Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction.
Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction.
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DOI：
10.1371/journal.pone.0153844
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发表时间：
2016
期刊：
影响因子：
3.7
通讯作者：
Anglesio MS
中科院分区：
文献类型：
--
作者：
Talhouk A;Kommoss S;Mackenzie R;Cheung M;Leung S;Chiu DS;Kalloger SE;Huntsman DG;Chen S;Intermaggio M;Gronwald J;Chan FC;Ramus SJ;Steidl C;Scott DW;Anglesio MS
许多高通量基因组研究的一个主要弱点是缺乏对临床环境的考虑，在这种环境下，一次必须对一个患者进行评估。我们从卵巢癌和霍奇金淋巴瘤患者的NanoString基因表达数据中检查了可推广的和平台特异性的变异来源。提出了一种适用于单患者分子检测的基于参考的策略，用于批次效应校正。所提出的方案提高了已建立的霍奇金淋巴瘤分类器的性能，减少了批次间的错误分类，同时保持了准确性和精度。我们建议这种策略可以通过加速相关诊断的前瞻性验证和临床吸收来促进NanoString和类似分子测定的发展。
A major weakness in many high-throughput genomic studies is the lack of consideration of a clinical environment where one patient at a time must be evaluated. We examined generalizable and platform-specific sources of variation from NanoString gene expression data on both ovarian cancer and Hodgkin lymphoma patients. A reference-based strategy, applicable to single-patient molecular testing is proposed for batch effect correction. The proposed protocol improved performance in an established Hodgkin lymphoma classifier, reducing batch-to-batch misclassification while retaining accuracy and precision. We suggest this strategy may facilitate development of NanoString and similar molecular assays by accelerating prospective validation and clinical uptake of relevant diagnostics.