JMP Clinical. Release Notes. Version 5.0

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1 JMP Clinical Version 5.0 Release Notes Creativity involves breaking out of established patterns in order to look at things in a different way. Edward de Bono JMP, A Business Unit of SAS SAS Campus Drive Cary, NC 27513

2 JMP Clinical Release Notes Copyright 2014, SAS Institute Inc., Cary, NC, USA All rights reserved. Produced in the United States of America. Your use of this publication shall be governed by the terms established by the vendor at the time you acquire this publication. U.S. Government Restricted Rights Notice: Use, duplication, or disclosure of this software and related documentation by the U.S. government is subject to the Agreement with SAS Institute and the restrictions set forth in FAR , Commercial Computer Software-Restricted Rights (June 1987). SAS Institute Inc., SAS Campus Drive, Cary, North Carolina JMP, SAS and all other SAS Institute Inc. product or service names are registered trademarks or trademarks of SAS Institute Inc. in the USA and other countries. indicates USA registration. Other brand and product names are registered trademarks or trademarks of their respective companies.

3 JMP Clinical, Version Release Notes This document describes changes and enhancements from JMP Clinical, Version 4.1 to JMP Clinical, Version 5.0. Processes are described in the order in which they first appear in the JMP Clinical menu 1. General Features JMP and SAS Platform Updates JMP Clinical 5.0 is built on the latest JMP release, JMP For more information about the updates to JMP software that are included in this release, please see the New in JMP 11 web page. JMP Clinical 5.0 is built on the latest SAS release, SAS 9.4 M2. For more information about the enhancements to SAS analytical software that are included in this release, please seethe What s New in SAS 9.4 web page. Full installation instructions are available on the JMP Clinical website. Please note the following when you install JMP Clinical 5.0: You must uninstall JMP Clinical 4.1 first using either the Add or Remove Programs (Windows 7) or the Uninstall a program utility from the Control Panel. If you have already installed SAS 9.4 on your computer before installing JMP Clinical, you might need to run the install twice. Initially, SAS is updated, and when that installation has completed, you can re-start the installer again to install JMP Clinical. After installing, you will not see a desktop icon for JMP Clinical 5.0. If you want to create one, you can do so by navigating to the location of the JMP executable (typically C:\Program Files\SASHome\JMPClinical\11)) and creating a new shortcut to this file on your desktop. To change the icon used for the shortcut on Windows 7, right-click on the shortcut and choose Properties. Click Change Icon and navigate to the JMP Clinical icon in C:\Program Files\SASHome\JMPClinical\11\LifeSciences\Documentation\Icons\ JMPClinicalApp.ico. 1. Note: If you have a suggestion, comment, or encounter a bug in JMP Clinical 4.1, please click Send a Comment or a Feature Request under Clinical > Documentation and Help > Additional Resources, or details to Clinical@jmp.com. For bugs, it is especially helpful if you can attach a settings file for the JMP Clinical process in which you encountered the problem, along with a subset of your data that can be used to reproduce the error. If you cannot share a subset of your own data, but can reproduce the problem with one of our sample data sets, please send us a settings file for this so that we can replicate the error. We will make every effort to address the issue promptly. Thank you for taking the time to do this!

4 2 JMP Clinical, Version Release Notes Software Documentation Updates The User Guide has been updated to reflect all new and updated software features. The User Guide is available in both online and locally. The online version is updated on a regular basis and is the preferred source for information and help. For users who cannot access the Internet, a local version is provided. You are prompted during installation to select the documentation source. To switch between sources, open JMP Clinical, click File > Configure Life Sciences Settings and select the desired source for accessing the documentation. Click Run to update the settings. New Features Risk Based Monitoring Five new reports and methods have been added to JMP Clinical. These reports enable you to monitor the performance of each study site participating in the clinical trial and develop an overall assessment of the safety and quality risks associated with each study site. Individual processes are described below. Patient Profile Tables The Patient Profiler now generates patient-specific comprehensive tables listing all of the data, results and other information available for each patient being profiled, and places them on a single tab. To view this information, run the patient profiler for one or a group of patients, use the Subjects drill-down to select the patient whose data you want to review, and click on the new Tables tab. Use the Create Reports feature to generate a PDF- or RTF-formatted Report file containing the profile information. Review Builder The new Review Builder process provides a quick and easy means of building and performing a complete analysis of the data in a study. Results are accessed from a JMP journal. Reviews can consist of one or more reports that reviewed and reordered and then used to generate a final review package. Standardised MedDRA Queries (SMQs) JMP Clinical now uses your current version of the MedDRA dictionary to identify occurrences of SMQs using broad, narrow or algorithm criteria, summarize findings in distributions, and conduct incidence analyses. Further functionality allows you to identify which preferred or lower-level terms contributed to the SMQs. Crossover Analysis Support Added to Many JMP Clinical Reports Clinical trials using a cross-over design have become increasingly popular, particularly for those trials involving stable, chronic conditions, offers many benefits over more traditional parallel study designs. JMP Clinical now contains support for analysis and views for cross-over trials in the following reports: Adverse Event Distribution, Adverse Event Incidence Screen, Adverse Event Severity ANOVA, Adverse Event Resolution Screen, Events Distribution, Events Incidence Screen, Findings Distribution, Findings Baseline ANOVA, and Findings Time Trends.

