检测急性白血病和髓系疾病中的杂交融合转录本、异常转录本表达和特定单核苷酸变异与复发性基因重排。

IF 3.5 4区 医学 Q3 CELL BIOLOGY
Pathobiology Pub Date : 2024-01-01 Epub Date: 2023-07-25 DOI:10.1159/000532085
Yuewei Li, Kaifang Deng, Justin Kaner, Julia T Geyer, Madhu Ouseph, Frank Fang, Kemin Xu, Gail Roboz, Michael J Kluk
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引用次数: 0

摘要

导言:各种基因重排和分子改变是急性白血病和骨髓性疾病病理生物学的关键驱动因素;目前的分类系统越来越多地将这些发现纳入诊断算法。因此,临床实验室需要多功能工具,以检测数量和种类日益增多的具有临床意义的分子和细胞遗传学改变:方法:我们验证了一种基于 RNA 的新一代测序(NGS)检测方法,该方法可检测(方法:我们验证了一种基于 RNA 的新一代测序(NGS)检测方法,该方法能够检测:(i) 大量杂交融合转录本(包括罕见/新颖基因伴侣);(ii) 异常表达的 EVI1(MECOM)和 IKZF1(Del 外显子 4-7)转录本;(iii) KIT、ABL1 和 NPM1 的热点变异(与基因重排状态相关):对于杂交融合转录本,该检测方法对已知阳性和阴性样本的一致性为 98%-100%,分析灵敏度(即检测限)约为 0.8%。有潜在 EVI1 (MECOM) 易位的样本显示 EVI1 (MECOM) 表达增加。在正交反转录 PCR 中也能检测到异常的 IKZF1(Del 外显子 4-7)转录本。用该检测法检测到的 KIT、ABL1 和 NPM1 的特定热点突变与正交检测的一致性达到 100%。最后,我们还提供了几个示例样本,以强调该检测方法在临床上对病人检查的贡献:通过同时检测各种基因重排、异常表达转录本和热点突变的能力,这种基于 RNA 的 NGS 检测是临床实验室的一种宝贵工具,可补充急性白血病和骨髓疾病患者诊断工作和临床研究中使用的其他分子和细胞遗传学方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Detection of Hybrid Fusion Transcripts, Aberrant Transcript Expression, and Specific Single Nucleotide Variants in Acute Leukemia and Myeloid Disorders with Recurrent Gene Rearrangements.

Introduction: A variety of gene rearrangements and molecular alterations are key drivers in the pathobiology of acute leukemia and myeloid disorders; current classification systems increasingly incorporate these findings in diagnostic algorithms. Therefore, clinical laboratories require versatile tools, which can detect an increasing number and variety of molecular and cytogenetic alterations of clinical significance.

Methods: We validated an RNA-based next-generation sequencing (NGS) assay that enables the detection of: (i) numerous hybrid fusion transcripts (including rare/novel gene partners), (ii) aberrantly expressed EVI1 (MECOM) and IKZF1 (Del exons 4-7) transcripts, and (iii) hotspot variants in KIT, ABL1, NPM1 (relevant in the context of gene rearrangement status).

Results: For hybrid fusion transcripts, the assay showed 98-100% concordance for known positive and negative samples, with an analytical sensitivity (i.e., limit of detection) of approximately 0.8% cells. Samples with underlying EVI1 (MECOM) translocations demonstrated increased EVI1 (MECOM) expression. Aberrant IKZF1 (Del exons 4-7) transcripts detectable with the assay were also present on orthogonal reverse transcription PCR. Specific hotspot mutations in KIT, ABL1, and NPM1 detected with the assay showed 100% concordance with orthogonal testing. Lastly, several illustrative samples are included to highlight the assay's clinically relevant contributions to patient workup.

Conclusion: Through its ability to simultaneously detect various gene rearrangements, aberrantly expressed transcripts, and hotspot mutations, this RNA-based NGS assay is a valuable tool for clinical laboratories to supplement other molecular and cytogenetic methods used in the diagnostic workup and in clinical research for patients with acute leukemia and myeloid disorders.

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来源期刊
Pathobiology
Pathobiology 医学-病理学
CiteScore
8.50
自引率
0.00%
发文量
47
审稿时长
>12 weeks
期刊介绍: ''Pathobiology'' offers a valuable platform for the publication of high-quality original research into the mechanisms underlying human disease. Aiming to serve as a bridge between basic biomedical research and clinical medicine, the journal welcomes articles from scientific areas such as pathology, oncology, anatomy, virology, internal medicine, surgery, cell and molecular biology, and immunology. Published bimonthly, ''Pathobiology'' features original research papers and reviews on translational research. The journal offers the possibility to publish proceedings of meetings dedicated to one particular topic.
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