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Title: Phase 2 Trial of Brigatinib after Treatment with Next-Generation ALK  
  
inhibitors in Refractory ALK Rearranged NSCLC
Protocol Number: ARI-AT-002 Study Collaborator: Takeda Oncology IND\# 128883
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study contacts

| Principal Investigator USA Thomas E. Stinchcombe, MD  Duke University  DUMC 3198  25177 Morris Building  Durham, NC 27710  Phone 919-681-9509 Fax 919-681-9599  E-mail: Thomas.stinchcombe@duke.edu                                                                                                                                                                                                                                                                                                                    | Principal Investigator Canada Geoffrey Liu, MD Princess Margaret Cancer Centre 610-7-124 University Ave.  Toronto, ON Canada  M5G2M9 Phone: (416) 946-2000  E-mail: Geoffrey.Liu@uhn.ca   |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Principal Co-Investigator  Ross Camidge MD, PhD  University of Colorado  12605 E 16th Avenue  Aurora CO 80045  Phone: 720-848-0449 Fax: 720-848-0465  E-mail: Ross.Camidge@cuanschutz.edu Biostatistician  Xiaofei Wang, PhD  Duke University  Dept.of Biostatistics & Bioinformatics  Hock Plaza, 2424 Erwin Rd  Durham, NC 27710  Phone: (919) 681-5406  E-mail: Xiaofei.wang@duke.edu Criterium, Inc. (Project Management) 358 Broadway, Suite 201  Saratoga Springs, NY 12866  E-Mail: ARIAT002PM@criteriuminc.com |                                                                                                                                                                                           |  
Sponsor: Criterium, Inc. dba ATOMIC Funding Source: Takeda Oncology Protocol History: Original: September 17, 2015 Amendment 1 (Version 2): May 26, 2016 Amendment 2 (Version 3): October 4, 2016 Amendment 3 (Version 4): December 06, 2017 Amendment 4 (Version 5) April 18, 2018 Amendment 4 (Version 5.1) November 29, 2018 Amendment 5 (Version 6) May 20, 2019 Amendment 6 (Version 7) April 20, 2020  
| Version   | Main Changes                                                                                                                                           |                                                                                                          |
|-----------|--------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------|
| 1         |                                                                                                                                                        | Original                                                                                                 |
| 2         | -                                                                                                                                                      | Removal of Co-Investigators, updates to study collaborators and  contact information, addition of IND #; |
| -         | Clarifications, formatting, and spelling updates throughout;                                                                                           |                                                                                                          |
| -         | Section 1.3.5 updated with new findings;                                                                                                               |                                                                                                          |
| -         | Mechanism of resistance added to exploratory findings;                                                                                                 |                                                                                                          |
| -         | Inclusion 7 updated to allow study entry for subjects who cannot  undergo a biopsy;                                                                    |                                                                                                          |
| -         | Exclusion criteria 2 added to exclude patients who received prior  brigatinib treatment;                                                               |                                                                                                          |
| -         | Addition of ctDNA blood sample collection at C1D1 and D1 of odd  cycles;                                                                               |                                                                                                          |
| -         | SAE and pregnancy reporting process updated;                                                                                                           |                                                                                                          |
| -         | Addition of overdose reporting;                                                                                                                        |                                                                                                          |
| -         | Updates to section 9.2: Required documentation for site opening;                                                                                       |                                                                                                          |
| -         | Updates to enrollment procedures;                                                                                                                      |                                                                                                          |
| -         | Updates to section 9.4 due to change in EDC system and monitoring  of data.                                                                            |                                                                                                          |
| -         | Addition of Criterium Project manager's role throughout the protocol.                                                                                  |                                                                                                          |
| -         | Removal of Unanticipated problems;                                                                                                                     |                                                                                                          |
| -         | Updated Appendix B Model Patient Diary.                                                                                                                |                                                                                                          |
| 3         | -                                                                                                                                                      | Background and Rationale updated with new data                                                           |
| -         | Updates throughout removing references to UNC and LCCC 1523 to  reflect the transition of responsibilities to ATOMIC and Duke  Principal Investigator; |                                                                                                          |
| -         | Change of the Protocol number to ARI-AT-002;                                                                                                           |                                                                                                          |
| -         | Update to study team and contact information;                                                                                                          |                                                                                                          |
| -         | Addition of protocol signature page;                                                                                                                   |                                                                                                          |
| -         | Clarifications, formatting, and spelling updates throughout;                                                                                           |                                                                                                          |
| -         | New background information added;                                                                                                                      |                                                                                                          |
| -         | Update to Inclusion 7;                                                                                                                                 |                                                                                                          |
| -         | Update to Exclusion 6 to include wash out period;                                                                                                      |                                                                                                          |
| -         | Removal of therapy actions related to QTc Interval prolongation;                                                                                       |                                                                                                          |
| -         | Update to treatment modifications due to pneumonitis;                                                                                                  |                                                                                                          |
| -         | Update to prohibited medications and medications to be used with  caution due to updated safety profile;                                               |                                                                                                          |
| -         | Update to management of adverse events of note to reflect current safety profile;                                                                      |                                                                                                          |
| -         | Removal of treatment beyond disease progression;                                                                                                       |                                                                                                          |
| -         | Updates to Time and Events table and footnotes;                                                                                                        |                                                                                                          |
| -         | Clarification of tumor biopsy requirement;                                                                                                             |                                                                                                          |
| -         | Updates to SAE and Serious SAR reporting;                                                                                                              |                                                                                                          |
| -         | Updates to Data Safety Monitoring Plan;                                                                                                                |                                                                                                          |  
| Drug Substance: brigatinib                                     | ATOMIC Protocol Number: ARI-AT-002                                                                                                                                                                                   |                                                                     |                                         |
|----------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------------------------------------------------------|-----------------------------------------|
| -                                                              | Updated to data analysis plan                                                                                                                                                                                        |                                                                     |                                         |
| -                                                              | Removal of institution specific IRB reporting requirements;                                                                                                                                                          |                                                                     |                                         |
| -                                                              | Removal of single patient/subject exception.                                                                                                                                                                         |                                                                     |                                         |
| -                                                              | Removal of appendix Drugs with a Risk of Torsades de Pointes                                                                                                                                                         |                                                                     |                                         |
| 4                                                              | -                                                                                                                                                                                                                    | Revision to title of protocol                                       |                                         |
| -                                                              | The addition of 2 cohorts (one for patients who have only received  alectinib and one for patients who have tolerated brigatinib and  experienced disease progression and then will receive brigatinib 240  mg daily |                                                                     |                                         |
| -                                                              | Increased number of patients enrolled to 120 (40 per cohort)                                                                                                                                                         |                                                                     |                                         |
| -                                                              | Addition of information from the updated IB which included updated  information about the randomized phase 2 trial                                                                                                   |                                                                     |                                         |
| -                                                              | Updated information about the drug-drug interactions                                                                                                                                                                 |                                                                     |                                         |
| -                                                              | Additional changes were administrative to clarify questions  investigators have had over eligibility or tests.                                                                                                       |                                                                     |                                         |
| -                                                              | Inclusion criteria for previous therapies revised to reflect cohorts A, B, C                                                                                                                                         |                                                                     |                                         |
| -                                                              | Dose administration for Cohort C added                                                                                                                                                                               |                                                                     |                                         |
| -                                                              | Toxicities and dose modifications for Cohort C were added                                                                                                                                                            |                                                                     |                                         |
| -                                                              | Contact information was updated for safety reporting                                                                                                                                                                 |                                                                     |                                         |
| -                                                              | Product complaint/medication error instructions were added                                                                                                                                                           |                                                                     |                                         |
| -                                                              | Length of study revised to two years from amendment approval                                                                                                                                                         |                                                                     |                                         |
| 5                                                              | -                                                                                                                                                                                                                    | Inclusion criteria 3.1.11 -                                         | Revised contraception language; removed |
| hormonal contraception as an effective method of birth control |                                                                                                                                                                                                                      |                                                                     |                                         |
| -                                                              | Appendix C - Added information regarding co-administration of brigatinib  with CYP3A substrates                                                                                                                      |                                                                     |                                         |
| -                                                              | Pregnancy reporting language updated.                                                                                                                                                                                |                                                                     |                                         |
| 5.1                                                            | -                                                                                                                                                                                                                    | Page 2 (Study Contacts) adds Principal Investigator of Canada site. |                                         |
| -                                                              | Section 9.7 (Record Retention) updated to comply with Canadian law.                                                                                                                                                  |                                                                     |                                         |
| -                                                              | Appendix B and C removed from protocol by University Health Network  Research Ethics Board request, to be presented as auxiliary material for  the patient.                                                          |                                                                     |                                         |
| 6                                                              | -                                                                                                                                                                                                                    | Corrected Table of Content including page numbering.                |                                         |
| -                                                              | Administrative changes throughout to correct vertical spacing (reduced  number of pages to this document); section formatting and numbering;  sections headings; and page numbering in footer.                       |                                                                     |                                         |
| -                                                              | Clarified that no EOT visit is required with cohort changes from A or B to  C in Sections (Section 3.2.4. 3.3.3 and 6.4).                                                                                            |                                                                     |                                         |
| -                                                              | Clarifies dose modification regarding Grade 4 Non- Hematologic  Treatment Related AEs during Brigatinib 180mg Daily than Pneumonitis  (Section 4.4.3).                                                               |                                                                     |                                         |
| -                                                              | Corrected section references related to Concomitant Medications/ Juices/Herbal Supplements (within Section 4.6).                                                                                                     |                                                                     |                                         |
| -                                                              | Clarifies timeframe of Duration of Follow-up (Section 4.7, see also  footnote 4 Section 6.1).                                                                                                                        |                                                                     |                                         |  
| Drug Substance: brigatinib   | ATOMIC Protocol Number: ARI-AT-002                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |                                                                                              |
|------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------|
| -                            | Clarifies Section 6, including Schedule of Events (Section 6.1) and  Treatment Assessments (Section 6.3), Assessment of Efficacy  (Section 6.8) as follows:  - collection of information regarding prior cancer therapy;  - clarifies CT scans requirements. - Clarifies CT scan and brain MRI requirements and measurements. - Clarifies no EOT visit required with cohort changes from A or B  to cohort C.  - Clarifies timeframe of Duration of Follow-up.  - Clarifies that biopsies are required for patients treated on cohorts A  or B and enrolling in C.  - Specifies prior cancer therapy to be captured. - Clarifies tissue acquisition requirements. |                                                                                              |
| 7                            | -                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 | Updated to maintain one protocol version for all participating sites  (merging v5.1 and v6). |
| -                            | Adjusts left margins per ICH required minimum, and includes some  right margin readjustments.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     |                                                                                              |
| -                            | Updates References throughout to identify by authors (vs. numbers)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                |                                                                                              |
| -                            | Page 2 (Study Contacts) adds Canadian Site PI and updates some other  addresses                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |                                                                                              |
| -                            | Section 1.1 updated with recent research findings regarding brigatinib,  clarifies each cohort is evaluated independently                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |                                                                                              |
| -                            | Section 1.2 adds Canadian health systems use of IHC testing method and recent FDA approval of loritinib for patients with disease  progression.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   |                                                                                              |
| -                            | Sections 1.3 and 1.4 adds current and clarifies brigatinib information.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |                                                                                              |
| -                            | EOT visit clarified that EOT not needed for cohort changes from A or  B to C in Sections 3.2.4. 3.3.3 and 6.4.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |                                                                                              |
| -                            | Inclusion criteria Sections updated to confirm ALK positive status  allows CLIA or test approved for use in Canada (3.1.2); correct  subsection numbering (3.1.7 - 3.1.13); reference progressing on  lorlatinib for cohort A (3.2.1); and clarify no EOT visit for cohort A or  B participants entering cohort C; and biopsy required for cohort C  participants (3.2.4).                                                                                                                                                                                                                                                                                        |                                                                                              |
| -                            | Exclusion criteria Sections revisions include no washout for A or  cohort B participants entering cohort C (3.3.6); adds "as determined by  the investigator" to Clinically significant atrial arrhythmia (3.3.7); adds  new section "Another primary malignancy for which the patient is  currently receiving therapy" (3.3.8), and readjusts subsequent  subsection numbers (3.3.9 - 3.3.13)                                                                                                                                                                                                                                                                    |                                                                                              |
| -                            | Section 6.1 (Time/Events Table) expands columns to 12 cycles adding  new footnote 14 reference; updates "X" at Medical History (removes at  C1D1 & D8), all D1 cycle visits (adds for physical exam/vital signs,  ECOG, CBC/serum blood tests, and AEs); all D1 cycles for patient  diary and concomitant meds (add "Review"); and brain MRI timepoints  (moves to each 3rd cycle from each odd cycle - revised with protocol  v6) visit.                                                                                                                                                                                                                         |                                                                                              |  
| -   | Section 6.1 (Keynotes to footnotes) updates FN 9 to clarify ctDNA  blood samples collected only while patient receives treatment and adds  FN 14 allowing some telemedicine visits, at treating physician's  discretion, for non-scan even cycle visits.                                                                                             |
|-----|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| -   | Section 6.2 revised that patient diary (Appendix B) is a stand-alone  auxiliary patient document.                                                                                                                                                                                                                                                    |
| -   | Section 6.3 (Treatment Assessments) updates include adds paragraph  clarifying each odd day cycles (at 6.3.3) and each 3rd cycle (new 6.3.4)  visit assessments; updates odd day cycles (6.3.3); adds new subsection  for each 3rd cycle visit (6.3.4); and adds new subsection for non-scan  even cycles allowing some telemedicine visits (6.3.5). |
| -   | Section 6.4 (EOT Visit) revisions adds clarity for consistency with data  collection across participating centers (new paragraph 2); for AEs,  ctDNA blood sample collection; and for cohort C (previously cohort A  or B) participants.                                                                                                             |
| -   | Section 6.5 (Post-treatment/Follow-up Assessments) adds clarity for  recording data of EOT visit and long-term follow-ups.                                                                                                                                                                                                                           |
| -   | Section 7.3 (Documentation of non-serious AEs or SARs) adds clarity  for data recording with participants as both cohort A or B and cohort C.                                                                                                                                                                                                        |
| -   | Section 9.1, and throughout, updated references to IRB to include REB                                                                                                                                                                                                                                                                                |
| -   | Section 9.4 (Data Management) clarifies all data for each cohort is  captured independently from time of entry into cohort.                                                                                                                                                                                                                          |
| -   | Section 9.5.2 (Protocol Deviations) adds clarity for data capture and  regulatory reporting of missed assessments with use of telemedicine  visits.                                                                                                                                                                                                  |
| -   | Section 9.7 (Record Retention) adds Canada's required record retention  period per protocol v5.1                                                                                                                                                                                                                                                     |
| -   | Section 10 (Appendices) removes Appendix B and Appendix C per  protocol v5.1                                                                                                                                                                                                                                                                         |  
ARI-AT-002: Phase 2 Trial of Brigatinib after Treatment with Second-Generation ALK inhibitors in Refractory ALK Rearranged NSCLC
Amendment 7: April 20, 2020 Principal Investigator - USA Thomas E. Stinchcombe, MD Duke University DUMC 3198 25177 Morris Building Durham, NC 27710 Phone 919-681-9509 Fax 919-681-9599 E-mail: Thomas.stinchcombe@duke.edu
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signature page

