependent kinase inhibitor 2A/B gene deletions are markers of poor prognosis in Indian children with acute lymphoblastic leukemia. Pediatr Blood Cancer. 2018;65:e27001.
  • Fang Q, Yuan T, Li Y, et al. Prognostic significance of copy number alterations detected by multi-link probe amplification of multiple genes in adult acute lymphoblastic leukemia. Oncol Lett. 2018;15:5359–5367.
  • Gupta SK, Bakhshi S, Kumar L, et al. Gene copy number alteration profile and its clinical correlation in B-cell acute lymphoblastic leukemia. Leuk Lymphoma. 2017;58:333–342.
  • Kutlay NY, Pekpak E, Altiner S, et al. Prognostic impact of RUNX1 and ETV6 gene copy number on pediatric B-cell precursor acute lymphoblastic leukemia with or without hyperdiploidy. Int J Hematol. 2016;104:368–377.
  • Messina M, Chiaretti S, Fedullo AL, et al. Clinical significance of recurrent copy number aberrations in B-lineage acute lymphoblastic leukaemia without recurrent fusion genes across age cohorts. Br J Haematol. 2017;178:583–587.
  • Pfeifer H, Raum K, Markovic S, et al. Genomic CDKN2A/2B deletions in adult Ph + ALL are adverse despite allogeneic stem cell transplantation. Blood. 2018;131:1464–1475.
  • Huether R, Dong L, Chen X, et al. The landscape of somatic mutations in epigenetic regulators across 1,000 paediatric cancer genomes. Nat Commun. 2014;5:3630.
  • Cibulskis K, Lawrence MS, Carter SL, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213–219.
  • DePristo MA, Banks E, Poplin R, et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet. 2011;43:491–498.
  • Koboldt DC, Zhang Q, Larson DE, et al. VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res. 2012;22:568–576.
  • 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;25:2865–2871.
  • Rausch T, Zichner T, Schlattl A, et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28:i333–i339.
  • Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
  • McLaren W, Pritchard B, Rios D, et al. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics. 2010;26:2069–2070.
  • Robinson JT, Thorvaldsdottir H, Winckler W, et al. Integrative genomics viewer. Nat Biotechnol. 2011;29:24–26.
  • Plagnol V, Curtis J, Epstein M, et al. A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics. 2012;28:2747–2754.
  • Kuilman T, Velds A, Kemper K, et al. CopywriteR: DNA copy number detection from off-target sequence data. Genome Biol. 2015;16:49.
  • Irving J, Matheson E, Minto L, et al. Ras pathway mutations are prevalent in relapsed childhood acute lymphoblastic leukemia and confer sensitivity to MEK inhibition. Blood. 2014;124:3420–3430.
  • Forero-Castro M, Robledo C, Benito R, et al. Mutations in TP53 and JAK2 are independent prognostic biomarkers in B-cell precursor acute lymphoblastic leukaemia. Br J Cancer. 2017;117:256–265.
  • Stengel A, Schnittger S, Weissmann S, et al. TP53 mutations occur in 15.7% of ALL and are associated with MYC-rearrangement, low hypodiploidy, and a poor prognosis. Blood. 2014;124:251–258.
  • Salmoiraghi S, Montalvo ML, Ubiali G, et al. Mutations of TP53 gene in adult acute lymphoblastic leukemia at diagnosis do not affect the achievement of hematologic response but correlate with early relapse and very poor survival. Haematologica. 2016;101:e245–248.
  • Huguet F, Leguay T, Raffoux E, et al. Pediatric-inspired therapy in adults with Philadelphia chromosome-negative acute lymphoblastic leukemia: the GRAALL-2003 study. J Clin Oncol. 2009;27:911–918.
  • Jones CL, Bhatla T, Blum R, et al. Loss of TBL1XR1 disrupts glucocorticoid receptor recruitment to chromatin and results in glucocorticoid resistance in a B-lymphoblastic leukemia model. J Biol Chem. 2014;289:20502–20515.
  • Li JY, Daniels G, Wang J, et al. TBL1XR1 in physiological and pathological states. Am J Clin Exp Urol. 2015;3:13–23.
  • Ding LW, Sun QY, Tan KT, et al. Mutational landscape of pediatric acute lymphoblastic leukemia. Cancer Res. 2017;77:390–400.
  • Okosun J, Bodor C, Wang J, et al. Integrated genomic analysis identifies recurrent mutations and evolution patterns driving the initiation and progression of follicular lymphoma. Nat Genet. 2014;46:176–181.
  • Hunger SP, Loh ML, Whitlock JA, et al. Children’s Oncology Group’s 2013 blueprint for research: acute lymphoblastic leukemia. Pediatr Blood Cancer. 2013;60:957–963.
  • Smith M, Arthur D, Camitta B, et al. Uniform approach to risk classification and treatment assignment for children with acute lymphoblastic leukemia. J Clin Oncol. 1996;14:18–24.

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