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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. Single-Patient Molecular Testing with NanoString nCounter Data Using a Reference-Based Strategy for Batch Effect Correction. PLoS One 2016; 11:e0153844. [PMID: 27096160 PMCID: PMC4838303 DOI: 10.1371/journal.pone.0153844] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 04/05/2016] [Indexed: 12/20/2022] Open
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.
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Affiliation(s)
- Aline Talhouk
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Stefan Kommoss
- Department of Women’s Health, University Hospital Tuebingen, Tuebingen, Germany
| | - Robertson Mackenzie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Martin Cheung
- British Columbia Centre for Disease Control, Vancouver, Canada
| | - Samuel Leung
- Genetic Pathology Evaluation Centre (GPEC), Vancouver General Hospital and The University of British Columbia, Vancouver, Canada
| | - Derek S. Chiu
- Department of Statistics, University of British Columbia, Vancouver, Canada
| | - Steve E. Kalloger
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Pancreas Centre BC, Vancouver, Canada
| | - David G. Huntsman
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Genetic Pathology Evaluation Centre (GPEC), Vancouver General Hospital and The University of British Columbia, Vancouver, Canada
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
| | - Stephanie Chen
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, United States of America
| | - Maria Intermaggio
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Fong C. Chan
- Centre for Lymphoid Cancer, British Columbia Cancer Agency Cancer Research Centre, Vancouver, Canada
| | - Susan J. Ramus
- School of Women's and Children's Health, University of New South Wales, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer Agency Cancer Research Centre, Vancouver, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, British Columbia Cancer Agency Cancer Research Centre, Vancouver, Canada
| | - Michael S. Anglesio
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, Canada
- * E-mail:
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Deng MC, Alexander G, Wolters H, Shahzad K, Cadeiras M, Hicks A, Rowe T, Klingler TM, Eisen HJ. Low variability of intraindividual longitudinal leukocyte gene expression profiling cardiac allograft rejection scores. Transplantation 2010; 90:459-61. [PMID: 20720479 DOI: 10.1097/tp.0b013e3181e7e536] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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