U1小核rna的多样性及其突变诊断方法

IF 5.7 2区 医学 Q1 Medicine
Cancer Science Pub Date : 2025-05-27 DOI:10.1111/cas.70110
Takuma Nakashima, Tsubasa Miyauchi, Ryota Takeuchi, Yuriko Sugihara, Yusuke Funakoshi, Fumiharu Ohka, Sachi Maeda, Junko Hirato, Takako Yoshioka, Hajime Okita, Yoshitaka Narita, Yonehiro Kanemura, Yasuhiro Kojima, Yuko Watanabe, Ryuta Saito, Hiromichi Suzuki
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引用次数: 0

摘要

U1小核RNA (snRNA)突变是在各种恶性肿瘤中发现的复发性非编码改变,但由于其重复性,其鉴定已被证明具有挑战性。我们利用测序数据和泛基因组参考资料表征了U1 snRNA位点复杂的个体间多样性和基因组结构。我们的分析揭示了拷贝数变异和单核苷酸变异的多样性,这些变异在预计不会对功能产生重大影响的区域。与传统的基于线性参考的突变分析相比,泛基因组图显示出最好的准确性,成功地识别了以前无法检测到的突变。这强调了泛基因组图参考对癌症基因组研究的效用,特别是在重复和高度多样化的基因组区域。此外,我们开发了突变检测方法,采用靶向捕获测序,快速定量聚合酶链反应和基于剪接模式的机器学习方法,这些方法在识别U1 snRNA突变方面都具有很高的精度。我们的研究结果阐明了U1 snRNA位点的结构复杂性,并建立了在这些区域精确检测突变的可靠方法。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Diversity of U1 Small Nuclear RNAs and Diagnostic Methods for Their Mutations.

U1 small nuclear RNA (snRNA) mutations are recurrent non-coding alterations found in various malignancies, yet their identification has proven challenging due to their repetitive nature. We characterized the complex interindividual diversity and genomic architecture of U1 snRNA loci using sequencing data and a pangenome reference. Our analysis uncovered copy number variations and the diversity of single-nucleotide variants in regions not predicted to have significant functional impact. Compared to traditional linear reference-based analyses for mutations, the pangenome graph demonstrated the best accuracy, successfully identifying previously undetectable mutations. This underscores the utility of pangenome graph references for cancer genome research, particularly in repetitive and highly diverse genomic regions. Additionally, we developed mutation detection methods employing targeted capture sequencing, rapid quantitative polymerase chain reaction, and a machine learning approach based on splicing patterns, all exhibiting high precision in identifying U1 snRNA mutations. Our findings elucidate the structural complexity of U1 snRNA loci and establish robust methodologies for precise mutation detection in these regions.

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来源期刊
Cancer Science
Cancer Science ONCOLOGY-
CiteScore
9.90
自引率
3.50%
发文量
406
审稿时长
17 weeks
期刊介绍: Cancer Science (formerly Japanese Journal of Cancer Research) is a monthly publication of the Japanese Cancer Association. First published in 1907, the Journal continues to publish original articles, editorials, and letters to the editor, describing original research in the fields of basic, translational and clinical cancer research. The Journal also accepts reports and case reports. Cancer Science aims to present highly significant and timely findings that have a significant clinical impact on oncologists or that may alter the disease concept of a tumor. The Journal will not publish case reports that describe a rare tumor or condition without new findings to be added to previous reports; combination of different tumors without new suggestive findings for oncological research; remarkable effect of already known treatments without suggestive data to explain the exceptional result. Review articles may also be published.
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