Abstract：
Formalin-fixed paraffin-embedded (FFPE) tissue is the most common source of archived material for genomic medicine. However, FFPE tissue is suboptimal for high-throughput analyses, such as RNA sequencing, because the quality of nucleic acids in FFPE tissues is low. We compared RNA-seq with the nCounter system to evaluate use of FFPE tissue for genomic medicine. Twelve fresh frozen bladder cancer samples were analyzed by both RNA sequencing and nCounter, and matched FFPE samples, by nCounter. Gene-expression values obtained by these two platforms were compared by calculating Pearson correlation coefficients for each sample (across the set of matched genes) and for each matched gene (across the set of samples). For each sample, gene-expression levels measured by RNA sequencing highly correlated with those measured by nCounter (all Pearson\'s R > 0.8, P < 0.0001), as seen by hierarchical clustering. RNA sequencing results for fresh frozen tissues positively correlated with nCounter results for FFPE tissues (R ranged from 0.675 to 0.873, all P < 0.0001). Correlation and hierarchical-clustering analyses of nCounter data from the two specimens demonstrated a strong positive correlation between each group (R ranged from 0.779 to 0.977, all P < 0.0001). Our findings suggest that the nCounter system is useful for assaying archived-FFPE samples and that the gene-expression signatures obtained from FFPE samples represent those from fresh frozen tissues.
摘要：
福尔马林固定的石蜡包埋（FFPE）组织是基因组医学存档材料的最常见来源。然而,FFPE组织对于高通量分析来说是次优的，比如RNA测序，因为FFPE组织中的核酸质量较低。我们将RNA-seq与nCounter系统进行了比较，以评估FFPE组织在基因组医学中的应用。通过RNA测序和nCounter分析了12个新鲜的冷冻膀胱癌样品，和匹配的FFPE样品，由nCounter。通过计算每个样品(跨匹配基因集合)和每个匹配基因(跨样品集合)的Pearson相关系数来比较通过这两个平台获得的基因表达值。对于每个样本，通过RNA测序测量的基因表达水平与nCounter测量的基因表达水平高度相关（所有Pearson的R>0.8，P<0.0001），如分层聚类所示。新鲜冷冻组织的RNA测序结果与FFPE组织的nCounter结果呈正相关（R范围为0.675至0.873，均P<0.0001）。来自两个样本的nCounter数据的相关性和分层聚类分析表明各组之间存在强正相关（R范围为0.779至0.977，所有P<0.0001）。我们的发现表明，nCounter系统可用于测定存档的FFPE样品，并且从FFPE样品获得的基因表达特征代表来自新鲜冷冻组织的基因表达特征。