5 JMP Clinical, Version Release Notes3 The system detects a crossover if multiple TRTxxP or TRTxxA variables exist and the associated timing variables for the xx period exist and contain values and adjusts the analysis and report to account for the cross-over design. If a time measurement is not available, the analysis includes only the date component. Refer to the Cross-Over Analysis chapter in the JMP Clinical User Guide for more details. Support for Partial Date Imputation When date/time values are either partial or incomplete, JMP Clinical now invokes a first moment rule. In these cases, when a date/time component is not included in the ISO 8601 value, that value is assumed to be the first possible value. Chinese Language Support A Chinese-version of JMP Clinical is now available and fully supported. Users can now view all dialogs and most reports in Chinese, and import and analyze Chinese-language data that has been formatted according to CDISC standards. New Analyses and Reports Studies Combine Studies New! This new process creates a new study by combining two or more existing studies. The specified study data sets are concatenated with checks for STUDYID and USUBJID uniqueness, the data is saved to the specified folders and the new study is generated using the Add Study from Folders process. Review Builder New! The new Review Builder process provides a quick and easy means of building and performing a complete analysis of the data in a study. Results are accessed from a JMP journal. You can specify one analysis at a time, but a review can consist of multiple reports. You can add, delete, or reorder reports within the review. Finally, you can opt to create a final review package that optionally includes the study data. JMP Clinical, Version Release Notes Demographics and Visits Add Holiday or Event New! This new feature generates a data set for user-specified country-specific holidays or events (countries compiled from all of your defined studies) for identification within the Weekdays and Holidays report.

6 4 JMP Clinical, Version Release Notes Edit Holiday or Event Data Set New! This new feature enables you to edit your holiday and event data set and add multiple new holidays or events at one time. Events Standardised MedDRA 2 Queries Distribution New! This new analysis enables you to compare distributions of SMQs across treatment arms. You can view results either in stacked bar charts or tables and flag results for additional review. Standardised MedDRA Queries Incidence Screen New! This new process screens Standard MedDRA Query terms by performing a Cochran-Mantel-Haenszel test on all 2 x 2 tables constructed from event incidence and treatment arm. Output is a table of multiplicity-adjusted p-values, an accompanying volcano plot of relative risk and a SAS data set of indicator variables that can be used as input for other processes. Risk-Based Monitoring New! Risk-Based Monitoring New! This analysis generates a dashboard for risk-based monitoring of clinical trials. Update Study Risk Data Set New! This feature enables you to manually enter site-specific descriptive information as well as risk indicator information that might not typically be available in the study database. Define Risk Threshold Data Set New! A risk threshold data set is used to 1) define the risk levels for individual variables for RBM analyses 2) specify the contribution of each variable to overall indicators of site risk. This process allows users to define a new risk threshold data set for RBM analyses using a previously-defined risk threshold data set as a starting point. Several risk threshold data sets can be defined to evaluate the sensitivity of the Risk Based Monitoring analysis to varying assumptions and risk thresholds. Finally, several overall indicators are defined, allowing for the straightforward combination of related factors. Manage Risk Threshold Data Sets New! This feature enables you to delete risk threshold data sets that are no longer valid or useful for risk based monitoring of your study. 2. You must specify the location of the MedDRA *.asc files.

7 JMP Clinical, Version Release Notes5 Map Geocoding Help New! Select this new option to open a JMP table listing the latitude and longitude of more than 750,000 geographical locations worldwide, spread more than two tabs that list U.S. and non-u.s. cities. These entries can help individuals customize geographic information in order to geocode clinical trial sites. Fraud Detection Cluster Subjects across Study Sites New! This new process clusters subjects across study sites for the purpose of identifying subjects that have enrolled at two or more clinical sites. It constructs a cross domain data set of pre-dosing data and computes a distance matrix and performs hierarchical clustering of subjects across all of the study centers to identify pairs of subjects with a very small distance, indicating they might represent the same individual who has enrolled at multiple sites. Digit Preference New! This new analysis assesses the use of terminal digits by study sites when reporting their clinical findings. It can be used to identify those sites that might exhibit biases in rounding issues or other problems with how they report data as compared with all other sites in the study. Predictive Modeling Predictive Modeling Review New! This new process enables you to examine multiple dependent variables and models, all in a single interface. In addition, for any regression-based model, candidate scores are generated. Subgroup Analysis New! Interaction Trees New! This new process finds a subgroup of rows with a differentiated treatment effect (either positive or negative, depending on the direction specified) by testing interactions of predictor variables with a treatment variable and splitting on the best interaction effect. It currently adopts a prune-as-you-go approach, keeping only the best branch of the tree after each split. This process is particularly useful for identifying the unique combination of conditions that subjects can exhibit along with the treatment expected to result in the most beneficial or, conversely, the most deleterious, outcome. JMP Clinical, Version Release Notes Virtual Twins New! This new process fits a model to observed and counter-factual data to find a subgroup of rows with enhanced treatment effects. This process follows the following steps: 1. Fit a forest model to the response. 2. Compute

