G: Figure 2. Interpretation of the 95% confidence interval for the effect of treatment in a non-inferiority

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1 Appendix (A-I) A: Figure 1. RAPS clinical trial schema B: RAPS regimen for patients converting from warfarin to rivaroxaban C: Glossary D: Exclusion criteria E: RAPS laboratory criteria for antiphospholipid antibodies (apl) F: Table 1. RAPS trial assessment schedule G: Figure 2. Interpretation of the 95% confidence interval for the effect of treatment in a non-inferiority trial H: Changes to the protocol since first approval I: Monitoring, trial approvals and registrations NB The references cited in this appendix are included in the manuscript.

2 A: Figure 1. RAPS clinical trial schema

3 B: RAPS regimen for patients converting from warfarin to rivaroxaban; and clarification (explanatory notes added in bold font) Regimen for patients converting from warfarin to rivaroxaban For patients randomised to rivaroxaban, the warfarin should be stopped on the day of conversion from warfarin to rivaroxaban If the INR is 2.5, the rivaroxaban should be started the following morning If the INR is 2.6 to 3, the rivaroxaban should be started 2 days later in the morning If the INR is >3, the INR should be rechecked as required and the rivaroxaban should be started, as a morning dose: o when the INR is 2.6 to 3, the rivaroxaban should be started 2 days later in the morning o when the INR is 2.5, the rivaroxaban should be started the following morning When converting a patient from warfarin to rivaroxaban, the INR will be falsely elevated after rivaroxaban dosing. Therefore, the INR should not be used as a measure of anticoagulant activity of rivaroxaban. Clarification (explanatory notes added in bold font) 1. The protocol is entirely in accordance with the SPC 19 and should be used in that context. The SPC states: "For patients treated for DVT, PE and prevention of recurrence, VKA treatment should be stopped and arelto therapy should be initiated once the INR is 2.5."

4 2. The protocol states: "Regimen for patients converting from warfarin to rivaroxaban: For patients randomised to rivaroxaban, the warfarin should be stopped on the day of conversion from warfarin to rivaroxaban. This means that patients randomised to rivaroxaban should not take the next due dose of warfarin after randomisation, which will generally be either that evening or the following morning. If the INR is 2.5, the rivaroxaban should be started the following morning This means that if the INR is 2.5 on the baseline sample taken on the day of randomisation, then the rivaroxaban should be started the next morning (the patient having not taken the warfarin the evening of randomisation/the following morning (and of course from then onwards). Therefore the rivaroxaban will be started around 24 hours or more after the last warfarin dose If the INR is 2.6 to 3, the rivaroxaban should be started 2 days later in the morning This means that if the INR is 2.6 to 3, the rivaroxaban will be started around 48 hours or more after the last dose If the INR is >3, the INR should be rechecked as required and the rivaroxaban should be started, as a morning dose: o when the INR is 2.6 to 3, the rivaroxaban should be started 2 days later in the morning o when the INR is 2.5, the rivaroxaban should be started the following morning NB If the INR is between 2.5 and 2.6, then the INR result should be corrected upwards to 2.6 if the result is 2.55 and above and corrected downwards to 2.5 if the result is between

5 Note: when converting a patient from warfarin to rivaroxaban, the INR will be falsely elevated after dosing. Therefore, the INR should not be used as a measure of anticoagulant activity of rivaroxaban.

6 C: Glossary Adequate contraception Adequate contraception is defined as hormonal contraception or barrier method contraception. Sub-therapeutic anticoagulant therapy Patients who develop a new venous thromboembolic event while on warfarin with an INR (International Normalised ratio) of <2.0 (target INR 2.5, i.e. range ) will be considered to have had the event when sub-therapeutically anticoagulated. The same would apply if the patient was on a dose of another anticoagulant (e.g. low molecular weight heparin) administered at less than the manufacturer s recommended therapeutic dose for VTE at the time of the event. Thrombotic APS Thrombotic APS is defined as venous thromboembolism (VTE) associated with persistent positivity of one or more antiphospholipid antibodies (apl; i.e. lupus anticoagulant, IgG and/or IgM anticardiolipin and/or anti beta 2 glycoprotein 1 antibodies at >40 GPL or MPL units or > the 99th percentile of normal). Persistent apl positivity is defined as apl present on at least two consecutive occasions at least 12 weeks apart as defined in the International (Sydney) Consensus Statement criteria. 47 Clinical outcome events All thrombotic events, defined below, will be classified by the PI at the trial site. 1. Venous thromboembolism The diagnosis of symptomatic recurrent venous thromboembolism (VTE), i.e. deep-vein thrombosis