The signature below constitutes the approval of this protocol and the attachments, and provides the necessary assurances that this trial will be conducted according to all stipulations of the protocol, including all statements regarding confidentiality, and according to local legal and regulatory requirements and applicable U.S. federal regulations and ICH guidelines.
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protocol signature page

Study Protocol Number: ARI-AT-002 Study Protocol Title: Phase 2 Trial of Brigatinib after Treatment with SecondGeneration ALK inhibitors in Refractory ALK Rearranged NSCLC
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table of contents

| 1.0 BACKGROUND AND RATIONALE 12  1.1 Study Synopsis 12  1.2 Non-small Cell Lung Cancer (NSCLC) 13  1.3 Brigatinib (AP26113) 15  1.4 Rationale 35 1.5 Correlative Studies to Explore Mechanisms of Resistance 36  2.0 STUDY OBJECTIVES 37 2.1 Primary Objective 37 2.2 Secondary Objectives 37 2.3 Exploratory Objectives 38  2.4 Primary Endpoint 38  2.5 Secondary Endpoints 38  3.0 PATIENT ELIGIBILITY 39  3.1 Inclusion Criteria for all cohorts 39  3.2 Inclusion criteria for cohort assignment 40  3.3 Exclusion Criteria for cohorts A, B, and C 41  4.0 TREATMENT PLAN 42  4.1 Schema for cohorts A and B 42  4.2 Schema for cohort C 42  4.3 Treatment Dosage and Administration 43  4.4 Toxicities and Dosing Delays/Dose Modifications for cohorts A and B 43 4.5 Toxicities and dose modifications for cohort C 47  4.6 Concomitant Medications/Juices/Herbal Supplements 49  4.7 Prohibitive Palliative Radiotherapy 49   |
|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|  
| Drug Substance: brigatinib       |                                                                                                         |
|----------------------------------|---------------------------------------------------------------------------------------------------------|
| 4.8                              | Prohibited Systemic Therapy                                                                             |
| 4.9                              | Prohibited Medications/Juices/Herbal Supplements ................................................... 49 |
| 4.10                             | D Duration of Therapy                                                                                   |
| D Duration of Follow-up          |                                                                                                         |
| 4.11                             | Removal of Patients from Protocol Therapy                                                               |
| 4.12                             | Study Withdrawal .                                                                                      |
| 4.13                             |                                                                                                         |
| 5.0 DRUG INFORMATION             |                                                                                                         |
| 5.1                              | Investigational Agent Description and Management .                                                      |
| 6.0 EVALUATIONS AND ASSESSMENTS  |                                                                                                         |
| 6.1                              | Time and Events Table                                                                                   |
| 6.2                              | Pre-Study Assessments                                                                                   |
| 6.3                              | T Treatment Assessments                                                                                 |
| 6.4                              | EOT Visit                                                                                               |
| 6.5                              | Post-Treatment/Follow-up Assessments                                                                    |
| Correlative Studies Procedures . |                                                                                                         |
| 6.6                              | Assessment of Safety .                                                                                  |
| 6.7                              |                                                                                                         |
| 6.8                              | Assessment of Efficacy .                                                                                |
| 7.0 ADVERSE EVENTS .             |                                                                                                         |
| 7.1                              | Intentionally Blank                                                                                     |
| 7.2                              | Definitions                                                                                             |
| 7.3                              | Documentation of non-serious AEs or SARs .                                                              |
| SAEs or Serious SARs .           |                                                                                                         |
| 7.4                              |                                                                                                         |
| 7.5                              | Data and Safety Monitoring Plan                                                                         |
| 8.0 STATISTICAL CONSIDERATIONS . |                                                                                                         |
| 8.1                              | Study Design/Study Endpoints                                                                            |  
| Drug Substance: brigatinib                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | ATOMIC Protocol Number: ARI-AT-002   |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------|
| 8.2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Sample Size and Accrual 73           |
| 8.3                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | Data Analysis Plans 73               |
| 9.0 STUDY MANAGEMENT 74  9.1 Institutional Review Board (IRB) / Research Ethics Board REB)  Approval and Consent 74  9.2 Required Documentation 75  9.3 Enrollment Procedures 75  9.4 Data Management and Monitoring/Auditing 76  9.5 Adherence to the Protocol 76  9.6 Amendments to the Protocol 78  9.7 Record Retention 78  9.8 Obligations of Investigators 78  10.0 APPENDICES 79  Appendix A: ECOG Performance Status Appendix B: Patient Diary for Brigatinab (see as auxiliary patient document)  Appendix C: Prohibited Drugs, Juices and Herbal Supplements, and  Medications to be used with Caution (see as auxiliary patient  document) |                                      |  
11.0 REFERENCES ...................................................................................................... 80
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1.0 background and rationale

1.1 Study **Synopsis**
This multicenter phase II trial will evaluate brigatinib (AP261136) in patients with advanced non-small cell lung cancer (NSCLC) harboring an anaplastic lymphoma kinase (ALK) rearrangement, previously treated with a next generation ALK inhibitor such as ceritinib or alectinib.(Shaw et al. 2014; Soria et al. 2017; Peters et al. 2017; Hida et al. 2017). Ceritinib and alectinib are referred to as 'next generation,"
and are approved by the Food and Drug Administration (FDA) for patients with a confirmed *ALK* rearrangement (referred to as ALK+) who have progressed on or are intolerant of crizotinib, and alectinib and ceritinib is approved for treatment naïve patients. Alectinib, ceritinib, and crizotinib currently are recommended by the National Comprehensive Cancer Network (NCCN) as first- line therapy with category 1 recommendations; alectinib is the preferred therapy.( ) In addition, multiple other next generation inhibitors are in development. Brigatinib has also demonstrated significant activity in patients who have progressed on crizotinib, with responses reported for both intracranial and extracranial disease.(Kim et al. 2017)The activity of brigatinib in patients who have disease progression after ceritinib or alectinib has not been prospectively investigated. Brigatinib was compared to crizotinib in phase 3 trial of treatment naïve patients, and was found a statistically significant improvement in progression-free survival.  
There is increasing concern that patients who have been exposed to multiple therapies may have multiple mechanisms of resistance, including ALK dependent and ALK independent mechanisms of resistance. Therefore, patients will be divided into cohorts (A) patients who have progressed on multiple lines (>1) of ALK directed therapy, including at least one licensed or experimental next generation therapy (B) patients who have progressed on only alectinib.8 In an exploratory cohort (C) patients who tolerate but progress on 180mg brigatinib (as a part of the trial or as part of routine clinical care) will be treated with 240 mg brigatinib daily to determine if intra-patient dose escalation is safe and tolerable and is associated with greater activity at the higher doses.
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rationale for post alectinib cohort

Brigatinib is predicted to maintain activity against all *ALK* resistance mutations, and such resistance mutations are associated with progression in approximately 50% of patients treated with alectinib.(Gainor et al. 2016; Shaw et al. 2019; Lin, Riely, and Shaw 2017) Brigatinib inhibits ALK with approximately 2-fold greater potency than alectinib in vitro. Steady-state levels of exposure of brigatinib in patients treated with 90 mg daily for 7 days followed by 180 mg daily regimen of brigatinib are at least 2-fold higher than those achieved in patients treated with alectinib (600 mg twice daily), suggesting that brigatinib may also be less susceptible to pharmacologic resistance than alectinib.(Zhang et al. 2016) The mechanisms of resistance and resistance mutations may be unique for alectinib. Investigating brigatinib in patients who have progressed on only alectinib will create a more homogenous cohort, and there is a clinical need to assess the activity of other ALK inhibitors as alectinib is adopted as a first-line therapy. Rationale for dose escalation cohort. The rationale for escalation to 240 mg daily at disease progression is to attempt to overcome potential pharmacologic resistance at 180 mg daily brigatinib (i.e. to increase brigatinib exposure in order to have better activity against a given *ALK*
resistance mutation may be dose dependent or for increased exposure in the CNS to treat CNS disease progression). A higher dose of brigatinib may have inhibitory activity against resistance mutations, and better CNS penetration which is clinically relevant since many patients experience progressive CNS disease. In the phase 1/2 dose-limiting toxicities (DLT) were grade 3 alanine aminotransferase (ALT) in one patient at 240 mg daily and grade 4 dyspnea in one patient at 300 mg daily.(Gettinger et al. 2016)The maximum tolerated dose was not established. In patients who were treated with 240 mg daily, 300 mg daily or 120 mg twice daily (n=15) the grade 3 or 4 adverse events observed at (>5%) were fatigue
(13%), diarrhea (13%), headache (7%), vomiting (14%), increased lipase (13%),
hypertension (7%), and pyrexia (7%). Since exposure to lower starting doses of brigatinib has now been associated with an abrogation of early onset pulmonary symptoms at escalation to a higher dose (e.g. 90 mg for 7 days before increasing to 180mg as in ALTA), re-exploration of the tolerability and efficacy of 240 mg QD after tolerable exposure to 180 mg is appropriate clinical question for further study.
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study design

The study will enroll up to 40 patients in each of the cohorts, using a Simon twostage design, with a primary endpoint of objective response (complete response
(CR) + partial response (PR)) as assessed by the investigator. Each cohort is evaluated independently. Secondary objectives include estimating duration of response, progression free survival (PFS), intracranial and extracranial PFS, and overall survival (OS). Exploratory objectives include intracranial ORR among patients with measurable CNS disease. If the trial meets the primary efficacy endpoint an exploratory evaluation of molecular predictors of response and resistance, using both tumor tissue samples and circulating tumor DNA (ctDNA) from peripheral blood samples will be conducted.
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1.2 non-small cell lung cancer

