Blocking and randomization to improve molecular biomarker discovery.
Blocking and randomization to improve molecular biomarker discovery.
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DOI：
10.1158/1078-0432.ccr-13-3155
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发表时间：
2014-07-01
期刊：
影响因子：
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通讯作者：
Levine DA
中科院分区：
文献类型：
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作者：
Qin LX;Zhou Q;Bogomolniy F;Villafania L;Olvera N;Cavatore M;Satagopan JM;Begg CB;Levine DA
随机化和阻断有可能防止非生物效应对分子生物标志物发现的负面影响。然而，它们在实践中的应用却很少。为了证明随机化和阻断的逻辑可行性和科学效益，我们使用阻断随机化设计对子宫内膜肿瘤（n=96）和卵巢肿瘤（n=96）进行了一项microRNA研究，以控制非生物效应；我们对同一组肿瘤进行了第二次分析，没有采用阻断或随机分组。我们评估了两项研究中差异表达的经验证据。我们通过虚拟再杂交进行了模拟，以进一步评估阻断和随机化的影响。在随机数据集中，子宫内膜和卵巢肿瘤之间存在中度和不对称的差异表达（351/ 3523,10%）。在非随机数据集中观察到非生物学效应，1934个标记（55%）被称为差异表达（DE）。其中185例（185/351,53%）为DE， 1749例（1749/3172,55%）为非DE。在模拟中，当一次对所有样本进行随机化或在肿瘤组中平衡的批次样本中进行随机化时，阻断将真阳性率（TPR）从0.95提高到0.97，假阳性率（FPR）从0.02提高到0.002；当样品批次不平衡时，无论阻断与否，随机化的TPR（0.92）和FPR（0.10）都较差。归一化改进了真阳性标记的检测，但仍然保留了相当大的假阳性标记。应该在实践中使用随机化和阻断，以更充分地获得基因组学技术的好处。
Randomization and blocking have the potential to prevent the negative impacts of non-biological effects on molecular biomarker discovery. Their use in practice, however, has been scarce. To demonstrate the logistic feasibility and scientific benefits of randomization and blocking, we conducted a microRNA study of endometrial tumors (n=96) and ovarian tumors (n=96) using a blocked randomization design to control for non-biological effects; we profiled the same set of tumors for a second time using no blocking or randomization. We assessed empirical evidence of differential expression in the two studies. We performed simulations through virtual re-hybridizations to further evaluate the effects of blocking and randomization. There was moderate and asymmetric differential expression (351/3523, 10%) between endometrial and ovarian tumors in the randomized dataset. Non-biological effects were observed in the non-randomized dataset and 1934 markers (55%) were called differentially expressed (DE). Among them, 185 were deemed DE (185/351, 53%) and 1749 non-DE (1749/3172, 55%) in the randomized dataset. In simulations, when randomization was applied to all samples at once or within batches of samples balanced in tumor groups, blocking improved the true positive rate (TPR) from 0.95 to 0.97 and the false positive rate (FPR) from 0.02 to 0.002; when sample batches were unbalanced, randomization had a worse TPR (0.92) and FPR (0.10) regardless of blocking. Normalization improved the detection of true positive markers but still retained sizeable false positive markers. Randomization and blocking should be used in practice to more fully reap the benefits of genomics technologies.