PhUSE. PhUSE Computational Science Standard Analyses and Code Sharing Working Group

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1 PhUSE PhUSE Computational Science Standard Analyses and Working Group Script Discovery and Acquisition Project Team Screen Shots of the Displays Created Using Scripts 1

2 Table of Contents 1. Disclaimer Notice of Current Edition Additions and/or Revisions Purpose Acknowledgements Project Leader Contact Information References Appendices AE Severity AE Toxicity AE MedDRA Analysis Panel Demographics Disposition Liver

3 1. Disclaimer The opinions expressed in this document are those of the authors and do not necessarily represent the opinions of the Pharmaceuticals User Software Exchange (PhUSE), members' respective companies or organizations, or regulatory authorities. The content in this document should not be interpreted as a data standard and/or information required by regulatory authorities. 2. Notice of Current Edition This edition of the Screen Shots of the Displays Created Using Scripts Contributed by the FDA white paper is a minor revision of the white paper originally titled as Screen Shots of the Displays Created by JumpStart Programs. 3. Additions and/or Revisions Date Author Version Changes 2017-Mar-17 See Section 5 v1.0 First edition 2017-May-19 See Section 5 v1.1 Updated the title and purpose to more accurately reflect the purpose and use of the outputs of the analysis scripts provided by FDA. 4. Purpose The purpose of this document is to show the displays associated with the scripts (SAS programs) contributed to the PhUSE Script Repository in 2016 by the Food and Drug Administration (FDA). These programs were developed by the Center for Drug Evaluation and Research s Office of Computational Science as tools to help reviewers with the analysis of sponsorsubmitted study data in Clinical Data Interchange Standards Consortium-compliant study data tabulation model format. The SAS programs encompass the following analysis panels: Adverse Events Analysis Panel, which provides users with different analyses to facilitate understanding of the adverse events present in the study and the frequency of their occurrence by treatment arm. 3

4 Adverse Event Toxicity, which provides users with analyses of adverse events by toxicity grades and shows information on subjects experiencing adverse events corresponding to user-selected Medical Dictionary for Regulatory Activities (MedDRA) levels in the treatment and control arms. Adverse Events MedDRA Analysis Panel, which enables users to see events that occurred in the study according to their place in the MedDRA hierarchy and allows them to compare any two arms according to a number of statistics. Demographic Analysis Panel, which provides users with an overview of the number and percent of subjects that correspond to various variables in the demographics dataset. Disposition Analysis Panel, which details the number and percent of cases that correspond to the disposition dataset. Liver Lab Analysis Panel, which provides users with an overview of the number and percent of subjects who have predefined abnormalities in lab test values for alanine aminotransferase, aspartate aminotransferase, total bilirubin, and alkaline phosphatase. The displays provided here are not necessarily consistent with regulatory guidance documents or white papers created by the PhUSE Analysis and Display White Papers (ADW) Project Team. We do not recommend that sponsors create these tables and figures instead of those already in a sponsor s standards library or those that are recommended by the PhUSE ADW project team. Instead, these displays inform sponsors of what the FDA may see early in their review process. Updates or modifications to a sponsor s standards may be warranted if conceptual gaps are identified. However, sponsors may want to run the contributed programs to ensure the FDA will be able to run them without errors. The contributed programs were shared with the PhUSE Script Repository Discovery and Acquisition Project Team and the programs have been uploaded to the PhUSE Script Repository in GitHub [1]. If interested in ensuring the FDA will be able to run the programs without errors or in duplicating the displays, sponsors can start with and access the codes provided in the PhUSE Script Repository in GitHub by following these links: Index of all scripts: Index of FDA Analytical Scripts: Once a script is tested, it will be in the tested/sas folder 4

5 5. Acknowledgements The primary contributors include Rebeka Revis, Hamning Tu, Mary Nilsson, Ted Peterson, and Bobbie Witczak. Thank you to Casie Polanco for editorial support. Thank you to all the original authors of the scripts and those involved with updates to the scripts over time. 6. Project Leader Contact Information Rebeka Revis Eli Lilly & Company Indianapolis, IN Work Phone: (317) References 1. Slain J, Tu H. CS07: Get a Jump Start on Clinical Data Analysis and Visualization with Standard Scripts. PhUSE Wiki. Available at: Accessed 13 Feb

