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Article

A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia

  • Authors:
    • Rong Liu
    • Shunqiao Feng
    • Yanchun Li
    • Hongchao Pan
    • Chao Liang
    • Yanhui Su
    • Jiahao Dong
    • Benshang Li
    • Zhong Chen
    • Xiaodai Cui
  • View Affiliations / Copyright

    Affiliations: Department of Hematology, Children's Hospital of Capital Institute of Pediatrics, Beijing 100020, P.R. China, Beijing Hightrust Diagnostics, Co., Kindstar Globalgene Technology, Inc., Beijing 100176, P.R. China, Shanghai Simplegene Clinical Laboratory, Co., Kindstar Globalgene Technology, Inc., Shanghai 200025, P.R. China, Key Laboratory of Pediatric Hematology and Oncology Ministry of Health, Department of Hematology and Oncology, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, P.R. China, Department of Key Laboratory, Children's Hospital of Capital Institute of Pediatrics, Beijing 100020, P.R. China
  • Article Number: 21
    |
    Published online on: November 22, 2022
       https://doi.org/10.3892/ol.2022.13607
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Abstract

Fusion genes are products of chromosomal translocations that generate either a dysregulated partner gene or a chimeric fusion protein with new properties, and contribute significantly to leukemia development and clinical risk stratification. However, simultaneous detection of several hundreds of fusion genes has always been a challenge in a clinical laboratory setting. In the present study, a total of 182 pediatric patients with leukemia were screened for fusion genes by employing a novel genomic DNA‑, instead of RNA‑, based next‑generation sequencing (NGS) method. This involved the comparison of the multiply targeted capture sequencing method with a detection panel of 270 fusion genes (MTCS‑270) with an RNA‑based multiplex reverse transcription‑PCR technique with a detection panel of 57 fusion genes (MRTP‑57). MRTP‑57 has been well established in the clinical lab at Beijing Hightrust Diagnostics, Co. (Beijing, China) for an up‑front leukemia diagnosis and served as the control technique in the present study. In the series, MTCS‑270 and MRTP‑57 yielded a positive fusion gene detection rate of 50.0% (91/182) and 41.8% (76/182), respectively, indicating an advantage of MTCS‑270 over MRTP‑57 in overall detection sensitivity. Specifically, all the fusion genes detected by MRTP‑57 were also identified by MTCS‑270, clearly signifying the respectable detection accuracy of MTCS‑270. Notably, across the patients screened, MTCS‑270 identified more samples with fusion genes than MRTP‑57, illustrating a broader fusion gene detection coverage by MTCS‑270. The present study provides solid evidence that this DNA‑based NGS approach can be used as a potential detection tool together with other well‑established molecular cytogenetic methods for leukemia management, and to the best of our knowledge, represents the largest leukemia fusion gene identification analysis by genomic NGS.
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1 

Arber DA, Orazi A, Hasserjian R, Thiele J, Borowitz MJ, Le Beau MM, Bloomfield CD, Cazzola M and Vardiman JW: The 2016 revision to the World Health Organization classification of myeloid neoplasms and acute leukemia. Blood. 127:2391–2405. 2016. View Article : Google Scholar : PubMed/NCBI

2 

Wiemels J: Chromosomal translocations in childhood leukemia: Natural history, mechanisms, and epidemiology. J Natl Cancer Inst Monogr. 39:87–90. 2008. View Article : Google Scholar : PubMed/NCBI

3 

Conneely SE and Rau RE: The genomics of acute myeloid leukemia in children. Cancer Metastasis Rev. 39:189–209. 2020. View Article : Google Scholar : PubMed/NCBI

4 

Taylor J, Xiao W and Abdel-Wahab O: Diagnosis and classification of hematologic malignancies on the basis of genetics. Blood. 130:410–423. 2017. View Article : Google Scholar : PubMed/NCBI