7 (DVT) or non-fatal or fatal pulmonary embolism (PE) is based on the following: DVT is diagnosed objectively on venous doppler or duplex scanning or venography. PE is diagnosed objectively on computed tomography pulmonary angiogram (CTPA) or ventilation/perfusion (V/Q) lung scanning. Fatal PE: the diagnosis of fatal PE is based on objective diagnostic testing, autopsy, or death which cannot be attributed to a documented cause and for which PE cannot be ruled out (unexplained death). 2. Other thrombotic events a) Arterial thrombosis/thromboembolism Stroke is defined as a sudden focal neurologic deficit of presumed cerebrovascular etiology that persists beyond 24 hours and is not due to another identifiable cause. An event matching this definition but lasting less than 24 hours is considered to be a transient ischemic attack. The diagnosis of stroke is based on brain imaging (computed tomography or magnetic resonance imaging). Systemic embolism is defined as abrupt vascular insufficiency associated with clinical or radiological evidence of arterial occlusion in the absence of another likely mechanism (e.g. atherosclerosis, instrumentation, or trauma). Myocardial infarction (MI) is defined by typical symptoms, cardiac biomarker elevation and electrocardiogram changes, or confirmation at autopsy. Deaths are classified as either vascular (e.g. due to stroke, embolism, myocardial infarction, or arrhythmia) or non-vascular (e.g. malignancy or infection). b) Microvascular thrombosis

8 Thrombosis in the microvasculature, generally associated with evidence of organ dysfunction in patients with thrombotic APS, is diagnosed on histological examination of a tissue biopsy. Categorisation of bleeds: Major bleeding Major bleeding is defined as clinically overt bleeding associated with any of the following: fatal outcome, involvement of a critical anatomic site (intracranial, spinal, ocular, pericardial, articular, retroperitoneal, or intramuscular with compartment syndrome), fall in hemoglobin concentration of at least 20 g/l, transfusion of 2 or more units of red blood cells, or permanent disability. Clinically relevant non-major bleeding Clinically relevant non-major bleeding is defined as overt bleeding not meeting the criteria for major bleeding but associated with medical intervention, unscheduled contact (visit or telephone) with a physician, temporary interruption of study drug (i.e. delayed dosing), or associated with any other discomfort such as pain or impairment of activities of daily life. Minor bleeding Bleeding events that do not meet the criteria of major or clinically relevant non-major bleeding are defined as minor.

9 D: Exclusion criteria 1. Previous arterial thrombotic event due to APS 2. Recurrent venous thromboembolic events whilst on warfarin at a therapeutic INR of Pregnant or lactating women 4. Severe renal impairment (creatinine clearance < 30 ml/min) 5. Liver function tests (alanine transaminase > 2 x upper limit of normal) 6. Cirrhotic patients with Child Pugh B or C 7. Thrombocytopenia (platelets < 75 x 10 9 /L) 8. Non-compliance on warfarin (based on clinical assessment) 9. Patients on azole antifungals (e.g. ketoconazole, itraconazole, voriconazole and posaconazole) 10. Patents on Human Immunodeficiency Virus (HIV) protease inhibitors (e.g. ritonavir) 11. Patients on strong CYP3A4 inducers (e.g. rifampicin, phenytoin, carbamazepine, phenobarbital or St. John's Wort) 12. Patients on dronedarone 13. Patients less than 18 years of age 14. Refusal to consent to the site informing GP and healthcare professional responsible for anticoagulation care, of participation

