Large Chromosomal Rearrangements Yield Biomarkers to Distinguish Low-Risk From Intermediate- and High-Risk Prostate Cancer  George Vasmatzis, PhD, Farhad Kosari, PhD, Stephen J. Murphy, PhD, Simone Terra, MD, Irina V. Kovtun, PhD, Faye R. Harris, BS, Shabnam Zarei, MD, James B. Smadbeck, PhD, Sarah H. Johnson, MS, Athanasios G. Gaitatzes, MS, Terry M. Therneau, PhD, Laureano J. Rangel, BS, Ryan A. Knudson, BS, Patricia Greipp, DO, William R. Sukov, MD, Darlene L. Knutson, BS, Sara M. Kloft- Nelson, BS, R. Jeffrey Karnes, MD, John C. Cheville, MD  Mayo Clinic Proceedings  Volume 94, Issue 1, Pages 27-36 (January 2019) DOI: 10.1016/j.mayocp.2018.06.028 Copyright © 2018 Mayo Foundation for Medical Education and Research Terms and Conditions

Figure 1 Study design for the discovery (top panel) and validation (bottom panel) sets. Numbers on the plot denote the size of samples in insignificant prostate cancer, large volume GS6, GS7, and GS8 and higher (GS8+) categories. Light blue and red shaded areas on the prostate drawings represent Gleason patterns 3 and 4, respectively, and dark blue areas represent GS8+ tumors. GS# = Gleason score #. Mayo Clinic Proceedings 2019 94, 27-36DOI: (10.1016/j.mayocp.2018.06.028) Copyright © 2018 Mayo Foundation for Medical Education and Research Terms and Conditions

Figure 2 Scatterplots of junction counts (A) and event counts (B) stratified by risk categories. Numbers in red denote P values for groups calculated using the Wilcoxon test in comparison with the LRP category. GP# = Gleason pattern #; GS# = Gleason score #; LRP = low risk of progression; LV = large volume. Mayo Clinic Proceedings 2019 94, 27-36DOI: (10.1016/j.mayocp.2018.06.028) Copyright © 2018 Mayo Foundation for Medical Education and Research Terms and Conditions

Figure 3 A, Genome plot of Gleason pattern 4 in Gleason score 7 cancer. Deleted areas (red) and gained areas (blue) are color coded to depict aneuploidy. B, Composite graph compiling data from all cases yields the commonly gained (blue) and commonly deleted (red) gene loci across the genome. The x-axis is the gene loci count as they appear across the genome. The y-axis is the case count for both types of alterations, except that the count for deletions was inverted to distinguish from the gains. C, Correlation plot of the deleted counts vs the gained counts for all gene loci CNV = copy number variation. Mayo Clinic Proceedings 2019 94, 27-36DOI: (10.1016/j.mayocp.2018.06.028) Copyright © 2018 Mayo Foundation for Medical Education and Research Terms and Conditions

Figure 4 Composite graph compiling data from multiple cases yields the commonly gained (blue) and commonly deleted (red) genes across the genome that are preferentially in intermediate- and high-risk cases vs low-risk cases. The y-axis is the log10 of the P value calculated using a binomial test and inverted for deletions. Commonly deleted and gained loci selected for further validation by fluorescence in situ hybridization are annotated. Mayo Clinic Proceedings 2019 94, 27-36DOI: (10.1016/j.mayocp.2018.06.028) Copyright © 2018 Mayo Foundation for Medical Education and Research Terms and Conditions

Figure 5 Receiver operating characteristic (ROC) curves for the 6 potential biomarkers in low risk of progression to GS6 cancers vs other groups. ROC curves in red, blue, green, and black are for large volume GS6, GP3 in GS7, GP4 in GS7, and GP4 in GS8 and higher tumors, respectively. The insets are scatterplots of abnormal cells in different categories, and the text above each category is the area under the ROC curve for that category. Except RB1, all other fluorescence in situ hybridization probes were statistically significant (P≤.01). The P values for GP4 in GS7 and G8 and higher tumors in comparison with those for indolent GS6 tumors are generally more significant (see Discussion). GP# = Gleason pattern #; GS# = Gleason score #. Mayo Clinic Proceedings 2019 94, 27-36DOI: (10.1016/j.mayocp.2018.06.028) Copyright © 2018 Mayo Foundation for Medical Education and Research Terms and Conditions