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IF 4.8 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Biomolecules Pub Date : 2025-01-18 DOI:10.3390/biom15010146

Michele Massimino, Elena Tirrò, Stefania Stella, Cristina Tomarchio, Sebastiano Di Bella, Silvia Rita Vitale, Chiara Conti, Marialuisa Puglisi, Rosa Maria Di Crescenzo, Silvia Varricchio, Francesco Merolla, Giuseppe Broggi, Federica Martorana, Alice Turdo, Miriam Gaggianesi, Livia Manzella, Andrea Russo, Giorgio Stassi, Rosario Caltabiano, Stefania Staibano, Paolo Vigneri

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引用次数: 0

摘要

背景：尽管葡萄膜黑色素瘤（UM）的诊断和治疗取得了进展，但仍有约50%的患者发生远处转移，因此总生存率很低。分子图谱分析发现了几种可将葡萄膜黑色素瘤患者分为不同风险类别的基因改变。然而，这些基因改变目前分散在多项研究和几种方法中，因此需要一个明确的工作流程，以便进行标准化和可重复的分子分析：方法：根据 "癌症基因组图谱-UM"（TCGA-UM）研究公布的结果，我们开发了一个基于 NGS 的基因面板（称为 UMpanel），将突变集分为四类：启动性改变（CYSLTR2、GNA11、GNAQ 和 PLCB4）、预后性改变（BAP1、EIF1AX、SF3B1 和 SRSF2）、新兴生物标志物（CDKN2A、CENPE、FOXO1、HIF1A、RPL5 和 TP53）和染色体异常（1、3 和 8 号染色体不平衡）。结果：我们利用商业基因面板、参考突变 DNA 和 Sanger 测序进行了比较分析，发现与作为验证组的 TCGA-UM 队列相比，我们的方法成功地预测了生存率，并具有很高的特异性和灵敏度：我们的研究结果表明，基于 NGS 的可重复工作流程是对 UM 患者进行临床分层的可靠工具。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

An Optimized NGS Workflow Defines Genetically Based Prognostic Categories for Patients with Uveal Melanoma.

Background: Despite advances in uveal melanoma (UM) diagnosis and treatment, about 50% of patients develop distant metastases, thereby displaying poor overall survival. Molecular profiling has identified several genetic alterations that can stratify patients with UM into different risk categories. However, these genetic alterations are currently dispersed over multiple studies and several methodologies, emphasizing the need for a defined workflow that will allow standardized and reproducible molecular analyses.

Methods: Following the findings published by "The Cancer Genome Atlas-UM" (TCGA-UM) study, we developed an NGS-based gene panel (called the UMpanel) that classifies mutation sets in four categories: initiating alterations (CYSLTR2, GNA11, GNAQ and PLCB4), prognostic alterations (BAP1, EIF1AX, SF3B1 and SRSF2), emergent biomarkers (CDKN2A, CENPE, FOXO1, HIF1A, RPL5 and TP53) and chromosomal abnormalities (imbalances in chromosomes 1, 3 and 8).

Results: Employing commercial gene panels, reference mutated DNAs and Sanger sequencing, we performed a comparative analysis and found that our methodological approach successfully predicted survival with great specificity and sensitivity compared to the TCGA-UM cohort that was used as a validation group.

Conclusions: Our results demonstrate that a reproducible NGS-based workflow translates into a reliable tool for the clinical stratification of patients with UM.

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来源期刊

Biomolecules Biochemistry, Genetics and Molecular Biology-Molecular Biology

CiteScore

9.40

自引率

3.60%

发文量

1640

审稿时长

18.28 days

期刊介绍： Biomolecules (ISSN 2218-273X) is an international, peer-reviewed open access journal focusing on biogenic substances and their biological functions, structures, interactions with other molecules, and their microenvironment as well as biological systems. Biomolecules publishes reviews, regular research papers and short communications. Our aim is to encourage scientists to publish their experimental and theoretical results in as much detail as possible. There is no restriction on the length of the papers. The full experimental details must be provided so that the results can be reproduced.