10 E: RAPS laboratory criteria for antiphospholipid antibodies (apl) Persistent antiphospholipid antibodies i.e. present on two or more occasions at least 12 weeks apart The diagnosis of apl is based on the Sapporo (Sydney) International Consensus Criteria, and International Society of Thrombosis and Haemostasis Scientific Subcommittee (ISTH SCC) and British Committee for Standards in Haematology (BCSH) guidance. 11,47,54 Lupus anticoagulant (LA) Patients not receiving anticoagulants (warfarin/other vitamin K antagonist (VKA) or therapeutic dose heparin/lmwh) Testing should be performed using accepted testing such as the Dilute Russell Viper Venom time (DRVVT) or the dilute activated partial thromboplastin time (APTT) assay or other appropriate assays as per BCSH/ISTH guidelines. Mixing tests and confirmatory procedures (high phospholipid, different phospholipid composition, or platelet neutralisation procedure) must be included to demonstrate an inhibitor (mixing tests) and show phospholipid dependence. Lupus anticoagulant (LA) testing in patients on VKA At least one of the following should be positive: 1) Taipan snake venom time (TVT) 2) DRVVT: Screening and confirmatory steps on equal volume (50:50) mixtures of patient and normal plasma. If the screening step on the mixture is abnormal, this may be taken as grounds for considering that an inhibitor is present and the confirmatory step will demonstrate phospholipid dependence. The

11 calculation of results should be according to the laboratory SOP/manufacturers recommendations. Points to note: The DRVVT and TVT are appropriate, but other methods may also be used (e.g. Acticlot dilute PT). Due to the dilution effect, negative testing in mixing studies does not exclude the presence of a LA Patients on low molecular weight/unfractionated heparin may have false positive results, therefore do not include these The APTT is not suitable due to the prolongation caused by warfarin The DRVVT may be performed on unmixed plasma if the INR is <1.5, and should be performed on a 50:50 mix with normal plasma if the INR is Anticardiolipin (acl) IgG and/or IgM Moderate/high positive: >the 99 th centile of the normal range Anti-β2-glycoprotein 1 antibodies (anti-β2-gp1) IgG and/or IgM Moderate/high positive: >the 99 th centile of the normal range

12 Site of apl testing This may be a RAPS trial site or other hospital. If the latter, this will be reflected in the baseline CRF and the cut offs for abnormal results should be provided to the Trial Manager.

13 F: Table 1. RAPS trial assessment schedule Assessment (Procedure/activity) Consent Medical History Demographics Screening Baseline Visit 1 Day 42 (ideally - 12days+14 days) Visit 2 Day 90 (ideally ±14days) Visit 3 Day 180 (ideally ±14days) Visit 4 Day 210 (ideally ±14days) Patient review Height Weight BMI Blood pressure FBC U&E, CrCl LFTs Anti-DNA apl 20 ml citrated blood sample for trial assessments (all patients) 20 ml blood sample for the translational research (optional) Pregnancy tests Current medication Document INRs Dispensation rivaroxaban Drug accountability of rivaroxaban Enquiry for bleeding symptoms Enquiry for recurrent thrombosis QoL questionnaire Timing of screening tests: The following tests are repeated if screening was more than 14 days prior to randomisation:

14 Full blood count (FBC) Urea and electrolytes (U&E) and creatinine clearance (CrCl) (to be calculated using the Cockcroft & Gault formula) 48,49 Liver function tests (LFTs) to include ALT * Anti-DNA tests no more than three months prior to randomisation, i.e. testing for anti-dna is not required within 30 days prior to randomisation ** Patients are diagnosed with thrombotic APS (Appendix: C) prior to trial entry. Results and dates of routine apl tests establishing a diagnosis of thrombotic APS are documented in the CRF (i.e. testing for apl is not required within 30 days prior to randomisation). Laboratory criteria for apl are detailed in the appendix (E). apl are reassessed at baseline using established methods, to define apl status at trial entry. + INR to be performed only in patients randomised to remain on warfarin