5 

Xiong FF, Li BS, Zhang CX, Xiong H, Shen SH and Zhang QH: A pipeline with multiplex reverse transcription polymerase chain reaction and microarray for screening of chromosomal translocations in leukemia. Biomed Res Int. 2013:1350862013. View Article : Google Scholar : PubMed/NCBI

6 

Wang Q, Xia J, Jia P, Pao W and Zhao Z: Application of next generation sequencing to human gene fusion detection: Computational tools, features and perspectives. Brief Bioinform. 14:506–519. 2013. View Article : Google Scholar : PubMed/NCBI

7 

de Boer EN, Johansson LF, de Lange K, Bosga-Brouwer AG, van den Berg E, Sikkema-Raddatz B and van Diemen CC: Detection of fusion genes to determine minimal residual disease in leukemia using next-generation sequencing. Clin Chem. 66:1084–1092. 2020. View Article : Google Scholar : PubMed/NCBI

8 

Chen B, Jiang L, Zhong ML, Li JF, Li BS, Peng LJ, Dai YT, Cui BW, Yan TQ, Zhang WN, et al: Identification of fusion genes and characterization of transcriptome features in T-cell acute lymphoblastic leukemia. Proc Natl Acad Sci USA. 115:373–378. 2018. View Article : Google Scholar : PubMed/NCBI

9 

Jin Y, Wang X, Hu S, Tang J, Li B and Chai Y: Determination of ETV6-RUNX1 genomic breakpoint by next-generation sequencing. Cancer Med. 5:337–351. 2016. View Article : Google Scholar : PubMed/NCBI

10 

Levy MA, Santos S, Kerkhof J, Stuart A, Aref-Eshghi E, Guo F, Hedley B, Wong H, Rauh M, Feilotter H, et al: Implementation of an NGS-based sequencing and gene fusion panel for clinical screening of patients with suspected hematologic malignancies. Eur J Haematol. 103:178–189. 2019. View Article : Google Scholar : PubMed/NCBI

11 

Pallisgaard N, Hokland P, Riishøj DC, Pedersen B and Jørgensen P: Multiplex reverse transcription-polymerase chain reaction for simultaneous screening of 29 translocations and chromosomal aberrations in acute leukemia. Blood. 92:574–588. 1998. View Article : Google Scholar : PubMed/NCBI

12 

Quessada J, Cuccuini W, Saultier P, Loosveld M, Harrison CJ and Lafage-Pochitaloff M: Cytogenetics of pediatric acute myeloid leukemia: A review of the current knowledge. Genes (Basel). 12:9242021. View Article : Google Scholar : PubMed/NCBI

13 

Iijima-Yamashita Y, Matsuo H, Yamada M, Deguchi T, Kiyokawa N, Shimada A, Tawa A, Takahashi H, Tomizawa D, Taga T, et al: Multiplex fusion gene testing in pediatric acute myeloid leukemia. Pediatr Int. 60:47–51. 2018. View Article : Google Scholar : PubMed/NCBI

14 

Ampatzidou M, Papadhimitriou SI, Paterakis G, Pavlidis D, Tsitsikas Κ, Kostopoulos IV, Papadakis V, Vassilopoulos G and Polychronopoulou S: ETV6/RUNX1-positive childhood acute lymphoblastic leukemia (ALL): The spectrum of clonal heterogeneity and its impact on prognosis. Cancer Genet. 224–225. 1–11. 2018.PubMed/NCBI

15 

Moorman AV, Ensor HM, Richards SM, Chilton L, Schwab C, Kinsey SE, Vora A, Mitchell CD and Harrison CJ: Prognostic effect of chromosomal abnormalities in childhood B-cell precursor acute lymphoblastic leukaemia: Results from the UK medical research council ALL97/99 randomised trial. Lancet Oncol. 11:429–438. 2010. View Article : Google Scholar : PubMed/NCBI

16 

Gu Z, Churchman M, Roberts K, Li Y, Liu Y, Harvey RC, McCastlain K, Reshmi SC, Payne-Turner D, Iacobucci I, et al: Genomic analyses identify recurrent MEF2D fusions in acute lymphoblastic leukaemia. Nat Commun. 7:133312016. View Article : Google Scholar : PubMed/NCBI

