Interlaboratory Performance of a Microarray-Based Gene Expression Test to Determine Tissue of Origin in Poorly Differentiated and Undifferentiated Cancers

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Presentation transcript:

Interlaboratory Performance of a Microarray-Based Gene Expression Test to Determine Tissue of Origin in Poorly Differentiated and Undifferentiated Cancers Catherine I. Dumur, Maureen Lyons-Weiler, Christin Sciulli, Carleton T. Garrett, Iris Schrijver, Tara K. Holley, Juan Rodriguez-Paris, Jonathan R. Pollack, James L. Zehnder, Melissa Price, Jill M. Hagenkord, C. Ted Rigl, Ljubomir J. Buturovic, Glenda G. Anderson, Federico A. Monzon The Journal of Molecular Diagnostics Volume 10, Issue 1, Pages 67-77 (January 2008) DOI: 10.2353/jmoldx.2008.070099 Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 1 Study design. Sixty frozen tissue specimens from metastatic and primary tumors were assayed at four sites, three academic laboratories and one commercial laboratory, to adequately represent the variability found during routine clinical testing in molecular diagnostics laboratories. Microarray data files for samples passing quality control criteria only were analyzed by Pathwork Diagnostics, and reports were evaluated by pathologists (blinded). Data were compared between laboratories to determine reproducibility of the assay. The Journal of Molecular Diagnostics 2008 10, 67-77DOI: (10.2353/jmoldx.2008.070099) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 2 Example of Pathwork TOO report. Results shown are for study specimen 06-0360 from site 1. A SS ≥30 is the cutoff value to indicate a positive call, and an SS <5 confirms a negative call for each TOO. The Journal of Molecular Diagnostics 2008 10, 67-77DOI: (10.2353/jmoldx.2008.070099) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 3 Comparison of reproducibility of gene expression measurements and SS between test sites, as measured by the Pearson correlation coefficient. Data for 1668 genes normalized with the MAS5 and Pathwork TOO test algorithms show that correlation coefficients are significantly higher for the Pathwork SE value (Wilcoxon one-sided paired test, P = 0.01563) than those achieved with MAS5 normalization. Reproducibility across laboratories is further improved by the calculation of the SS from the SE data. The Journal of Molecular Diagnostics 2008 10, 67-77DOI: (10.2353/jmoldx.2008.070099) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions

Figure 4 Bland-Altman plots graph the difference between the SS for the true TOO between sites (y axis) versus the average of the SS (x axis) of any given pair of sites. The mean and ± 1.96 SD intervals are shown by dotted and plain horizontal lines, respectively. The coefficients of reproducibility (CR) and percentage of outliers are indicated for each comparison. The number of samples included in each comparison were n = 51 (A), n = 54 (B), n = 51 (C), n = 53 (D), n = 51 (E), and n = 50 (F). The Journal of Molecular Diagnostics 2008 10, 67-77DOI: (10.2353/jmoldx.2008.070099) Copyright © 2008 American Society for Investigative Pathology and Association for Molecular Pathology Terms and Conditions