Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction
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.
|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|
|URL link to publisher's version||http://www.ncbi.nlm.nih.gov/pubmed/27096160|
|OpenAccess link to author's accepted manuscript version||https://publications.gimr.garvan.org.au/open-access/13959|