17 

Byron SA, Keuren-Jensen KV, Engelthaler DM, Carpten JD and Craig DW: Translating RNA sequencing into clinical diagnostics: Opportunities and challenges. Nat Rev Genet. 17:257–271. 2016. View Article : Google Scholar : PubMed/NCBI

18 

Zhan D, Zhang Y, Xiao P, Zheng X, Ruan M, Zhang J, Chen A, Zou Y, Chen Y, Huang G, et al: Whole exome sequencing identifies novel mutations of epigenetic regulators in chemorefractory pediatric acute myeloid leukemia. Leuk Res. 65:20–24. 2018. View Article : Google Scholar : PubMed/NCBI

19 

Zhao J, Liang JW, Xue HL, Shen SH, Chen J, Tang YJ, Yu LS, Liang HH, Gu LJ, Tang JY and Li BS: The genetics and clinical characteristics of children morphologically diagnosed as acute promyelocytic leukemia. Leukemia. 33:1387–1399. 2018. View Article : Google Scholar : PubMed/NCBI

20 

Ruiz-Argüelles GJ, Garcés-Eisele J, Reyes-Núñez V, Gómez-Rangel JD and Ruiz-Delgado GJ: More on geographic hematology: The breakpoint cluster regions of the PML/RARalpha fusion gene in Mexican Mestizo patients with promyelocytic leukemia are different from those in Caucasians. Leuk Lymphoma. 45:1365–1368. 2004. View Article : Google Scholar : PubMed/NCBI

21 

Livak KJ and Schmittgen TD: Analysis of relative gene expression data using real-time quantitative PCR and the 2(−Delta Delta C(T)) method. Methods. 25:402–408. 2001. View Article : Google Scholar : PubMed/NCBI

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Copy and paste a formatted citation
Spandidos Publications style
Liu R, Feng S, Li Y, Pan H, Liang C, Su Y, Dong J, Li B, Chen Z, Cui X, Cui X, et al: A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia. Oncol Lett 25: 21, 2023.
APA
Liu, R., Feng, S., Li, Y., Pan, H., Liang, C., Su, Y. ... Cui, X. (2023). A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia. Oncology Letters, 25, 21. https://doi.org/10.3892/ol.2022.13607
MLA
Liu, R., Feng, S., Li, Y., Pan, H., Liang, C., Su, Y., Dong, J., Li, B., Chen, Z., Cui, X."A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia". Oncology Letters 25.1 (2023): 21.
Chicago
Liu, R., Feng, S., Li, Y., Pan, H., Liang, C., Su, Y., Dong, J., Li, B., Chen, Z., Cui, X."A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia". Oncology Letters 25, no. 1 (2023): 21. https://doi.org/10.3892/ol.2022.13607
Copy and paste a formatted citation
x
Spandidos Publications style
Liu R, Feng S, Li Y, Pan H, Liang C, Su Y, Dong J, Li B, Chen Z, Cui X, Cui X, et al: A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia. Oncol Lett 25: 21, 2023.
APA
Liu, R., Feng, S., Li, Y., Pan, H., Liang, C., Su, Y. ... Cui, X. (2023). A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia. Oncology Letters, 25, 21. https://doi.org/10.3892/ol.2022.13607
MLA
Liu, R., Feng, S., Li, Y., Pan, H., Liang, C., Su, Y., Dong, J., Li, B., Chen, Z., Cui, X."A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia". Oncology Letters 25.1 (2023): 21.
Chicago
Liu, R., Feng, S., Li, Y., Pan, H., Liang, C., Su, Y., Dong, J., Li, B., Chen, Z., Cui, X."A genomic DNA‑based NGS method for the simultaneous detection of multiple fusion genes in pediatric leukemia". Oncology Letters 25, no. 1 (2023): 21. https://doi.org/10.3892/ol.2022.13607
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