Factors that determine treatment for non-small cell lung cancer (NSCLC) include histology, age, comorbidities, and presence or absence of driver mutations or rearrangements. One such oncogenic driver that influences treatment is the novel fusion oncogene resulting from an inversion in chromosome 2 of two genes: the echinoderm microtubule-associated protein-like 4 (EML4) and the anaplastic lymphoma kinase (ALK) gene. ALK rearrangements are more commonly (but not exclusively) detected in NSCLC patients with adenocarcinoma, patients with a history of light or never smoking, and younger patients. The prevalence among patients with adenocarcinoma is estimated to be 8% (95% confidence interval (CI), 6 to 10%).(Kris et al. 2014; Barlesi et al. 2016). Given that ALK rearrangements are not exclusively found in these groups, current practice guidelines recommend reflexive testing in all patients with non-squamous NSCLC. Current FDA approved methods of detecting ALK rearrangements are the fluorescence in situ hybridization (FISH), and more recently immunohistochemistry (IHC) testing. (Lindeman et al. 2018) Additional methods that can detect ALK fusions include PCR-based methods and more recently DNA- and RNA-based next generation sequencing (NGS) assays from tumor and/or ctDNA. The Canadian health system has adopted an IHC testing method nationally, and there is increasing adoption of tumor and ctDNA NGS testing methods. (Lindeman et al. 2018; Cutz et al. 2014; Wynes et al. 2014)
Crizotinib, an ALK inhibitor, is a standard first-line treatment for NSCLC patients with this genetic rearrangement, so called ALK+ disease. This is based on superior objective response rates (ORR) and progression free survival (PFS) in phase 3 trials of crizotinib compared to chemotherapy in the first and second line treatment of advanced ALK+ NSCLC patients. A phase 3 trial compared ceritinib to platinum-pemetrexed and demonstrated a statistically significant improvement in PFS as assessed by the independent review committee (IRC) (HR of 0.55, 95% CI, 0.42-0.73, p<0.00001; median PFS 16.6 and 8.1 months, respectively) and superior ORR (72.5% vs 26.7%) with ceritinib.(Soria et al. 2017) The most common grade 3 or 4 AE's were ALT (31%), and AST (17%). The median relative dose intensity was 78.4%. Two phase 3 trials have compared alectinib to crizotinib in ALK therapy naïve patients, and have demonstrated a superior ORR and PFS with alectinib. A phase 3 trial in Japan compared alectinib to crizotinib in patients with ALK + NSCLC who had not previously been treated with an ALK inhibitor. (Hida et al. 2017; Peters et al. 2017) The independent data monitoring committee stopped enrollment to the trial early since alectinib had demonstrated a statistically significant improvement in PFS.4 Patients assigned to alectinib compared to crizotinib had a statistically higher ORR (92% vs 79%), a lower rate of grade 3 or 4 AE's (26% vs 52%), treatment discontinuations due to AE's (9% vs 20%), and a longer PFS (hazard ratio (HR) of 0.34; 95% CI, 0.17 to 0.71; p<0.0001; median not reached and 10.2 months, respectively). An international trial compared alectinib to crizotinib and revealed a superior ORR by investigator (82.9% vs 75.5%, p=0.09), and PFS by IRC (HR of 0.50, 95% CI, 0.36 to 0.70; p<0.001; median PFS of 25.7 and 10.4 months, respectively). The grade 3 to 5 AE's were lower in the alectinib than the crizotinib arms (41% vs 51%). The time to CNS disease progression was significantly longer in the alectinib arm compared to the crizotinib arm (HR of 0.16, 95% CI, 0.10-0.28, p<0.001), and the 12-month rate of CNS progression was 9.4% and 41.4%, respectively The current NCCN recommend crizotinib, ceritinib, and alectinib as first-line therapies (category 1) with alectinib being the preferred therapy.6 These phase 3 trials and the NCCN guidelines have led to the adoption of second-generation ALK TKI's as first-line therapy. Recently lorlatinib was approved by the FDA for patients with disease progression after alectinib, after ceritinib, or crizotinib and one other ALK TKI.(Solomon et al. 2018) Brigatinib, a next generation ALK inhibitor with broad activity against crizotinib resistance mutations and promising CNS activity. It was approved by the FDA for patients who have progressed on or were intolerant of crizotinib. Brigatinib was investigated in a two-arm randomized phase 2 trial of 90 mg daily and 90 mg daily for 7 days followed by 180 mg daily.(Kim et al. 2017) The primary endpoint was ORR, and secondary end-points were PFS and CNS response. In the 90 mg daily arm the ORR by IRC was 48% (95% CI, 39-58%), and the median PFS was 9.2 months (95% CI, 7.4 to not reached). In the 90 mg daily followed by 180 mg daily the ORR by IRC was 53% (95% CI, 43-62%), and the median PFS was 15.6 months (95% CI, 11.0 to not reached). The intracranial response rate in patients with measurable CNS disease by independent radiological review on the 90 mg daily arm (n=26) was 42% (95% CI, 23-635), and in the 90 mg daily followed by 180 mg daily arm (n=18) was 67% (95% CI, 41%-87%). In the 90 mg daily followed by 180 mg daily the grade ≥3 AE's observed at a rate of ≥ 2% of patients were: dyspnea (2%), back pain (2%), increase phosphokinase (9%), rash (3%), and hypertension (6%). Episodes of QT prolongation were not observed.  
At this time the activity of brigatinib after ceritinib, or alectinib has not been prospectively studied.
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1.3 brigatinib (ap26113)

Brigatinib (AP26113) is a novel, orally-active tyrosine kinase inhibitor (TKI) discovered and developed by ARIAD Pharmaceuticals, a subsidiary of Takeda Oncology. Primary targets are activated, mutant forms of anaplastic lymphoma kinase (ALK) and c-ros oncogene 1 (ROS1), which play important roles in nonsmall cell lung cancer (NSCLC) and other cancers.  
1.3.1 **Pharmacology Summary**
A series of in vitro and in vivo studies have been performed to characterize the pharmacodynamic profile of brigatinib. These studies have demonstrated that brigatinib potently inhibits activated variants of ALK, such as echinoderm microtubule-associated protein like (EML4)-ALK, and variants of ALK, including the L1196M gatekeeper mutation, that confers resistance to crizotinib. No ALK mutations have been identified in in vitro mutagenesis assays that confer resistance to brigatinib at clinically achievable concentrations. Overall, the data established that brigatinib has a promising profile as an antitumor agent, and they provided a strong rationale for conducting a clinical development program in cancer patients.
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1.3.2 absorption distribution metabolism and

Brigatinib is bioavailable after oral administration in multiple animal species, and in rats and monkeys has been shown to be a low clearance compound that is extensively distributed in extravascular compartments. In vitro, brigatinib was moderately bound to plasma proteins in mouse, rat, monkey and human and also did not show preferential partitioning into red blood cells (RBCs). Brigatinib is a Permeability-glycoprotein (P-gp) substrate. Overall, the metabolism of brigatinib in rats, monkeys, and humans (both in vitro and in vivo) was qualitatively similar with no unique human metabolites observed. N-demethylation leading to AP26123 was identified as the main biotransformation pathway in liver microsomes and hepatocytes. Other minor metabolites were present in insignificant amounts in hepatocyte incubations and did not contribute substantially to brigatinib metabolism. Analysis of rat, monkey, and human urine, and feces of rats by liquid chromatography/tandem mass spectrometry (LC/MS/MS) showed that AP26123 also was the principal metabolite in these matrices. In [14C]-brigatinib ADME studies in rats, monkeys, and humans, the majority of the circulating radioactivity was attributed to the parent drug brigatinib (>60%). The metabolite AP26123 accounted for <10% of circulating radioactivity. In vitro studies suggest that brigatinib and its metabolite, AP26123, do not inhibit CYPs 1A2, 2B6, 2C8, 2C9, 2C19, 2D6, and 3A4/5 at therapeutically relevant drug concentrations. Thus, clinical DDIs due to inhibition of CYPs by brigatinib and AP26123 are highly unlikely.
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1.3.3 toxicology summary

The nonclinical safety and toxicity profile of brigatinib was characterized in acute toxicity studies in mice and rats, range-finding and 28-day Good Laboratory Practice (GLP) toxicology studies in rats and cynomolgus monkeys, in vitro genotoxicity studies, and a phototoxicity study in rats. A summary of toxicology observations is summarized in the investigator brochure. A single oral dose of brigatinib was tolerated in mice at doses up to 75 mg/kg and in rats at doses up to 125 mg/kg. Dose-dependent increases in mortality occurred at dose levels ≥125 mg/kg in mice and ≥250 mg/kg in rats. In the 28-day GLP oral toxicology/toxicokinetics study in rats, oral administration of brigatinib at doses of 30 or 60 mg/kg/day resulted in a dosedependent increase in mortality, which led to the cessation of dosing in the 60 mg/kg/day dose group toward the end of Week 1. A clear spectrum of clinical signs of toxicity preceded the deaths of the animals. The key histopathological findings in rats at the 30 and 60 mg/kg/day dose levels that died prematurely and in some 30 mg/kg/day rats that survived the 28-day treatment period were minimal to marked hematopoietic hypocellularity in the bone marrow in conjunction with lymphoid depletion in the spleen, thymus and other lymphoid tissues, which raise the potential for immunosuppressive effects of brigatinib. Other notable brigatinib-related gross anatomic or microscopic findings, including bone and gastrointestinal pathologies, were seen primarily in rats that died prematurely. Brigatinib was physically well tolerated by rats in the 15 mg/kg/day dose group, and by most rats in the 30 mg/kg/day dose group. Reversible, dose-related reductions in group mean body weight, body weight gain, and food consumption were noted at these dose levels from Day 7 until the end of the dosing period. Based on the incidence and severity of gross anatomic and microscopic lesions and mortality observed at the 30 mg/kg/day brigatinib dose level, the no-observed adverse effect level (NOAEL) of brigatinib was considered to be 15 mg/kg/day, which corresponded to a Cmax of 1437 ng/mL and 1527 ng/mL, and AUC0-24 of 21716 h•ng/mL and 23550 h•ng/mL on Day 28 for males and females, respectively. In the 28-day GLP monkey oral toxicology/toxicokinetic study, clinical signs of toxicity, moribundity, and mortality were evident beginning on Day 3 after daily oral administration of 45 mg/kg/day brigatinib. Consequently, dosing of all animals in the 45 mg/kg/day dose group was stopped on Day 7 or 8. The cause of premature death was attributed to brigatinib-related gastrointestinal toxicity, which involved all segments of the gastrointestinal tract, but was most severe in the stomach and small intestines. Other prominent histopathological findings in monkeys that died prematurely and in animals treated with 15 and 45 mg/kg/day brigatinib that survived to the terminal sacrifice on Day 30 were generally similar to those seen in rats, including lymphoid atrophy/necrosis and bone marrow hypocellularity. No brigatinib-related changes were seen at terminal sacrifice in the 7.5 mg/kg/day treatment group, or in any dose group at the end of the 28-day recovery period. Based on these results, the NOAEL was considered to be 7.5 mg/kg/day brigatinib, corresponding to a Cmax of 526 ng/mL and 560 ng/mL, and AUC0-24 of 3408 h•ng/mL and 3358 h•ng/mL on Day 28 for males and females, respectively. No evidence of cutaneous phototoxicity or ocular phototoxicity was observed in rats after a single oral administration of brigatinib at doses as high as 60 mg/kg. A bacterial reverse mutation assay and a chromosomal aberration test in human peripheral blood lymphocytes revealed no evidence of brigatinib genotoxic activity. In summary, the nonclinical safety and toxicity profile of brigatinib was adequately characterized in appropriate animal and in vitro models to inform the design of clinical studies of brigatinib, determine potential risks associated with its administration to patients, and provide recommendations for clinical monitoring.
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1.3.4 preclinical data

The activity of brigatinib against 293 recombinant human protein kinases was analyzed in an in vitro kinase assay. At a concentration of 1 μM, brigatinib was found to inhibit the activity of 36 kinases (12%) by at least 90%. More detailed analysis of the kinases with greatest sensitivity showed that 1 kinase, ALK, was inhibited with a 50% inhibitory concentration (IC50) <1 nM. Eleven kinases, including ROS1, FAK, FLT3, CHK2, and EGFR-L858R were inhibited with IC50 values between 1 nM and 10 nM. Nineteen kinases, including EGFRL858R/T790M, ERBB2, and CHK1, were inhibited with IC5 0 values between 10 nM and 50 nM. Twelve kinases, including IGF-1R and native EGFR, were inhibited with IC50 values between 50 nM and 100 nM
These studies demonstrated that brigatinib potently inhibited the kinase activity of ALK, and inhibited the activity of ROS1, mutant EGFR, and to a lesser extent IGF-1R, prompting further analysis of these kinases in non-clinical experiments.
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1.3.5 anaplastic lymphoma kinase inhibitory

In nonclinical studies, brigatinib has been shown to:  
- Inhibit growth of ALK+ human tumor-derived cell lines with potency and selectivity approximately 10-fold greater than that of crizotinib
- Potently inhibit ALK variants with secondary mutations that confer resistance to crizotinib, ceritinib, or alectinib
- Suppress the emergence of any resistant ALK mutant in an in vitro mutagenesis assay, at concentrations that can be achieved clinically
- Induce regressions or inhibit growth of tumor xenografts driven by native ALK or mutant variants that confer clinical resistance
- Prolong survival of mice in an ALK-dependent orthotopic brain tumormodel
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1.3.6 in vitro activity in