6 Contributed by the FDA Standard Analyses and 8. Appendices 8.1. AE Severity Analysis 1: Adverse Events by Arm Greater than 2 Adverse Events by Organ Class and Term NDA/BLA: Study: 123 Analysis run date: :22:04 AM Where subject count is the number of subjects in the treatment arm experiencing at least one adverse event per organ class and term and greater than 2 of subjects in any arm experienced at least one adverse event Placebo Treatment Total Body System or Organ Class Dictionary-Derived Term N=577 N=575 N=1,152 Blood And Lymphatic System Disorders Anaemia Blood And Lymphatic System Disorders Iron Deficiency Anaemia Cardiac Disorders Right Ventricular Failure Cardiac Disorders Palpitations Cardiac Disorders Atrial Fibrillation Ear And Labyrinth Disorders Vertigo Endocrine Disorders Hypothyroidism Gastrointestinal Disorders Diarrhoea Gastrointestinal Disorders Nausea Gastrointestinal Disorders Vomiting Gastrointestinal Disorders Abdominal Pain Gastrointestinal Disorders Abdominal Pain Upper Gastrointestinal Disorders Abdominal Distension Gastrointestinal Disorders Dyspepsia Gastrointestinal Disorders Abdominal Discomfort

7 Contributed by the FDA Standard Analyses and Analysis 2: Serious Adverse Events by Arm Serious Adverse Events by Organ Class and Term NDA/BLA: Study: 123 Analysis run date: :22:04 AM Where subject count is the number of subjects in the treatment arm experiencing at least one serious adverse event per organ class and term Placebo Treatment Total Body System or Organ Class Dictionary-Derived Term N=577 N=575 N=1,152 Blood And Lymphatic System Disorders Anaemia Blood And Lymphatic System Disorders Haemorrhagic Anaemia Blood And Lymphatic System Disorders Idiopathic Thrombocytopenic Purpura Blood And Lymphatic System Disorders Leukopenia Blood And Lymphatic System Disorders Neutropenia Blood And Lymphatic System Disorders Thrombocytopenia Cardiac Disorders Right Ventricular Failure Cardiac Disorders Atrial Fibrillation Cardiac Disorders Atrial Flutter Cardiac Disorders Acute Right Ventricular Failure Cardiac Disorders Cardiac Arrest Cardiac Disorders Supraventricular Tachycardia Cardiac Disorders Cardio-Respiratory Arrest Cardiac Disorders Cardiogenic Shock Cardiac Disorders Cardiopulmonary Failure

8 Contributed by the FDA Standard Analyses and Analysis 3: Adverse Events by Severity and Arm Adverse Events by Severity Level NDA/BLA: Study: 123 Analysis run date: :22:04 AM Where the number in each column is the number of adverse events per treatment arm at the stated severity level. Body System or Organ Class Dictionary-Derived Term Mild Moderate Severe Not Applicabl e Mild Moderate Severe Not Applicabl e Nervous System Disorders Headache General Disorders And Administration Site Cond Disease Progression Gastrointestinal Disorders Diarrhoea Gastrointestinal Disorders Nausea Respiratory, Thoracic And Mediastinal Disorders Pulmonary Arterial Hypertension Respiratory, Thoracic And Mediastinal Disorders Dyspnoea Infections And Infestations Upper Respiratory Tract Infection Musculoskeletal And Connective Tissue Disorde Pain In Jaw General Disorders And Administration Site Cond Oedema Peripheral Nervous System Disorders Dizziness Infections And Infestations Nasopharyngitis Musculoskeletal And Connective Tissue Disorde Pain In Extremity Gastrointestinal Disorders Vomiting Musculoskeletal And Connective Tissue Disorde Myalgia Respiratory, Thoracic And Mediastinal Disorders Cough Musculoskeletal And Connective Tissue Disorde Arthralgia Cardiac Disorders Right Ventricular Failure Placebo Treatment Total 8

