(r) GILEAU STATISTICAL ANALYSIS PLAN Study Title: A Randomized, Double-blind, Placebo- and Active -controlled, Multicenter, Phase 3 Study to Assess the Efficacy and Safety of Filgotinib Administered for 52 weeks Alone and in Combination with Methotrexate (MTX) to Subjects with Moderately to Severely Active Rheumatoid Arthritis Who Are Naïve to MTX Therapy Name of Test Drug: Filgotinib Study Number: GS-US-417-0303 Protocol Version (Date): Amendment 1: 05 July 2016 Analysis Type: Week 24 Analysis and Final Analysis Analysis Plan Version: Final Draft Analysis Plan Date: 06 August 2018 Analysis Plan Author(s): PPD CONFIDENTIAL AND PROPRIETARY INFORMATION Filgotinib GS-US-417-0303 Statistical Analysis Plan –Final Analysis Final Draft TABLE OF CONTENTS TABLE OF CONTENTS ..............................................................................................................................................2 LIST OF IN-TEXT TABLES........................................................................................................................................4 LIST OF IN-TEXT FIGURES ......................................................................................................................................4 LIST OF ABBREVIATIONS........................................................................................................................................5 PHARMACOKINETIC ABBREVIATIONS................................................................................................................8 1. INTRODUCTION ................................................................................................................................................9 1.1. Study Objectives ......................................................................................................................................9 1.2. Study Design ..........................................................................................................................................10 1.3. Sample Size and Power..........................................................................................................................11 2. TYPE OF PLANNED ANALYSIS ....................................................................................................................13 2.1. Data Monitoring Committee Analyses...................................................................................................13 2.2. Week 24 Analysis ..................................................................................................................................13 2.3. Final Analysis ........................................................................................................................................13 3. GENERAL CONSIDERATIONS FOR DATA ANALYSES ............................................................................14 3.1. Analysis Sets ..........................................................................................................................................14 3.1.1. All Randomized Analysis Set...............................................................................................14 3.1.2. Full Analysis Set ..................................................................................................................14 3.1.3. Per-Protocol Analysis Set.....................................................................................................14 3.1.4. Safety Analysis Set...............................................................................................................15 3.1.5. Pharmacokinetic Analysis Set ..............................................................................................15 CCI 3.2. Subject Grouping ...................................................................................................................................16 3.3. Strata and Covariates..............................................................................................................................16 3.4. -Examination of Subject Subgroups ........................................................................................................17 3.5. Multiple Comparisons............................................................................................................................17 3.6. Missing Data and Outliers......................................................................................................................19 3.6.1. Missing Data ........................................................................................................................19 3.6.2. Outliers.................................................................................................................................19 3.7. Data Handling Conventions and Transformations .................................................................................19 3.8. Analysis Visit Windows.........................................................................................................................20 3.8.1. Definition of Study Day .......................................................................................................20 3.8.2. Analysis Visit Windows.......................................................................................................21 3.8.3. Selection of Non-Efficacy Data in the Event of Multiple Records in an Analysis Visit Window ........................................................................................................23 4. SUBJECT DISPOSITION ..................................................................................................................................25 4.1. Subject Enrollment and Disposition.......................................................................................................25 4.2. Extent of Study Drug Exposure and Adherence.....................................................................................26 4.2.1. Duration of Exposure to Study Drug....................................................................................26 4.2.2. Adherence to Study Drug.....................................................................................................27 4.3. Protocol Deviations................................................................................................................................28 5. BASELINE CHARACTERISTICS....................................................................................................................29 5.1. Demographics and Other Baseline Characteristics ................................................................................29 5.2. Baseline Disease Characteristics............................................................................................................29 5.3. Medical History......................................................................................................................................31 CONFIDENTIAL Page 2 06 August 2018 Filgotinib GS-US-417-0303 Statistical Analysis Plan –Final Analysis Final Draft 6. EFFICACY ANALYSES ...................................................................................................................................32 6.1. General Considerations ..........................................................................................................................32 6.1.1. Tender/Swollen Joint Counts (TJC/SJC)..............................................................................33 6.1.2. Global Assessment of Disease Activity................................................................................34 6.1.3. Health Assessment Questionnaire Disability Index (HAQ-DI)............................................34 6.2. Primary Efficacy Endpoint.....................................................................................................................35 6.2.1. Definition of the Primary Efficacy Endpoint .......................................................................35 6.2.2. Statistical Hypothesis for the Primary Efficacy Endpoint....................................................35 6.2.3. Primary Analysis of the Primary Efficacy Endpoint ............................................................36 6.2.4. Sensitivity Analysis of the Primary Endpoint ......................................................................36 6.2.5. Subgroup Analysis of the Primary Endpoint........................................................................37 6.3. Key Secondary Efficacy Endpoints........................................................................................................37 6.3.1. Definition of Key Secondary Efficacy Endpoints ................................................................38 6.3.2. Analysis Methods for Key Secondary Efficacy Endpoints ..................................................39 6.3.3. Sensitivity Analysis for Key Secondary Efficacy Endpoints ...............................................40 6.3.4. Subgroup Analysis of Key Secondary Endpoints.................................................................42 6.4. Other Secondary Efficacy Endpoints .....................................................................................................42 6.4.1. Definition of Other Secondary Efficacy Endpoints..............................................................43 6.4.2. Analysis Methods for Other Secondary Efficacy Endpoints................................................46 6.5. Changes From Protocol-Specified Efficacy Analyses............................................................................49