In a panel of 7 anaplastic large cell lymphoma (ALCL) and NSCLC cell lines that express nucleophosmin-ALK (NPM-ALK) or EML4-ALK fusions, the concentration of brigatinib that inhibited growth by 50% (GI50) ranged from 4 nM
to 31 nM, and the concentration that inhibited ALK phosphorylation by 50%
(IC50) ranged from 1.5 nM to 12 nM. Across 3 ALK-negative ALCL and NSCLC cell lines, the GI50 values for brigatinib ranged from 503 nM to 2387 nM.  
Overall, brigatinib potently inhibited ALK activity and proliferation in all ALK+ cell lines tested, and exhibited >100-fold selectivity over ALK-negative lines. In contrast, crizotinib exhibited 10-fold lower potency compared to brigatinib in ALK+ cell lines, and only approximately 10-fold selectivity over ALK-negative lines. AP26123, the principal metabolite of brigatinib in vivo, was included in a subset of these studies and found to have slightly reduced anti-ALK activity compared to brigatinib. The cellular activity of brigatinib was also compared to that of crizotinib, ceritinib, and alectinib in Ba/F3 cells whose viability was dependent on activity of a native EML4-ALK fusion, or fusions containing mutations in the ALK kinase domain that have been previously been associated with resistance in clinical or nonclinical studies.10,12,13 Brigatinib inhibited the viability of cells expressing native EML4-ALK with potency 8-fold greater than that of crizotinib (IC50 of 14 nM versus 107 nM). Brigatinib also inhibited the viability of cells expressing all 17 ALK mutants (IC50 values of 9 to 184 nM), with potency substantially greater than that of crizotinib (IC50 values of 170 to 1109 nM) for all 17 mutants except L1198F, which has been associated with resistance to ceritinib but not crizotinib. The relationship between TKI potency in these cellular assays and levels of TKI exposure in patients (mean steady state plasma concentrations), corrected for the functional effects of protein binding, was analyzed (Figure 1). For crizotinib, drug levels in patients exceed the IC50 for native EML4-ALK, but did not exceed, by at least 2-fold, the IC50 for variants that have been associated with crizotinib resistance. In contrast, based on PK data from the ongoing phase 1/2 trial, brigatinib plasma concentrations in patients dosed at 90 or 180 mg daily were found to exceed the IC50 values for native EML4-ALK and all 17 resistance mutants by at least 2-fold, with the exception of the G1202R mutant, whose IC50 was substantially exceeded by brigatinib levels achieved at 180 mg but not 90 mg daily dosing. A similar analysis of ceritinib and alectinib revealed that certain mutations increased the inhibitory concentrations to levels that were not exceeded, by at least 2-fold, by steady state plasma concentrations at the recommended phase 2 doses (Figure 1). These include T1151Tins, L1152R, L1152P, L1198F, and G1202R for ceritinib, and T1151Tins, I1171N, V1080L, and G1202R for alectinib. Finally, a cell-based accelerated mutagenesis assay was performed to more broadly assess the mutational liabilities of brigatinib and crizotinib. While this assay successfully identified mutations that cause clinical resistance to crizotinib, no mutations in ALK were identified that had an IC50 that exceeded the concentrations of brigatinib achieved in patients dosed with 90 or 180 mg. Taken together, these results demonstrate that brigatinib has pan-ALK inhibitory activity in vitro and is the only ALK TKI predicted to retain potent activity against all secondary ALK mutants described to date. (Figure 1).
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figure 1

50% maximal inhibitory concentration (IC50) values of Ba/F3 cells dependent on expression of EML4 ALK (native) or kinase domain mutated EML4 ALK variants (n=17). Data for each cell line are derived from at least 3 independent experiments (error bars=standard deviation). Dashed horizontal lines indicate the mean steady state (SS) concentrations of each drug (expressed as the average plasma drug concentration over the dosing interval determined by dividing: AUC0-24, ss by 24 h, or Cave,ss) corrected for the functional effects of protein binding (2.7, 2.7, 4.1, and 2.0-fold for crizotinib, ceritinib, alectinib, and brigatinib, respectively;10, 14,15 at the recommended phase 2 doses:  
a: Crizotinib: 250 mg BID, 266 nM (Cave,ss [719 nM]/2.7)
b: Ceritinib: 750 mg QD, 456 nM (Cave,ss [1232 nM]/2.7)1 c: Alectinib: 600 mg BID, 302 nM (Cave,ss [1120]/3.7)
d: Brigatinib 180 mg QD, 724 nM (Cave,ss [1477 nM]/2.0) and 90 mg QD, 291 nM
(Cave,ss [582 nM]/2.0) (Data on file,Takeda Pharmaceuticals, Inc.)
For each TKI, mutants for which the clinically effective concentration did not exceed the IC50by at least 2-fold are indicated in red text. *For brigatinib, G1202R
met this criterion based on exposure in patients dosed with 90 mg daily, but no mutants met this criterion based on exposure in patients dosed with 180 mg daily.
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1.3.7 in vivo activity in

The in vivo activity of brigatinib was examined in ALK+ KARPAS-299 (ALCL) and H3122 (NSCLC) xenograft models. Daily oral administration of brigatinib (10, 25, and 50 mg/kg) led to a dose-dependent inhibition of tumor growth in both models, with a dose level of 25 mg/kg inhibiting tumor growth by 89% in the KARPAS-299 model and inducing tumor regression by >90% in the H3122 model. In both models, a prolonged inhibition of ALK signaling was observed after administration of 25 mg/kg brigatinib, with >90% and >60% reductions in levels of phosphorylated ALK observed 10 and 24 hours after dosing, respectively. Additional in vivo tumor studies were conducted using Ba/F3 cell lines engineered to express native EML4-ALK, a crizotinib-resistant variant (L1196M), and the most recalcitrant mutant identified in in vitro assays (G1202R). Mice bearing subcutaneous tumors expressing native EML4-ALK or EML4- ALK/L1196M were administered vehicle, brigatinib, or crizotinib orally once daily. Crizotinib induced the regression of tumors expressing native EML4- ALK at the highest dose tested (200 mg/kg), but did not show antitumor activity in the EML4-ALK/L1196M model at this same dose. In contrast, brigatinib (50 mg/kg) induced tumor regression in both models. In mice bearing tumors expressing EML4- ALK/G1202R, brigatinib (50 mg/kg) inhibited tumor growth by 88%, while crizotinib (200 mg/kg) inhibited tumor growth by 46%. Doses of ceritinib (50 mg/kg) and alectinib (60 mg/kg) that strongly inhibited growth of native EML4- ALK tumors (by >95%) had little to no impact on growth of EML4- ALK/G1202R tumors (≤15% inhibition of tumor growth).
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1.3.8 in vivo activity in

Activity of brigatinib in the CNS was assessed in vivo using an orthotopic brain tumor model. ALK+ H2228 (NSCLC) cells were injected intracranially to form tumors in the brain and tumor-bearing mice were treated with vehicle, crizotinib or brigatinib. Daily oral administration of crizotinib at 100 mg/kg extended median survival to 48 days compared to 28 days in vehicle-treated mice (Figure 2). Compared to crizotinib-treated mice, daily oral dosing with 25 and 50 mg/kg brigatinib significantly prolonged median survival to 62 days and >65 days, respectively (Figure 2). Histological findings demonstrated a significant reduction in tumor burden in the brains of mice treated with 50 mg/kg brigatinib compared with crizotinib-treated mice.10  
Figure 2:
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1.3.9 clinical data

As of 01 August 2017, 634 patients have been enrolled in Takeda-sponsored clinical trials of brigatinib in cancer patients (phases 1, 2, and 3), and 263 subjects have been enrolled in clinical pharmacology studies. Three company-sponsored clinical studies with brigatinib are being conducted in adult cancer patients as of August 2017:  
- A phase 1/2 study of the safety, tolerability, PK and preliminary antitumor activity of brigatinib in advanced malignancies, including ALK+ NSCLC (Study AP26113-11-101).  
- A pivotal phase 2 study in patients with locally advanced or metastatic ALK+
NSCLC whose disease has progressed on therapy with crizotinib (Study AP26113- 13-201; ALTA).  
- A pivotal randomized phase 3 study of brigatinib versus crizotinib in patients with locally advanced or metastatic ALK+ NSCLC and no previous treatment with an ALK inhibitor (Study AP26113-13-301; ALTA 1L).
An EAP (Study AP26113-16-901) to provide brigatinib to patients with ALK+ NSCLC who are resistant or intolerant to at least 1 prior ALK TKI and for whom brigatinib therapy is requested by the investigator was initiated in 2016 and was closed after brigatinib was granted accelerated approval in the US in April 2017. A similar EAP is ongoing in Europe. As of 25 July 2017, approximately 139 patients have been exposed to brigatinib in the Post-Marketing setting in the US and as of 14 July 2017, 265 patients have been exposed to brigatinib through EAP in the US and Europe.  
The following clinical pharmacology studies have been completed or are ongoing:  
- An ethnobridging study to determine the PK of orally administered brigatinib in healthy Japanese and Caucasian subjects (Study AP26113-13-102).  
- A study to provide a preliminary assessment of the effect of a high-fat meal on the relative bioavailability and PK of a single dose of brigatinib administered orally to healthy subjects (Study AP26113-13-103).  
- An ADME study with [14C]brigatinib (Study AP26113-13-104). - A DDI study evaluating the effects of rifampin, itraconazole, and gemfibrozil on the PK of brigatinib in healthy subjects (Study AP26113-15-105).  
- A BE study between 30 mg brigatinib tablets and 90 mg brigatinib tablets in healthy subjects (Study AP26113-15-106).  
- A study evaluating the PK of brigatinib in subjects with chronic hepatic impairment and matched healthy subjects (Study AP26113-15-107). This study
- is ongoing. - A study evaluating the PK of brigatinib in subjects with chronic renal impairment and matched healthy subjects (Study AP26113-15-108). This study is ongoing.  
- A study to provide a definitive assessment of the effect of a high-fat meal on the relative bioavailability and PK of a single dose of brigatinib administered orally to healthy subjects (Study AP26113-16-109).  
- A BE study between 30 mg brigatinib tablets and 180 mg brigatinib tablets in healthy subjects (Study AP26113-16-110).
Detailed information about these studies is provided in Section 5.2.
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clinical pharmacology studies

An overview is presented of the final PK and safety results for the 7 completed clinical pharmacology studies performed in healthy subjects: Study AP26113-13102 (Ethnobridging), Study AP26113-13-103 (Preliminary Food-Effect), Study AP26113-13-104 (ADME), Study AP26113-15-105 (DDI), Study AP26113-15-106 (30 mg vs 90 mg tablet BE), Study AP26113-16-109 (Pivotal Food-Effect) and Study AP26113-16-110 (30 mg vs 180 mg tablet BE) Study descriptions for the 2 ongoing clinical pharmacology studies in subjects with impaired end-organ function are also described although results are not available: Study AP26113-15-107 (Hepatic Impairment) and Study AP26113-15-108 (Renal Impairment).
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ethnobridging study (study ap26113-13-102)

This was a double-blind, randomized, placebo-controlled, single ascending dose study of PO- administered brigatinib in healthy subjects (24 Japanese and 24 Caucasian subjects). Three of the 6 cohorts consisted of 8 Japanese (6 active:2 placebo) subjects each and the other 3 cohorts consisted of 8 Caucasian (6 active:2 placebo) subjects each. The single doses of brigatinib tested were 90 mg, 120 mg, and 180 mg administered under fasting conditions. Each dose was tested in 2 cohorts, 1 of Caucasian subjects and 1 of Japanese subjects. Following single PO doses, plasma brigatinib concentrations reached a maximum at approximately 2.0 to 3.5 hours and then declined in a multi-exponential manner with all subjects showing quantifiable concentrations up to 72 hours postdose. The arithmetic mean Cmax increased with an increase in dose from 401.8 ng/mL and 451.3 ng/mL for Japanese and Caucasian subjects at 90 mg, respectively, to 640.3 ng/mL and 712.3 ng/mL for Japanese and Caucasian subjects at 180 mg, respectively. Although the mean peak concentration generally appeared higher for the Caucasian population, there was also higher intersubject variability with this population when compared with the Japanese population. The GeoMean coefficient of variation (CV%) Cmax with Caucasian subjects ranged from 41.2% to 65.2% across treatments when compared with the GeoMean CV% Cmax for Japanese subjects, which ranged from 26.6% to 37.0% across treatments. The mean AUC0-∞ increased from 6064 h•ng/mL and 6783 h•ng/mL for Japanese and Caucasian subjects at 90 mg, respectively, to 9910 h•ng/mL and 12149 h•ng/mL for Japanese and Caucasian subjects at 180 mg, respectively. Similar to the observation with Cmax, AUC0-∞ estimated for Caucasian subjects generally appeared higher with higher variability when compared with Japanese subjects. Given the variability, assessment of race on single dose PK parameters of brigatinib indicated that Caucasian and Japanese subjects had comparable systemic exposure at the studied dose levels. A could not be ruled out due to variability. Mean t½ was comparable across populations and dose levels and ranged from approximately 20 to 26 hours following single dose administration. Brigatinib was safe and well tolerated in healthy male and female Caucasian and Japanese subjects in this study after single PO dose administration of 90, 120, and 180 mg. Based on these single-dose PK findings, the PK of brigatinib appears to be similar between Japanese and Caucasian subjects.
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preliminary food-effect study (study ap26113-13-103)

The objective of this randomized, open-label study was to rule out a clinically significant food effect by assessing the effect of high-fat conditions on the PK and relative bioavailability of brigatinib as compared to fasting conditions. This study was designed to be a preliminary food-effect assessment intended to guide further development of brigatinib. Healthy male or female (of non-childbearing potential) adult subjects were eligible for study participation. Doses were administered in the fasting state or after the completion of a standard high-fat meal. Ten healthy subjects were enrolled (evaluable for safety) and 8 subjects were considered evaluable for all PK comparisons. Single PO doses of brigatinib 180 mg (6 x 30 mg tablets) were administered on Day 1 and subjects remained at the research site until at least 96 hours postdose (Day 4).  
When administered under fasting conditions, the median (range) time to reach first Cmax (Tmax) for brigatinib was 2.5 hours (range: 1 to 6 hours) after intake of the 180 mg brigatinib dose. After administration following a high-fat meal, median (range) Tmax was 6 hours (range: 1 to 8 hours). GeoMean Cmax for the fasted and high-fat regimens were 804.5 ng/mL and 612 ng/mL, respectively, representing a 24% decrease under fed conditions. Importantly, GeoMean AUC0-∞ values for the fasted and high-fat regimens were similar at 15607 h•ng/mL and 15488 h•ng/mL, respectively.The limits of the 90% CIs of the estimated GeoMean ratios of Cmax (67.766, 85.401) did not fall within the 80% to 125% margin, suggesting the presence of an effect of food on brigatinib absorption. However, the limits of the 90% CIs of the estimated GeoMean ratios for both AUC0-∞ (88.163, 113.479) and AUC0-t (88.086, 107.147) fell within the 80% to 125% margins required to support the absence of a clinically relevant effect of food intake on brigatinib PK.  
Brigatinib was well tolerated in healthy subjects under both fasted and fed conditions.
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[14c]adme study (study ap26113-13-104)