9 Contributed by the FDA Standard Analyses and Analysis 4: Serious Adverse Events by Severity and Arm Serious Adverse Events by Organ Class and Term NDA/BLA: Study: 123 Analysis run date: :22:04 AM Where subject count is the number of subjects in the treatment arm experiencing at least one serious adverse event per organ class and term Placebo Treatment Total Body System or Organ Class Dictionary-Derived Term N=577 N=575 N=1,152 Blood And Lymphatic System Disorders Anaemia Blood And Lymphatic System Disorders Haemorrhagic Anaemia Blood And Lymphatic System Disorders Idiopathic Thrombocytopenic Purpura Blood And Lymphatic System Disorders Leukopenia Blood And Lymphatic System Disorders Neutropenia Blood And Lymphatic System Disorders Thrombocytopenia Cardiac Disorders Right Ventricular Failure Cardiac Disorders Atrial Fibrillation Cardiac Disorders Atrial Flutter Cardiac Disorders Acute Right Ventricular Failure Cardiac Disorders Cardiac Arrest Cardiac Disorders Supraventricular Tachycardia Cardiac Disorders Cardio-Respiratory Arrest Cardiac Disorders Cardiogenic Shock Cardiac Disorders Cardiopulmonary Failure

10 Analysis 5.1: Relative Risk Placebo vs Treatment Placebo Treatment Body Relative Lower Upper System Dictionary-Derived Term Risk 95 CI 95 CI Immun Hypersensitivity ( 1.1, 70.6) Card Cyanosis ( 0.7, 49.5) Metab Fluid Overload ( 0.7, 49.5) Metab Gout ( 1.3, 26.6) Gastr Gingival Bleeding ( 0.6, 42.5) Vasc Hypertension ( 1.2, 15.1) Infec Otitis Externa ( 0.4, 35.6) Infec Viral Upper Respiratory Tract ( 0.4, 35.6) Musc Systemic Sclerosis ( 0.4, 35.6) Skin Dermatitis Contact ( 0.4, 35.6) Blood Iron Deficiency Anaemia ( 1.1, 8.2) Card Bundle Branch Block Right ( 0.3, 28.7) Eye Eye Pruritus ( 0.3, 28.7) Eye Ocular Hyperaemia ( 0.3, 28.7) 10

11 Analysis 5.2: Relative Risk and 95 Interval Analysis Relative Risk and 95 Confidence Interval Analysis Hypersensitivity Cyanosis Fluid Overload Gout Gingival Bleeding Hypertension Otitis Externa Viral Upper Respiratory Tract Systemic Sclerosis Dermatitis Contact Iron Deficiency Anaemia Bundle Branch Block Right Eye Pruritus Ocular Hyperaemia Irritable Bowel Syndrome Mouth Ulceration Feeling Hot Hyperthermia Laryngitis Onychomycosis Animal Bite Foot Fracture Liver Function Test Abnormal Hypercholesterolaemia Arthritis Breast Cancer Sinus Headache Interstitial Lung Disease Dermatitis Swelling Face

12 Analysis 6.1: Odds Ratio Placebo vs Treatment Placebo Treatment Body Odds Lower Upper System Dictionary-Derived Term Ratio 95 CI 95 CI Immun Hypersensitivity ( 1.3, 399.3) Metab Gout ( 1.3, 56.2) Card Cyanosis ( 0.7, 277.9) Metab Fluid Overload ( 0.7, 277.9) Gastr Gingival Bleeding ( 0.6, 237.7) Vasc Hypertension ( 1.2, 24.1) Infec Otitis Externa ( 0.4, 197.7) Infec Viral Upper Respiratory Tract ( 0.4, 197.7) Musc Systemic Sclerosis ( 0.4, 197.7) Skin Dermatitis Contact ( 0.4, 197.7) Blood Iron Deficiency Anaemia ( 1.0, 10.8) Inv Liver Function Test Abnormal ( 0.5, 30.6) Musc Arthritis ( 0.5, 30.6) Card Bundle Branch Block Right ( 0.2, 157.8) 12

13 Analysis 6.2: Odds Ratio and 95 Interval Analysis Odds Ratio and 95 Confidence Interval Analysis Hypersensitivity Gout Cyanosis Fluid Overload Gingival Bleeding Hypertension Otitis Externa Viral Upper Respiratory Tract Systemic Sclerosis Dermatitis Contact Iron Deficiency Anaemia Liver Function Test Abnormal Arthritis Bundle Branch Block Right Eye Pruritus Ocular Hyperaemia Irritable Bowel Syndrome Mouth Ulceration Feeling Hot Hyperthermia Laryngitis Onychomycosis Animal Bite Foot Fracture Hypercholesterolaemia Breast Cancer Sinus Headache Interstitial Lung Disease Dermatitis Swelling Face

