Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples:: a comparison to snap-frozen material using oligonucleotide microarrays
Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples:: a comparison to snap-frozen material using oligonucleotide microarrays
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DOI：
10.1007/s00428-007-0412-9
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发表时间：
2007-06-01
期刊：
影响因子：
3.5
通讯作者：
Hansmann, Martin-Leo
中科院分区：
文献类型：
--
作者：
Frank, Matthias;Doering, Claudia;Hansmann, Martin-Leo
寡核苷酸微阵列被广泛用于大规模研究基因表达。一个主要的限制是依赖冷冻材料来获得高质量的核糖核酸，因为大多数临床标本都是福尔马林固定和石蜡包埋的(FFPE)。使用微阵列分析这些样品的能力将扩大可调查的样品库存多种多样。我们对研究两种恶性肿瘤的快速冷冻组织和FFPE组织进行了比较。从两种肿瘤材料中获得基因表达谱。在Affymetrix GeneChips(R)(美国加利福尼亚州帕洛阿尔托)上，分别对Snap冷冻和FFPE标本的独立处理的三联体进行两轮扩增和杂交。在FFPE和冷冻材料中都发现了差异表达的基因。归一化后，所有重复序列的相关系数(R)均大于0.95。仅将FFPE与冷冻复制品进行直接比较，得出的平均R值为0.86，这使得“混合”调查变得不可行。在5个以上的差异表达基因中(FFPE中800个，冰冻材料中685个)，无论使用何种材料，都能同时检测到50%以上(419个基因)，这与不同基因表达分析平台的其他比较类似。因此，仅使用FFPE材料进行全球基因表达分析似乎是可行的，其结果与冷冻组织研究几乎相似。
Oligonucleotide microarrays are widely used to investigate gene expression in a large-scale approach. A major limitation is the dependency on frozen material to obtain high-quality ribonucleic acid because most clinical specimens are formalin-fixed and paraffin-embedded (FFPE). The ability to analyze these samples using microarrays would enlarge the investigable sample stocks manifold. We conducted a comparison of snap-frozen and FFPE tissues investigating two malignomas. Gene expression profiles were obtained from both materials of the tumors. Independently processed triplicates of snap-frozen and FFPE specimen, respectively, were two-round-amplified and hybridized on Affymetrix GeneChips (R) (Palo Alto, CA, USA). Differentially expressed genes were identified in both FFPE and frozen material. All replicates had a correlation coefficient (R) of greater than 0.95 after normalization. Only direct comparison of FFPE to frozen replicates resulted in a mean R of 0.86, rendering a "mixed" investigation unfeasible. More than 50% (419 genes) of the more than fivefold differentially expressed genes (800 in FFPE, 685 in frozen material) were detected concomitantly regardless of the material used, which is similar to other comparisons of different gene expression analysis platforms. Thus, global gene expression analyses using solely FFPE material seem to be feasible with nearly comparable results to frozen tissue studies.