15 G: Figure 2. Interpretation of the 95% confidence interval for the effect of treatment in a noninferiority trial If the upper end of the 95% CI does not cross the non-inferiority limit of 20% (corresponding to Z= on the logarithmic scale), then rivaroxaban will be regarded as non-inferior (see B and C in Figure 2). If the mean difference is negative and the 95% CI does not include a difference of zero then we can conclude that rivaroxaban is superior to warfarin (see A in figure 2). 66 Error bars are 2-sided 95% confidence intervals (CIs). Z is the non-inferiority limit. The shaded area to the left of Z indicates non-inferiority of the new treatment. Example A: The whole of the CI is to the left of zero, so the new treatment is superior. Example B: The CI lies to the left of Z and includes zero, so the new treatment is non-inferior but is not shown to be superior.

16 Example C: The whole of the CI lies to the left of Z and to the right of zero, so the new treatment is noninferior (on the basis of the pre-specified non-inferiority limit), but it is also inferior as a treatment effect of zero is excluded. Example D: The CI is wide and includes both Z and zero, so the difference is not significant and the decision regarding non-inferiority is inconclusive. Example E: The CI excludes zero but includes Z, so the difference is significant but the decision regarding non-inferiority is inconclusive. Example F: The whole of the CI is to the right of Z, so the new treatment is inferior.

17 H: Changes to the protocol since first approval The required power was reduced from 90% to 80%, but the anticipated rate of non evaluable patients was maintained at 12% based on our experiences with recruiting the first 84 patients, where initial recruitment was a little slower than anticipated. The total sample size required was therefore reduced from 156 to 116 patients and the planned recruitment period was increased from 10 to 18 months. This change was approved by the Trial Steering Committee (TSC). Other minor changes to the protocol were removal of the Independent Event Adjudication Committee and permission to transfer any unused rivaroxaban to hospital stock at the end of the trial. The exclusion criteria concerning informing the patient s GP was expanded to include informing their healthcare professional responsible for anticoagulation care. The requirement for the patient to have been on six months of therapeutic warfarin target INR 2.5 (range ), was reduced to a minimum of three months, and this is reflected in current national guidelines. 9 A change to the protocol was required with the release of an updated version of the rivaroxaban SPC, where dosing patients with a creatinine clearance of ml/min with 15mg of rivaroxaban would be determined by the local clinical care team and following the SPC. The regimen for converting patients from warfarin to rivaroxaban was changed to state that patients should stop warfarin on the day of conversion from warfarin to rivaroxaban, i.e. that patients randomised to rivaroxaban should not take the next due dose of warfarin after randomisation, which will generally be either that evening or the following morning. The follow-up visit time point windows were reduced to encourage patient visits within the ideal visit schedule and ideally was inserted to allow for visits outside of the schedule. A further change of the rivaroxaban SPC, necessitated the addition of an exclusion criterion concerning avoidance of dronedarone and wording for the avoidance of dronedarone while on rivaroxaban. Markers of in vivo coagulation activation, F1.2, TAT and D-dimer, included in RAPS translational work, were incorporated into the trial protocol.

18 I: Monitoring, trial approvals and registrations Central and on-site monitoring will be carried out throughout the trial to ensure safety and quality in accordance with requirements detailed in the trial Monitoring and Quality Management Plan. An IDMC will monitor the progress of the trial, including patient recruitment, safety events and interim results. The trial will be conducted in accordance with the principles of the Declaration of Helsinki (version 2008). It will be conducted in compliance with the approved protocol, the principles of GCP as laid down by the Commission Directive 2005/28/EC with the implementation in national legislation in the UK by Statutory Instrument 2004/1031 (The Medicines for Human Use (Clinical Trials) Regulations 2004) and subsequent amendments, the UK Data Protection Act (DPA number: Z ) and the National Health Service (NHS) Research Governance Framework for Health and Social Care (RGF).

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