14 8.2. AE Toxicity Analysis 1: Toxicity Grade Summary Toxicity Grade Summary NDA/BLA: Study: 123 Analysis run date: :06:12 PM Where subject count is the number of subjects experiencing at least one adverse event at the stated toxicity grade using the maximum toxicity grade per subject Treatment N=254 Control N=239 Total NOTES: All Grades Grades 3/4/5 All Grades Grades 3/4/5 1 This analysis uses the safety population and only counts adverse events that start between a subject's first exposure and 30 days after the subject's last exposure 14

15 Contributed by the FDA Standard Analyses and Analysis 2: Preferred Term Analysis by Toxicity Grade (V1) Preferred Term Analysis by Toxicity Grade NDA/BLA: Study: 123 Analysis run date: :06:12 PM Where subject count is the number of subjects experiencing at least one adverse event at the stated toxicity grade using the maximum toxicity grade per subject, organ class, and term Body System or Organ Class Dictionary-Derived Term Treatment N=254 Blood And Lymphatic System Disorders Anaemia Blood And Lymphatic System Disorders Eosinophilia Blood And Lymphatic System Disorders Iron Deficiency Anaemia Blood And Lymphatic System Disorders Leukocytosis Blood And Lymphatic System Disorders Leukopenia Blood And Lymphatic System Disorders Lymphadenopathy Blood And Lymphatic System Disorders Lymphoid Tissue Hyperplasia Blood And Lymphatic System Disorders Lymphopenia Blood And Lymphatic System Disorders Microcytic Anaemia Blood And Lymphatic System Disorders Neutropenia Blood And Lymphatic System Disorders Normochromic Normocytic Anaemia Blood And Lymphatic System Disorders Thrombocytopenia Cardiac Disorders Acute Coronary Syndrome Cardiac Disorders Angina Pectoris Control N=239 All Grades Grades 3/4/5 All Grades Grades 3/4/5 15

16 Analysis 3: Preferred Term Analysis by Toxicity Grade (V2) Preferred Term Analysis by Toxicity Grade NDA/BLA: Study: 123 Analysis run date: :06:12 PM Where subject count is the number of subjects experiencing at least one adverse event at the stated toxicity grade using the maximum toxicity grade per subject, organ class, and term Adverse Event Blood And Lymphatic System Disorders Treatment N=254 Control N=239 All Grades Grades 3/4/5 All Grades Grades 3/4/5 Anaemia Eosinophilia Iron Deficiency Anaemia Leukocytosis Leukopenia Lymphadenopathy Lymphoid Tissue Hyperplasia Lymphopenia Microcytic Anaemia Neutropenia Normochromic Normocytic Anaemia Thrombocytopenia

