Department of Health Science and Technology, Seoul National University, 1 Gwanak-ro, Gwanak-gu, 08826 Seoul, Republic of Korea.
Department of Pathology and Translational Medicine, Seoul National University Bundang Hospital, Seoul National University College of Medicine, 82 Gumi-ro 173beon-gil, Bundang-gu, 13620 Seongnam, Republic of Korea.
Brief Bioinform. 2024 Jul 25;25(5). doi: 10.1093/bib/bbae423.
Microsatellite instability (MSI), a phenomenon caused by deoxyribonucleic acid (DNA) mismatch repair system deficiencies, is an important biomarker in cancer research and clinical diagnostics. MSI detection often involves next-generation sequencing data, with many studies focusing on DNA. Here, we introduce a novel approach by measuring microsatellite lengths directly from ribonucleic acid sequencing (RNA-seq) data and comparing its distribution to detect MSI. Our findings reveal distinct instability patterns between MSI-high (MSI-H) and microsatellite stable samples, indicating the efficacy of RNA-based MSI detection. Additionally, microsatellites in the 3'-untranslated regions showed the greatest predictive value for MSI detection. Notably, this efficacy extends to detecting MSI-H samples even in tumors not commonly associated with MSI. Our approach highlights the utility of RNA-seq data in MSI detection, facilitating more precise diagnostics through the integration of various biological data.
微卫星不稳定性 (MSI) 是一种由脱氧核糖核酸 (DNA) 错配修复系统缺陷引起的现象，是癌症研究和临床诊断中的一个重要生物标志物。MSI 检测通常涉及下一代测序数据，许多研究都集中在 DNA 上。在这里，我们介绍了一种新的方法，通过直接从核糖核酸测序 (RNA-seq) 数据中测量微卫星的长度，并比较其分布来检测 MSI。我们的研究结果揭示了 MSI 高（MSI-H）和微卫星稳定样本之间的明显不稳定模式，表明基于 RNA 的 MSI 检测的有效性。此外，3'非翻译区中的微卫星显示出对 MSI 检测的最大预测价值。值得注意的是，即使在通常与 MSI 无关的肿瘤中，这种功效也可以延伸到检测 MSI-H 样本。我们的方法突出了 RNA-seq 数据在 MSI 检测中的实用性，通过整合各种生物数据，促进更精确的诊断。
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