This was an open-label, non-randomized, mass balance study performed in 6 healthy male subjects to investigate the absorption, metabolism, and excretion of brigatinib. On Day 1, each subject received a single 180 mg PO dose of [14C]brigatinib (approximately 100 µCi). Serial PK sampling (blood, urine, feces) and safety assessments were conducted up to 216 hours postdose (morning of Day 10) or until the release criterion was met.[14C]radioactivity concentrations in plasma above the detectable level were observed up to 96 hours postdose in all 6 subjects, and in 4 of 6 subjects at 120 hours postdose. Brigatinib plasma concentrations were observed up to 240 hours postdose in all 6 subjects and in 5 of the 6 subjects who were still in the study at 264 hours postdose. Plasma brigatinib concentrations closely followed the plasma radioactivity concentrations. GeoMean plasma Cmax for both total radioactivity and brigatinib was approximately 1,000 ng/mL (Cmax for [14C]brigatinib equivalents was 7.6% higher than Cmax for brigatinib), and the median Tmax was 2 hours. The GeoMean exposure to total radioactivity in terms of AUC0-t and AUC0-∞ was close to approximately 20,000 h•ng/mL and only marginally higher (3.5% and 6.4% higher, respectively), than the values for brigatinib. The respective exposure PK parameter values (Cmax, Tmax, AUC) in plasma were very similar for brigatinib and TRA, indicating that concentrations of metabolites, if any, were negligible compared to those of brigatinib. The mean (±SD) total recovery of the administered radioactivity was 89.75±1.44%, of which 24.99±1.89% and 64.76±2.36% were recovered in urine and feces, respectively, indicating that feces was the major route of excretion of dosed [14C]brigatinib, although urinary excretion also contributed to drug elimination. Most of the radioactivity (approximately 80% of the dose) had been recovered by 120 hours postdose. Following PO administration of [14C]brigatinib, parent brigatinib was the major circulating radioactive component accounting for 91.5% of the plasma radioactivity. AP26123 was the principal metabolite observed and was present at 3.5% in the plasma. No other metabolites greater than 2% of the total plasma radioactivity were observed. Similarly in 0 to 240 hours pooled urine, parent brigatinib was the major species observed (85.57%) with AP26123 being the sole metabolite detected (6.17%). The major radioactive component in 0 to 240 hours pooled feces was brigatinib, accounting for 40.91% of the fecal TRA. Metabolites identified in feces were M36 (N-desmethyl brigatinib; AP26123), M28 (brigatinib cysteine conjugate), M25 (brigatinib N-oxide; AP32830), and M27 (monooxy-brigatinib), accounting for 39.13%, 14.03%, 1.04%, and 0.59% of the fecal TRA, respectively. Overall, the metabolism of brigatinib in humans was qualitatively similar to nonclinical toxicology species (rat and monkey) with no unique human metabolites observed.  
A single 180 mg PO dose of [14C]brigatinib was safe and well tolerated in the healthy male subjects in this study.
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ddi study of brigatinib with

In vitro studies demonstrated that brigatinib is primarily metabolized by CYP2C8 and CYP3A4, and is a substrate of the efflux transporter P-gp. This study was conducted to determine whether strong inhibitors of CYP2C8 or CYP3A4 (gemfibrozil and itraconazole, respectively) and a strong inducer of both enzymes, as well as P-gp, (rifampin) alter the single dose PK of brigatinib in healthy subjects. This was a single-center, 3-part, open-label, single-dose, 1-sequence, crossover study evaluating the effects of gemfibrozil (Part 1), rifampin (Part 2), and itraconazole (Part 3) on brigatinib PK in healthy subjects. In each part of the study, subjects received a single PO dose of brigatinib indose-proportional relationship treatment period 1. In treatment period 2, subjects were pretreated with the CYP inhibitor or inducer for either 4 or 6 days prior to co-administration with brigatinib. Subjects received the following treatments:
- Part 1: Gemfibrozil DDI Study Treatment period 1: 90 mg brigatinib. Treatment period 2: 600 mg gemfibrozil twice daily (BID) + 90 mg brigatinib. - Part 2: Rifampin DDI Study Treatment period 1: 180 mg brigatinib. Treatment period 2: 600 mg rifampin QD + 180 mg brigatinib. - Part 3: Itraconazole DDI Study Treatment period 1: 90 mg brigatinib. Treatment period 2: 200 mg itraconazole BID + 90 mg brigatinib.  
Subjects received the single doses of brigatinib following an overnight fast of at least 10 hours at approximately the same time on each dosing day. During treatment period 2, the CYP inducer or inhibitor was administered first for either 4 or 6 days, followed by co-administration with brigatinib. A washout period of at least 16 days between brigatinib doses was implemented and blood samples for brigatinib plasma PK characterization were collected for at least 120 hours following each brigatinib dose for all 3 study parts.
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part 1 gemfibrozil ddi study

Twenty healthy subjects were enrolled in Part 1 of the study and received at least 1 dose of the study drug in the treatment phase, and were included in the PK and safety populations. One subject was discontinued from the study due to vomiting within 4 hours of dosing in treatment period 2 and therefore, 19 subjects were evaluable for statistical PK comparisons. Median Tmax of brigatinib was similar for the 2 treatment periods. Compared with brigatinib administered alone, co-administration with gemfibrozil reduced the Cmax of brigatinib by 41% and the AUC0-∞ and AUC0-120 of brigatinib were decreased by 11.5% and 14.7%, respectively. The percent GeoMean ratio for Cmax was 59.086% with a 90% CI of 53.847 to 64.835. The percent GeoMean ratios and 90% CI for AUC0-∞ and AUC0-120 were 88.469% (83.186, 94.088) and 85.339% (80.036, 90.993), respectively. Although exposure to brigatinib was reduced following gemfibrozil administration, the degree of decrease for each parameter is well within the typical observed interpatient PK variability for brigatinib in patients under SS conditions. Therefore, CYP2C8 does not appear to contribute meaningfully to the clearance of brigatinib in vivo. No dose modification is required for brigatinib during co-administration with strong CYP2C8 inhibitors. Single PO doses of 90 mg brigatinib alone and when co-administered with gemfibrozil were well tolerated. No deaths or serious adverse events (SAEs) occurred during the study.
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part 2 rifampin ddi study

Twenty healthy subjects were enrolled in Part 2 of the study and all subjects received at least 1 dose of the study drug in the treatment phase, and were included in the PK and safety populations. One subject was discontinued from the study due to elevated liver enzymes approximately 21 days after dosing in treatment period 2 and therefore, 19 subjects were evaluable for statistical PK comparisons.  
Median Tmax of brigatinib was similar for both treatment periods. Compared with brigatinib administered alone, co-administration with rifampin reduced the Cmax of brigatinib by 59.5%; AUC0-∞ and AUC0-120 were decreased by 80.4% and 80.0%, respectively. The percent GeoMean ratio for Cmax was 40.478% with 90% CI (36.833, 44.484). The GeoMean ratios and 90% CI for AUC0-∞ and AUC0-120 were 19.582% (18.151, 21.127) and 20.021% (18.562, 21.594), respectively. Co-administration of multiple 600 mg daily doses of rifampin with a single 180 mg brigatinib dose resulted in a statistically significant decrease in brigatinib Cmax by 59.5%. A 5-fold higher apparent oral clearance after extravascular administration, calculated using the observed value of the last quantifiable concentration (CL/F) of brigatinib was observed, and brigatinib AUC0-∞ and AUC0-120 were decreased by 80.4% and 80.0%, respectively, relative to a single 180 mg brigatinib dose given alone. *Therefore, the concomitant use of strong and moderate CYP3A inducers with* brigatinib should be avoided. Single PO doses of 180 mg brigatinib alone and when co-administered with rifampin were well tolerated. No deaths or serious AEs occurred during Part 2 of the study.
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part 3 itraconazole ddi study

Twenty healthy subjects were enrolled in Part 3 of the study and all subjects received at least 2 doses of study drug and completed the treatment phase, and were included in the PK and safety populations. The median Tmax of brigatinib was similar for the 2 treatments. Compared with brigatinib administered alone, co-administration with itraconazole resulted in an increase in brigatinib Cmax. The GeoMean ratio for brigatinib Cmax was 121.165% with an associated 90% CI of 113.318 to 129.554. AUC0-∞ and AUC0-120 GeoMean ratios (90% CI) were 201.165% (183.917, 220.030) and 182.069% (171.579, 193.201), demonstrating increases by 101.2% and 82.1 respectively, in the presence of itraconazole. The t½ of brigatinib was prolonged from 30 to 45 hours in the presence of itraconazole. Itraconazole, a strong CYP3A4 and a P-gp inhibitor, had a moderate effect on the PK of brigatinib. Co-administration of multiple 200 mg BID doses of itraconazole with a single 90 mg brigatinib dose resulted in a statistically significant increase in brigatinib Cmax by 21.2%. A 2-fold decrease in CL/F of brigatinib was observed and brigatinib AUC0-∞ and AUC0-120 were increased by brigatinib dose given alone. Accordingly, the concomitant use of strong CYP3A inhibitors with brigatinib should be avoided. If concomitant use of strong CYP3A inhibitors cannot be avoided, the dose of brigatinib should be reduced by approximately 50% (ie, from 180 mg to 90 mg or from 90 mg to 60 mg considering the available tablet strengths). After discontinuation of a strong CYP3A inhibitor, the brigatinib dose that was tolerated prior to the initiation of the strong CYP3A inhibitor should be resumed.Single PO doses of 90 mg brigatinib alone and when co-administered with itraconazole were well tolerated. No deaths or SAEs occurred during Part 3 of the study, and no subject was discontinued from the study due to an AE.101.2% (2fold) and 82.1% (<2-fold), respectively, relative to a single 90 mg
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hepatic impairment study (study ap26113-15-107)

This study is an open-label, single-dose, parallel-group, inpatient, non-randomized study conducted in patients with chronic hepatic impairment and matched healthy subjects. A total of approximately 27 participants will be enrolled into the study, including 18 patients with hepatic impairment (6 each with Child-Pugh classes A, B, and C) and approximately 9 matched healthy controls. Patients with hepatic impairment will be matched with healthy subjects by age, sex, body mass index (BMI), and, if possible, smoking habits. Each participant will receive a single 90 mg PO dose of brigatinib in the morning of study Day 1 under fasting conditions and will remain in the clinic to complete PK sampling through 192 hours. This study is ongoing.
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renal impairment study (study ap26113-15-108)

This study is an open-label, parallel-group, inpatient, non-randomized, single-dose study conducted in patients with severe renal impairment and matched healthy subjects with normal renal function Approximately 8 subjects with severe renal impairment are planned to be enrolled along with 8 matched healthy subjects with normal renal function. Patients with renal impairment will be matched to the greatest extent possible with healthy subjects by age, sex, BMI and, if possible, smoking habits. Each participant will receive a single 90 mg PO dose of brigatinib in the morning of study Day 1 under fasting conditions and will remain in the clinic to complete blood and urine PK sampling through 168 hours. This study is ongoing.
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pivotal food-effect study (study ap26113-16-109)

Study AP26113-16-109 was conducted to provide a definitive assessment of the effect of a high-fat meal on the PK of a single PO dose of brigatinib, administered using the commercial 90 mg tablet formulation, in healthy subjects. This was a single-dose, randomized, open-label, 2-period, 2-sequence crossover study in healthy subjects. Single PO doses of brigatinib 180 mg (2 x 90 mg tablets) were administered after consumption of a high-fat meal or under fasting conditions. Each study drug administration was separated by a washout interval of at least 16 days. PK blood samples were collected and safety assessments were conducted at designated time points from predose until 168 hours postdose. A total of 24 subjects were randomized and were administered at least 1 dose of study drug and were included in the safety and PK populations. Three subjects were discontinued from the study prior to treatment period 2; therefore, 21 subjects completed the study and are included in the final statistical analyses. Two subjects were withdrawn early due to positive breath carbon monoxide test results; and 1 subject was withdrawn early due to noncompliance with clinic rules. Median brigatinib Tmax was 2 hours after dosing brigatinib 180 mg in the fasted state and 5.0 hours after dosing brigatinib in the fed state. The observed GeoMean Cmax was approximately 13% lower after dosing in the fed state (604.6 ng/mL) than after dosing in the fasted state (701.3 ng/mL). GeoMean values for AUC0-t were similar for both fasted and fed treatments (13054 h•ng/mL and 12742 h•ng/mL after dosing in the fasted and fed states, respectively). GeoMean values for AUC0-∞ were similar after dosing in the fasted state and fed state (13261 h•ng/mL and 12944 h•ng/mL, respectively).The results of the analyses conducted to evaluate the effect of a high-fat meal on brigatinib Cmax, AUC0-t, and AUC0-∞, demonstrated that the limits of the 90% CI of the estimated mean ratio of AUC0-t (89.396, 107.399) and AUC0-∞ (89.430, 107.386) fell within the 80% to 125% margins, but the lower bound of the 90% CI for Cmax (78.261, 96.752) fell below the 80% lower margin required to conclude BE between the fasted and fed treatments, with food intake reducing the GeoMean Cmax (estimated mean ratio was 87.016%) by approximately 13%. Brigatinib median Tmax was delayed by 3 hours after dosing in the fed state compared to the fasted state. Overall, the observed 13% decrease in plasma Cmax following a high-fat meal was small relative to typical variability in Cmax observed for brigatinib in patients under SS conditions (approximately 60% CV). Without a corresponding decrease in AUC when brigatinib is administered with a high-fat meal, these changes in Cmax are not considered to be clinically important for the safety and efficacy of brigatinib. Therefore, brigatinib may be administered without regard to food intake.
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concentration-qtc analysis

