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Small Nucleolar RNA Score: An Assay to Detect Formalin-Overfixed Tissue

机译：小核仁RNA评分：测定以检测福尔马林过夹的组织

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摘要

Although there are millions of formalin-fixed paraffin-embedded (FFPE) tissue blocks potentially available for scientific research, many are of questionable quality, partly due to unknown fixation conditions. We analyzed FFPE tissue biospecimens as part of the NCI Biospecimen Preanalytical Variables (BPV) program to identify microRNA (miRNA) markers for fixation time. miRNA was extracted from kidney and ovary tumor FFPE blocks (19 patients, cold ischemia 2 hours) with 6, 12, 24, and 72 hours fixation times, then analyzed using the WaferGen SmartChip platform (miRNA chip with 1036 miRNA targets). For fixation time, principal component analysis of miRNA chip expression data separated 72 hours fixed samples from 6 to 24 hours fixed samples. A set of small nuclear RNA (snRNA) targets was identified that best determines fixation time and was validated using a second independent cohort of seven different tissue types. A customized assay was then developed, based on a set of 24 miRNA and snRNA targets, and a simple snoRNA score defined. This score detects FFPE tissue samples with fixation for 72 hours or more, with 79% sensitivity and 80% specificity. It can therefore be used to assess the fitness-for-purpose of FFPE samples for DNA or RNA-based research or clinical assays, which are known to be of limited robustness to formalin overfixation.
机译：虽然有数百万福尔马林固定的石蜡嵌入式（FFPE）组织块可能可用于科学研究，但许多质量是可疑的，部分原因是未知的固定条件。我们分析了FFPE组织生物开发，作为NCI生物开始的一部分，用于鉴定用于固定时间的MicroRNA（miRNA）标记。用6,12,24和72小时的固定时间从肾脏和卵巢肿瘤FFPE嵌段（19例，冷缺血2小时）中提取miRNA，然后使用晶圆智能芯片平台（MiRNA芯片具有1036 miRNA靶标）分析。对于固定时间，MiRNA芯片表达数据的主要成分分析分离72小时固定样品的固定样品固定样品。鉴定了一组小核RNA（SNRNA）靶标，最佳地确定固定时间，并使用第二个不同组织类型的第二个独立队列进行验证。然后基于一组24 miRNA和SnRNA靶标进行定制的测定，并定义了简单的Snorna评分。该得分检测到固定72小时或更长时间的FFPE组织样品，灵敏度为79％和80％。因此，它可以用于评估用于DNA或RNA的研究或临床测定的FFPE样品的适应性，已知是对福尔马林过混件有限的鲁棒性。

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