Impact of RNA degradation on gene expression profiling.
Impact of RNA degradation on gene expression profiling.
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DOI：
10.1186/1755-8794-3-36
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发表时间：
2010-08-09
影响因子：
2.7
通讯作者：
Gaedcke J
中科院分区：
文献类型：
--
作者：
Opitz L;Salinas-Riester G;Grade M;Jung K;Jo P;Emons G;Ghadimi BM;Beissbarth T;Gaedcke J
基因表达谱分析是一种高度敏感的技术，用于分析肿瘤样品以进行医学预后。RNA质量和降解影响基因表达谱的分析结果。这种影响对特征的影响及其医学影响尚不完全清楚。由于患者样本对于临床研究非常有价值，因此有必要建立RNA质量标准，以便能够在后续分析中使用这些样本。为了研究RNA完整性对基因表达谱的影响，使用全基因组表达阵列。我们使用的肿瘤活检标本来自诊断为局部晚期直肠癌的患者。为了模拟降解，将所有患者的分离的总RNA以时间依赖性方式进行热诱导降解。然后进行表达谱分析，并对数据进行生物信息学分析以评估差异。患者之间的生物学差异在很大程度上超过了RNA降解引起的差异。只有相对少量的探针（41，000个中的275个）显示出由于降解而产生的显著影响。由于RNA降解而显示出最强效应的基因尤其是具有短mRNA和探针位置靠近5'端的那些基因。来自肿瘤样品的降解RNA（RIN > 5）仍然可以用于进行基因表达分析。与RNA降解所施加的效应相比，观察到患者之间的生物学差异要高得多。然而，当使用降解的RNA时，存在基因，非常短的基因和探针结合侧接近5'末端的基因，其应当从基因表达分析中排除。这些结果仅限于Agilent 44 k微阵列平台，在转移到其他设置时应仔细解释。
Gene expression profiling is a highly sensitive technique which is used for profiling tumor samples for medical prognosis. RNA quality and degradation influence the analysis results of gene expression profiles. The impact of this influence on the profiles and its medical impact is not fully understood. As patient samples are very valuable for clinical studies, it is necessary to establish criteria for the RNA quality to be able to use these samples in later analysis. To investigate the effects of RNA integrity on gene expression profiling, whole genome expression arrays were used. We used tumor biopsies from patients diagnosed with locally advanced rectal cancer. To simulate degradation, the isolated total RNA of all patients was subjected to heat-induced degradation in a time-dependent manner. Expression profiling was then performed and data were analyzed bioinformatically to assess the differences. The differences introduced by RNA degradation were largely outweighed by the biological differences between the patients. Only a relatively small number of probes (275 out of 41,000) show a significant effect due to degradation. The genes that show the strongest effect due to RNA degradation were, especially, those with short mRNAs and probe positions near the 5' end. Degraded RNA from tumor samples (RIN > 5) can still be used to perform gene expression analysis. A much higher biological variance between patients is observed compared to the effect that is imposed by degradation of RNA. Nevertheless there are genes, very short ones and those with the probe binding side close to the 5' end that should be excluded from gene expression analysis when working with degraded RNA. These results are limited to the Agilent 44 k microarray platform and should be carefully interpreted when transferring to other settings.
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影响因子：
--
作者：
Schroeder A;Mueller O;Stocker S;Salowsky R;Leiber M;Gassmann M;Lightfoot S;Menzel W;Granzow M;Ragg T
通讯作者：
Ragg T
影响因子：
12.3
作者：
Gentleman RC;Carey VJ;Bates DM;Bolstad B;Dettling M;Dudoit S;Ellis B;Gautier L;Ge Y;Gentry J;Hornik K;Hothorn T;Huber W;Iacus S;Irizarry R;Leisch F;Li C;Maechler M;Rossini AJ;Sawitzki G;Smith C;Smyth G;Tierney L;Yang JY;Zhang J
通讯作者：
Zhang J
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
2.1
作者：
Irizarry, RA;Hobbs, B;Speed, TP
通讯作者：
Speed, TP
影响因子：
3.5
作者：
Thompson, Karol L;Pine, P Scott;Rosenzweig, Barry A;Turpaz, Yaron;Retief, Jacques
通讯作者：
Retief, Jacques