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

Liu,Rong; Feng,Shunqiao; Li,Yanchun; Pan,Hongchao; Liang,Chao; Su,Yanhui; Dong,Jiahao; Li,Benshang; Chen,Zhong; Cui,Xiaodai

doi:10.3892/ol.2022.13607

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
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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
Published online on: November 22, 2022 https://doi.org/10.3892/ol.2022.13607
Article Number: 21

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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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