17 Contributed by the FDA Standard Analyses and 8.3. AE MedDRA Analysis Panel Analysis 1: Two-Term MedDRA Analysis (V1) Adverse Events Two-Term MedDRA Analysis by System Organ Class and Preferred Term NDA/BLA: Study: 123 Analysis run date: :06:12 PM Where subject count is the number of subjects experiencing at least one adverse event at the stated toxicity grade using the maximum toxicity grade per subject, system organ class, and preferred term System Organ Class Preferred Term Treatment N=254 All Grades Blood and lymphatic system disorders Anaemia (7.12, 15.09) (4.20, 11.14) 3.5 (-1.48, 8.52) Blood and lymphatic system disorders Eosinophilia (0.01, 2.17) (0.01, 2.31) 0.0 (-1.15, 1.10) Blood and lymphatic system disorders Iron deficiency anaemia (0.01, 2.17) (0.00, 1.53) 0.4 (-0.38, 1.16) Blood and lymphatic system disorders Leukocytosis (0.01, 2.17) (0.00, 1.53) 0.4 (-0.38, 1.16) Blood and lymphatic system disorders Leukopenia (0.01, 2.17) (0.10, 2.99) -0.4 (-1.83, 0.94) Blood and lymphatic system disorders Lymphadenopathy (0.01, 2.17) (0.10, 2.99) -0.4 (-1.83, 0.94) Blood and lymphatic system disorders Lymphoid tissue hyperplasia (0.00, 1.44) (0.01, 2.31) -0.4 (-1.24, 0.40) Blood and lymphatic system disorders Lymphopenia (0.64, 4.53) (0.46, 4.23) 0.3 (-2.06, 2.65) Blood and lymphatic system disorders Microcytic anaemia (0.00, 1.44) (0.01, 2.31) -0.4 (-1.24, 0.40) Blood and lymphatic system disorders Neutropenia (0.01, 2.17) (0.46, 4.23) -1.3 (-3.08, 0.52) Blood and lymphatic system disorders Normochromic normocytic anaemia (0.10, 2.82) (0.01, 2.31) 0.4 (-0.99, 1.73) Blood and lymphatic system disorders Thrombocytopenia (1.63, 6.62) (0.26, 3.62) 2.3 (-0.39, 4.96) Lower CL Upper CL Control N=239 All Grades Lower CL Upper CL Risk Difference Risk Difference Confidence Interval Lower CL Upper CL 17

18 Contributed by the FDA Standard Analyses and Analysis 2: Two-Term MedDRA Analysis Adverse Events Two-Term MedDRA Analysis by System Organ Class and Preferred Term; Sorted by Relative Risk NDA/BLA: Study: 123 Analysis run date: :06:12 PM Where subject count is the number of subjects experiencing at least one adverse event at the stated toxicity grade using the maximum toxicity grade per subject, system organ class, and preferred term Eye disorders Adverse Event Treatment N=254 All Grades Lower CL Upper CL Control N=239 All Grades Lower CL Upper CL Relative Risk Confidence Interval Confidence Interval Confidence Interval Relative Odds Lower CL Upper CL Risk Lower CL Upper CL Ratio Lower CL Upper CL Retinal detachment (5.19, 12.36) (0.00, 1.53) 8.3 (4.88, 11.65) 40.5* (2.47, ) 44.1* (2.66, ) 0.00 Chorioretinopathy (8.11, 16.43) (0.01, 2.31) 11.4 (7.34, 15.45) 28.2 (3.88, ) 31.9 (5.19, ) 0.00 Visual impairment (1.12, 5.60) (0.00, 1.53) 2.8 (0.74, 4.77) 14.1* (0.81, ) 14.5* (0.82, ) 0.02 Macular oedema (0.43, 3.98) (0.00, 1.53) 1.6 (0.04, 3.11) 8.5* (0.46, ) 8.6* (0.46, ) 0.12 Detachment of retinal pigment epithelium (1.37, 6.11) (0.01, 2.31) 2.7 (0.43, 5.03) 7.5 (0.95, 59.73) 7.7 (1.02, ) 0.04 Vitreous floaters (0.87, 5.07) (0.01, 2.31) 1.9 (-0.10, 3.98) 5.6 (0.68, 46.55) 5.8 (0.69, ) 0.12 Age-related macular degeneration (0.10, 2.82) (0.00, 1.53) 0.8 (-0.30, 1.87) 4.7* (0.23, 97.52) 4.7* (0.23, 99.29) 0.50 Diplopia (0.10, 2.82) (0.00, 1.53) 0.8 (-0.30, 1.87) 4.7* (0.23, 97.52) 4.7* (0.23, 99.29) 0.50 Orbital oedema (0.10, 2.82) (0.00, 1.53) 0.8 (-0.30, 1.87) 4.7* (0.23, 97.52) 4.7* (0.23, 99.29) 0.50 Retinopathy (0.10, 2.82) (0.00, 1.53) 0.8 (-0.30, 1.87) 4.7* (0.23, 97.52) 4.7* (0.23, 99.29) 0.50 Risk Difference Risk Difference Odds Ratio P-value 18

19 8.4. Demographics Analysis 1: Overview Demographic Baseline Characteristics: Overview NDA12345 Study: 123 Analysis run date: :21:03 AM Demographic Baseline Characteristics Placebo Treatment Overall Age Mean (SE) Min Q1 Median Q3 Max N=582 N=574 N= (15.6) 48.2 (15.2) 48.1 (15.4) Age Group Age under 50 years Age 50 and over Sex F M Race Asian Black Or African American Hispanic White Other Ethnicity Missing