Electrocardiogram (ECG) and time-matched PK data were available from a subset of the 137 patients enrolled in Study AP26113-11-101. Specifically, a total of 110 patients administered brigatinib doses ranging from 30 mg to 240 mg QD contributed PK time -matched ECG data to this concentration-QTc analysis, with 29 patients receiving the recommended 90 mg to 180 mg QD dose regimen. Therefore, data over a wide concentration range, including concentrations higher than those observed with the recommended dose regimen, contributed to the analysis, and brigatinib had no clinically significant effect on cardiac repolarization as assessed by concentration-QTc analysis. The one-sided upper 95% confidence bound of the predicted change from baseline in QTc corrected by Fridericia's formula (QTcF) was -4.7 milliseconds
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phase 2 study ap26113-13-201 (alta)

This is a pivotal phase 2, randomized, multicenter, international study of brigatinib in patients with ALK+ NSCLC who previously progressed on crizotinib. A total of 222 patients were randomized 1:1 to receive brigatinib in 1 of 2 different dosing regimens: (A) 90 mg QD, continuously, or (B) 90 mg QD for 7 days, then 180 mg QD, continuously (90 mg to180 mg QD). For both treatment regimens, dose modifications (dose interruptions, dose reductions) were allowed. Eligible patients had histologically or cytologically confirmed locally advanced or metastatic NSCLC with documented ALK rearrangement by a positive result from the Vysis® ALK. Break-Apart fluorescence in situ hybridization (FISH) Probe Kit; or documented ALK positivity by a different test and tissue available for the Vysis® FISH test to be performed centrally. Patients were required to have progressive disease (PD) while on crizotinib. The first patient was randomized in June 2014 and the last patient was randomized in September 2015. Treatment and follow up are ongoing. The primary endpoint of this study was confirmed ORR as assessed by the investigator, per RECIST, Version 1.1. Secondary endpoints include confirmed ORR as assessed by a central IRC; CNS response assessed by an IRC (ORR and PFS in patients who had active brain metastases); time to response; DOR; time on treatment; disease control rate (DCR); PFS; OS; safety and tolerability; SS plasma level of brigatinib for use in population PK modeling; and patient-reported symptoms of lung cancer and health-related quality of life scores, assessed with the European Organisation for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire (QLQ-C30, Version 3.0). The study is being conducted at approximately 100 study centers in 18 countries in North America, Europe, Asia, and Australia. Overall, 222 patients were enrolled into the study in 18 countries; 105 patients at 38 sites in 12 countries in Europe (Austria, Belgium, Denmark, France, Germany, Italy, Netherlands, Norway, Spain, Sweden, Switzerland, and the United Kingdom); 68 patients at 17 sites in 4 countries in the Asian Pacific region (Australia, Hong Kong, Republic of South Korea, and Singapore); and 49 patients at 16 sites in North America (Canada and US). Overall, the median age was 54.0 years (range: 18 to 82); over half the patients were female (56.8%, 126/222), while 23.5% were ≥65 years. At baseline, the ECOG performance status was 2 for 7.2% (16/222) of all patients (6.3% [7/112] in Arm A and 8.2% [9/110] in Arm B). The NSCLC histopathological classification was adenocarcinoma for the majority (96.8% [215/222]) of all patients (95.5% [107/112] in Arm A and 98.2% [108/112] in Arm B). The majority of patients had a local or centrally confirmed ALK Vysis FISH test result (89.2% [198/222] of all patients; 89.3% [100/112] in Arm A and 89.1% [98/110] in Arm B). Crizotinib was the most recent prior systemic therapy at baseline for 95.9% (213/222) of all patients (95.5% [107/112] in Arm A and 96.4% [106/110] in Arm B). The best response to the prior crizotinib therapy was a partial response (PR) for 60.8% (135/222) of all patients (58.0% [65/112] in Arm A and 63.6% [70/110] in Arm B), and 3.2% (7/222) of all patients had achieved a complete response (CR) with crizotinib (4.5% [5/112] in Arm A and 1.8% [2/110] in Arm B). The majority of patients had received prior chemotherapy (73.9% [164/222] of all patients; 74.1% [83/112] in Arm A and 73.6% [81/110] in Arm B) and prior platinum-based chemotherapy (73.4% [163/222] of all patients; 74.1% [83/112] in Arm A and 72.7% [80/110] in Arm B). Brain metastases at baseline, as assessed by the investigator, were present in 69.4% (154/222) of all patients (71.4% [80/112] in Arm A and 67.3% [74/110] in Arm B)
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objective response rate

The investigator-assessed confirmed ORR was 45.5% (51/112) of patients in Arm A and 55.5% (61/110) of patients in Arm B. The best overall response was a confirmed PR for 43.8% (49/112) of patients in Arm A and 50.9% (56/110) of patients in Arm B, and a confirmed CR for 1.8% (2/112) of patients in Arm A and 4.5% (5/110) of patients in Arm B. Prospectively defined criteria for efficacy stated that a treatment regimen will be considered to have achieved the primary objective when the investigator-assessed ORR is shown to be significantly higher than 20% at a two-sided alpha level of 0.025 at the primary analysis for that regimen; the lower limit of the 97.5% CI rules out an alternate rate of 20% when the true rate is 35% or higher. Therefore, these prospectively defined criteria for efficacy were met (the lower limit of the 97.5% CI exceeds 20%) with statistical significance for investigator-assessed ORR in both arms: 45.5% for Arm A (97.5% CI: 34.8, 56.5) and 55.5% for Arm B (97.5% CI: 44.3, 66.2). The IRC-assessed confirmed ORR was 50.9% (57/112) of patients in Arm A and 54.5% (60/110) of patients in Arm B. IRC-assessed confirmed CR was observed in 5.4% (6/112) of patients in Arm A and 5.5% (6/110) of patients in Arm B
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progression-free survival

Investigator-assessed PFS in the ITT population is presented in Figure XX. Median (KM estimate) for investigator-assessed PFS was 9.2 months (95% CI: 7.4, 11.1) in Arm A and 15.6 months (95% CI: 11.1, 19.4) in Arm B. In Arms A and B, 73/112 (65%) and 55/110 (50%) events have been observed, respectively. The hazard ratio observed between the two arms is 0.64 (95% CI: 0.45, 0.91). Median (KM estimate) for IRC-assessed PFS was 9.2 months (95% CI: 7.4, 12.8) in Arm A and 16.7 months (95% CI: 11.6, NE) in Arm B. In Arms A and B, 60/112 (53.6%) and 45/110 (40.9%) events have been observed, respectively. The hazard rat in between the two arms is 0.69 (95% CI: 0.47, 1.02).  
Overall survival OS by arm is shown in Figure 5.n. Median OS has not been reached in Arm A (95% CI: 20.2, NE) and is 27.6 months (95% CI 27.6, NE) in Arm B, with 42/112 (37.5%) and 32/110 (29.1%) events observed in Arm A and Arm B, respectively. The hazard ratio observed between the 2 arms is 0.67 (95% CI: 0.42, 1.06).
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cns efficacy

To evaluate the potential for brigatinib anti-tumor activity in the CNS, an additional IRC assessment was performed to assess efficacy endpoints in the intracranial CNS in randomized patients with active brain metastases assessed by MRI at enrollment. Contrast -enhanced brain MRI scans were analyzed by neuroradiologists in an independent central review. The reviewers were blinded to investigator assessment and treatment assignment. Up to 5 measurable brain metastases could be chosen as target lesions by the independent reviewers. Response in patients with at least 1 measurable brain lesion (≥10 mm) was defined as a ≥30% decrease in the sum of the longest diameters of target lesions and nonprogression in non-target lesions. Response in patients with only nonmeasureable brain metastases was defined as disappearance of all lesions (CR). Of the 222 patients in the ITT population, 217 patients had baseline MRI scans of the brain read by IRC, and 153 patients had brain metastases identified by IRC at baseline. - 44 patients with measurable lesions; of which, 34 patients had at least 1 active brain metastasis at baseline identified by the investigator (with 'active' defined as no prior history of radiation to the brain or clear progression after local radiotherapy). - 109 patients had only nonmeasureable lesions at baseline; of which, 67 patients who had a least 1 active brain metastasis at baseline identified by the investigator. The IRC database extraction included a last scan date of 28 February 2017 for all patients with brain metastases at baseline and 24 January 2017 for patients with measurable brain metastases at baseline.
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intracranial orr

Patients with Measureable Brain Metastases at Baseline At this database extraction, the IRC-assessed confirmed intracranial ORR was 50.0% (13/26) for patients in Arm A and 66.7% (12/18) for patients in Arm B for patients with measurable brain metastases at baseline. Confirmed intracranial CR was the best response for 7.7% (2/26) of patients in Arm A and for no patients (0/18) in Arm B. Confirmed intracranial PR was the best response for 42.3% (11/26) of patients in Arm A and 66.7% (12/18) of patients in Arm B. The intracranial DCR for patients with measureable brain metastases at baseline was 84.6% (22/26) of patients in Arm A and 83.3% (15/18) of patients in Arm B. Patients with Only Nonmeasurable Brain Metastases at Baseline For patients with only non-measureable brain metastases at baseline, intracranial ORR was observed in 7.4% (4/54) of patients in Arm A and 18.2% (10/55) of patients in Arm B. Intracranial response for patients with only non-measureable brain metastases is defined for purposes of this study as complete radiographic disappearance of lesions and is the only response possible for patients with only non-measureable lesions. The intracranial DCR for patients with non-measureable brain metastases at baseline was 74.1% (40/54) of patients in Arm A and 87.3% (48/55) of patients in Arm B.
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phase 2 study ap26113-13-201 (alta)

TEAEs that occurred in >20% of patients overall were nausea (42.5%), diarrhea (35.6%), cough (34.2%), headache (32.9%), vomiting (32.9%), fatigue (27.9%), dyspnea (25.6%), blood creatine phosphokinase (CPK) increased (25.6%),
decreased appetite (24.7%), hypertension (22.4%), and constipation (21.0%). The most common TEAE in both Arm A and Arm B was nausea (occurring in 37.6% and 47.3% of patients, respectively).
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grade >=3 teaes and treatment-related

Treatment-emergent AEs Grade ≥3 occurred in 62.1% (136/219) of patients overall and in similar proportions in Arm A and in Arm B (58.7% [64/109] and 65.5% [72/110], respectively). Treatment-emergent AEs Grade ≥3 by PT (occurring in ≥2% of all patients) that occurred in a greater proportion (≥50% relative increase) of patients in Arm A than in Arm B were neoplasm progression (15.6% [17/109] vs 7.3% [8/110], respectively), lipase increased (4.6% [5/109] vs 3.6% [4/110], respectively), and neutrophil count decreased (3.7% [4/109] vs 1.8% [2/110], respectively); and a greater proportion (≥50% relative increase) of patients in Arm B than in Arm A were blood CPK increased (12.7% [14/110] vs 4.6% [5/109], respectively). The most common treatment-related TEAE Grade ≥3 in Arm A was lipase increased and hypertension (3.7% [4/109] for each) and in Arm B was blood CPK increased (10.9% [12/110]). A greater proportion (≥50% relative increase) of patients in Arm B than in Arm A had blood CPK increased (10.9% [12/110] vs 2.8% [3/109], respectively), pneumonitis (3.6% [4/110] vs 1.8% [2/109],
respectively), and rash (3.6% [4/110] vs 0.9% [1/109], respectively). No treatment-related TEAEs Grade ≥3 occurring in ≥2% of all patients occurred in a greater proportion (≥50% relative increase) of patients in Arm A than in Arm B.  
Overall, 49.8% (109/219) of patients experienced a treatment-emergent AEs (TEAE) that led to dose interruption of any duration. A greater proportion of patients in Arm B than in Arm A had a TEAE that led to dose interruption (59.1% [65/110] vs 40.4% [44/109], respectively). The TEAEs occurring in ≥3% of patients overall by PT that led to dose interruption were blood CPK increased (5.5% [12/219]), pneumonitis (4.6% [10/219]), neoplasm progression (4.1% [9/219]), lipase increased (3.2% [7/219]) and vomiting (3.2% [7/219]). The most common TEAEs that led to dose interruption in Arm A were neoplasm progression, vomiting, and pyrexia; in Arm B, the most comment TEAEs that led to dose interruption were blood CPK increased, pneumonitis, rash, and lipase increased. TEAEs that led to dose reduction occurred in 9.2% (10/109) of patients in Arm A and 30.0% (33/110) of patients in Arm B. The only TEAE leading to dose reduction that occurred in ≥2% of patients overall by PT was blood CPK increased (4.1% [9/219]), which occurred in 1.8% (2/109) of patients in Arm A and 6.4% (7/110) of patients in Arm B. TEAEs that led to discontinuation of brigatinib occurred in 7.3% (16/219) of patients overall, 3.7% (4/109) of patients in Arm A and 10.9% (12/110) of patients in Arm B. A greater proportion (≥50% relative increase) of patients in Arm B than in Arm A had a TEAE that led to brigatinib discontinuation (10.9% [12/110] vs 3.7% [4/109], respectively). The most common TEAE (occurring in ≥2 patients overall) that led to brigatinib discontinuation by PT were pneumonitis (1.8% [4/219]), neoplasm progression (0.9% [2/219]), and pneumonia (0.9% [2/219]).
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specific adverse events of clinical