8 6 JMP Clinical, Version Release Notes individual treatment effects by scoring actual and counter-factual data 3. Fit a standard tree model to the estimated treatment effects. SAS Data Set Utilities Assign Default Data Sets New! This new feature enables you to specify the data sets that are loaded by default for a study. Assign Wide Variable Roles New! This new feature enables you to assign default roles to variables in a wide data set. Running this process first can greatly facilitate running and validating multiple predictive modeling processes in which identical parameters are specified. It is also useful when adjusting parameter specification. Convert Character Date New! This new process takes an ISO 8601 character date (which could include time), strips off the date part and add a numeric version of the variable to the data table (which can be saved with the new variable). Running this process enables you to subsequently filter your results based on a numeric variable. Enhancements and Updates Multiple Processes AE/Events/Interventions (or "Medical Monitor") Distribution Analysis All JMP Clinical Distribution reports have been extensively redesigned to include percent calculations. In addition, new report grouping and stacking tools to generate several styles of reports have been added to output dashboards. Category and subcategory histograms are now displayed in results. The ability to specify term level and options to specify the type of event/intervention (pre-treatment, treatment emergent, on treatment, or post-treatment) have been added and distribution results can now be broken out by demographic grouping and event/intervention categorization. Two new options for determining event type have been added. The first includes On Treatment Adverse Events that occur on or after the first dose of study drug and at or before the last dose of drug. The second includes Off Treatment Follow Up Events that occur after the last dose of drug. An offset that counts the number of days after the last date of dosing to consider when off treatment follow-up begins has also been added.

9 JMP Clinical, Version Release Notes7 Events/Findings Incidence Screens A drill-down option enabling you to create a plot that shows the ratio of the odds for those with a specified risk factor to the odds for those without the risk factor. This feature can be used to estimate the relative risk when the probability of positive response is small. Create Report A Page Setup option has been added to the dialog that opens when Create Report is selected on the Results dashboard. This new option enables you to customize the format and features of the generated report. ALL Time to Event Reports A Competing Causes section that includes a Weibull fit and corresponding hazard plot showing event risk over time, has been added to the Results. All Findings Analyses Visual presentation of results has been greatly improved. Colors are consistent and the display of missing time points, nested visits/time points has been enhanced. All Predictive Modeling Processes Algorithms to optimize predictor filtering have been added. These enable more effective removal of correlated markers from the final candidate set of predictors. In addition, for any regression-based model, candidate scores and scoring codes are generated. Studies Domain Viewer The Results dashboard for this report now includes the embedded data table, open and visible, for the selected domain. The table is updated whenever a new domain is selected. A new Remove Stable Records drill-down has been added. This new feature enables you to more easily identify rows that are new or contain updates or other modifications. JMP Clinical, Version Release Notes Demographics and Visits Study Visits Visit counts are now displayed as a stacked chart, colored by treatment. A table summarizing the number of subjects attending each visit is also displayed. Weekdays and Holidays The ability to add country-specific holidays or events has been added.

10 8 JMP Clinical, Version Release Notes Events AE Time to Event This analysis can now be run for blinded studies and for studies with just one ARM. An option has been added for specifying whether to model the time to the first event or the incidence density (either for the first or for all events) Findings Box Plots The option for specifying visit number as a time scale has been added and specified by default. This generates an enhanced view that aids in understanding the distributions of findings measurements across visits of the trial. Subject Utilities Profile Subjects An option to group y-axis values by category has been added. This report now generates patient-specific comprehensive tables listing all of the data, results and other information available for each patient being profiled, and places them on a single tab. Tables can be customized and formatted according to user-defined templates. The Create Reports feature can be used to generate a PDF- or RTF-formatted Report file containing the profile information. Fraud Detection Perfect Scheduled Attendance Enhancements include the addition of a chi-square-statistic with options for performing an exact test and a volcano plot that can be used to screen visit-site combinations of interest Predictive Modeling General Linear Model Selection This process now includes elastic net, making this process more robust with correlated markers.

11 JMP Clinical, Version Release Notes9 Logistic Regression SAS PROC HPLOGISTIC, which uses high-performance computing to speed up processing, can now optionally be used instead of SAS PROC LOGISTIC. JMP Clinical, Version Release Notes

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