针对 MGI DNBSEQ-G50 平台的临床 RNA 测序协议 Oncobox 的改编和实验验证

IF 0.6 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Biochemistry (Moscow), Supplement Series B: Biomedical Chemistry Pub Date : 2024-03-19 DOI:10.1134/S1990750823600589
N. R. Khilal, M. V. Suntsova, D. I. Knyazev, A. A. Guryanova, T. F. Kovaleva, M. I. Sorokin, A. A. Buzdin, N. Y. Katkova
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引用次数: 0

摘要

摘要RNA测序(RNAseq)是目前对基因表达进行高通量 RNA 级分析的首选方法。此外,RNAseq 数据还可用于预测多种癌症生物标志物,如微卫星不稳定性、肿瘤突变负荷、基因特征和免疫组化标志物表达。在这种分析中,核心步骤是与已有的正常/健康对照组织图谱库进行比较。然而,技术上不同的 RNAseq 平台和方案通常提供的基因表达输出结果兼容性较差,由于平台/方案的特异性偏差,很难汇集在一起进行直接比较分析。我们最近发布了用于 Illumina 平台的 Oncobox RNA 样品制备和测序方案,经临床前和临床研究验证,该方案可用于癌症分子诊断中的基因表达分析,以实现个性化治疗。在此,我们报告了针对 MGI 测序平台竞争对手的 DNBSEQ-G50 引擎对该方案的调整。我们展示了使用 Illumina 和 MGI 测序平台对相同的 16 个经福尔马林固定、石蜡包埋的实验性癌症模型生物样本进行 RNAseq 分析所获得的共同聚类和相似的基因表达图谱。所采用的 Oncobox 方案能够保留病例与正常值的比率、分子通路激活的计算值以及预测的癌症药物效率评分。我们的研究结果表明,Oncobox 分子诊断可同时用于 Illumina 和 MGI 测序平台的临床应用。这也证明,在使用 Oncobox 方案时,无需对特定数据进行协调,就能将两种平台获得的分子图谱进行比较,例如与之前发表的 ANTE 正常组织实验面板进行比较。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Adaptation and Experimental Validation of Clinical RNA Sequencing Protocol Oncobox for MGI DNBSEQ-G50 Platform

RNA sequencing (RNAseq) is currently a method of choice for the high-throughput RNA-level analysis of gene expression. Furthermore, RNAseq data can be used for the prediction of numerous cancer biomarkers e.g. microsatellite instability, tumor mutational burden, gene signatures, and immunohistochemical markers expression. In this analysis, central step is comparison with the pre-existing pool of normal/healthy control tissue profiles. However, technically different RNAseq platforms and protocols usually provide poorly compatible gene expression outputs that can be difficult to pool together and analyze in a direct comparison due to platform/protocol-specific bias. We recently published Oncobox RNA sample preparation and sequencing protocol for Illumina platform that can be used for the analysis of gene expression in cancer molecular diagnostics to personalize treatments, as validated in preclinical and clinical studies. Here we report adaptation of this protocol for DNBSEQ-G50 engine of a competitor MGI sequencing platform. We demonstrate common clustering and similar gene expression portraits for the RNAseq profiles obtained for the same 16 formalin-fixed, paraffin-embedded model experimental cancer biosamples using both Illumina and MGI sequencing platforms. The adopted Oncobox protocol enables retention of the case-to-normal ratios, calculated values of molecular pathway activation, and also of predicted cancer drug efficiency scores. Our findings suggest clinical applicability of Oncobox molecular diagnostics with both Illumina and MGI sequencing platforms. This also evidence that no specific data harmonization is needed to compare the molecular profiles obtained with either platform when using the Oncobox protocol, e.g. with the previously published ANTE experimental panel of normal tissues.

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来源期刊
CiteScore
1.10
自引率
0.00%
发文量
31
期刊介绍: Biochemistry (Moscow), Supplement Series B: Biomedical Chemistry   covers all major aspects of biomedical chemistry and related areas, including proteomics and molecular biology of (patho)physiological processes, biochemistry, neurochemistry, immunochemistry and clinical chemistry, bioinformatics, gene therapy, drug design and delivery, biochemical pharmacology, introduction and advertisement of new (biochemical) methods into experimental and clinical medicine. The journal also publishes review articles. All issues of the journal usually contain solicited reviews.
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