Early Onset Pulmonary Event (EOPE)
As of a database extraction date of 21 February 2017, out of 219 treated patients, 4 patient cases were determined to meet the criteria for definite EOPE, and 10 cases met the criteria for possible EOPE. In total, 14 of 219 (6.4%) patients overall had an event that was at least possibly an EOPE. All EOPEs occurred at a dose of 90 mg QD, regardless of arm (ie, within the first 7 days of treatment in Arm B). No EOPEs were identified after escalation to 180 mg QD in Arm B. Median time of onset of EOPE was Day 2 (range: 1 to 9). Of the 14 patients who had an EOPE (Arm A: 5/109 [4.6%] and Arm B: 9/110 [8.2%]), all occurred while patients were receiving brigatinib 90 mg QD. Eleven EOPE patient cases included SAEs, and 3 EOPE patient cases included only nonserious events. Seven (3.2%) patients had events that were Grade 1 or 2 only. Seven (3.2%) patients had events that were Grade ≥3, all of whom permanently discontinued brigatinib after the EOPE. There were 6 patients who had an EOPE with highest Grade of 3 or 4 (pneumonitis [n=4], radiation pneumonitis [n=1], pneumonia [n=1]). One patient (Patient 615-002) had a possible EOPE that was Grade 5. This patient developed pneumonia Grade 5 after taking brigatinib for 7 days (90 mg QD at event onset). At autopsy, microscopic examination revealed widespread dissemination of lung cancer, with spread to the paratracheal lymph nodes and left half of the chest, and lymphangitis carcinomatosis in the right lung. Additionally, histological changes in the right lung were compatible with diffuse alveolar damage, which indicated acute respiratory distress syndrome. Although the patient's lung cancer and infection were considered to be underlying causes of death, a contribution of brigatinib could not be ruled out, and this case was considered a possible EOPE given the association of events within 7 days of the start of brigatinib, as well as evidence for a pneumonitis-like process. In 7 of 14 (50.0%) patients experiencing EOPE, brigatinib was permanently discontinued after the EOPE (including the fatal case). All 7 patients who permanently discontinued had Grade ≥3 events. In 6 of 14 cases, brigatinib was interrupted and successfully resumed after resolution of the pulmonary event. In 1 of these 6 cases (Patient 588-001), brigatinib was continued during the event, with interruption for 1 day prior to escalating to 180 mg QD, and the events resolved. In 1 of 14 patient cases (Patient 590-003), the brigatinib dose was reduced to 60 mg QD without an interruption and the event resolved. Events resolved with dose interruption or brigatinib discontinuation (drug withdrawn). Steroids and antibiotics were administered in 11 of 14 (78.6%) and 4 of 14 (28.6%) patient cases, respectively. There were 7 patients who successfully resumed brigatinib or continued administration through the pulmonary event; 2 of the patients had a confirmed PR and 5 of the patients had stable disease as best response.
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later-onset pneumonitis events

Five patients each experienced a single later-onset pneumonitis event. Four of these occurred with the most recent dose being 180 mg QD, and 1 occurred at a dose of 90 mg QD. In 3 cases, brigatinib was successfully restarted without recurrence of pneumonitis. In 1 case, the patient had already permanently discontinued due to progression of disease. In the last case, the patient permanently discontinued brigatinib due to the event
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bradycardia

Bradycardia TEAEs of any grade occurred in 5.5% (12/219) of patients overall (Arm A: 6.4% [7/109] and Arm B: 4.5% [5/110]). Sinus bradycardia and bradycardia TEAEs occurred in 3.7% (8/219) and 1.8% (4/219) of patients overall, respectively. None of the bradycardia events were Grade ≥3. There were no dose reductions or treatment discontinuations due to bradycardia.
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hypertension

Hypertension TEAEs of any grade occurred in 22.4% (49/219) of patients overall (CSR AP26113-13-201 Table 14.3.3.4). Hypertension TEAEs were reported in a greater proportion of patients in Arm B than in Arm A (27.3% [30/110] vs 17.4% [19/109], respectively). Grade 3 hypertension TEAEs occurred in 6.8% (15/219) of patients overall; 5.5% (6/109) and 8.2% (9/110) of patients in Arm A and Arm B, respectively (CSR AP26113-13-201 Table 14.7.2.2). No Grade 4 hypertension has been reported. One patient in Arm A had retinopathy hypertensive. One patient in each arm (0.9%) had a dose reduction due to hypertension. No patient discontinued brigatinib due to hypertension.
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elevated insulin/hyperglycemia events

Elevated insulin/hyperglycemia TEAEs of any grade occurred in 5.5% (6/109) in Arm A and 11.8% (13/110) in Arm B. The elevated insulin/hyperglycemia events that occurred in >2 patients in either treatment arm by PT were hyperglycemia (3.7% [4/109] of patients in Arm A and 5.5% [6/110] of patients in Arm B) and diabetes mellitus (0.9% [1/109] of patients in Arm A and 4.5% [5/110] of patients in Arm B). Elevated insulin/hyperglycemia events Grade ≥3 occurred in only 1 patient; this patient had a Grade 3 event of diabetes mellitus (which was also present in the previous 31 May 2016 data extraction) (Study AP26113-13-201 Table 14.3.7.2.7). No patients have had dose reduction or treatment discontinuation due to increased insulin/hyperglycemia TEAEs.  
Pancreatic Events Pancreatic TEAEs based on laboratory elevations (pancreatic enzyme elevations) of any grade occurred in 20.5% (45/219) of patients overall. No patients experienced clinical pancreatitis. A greater proportion of patients in Arm B than in Arm A had pancreatic events of any grade (24.5% [27/110] vs 16.5% [18/109], respectively). Pancreatic events Grade ≥3 occurred in 5.9% of patients overall (Arm A: 5.5% [6/109] and Arm B: 6.4% [7/110]) (Study AP26113-13-201 Table 14.3.7.5.6). Amylase increased led to dose reduction in 0.9% of patients overall (1 patient in each arm). Lipase increased led to dose reduction in 0.9% of patients (1/109) in Arm A and 1.8% of patients (2/110) in Arm B. No patients discontinued treatment due to TEAEs of lipase increased or amylase increased.
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hepatic events

Hepatic TEAEs of any grade occurred in 21.9% (48/219) of patients overall, and occurred in 19.3% (21/109) of patients in Arm A and in 24.5% (27/110) of patients in Arm B. The most common hepatic events that occurred in >2 patients overall by PT were AST increased (15.1% [33/219] of patients overall; 10.1% [11/109] in Arm A and 20.0% [22/110] in Arm B) and ALT increased (12.8% [28/219] of patients overall; 10.1% [11/109] in Arm A and 15.5% [17/110] in Arm B). Grade 3 to 4 ALT increased TEAEs occurred in 3 patients (all in Arm B; 2.7%) and Grade 3 to 4 AST increased TEAEs occurred in 2 patients (both in Arm; 1.8%) (Study AP26113-13201 Table 14.3.7.3.8). One patient had a dose reduction due to a hepatic event. No patient discontinued treatment due to a hepatic event. There were no TEAEs of clinical hepatic failure, and no patients satisfied the laboratory criteria threshold for a possible Hy's Law case.
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vision impairment events

Vision impairment events of any grade occurred in 15.1% (33/219) of patients overall (Arm A: 11.0% [12/109] and Arm B: 19.1% [21/110]). The most common vision impairment event by PT in patients overall was vision blurred (5.0% [11/219]), which occurred in in a higher number of patient in Arm B compared with Arm A (7.3% [8/110] and 2.8% [3/109], respectively). Two patients had Grade 3 vision impairment events (macular oedema and cataract). Two patients have had a dose reduction due to vision impairment TEAEs (macular oedema, retinal oedema). No patients have discontinued treatment due to vision impairment TEAEs.  
1.4 **Rationale**
A significant population of ALK+ NSCLC patients exist that have progressed on or who were intolerant of next generation ALK inhibitor (e.g. ceritinib or alectinib). Brigatinib has demonstrated activity in patients who have progressed on crizotinib, but the activity of brigatinib in patients who have progressed on ceritinib, alectinib, or other next generation ALK inhibitors is unknown. Based on the preclinical data summarized in section 1.3, brigatinib has potent activity against known secondary ALK mutations suggesting it may retain activity as third-line treatment of ALK+ disease. Patients enrolled must have previously received a next generation ALK inhibitor other than brigatinib. Given that third-line treatment of ALK+ disease is analogous to a phase I population, we have chosen 20% as a clinically meaningful response rate that would justify further study of brigatinib in previously treated ALK+ disease. The recent data on brigatinib's activity in the central nervous system (CNS) provides additional rationale for study of this drug in refractory disease. We have elected to use the dose regimen (90mg PO QD for 7 days followed by 180mg PO QD continuously) from the above ongoing randomized Phase II trial of brigatinib as second-line treatment for cohorts A and B. For cohort C we have chosen the dose of 240 mg daily based on the phase I/II trial, and the fact all patients will have tolerated brigatinib at 180 mg daily.
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1.5 correlative studies to explore

The mechanisms of resistance to *ALK* inhibitors is an active area of investigation, and multiple mechanisms have been identified including *ALK* kinase domain mutations, *ALK* copy number gain, acquisition of oncogenic driver mutations and activation of the EGFR pathway. A substantial proportion of patients do not have an identifiable molecular mechanism of resistance. In a case series of 18 patients who underwent biopsy after experiencing disease progression on crizotinib, four patients had a mutation within the *ALK* tyrosine kinase domain and an additional patient had amplification of the *ALK* fusion gene.(Katayama et al. 2012) Other mechanisms of resistance identified include amplification of KIT and increased autophosphorylation of EGFR suggesting activation of the EGFR pathway as a mechanism of resistance. A similar case series of 11 patients identified secondary mutations in the tyrosine kinase domain (n=4), *ALK* copy number gain (n=2; one patient also demonstrated an *ALK* resistance mutation), *KRAS* mutation (n=2; one without the evidence of the original *ALK* rearrangement), EGFR mutation without evidence of a persistent *ALK*
rearrangement (n=1), and *ALK* rearrangement negative (n=1).(Doebele et al. 2012)
ALK secondary resistance mutations are identified in approximately 30% of patients after crizotinib, and include 1151Tins, C1156Y, L1196M, S 1206Y and G1269A.(Gainor et al. 2016) Tumor specimens from patients who received crizotinib or next generation *ALK* inhibitors were analyzed. In patients who received crizotinib *ALK* resistance mutations were identified in 20% of specimens, and *ALK* amplification (defined as ALK/centromere 2 ratio of > 2.0) was observed in 8% (none of which had an ALK resistance mutation). In contrast an *ALK*
resistance mutation was observed in 54% of the specimens of patients with disease progression on ceritinib, and 53% of specimens of patients with disease progression on alectinib. Collectively, these data suggest the rate of *ALK* resistance mutations is higher after next-generation ALK inhibitors and the most common resistance mutation is the G1202R. No association between ALK resistance mechanism and ceritinib response was observed in the initial trial but the number of patients with a known mutation was small (n=19).(Shaw et al. 2014) Preclinical models suggest that different ALK inhibitors have differing degrees of activity depending on the resistance mutation. Ceritinib has activity against the L1196M, G1296A, I1171T and S1206Y, but not against the ALK secondary mutations C1156Y, 1151Tins, G1202R and F1174C.(Friboulet et al. 2014) Patients treated with ceritinib have developed resistance mutations in G1202R or F1174. Patients previously treated with alectinib have been shown to develop V1180L and I1171T resistance mutations.22 Ceritinib demonstrated activity against the V1180L and I1171T mutations, brigatinib demonstrated activity against the V1180L mutation but less activity against the I1171T, and ASP3026 was active against V1180L and inactive against the I1171T mutation.(Katayama et al. 2014) Thus, ALK tyrosine kinase inhibitors may have differing level of clinical activity depending on the resistance mutation. None of the previous studies are definitive, but they suggest that an understanding of the molecular mechanisms of resistance at the time of initiating a new ALK inhibitor will be important in assessing the clinical activity of an ALK inhibitor. In this study, pre-treatment tumor samples will undergo next generation sequencing to explore for an association between mutation presence or absence and type of mutation as well as other mechanisms of resistance and response to brigatinib. Tumor samples at progression will be used to identify resistance mutations after brigatinib. Participation in the biopsy at the time of progression on brigatinib is optional since biopsies may not be feasible, patients may not be candidates for further therapy, or patients may need to proceed to the next line of therapy in an expedited time frame. There is increasing interest in detecting oncogenic mutations in ctDNA obtained from peripheral blood samples.(Oxnard et al. 2014; Cui et al. 2017; Newman et al. 2014; Wang et al. 2016)This will also be explored in the present study. The overall sensitivity, specificity, and accuracy of capture-based NGS of ctDNA was 54%, 100%, and 72%, respectively. Of 13 ALK positive samples were identified by capture-based NGS among 24 samples with positive tumor samples for ALK. An additional study revealed a sensitivity and specificity was 79% and 100%,
respectively. *ALK* rearrangements were successfully detected in 19 of 24 patients.  
Crizotinib resistance mutations were detected from a single patient. While the focus has been on the detection of *ALK* resistance mutations it is important to note the *ALK*
resistance mutations are detected in approximately 50% of patients with progressive disease on next-generation ALK inhibitors and there is a need to identify other mechanisms of resistance.
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2.0 study objectives 2.1 primary

