|Title||Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction|
|Publication Type||Journal Article|
|Year of Publication||2016|
|Authors||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|
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.