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Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction

Abstract

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.

Type Journal
ISBN 1932-6203 (Electronic) 1932-6203 (Linking)
Authors Talhouk, A.; Kommoss, S.; Mackenzie, R.; Cheung, M.; Leung, S.; Chiu, D. S.; Kalloger, S. E.; Huntsman, D. G.; Chen, S.; Intermaggio, M.; Gronwald, J.; Chan, F. C.; Ramus, S. J.; Steidl, C.; Scott, D. W.; Anglesio, M. S.;
Publisher Name PLoS ONE
Published Date 2016-01-01 00:00:00
Published Volume 11
Published Issue 4
Published Pages e0153844
URL http://www.ncbi.nlm.nih.gov/pubmed/27096160
Status Published In-print
OpenAccess Link https://publications.gimr.garvan.org.au/download.php?13959_13696/2016-Talhouk-PLoS One.pdf