20 Percentage () Project: Script Discovery and Acquisition Project Team Analysis 2: Age Groups Demographic Baseline Characteristics: Age Groups NDA12345 Study: 123 Analysis run date: :21:03 AM Age Group Placebo Treatment Overall N=582 N=574 N=1156 Age under 50 years Age 50 and over Age Groups Age under 50 years Age 50 and over Placebo 20

21 Analysis 3: Age Groups by Disposition Demographic Baseline Characteristics by Disposition Term: Age Groups NDA12345 Study: 123 Analysis run date: :21:03 AM The column shows the count of subjects in each demographic group per arm whose last disposition event is the disposition term shown. See the front page for further information. The column shows the proportion of the demographic group in each arm that the count represents. Standard Disposition Term Age Group Placebo Treatment Overall N=582 N=574 N=1156 Completed Age under 50 years Age 50 and over Death Age under 50 years Age 50 and over Unknown Age under 50 years Age 50 and over Analysis 4.1: Age Statistics - Table Demographic Baseline Characteristics: Age Statistics NDA12345 Study: 123 Analysis run date: :21:03 AM Age Statistic Placebo Treatment Overall N=582 N=574 N=1156 Mean (SE) 47.9 (15.6) 48.2 (15.2) 48.1 (15.4) Mode Min Q Median Q Max

22 Ages Project: Script Discovery and Acquisition Project Team Analysis 4.2: Age Statistics - Figure Age Statistics Placebo Treatment Overall Treatment Arms 22

23 Title: Screen Shots of the Displays Created by Using Scripts Contributed by the FDA Standard Analyses and Analysis 5: ry and Site ID Demographic Baseline Characteristics: ry and Site ID NDA12345 Study: 123 Analysis run date: :21:03 AM ry Site ID Placebo Treatment Overall N=582 N=574 N=1156 ARG AUS

24 8.5. Disposition Analysis 1: Disposition Events by Arm for All s Disposition Events by Arm for All s NDA12345 Study: 123 Analysis run date: :59:07 AM Category of Disposition Event Subcategory of Disposition Event Disposition Event Treatment Control Protocol Milestone Randomization Protocol Informed Consent Obtained All Eligibility Criteria Met Not All Eligibility Criteria Met Sample Collection Milestone Rcr Informed Consent Obtained Informed Consent Not Obtained Disposition Event Placebo Discontinuation Progression Of Disease Protocol Adverse Event Withdrawal By Physician Decision Death Other Non-Compliance With Study Drug Non-Compliance Lost To Follow-Up Analysis 2: Disposition Events by Arm for Exposed s Disposition Events by Arm for Exposed s NDA12345 Study: 123 Analysis run date: :59:07 AM Category of Disposition Event Subcategory of Disposition Event Disposition Event Treatment Control Protocol Milestone Missing Randomization Protocol Informed Consent Obtained All Eligibility Criteria Met Not All Eligibility Criteria Met Sample Collection Milestone Rcr Informed Consent Obtained Informed Consent Not Obtained Disposition Event Placebo Discontinuation Progression Of Disease Adverse Event Withdrawal By Physician Decision Death Other Non-Compliance With Study Drug Non-Compliance

25 Analysis 3: Time to Disposition Event by Arm for All s 25

26 Analysis 4: Time to Disposition Event by Arm for Exposed s 26

27 8.6. Liver Analysis 1: Liver Lab Tests Greater Than Upper Limit of Normal 27

28 Analysis 2.1: Combinations for Possible Hy s Law Cases at the Same Visit Analysis 2.2: Combinations for Possible Hy s Law Cases at Any Time during the Study 28

29 Analysis 2.3: Combinations for Possible Hy s Law Cases Patients at Any Time during the Study 29

30 Analysis 3: Baseline Lab Tests Maximum vs Baseline 30

31 Analysis 4: Maximum AST/ALT vs Maximum TB Lab Test Results per Charts 31

32 Analysis 5: Maximum Lab Test Results per by Study Day 32