Estimate ORR (rate of CR+PR) of brigatinib in patients with ALK+ NSCLC who have progressed on next generation ALK inhibitors
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2.2 secondary objectives

2.2.1 Further characterize treatment-related adverse events associated with brigatinib including at different doses in patients with ALK+NSCLC
2.2.2 Estimate duration of response in patients with ALK+ NSCLC
treated with brigatinib who have progressed after prior ALK inhibition 2.2.3 Estimate PFS in patients with ALK+ NSCLC treated with brigatinib who have progressed after prior ALK inhibition 2.2.4 Estimate intracranial and extra-cranial PFS in patients with ALK+
NSCLC treated with brigatinib who have progressed after prior ALK inhibition 2.2.5 Estimate OS in patients with ALK+ NSCLC treated with brigatinib who have progressed after prior ALK inhibition
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2.3 exploratory objectives

2.3.1 Explore association between presence and/or type of mutation or mechanism of resistance at baseline and efficacy outcomes (ORR and PFS)
2.3.2 Identify resistance mutations or other mechanisms of resistance after brigatinib by evaluating tumor samples at time of progression 2.3.3 Explore whether ctDNA from peripheral blood samples can identify development of resistance mutations 2.3.4 Estimate intracranial ORR in patients with ALK+ NSCLC treated with brigatinib who have progressed after prior ALK inhibition who have measurable CNS disease at baseline
2.4 Primary **Endpoint**
ORR as determined by RECIST 1.1 as assessed by the investigator
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2.5 secondary endpoints

2.5.1 The treatment-related adverse events will be assessed using the NCI CTCAE version 4.0 as assessed by the investigator.  
2.5.2 Duration of response is measured from the time measurement criteria are first met for CR/PR (whichever is first recorded) until the first date of progression
2.5.3 PFS with progression events as per RECIST 1.1 and as assessed by the investigator; PFS is defined from day 1 of treatment until progression of disease (either intracranial or extracranial) or death as a result of any cause  
2.5.4 Intracranial PFS is defined from day 1 of treatment until intracranial progression of disease or death as a result of any cause; extracranial PFS is defined from day 1 of treatment until extracranial progression of disease or death as a result of any cause. Only patients with brain metastases at baseline will be included in this analysis 2.5.5 OS is defined from day 1 of treatment until death as a result of any cause 2.5.6 Intracranial ORR as determined by RECIST 1.1 as assessed by the investigator
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3.0 patient eligibility

Patients must meet all of the following inclusion criteria to participate in this study:
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3.1 inclusion criteria for all

3.1.1 Locally advanced or metastatic NSCLC that has been cytologically or histologically confirmed 3.1.2 ALK positive status based on Clinical Laboratory Improvement Amendments (CLIA) or test approved for use in Canada. Diagnostic test may be based on ctDNA testing or based in tumor testing 3.1.3 ECOG PS ≤2
3.1.4 Age of ≥ 18 years  
3.1.5 Brain lesions may be used as target lesions if progressing, ≥10mm in longest diameter and if they were not previously treated with any of the following:
- Whole brain radiation therapy (WBRT) within 3 months - Stereotactic radiosurgery (SRS) - Surgical resection 3.1.6 Availability of core biopsy of progressive lesion taken within 60 days prior to D1 of treatment under study therapy or willing to undergo tumor biopsy: NOTE: All subjects must consent to provide tumor blocks or slides.  
- If archival tissue is not available and biopsies to obtain fresh tumor tissue cannot be performed with minimal risk to the subject, subjects may be permitted to enroll on the study with prior approval of the Study PI.  
- In the situation the patient undergoes biopsy within 60 days prior to D1 and there is insufficient tumor tissue for the correlative science part of the protocol, the patient will be permitted to enroll on the study with prior approval of the study PI
- In the situation the patient undergoes molecular testing or nextgeneration sequencing as part of standard care there must be sufficient tumor sample available for participation in the study (i.e. a next generation sequencing report is not sufficient for enrollment)
3.1.7 Recovered from toxicities related to prior anticancer treatment to ≤Grade 2 or baseline with the exception of alopecia 3.1.8 Have normal QT interval on ECG evaluation QT corrected Fridericia
(QTcF) of ≤ 450 ms in males or ≤ 470 ms in females  
| Absolute neutrophil count (ANC)   | ≥1500/µL                                                           |
|-----------------------------------|--------------------------------------------------------------------|
| Platelets                         | ≥75,000/µL                                                         |
| Hemoglobin                        | ≥ 10g/dL                                                           |
| AST /ALT                          | ≤ 2.5 x upper limit of normal (ULN); ≤ 5 x ULN if liver metastasis |
| Total serum bilirubin             | ≤ 1.5 x ULN                                                        |
| Serum creatinine                  | ≤ 1.5 x UNL                                                        |
| Serum amylase                     | ≤ 1.5 x UNL                                                        |  
3.1.9 Adequate organ function defined as:
3.1.10 At least 1 measurable lesion per RECIST version 1.1  
3.1.11 Female patients who:
- Are postmenopausal for at least 1 year before the screening visit, OR - Are surgically sterile, OR
- If they are of childbearing potential, agree to practice 2 effective methods of contraception, at the same time, from the time of signing the informed consent through *4 months* after the last dose of study drug, or agree to completely abstain from heterosexual intercourse. (Oral and implantable contraceptives are not considered effective forms of contraception for study purposes. See Appendix C (auxiliary patient document)).  
- Women of child-bearing potential (WOCBP) must have a negative serum pregnancy test within 7 days of D1 of treatment.  
3.1.12 Male patients, even if surgically sterilized (i.e., status post-vasectomy), who:
- Agree to practice effective barrier contraception during the entire study treatment period and through 4 *months* after the last dose of study drug, or
- Agree to completely abstain from heterosexual intercourse 3.1.13 Ability to provide signed informed consent and willing and able to comply with all study requirements.
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3.2 inclusion criteria for cohort

3.2.1 **Cohort A**: Progressive disease on any next generation ALK inhibitor exceptfirst line alectinib alone (eligible for study but assigned to cohort B) or brigatinib (any line). Patients who received previous therapy with lorlatinib will be assigned to cohort A.  
3.2.2 **Cohort B:** Progressive disease on first-line therapy with alectinib, and no other ALK inhibitors 3.2.3 **Cohort C:** Previous treatment brigatinib at 180 mg daily for ≥4 weeks without > grade 2 drug-related toxicities and with radiographic evidence of
progressive disease and no intervening systemic therapies such as chemotherapy, immunotherapy or another ALK inhibitor (radiation therapy allowed as intervening therapy).  
3.2.4 Patients who are treated on cohorts A and B will be allowed to enroll in cohort C if they meet the inclusion and exclusion criteria. Patients are required to undergo a biopsy before enrollment in cohort C. Patients who change cohorts from A or B to cohort C should not have EOT assessments completed and do not discontinue brigatinib, and should complete a new registration form and will be given a new subject number
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3.3 exclusion criteria for cohorts

Patients meeting any of the following exclusion criteria will not be able to participate in this study:  
3.3.1 History or the presence of pulmonary interstitial disease, drug-related or immune-related pneumonitis, or radiation pneumonitis requiring medical management within 6 months of trial enrollment 3.3.2 Prior treatment with brigatinib for cohorts A and B 3.3.3 History of or active significant gastrointestinal (GI) bleeding within 3 months 3.3.4 Malabsorption syndrome or other GI illness that could affect oral absorption of the study drug 3.3.5 Received cytotoxic chemotherapy, investigational agents or radiation within 7 days prior to D1 of study treatment 3.3.6 Received prior ALK TKI therapy within 7 days prior to D1 of treatment under study drug. 7 day wash out period is required after prior ALK inhibitor treatment for cohorts A and B. Patients enrolling in cohort C should continue brigatinib and 7 day wash out is not required).  
3.3.7 Have significant, uncontrolled, or active cardiovascular disease,specifically including, but not restricted to:
- Myocardial infarction (MI) within 6 months of trial enrollment
- Unstable angina within 6 months of trial enrollment
- Congestive heart failure (CHF) with 6 months prior to trial enrollment - Any history of ventricular arrhythmia - Cerebrovascular accident or transient ischemic attack within 6 months of D1 of study treatment
- Clinically significant atrial arrhythmia (as determined by the investigator)
or severe baseline bradycardia defined as resting heart rate < 60 beat per minute
- Uncontrolled hypertension defined as baseline SBP> 160 and DBP > 100 on 3 separate clinic visits or past history of hypertensive urgency, emergency, or encephalopathy
3.3.8 Another primary malignancy for which the patient is currently receiving therapy  
3.3.9 Have been diagnosed with another primary malignancy within the past 3 years
(except for adequately treated non-melanoma skin cancer, cervical cancer in situ, or prostate cancer, which are allowed within 3 years)
3.3.10 Have symptomatic CNS metastases which require an increasing dose of corticosteroids within the last 2 weeks to remain asymptomatic.  
3.3.11 Have active infection requiring intravenous antibiotics
3.3.12 Pregnant or breastfeeding  
3.3.13 Have any condition or illness that, in the opinion of the investigator, would compromise patient safety or interfere with evaluation of the study drug.
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4.0 treatment plan 4.1 schema

4.2 **Schema For Cohort C**  
  
 4.3 **Treatment Dosage And Administration** 4.3.1 **Cohorts A And B**  
Brigatinib will be administered at a dose of 90 mg (3 by 30 mg tablets) orally once a day (QD) for the first 7 days of cycle 1 followed by 180 mg (6 by 30 mg tablets) orally once a day continuously thereafter. NOTE: during cycle 1, patients will be seen on D8 to determine if dose escalation to 180mg is appropriate (see section 4.3.1 and 4.3.2. Should drug formulation change, equivalent doses in smaller numbers of capsules may be substituted to reduce patient pill burden in any cohort. A cycle of therapy will comprise 28 days of treatment, regardless of dose. Patients will be instructed to take the prescribed dose with water (recommended 240 mL(8 oz)) at the same time each day, and *without regard to food intake*.  
Patients who forget to take their scheduled dose of study drug should be instructed not to make up the missed dose. Patients who vomit immediately after taking a dose should be instructed NOT to retake the dose. All doses should be recorded in the patient diary, with a notation made by the patient if any dose is missed, or if a dose is vomited.
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4.3.2 cohort c

Brigatinib will be administered at 240 mg daily (8 by 30 mg tablets). A cycle of therapy will comprise 28 days of treatment, regardless of dose. Patients will be instructed to take the prescribed dose with water [recommended 240 mL (8 oz)] at the same time each day, and without regard to food intake. Patients who forget to take their scheduled dose of study drug should be instructed not to make up the missed dose. Patients who vomit immediately after taking a dose should be instructed NOT to retake the dose. All doses should be recorded in the patient diary, with a notation made by the patient if any dose is missed, or if a dose is vomited.
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4.4 toxicities and dosing delays/dose

Any patient who receives treatment on this protocol will be evaluable for toxicity.  
Each patient will be assessed periodically for the development of any AE according to the Time and Events table (Section 6.0). AE will be assessed according to the NCI CTCAE v4 for 30 days after dosing is completed. Of note, monitoring for signs of liver or vision dysfunction, monitoring serum levels of testosterone is recommended due to the safety profile of the ALK inhibitor crizotinib. Missed doses of brigatinib will be omitted and not made up. Unless otherwise noted in the tables below, treatment may be interrupted ≤ 2 weeks for any reason. If treatment is interrupted ≤ 2 weeks, subjects will proceed with treatment at the dose level recommended according to the tables below. In the event that brigatinib dosing is interrupted, the duration of cycle/treatment will not be extended. Therefore, if treatment is delayed on D1 of a cycle due to toxicity, and the patient does not begin therapy until D5 (for example), the start date of drug for that cycle remains D5, not D1 If treatment is delayed >2 weeks, then the patient should be discontinued from protocol mandated therapy and followed-up per protocol.  
| Grade1                                       | Dose Modification                                                                                                                                                                            | Criteria for Dose Escalation              |
|----------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------------------------|
| 1                                            | Continue 90mg daily                                                                                                                                                                          | Escalate to 180 mg daily D8 as  scheduled |
| 2                                            | Continue 90mg daily                                                                                                                                                                          | If AE returns to ≤ Grade 1 or             |
| (≤ 3 days)                                   | baseline at D8, escalate to 180mg  daily on D8                                                                                                                                               |                                           |
| 2                                            |                                                                                                                                                                                              |                                           |
| (≥ 3 days despite  optimal  supportive care) | If no recurrence of Grade 2 AE after  90 mg daily for 7 days, escalate to  120 mg daily. Do NOT escalate to  180 mg daily. If recurrence of Grade 2 after 90mg daily, do NOT escalate  dose. |                                           |
| 3                                            | Hold until event is Grade ≤ 1 or has returned to baseline, then  resume at 90mg daily Hold until event is ≤ Grade 1 or  returned to baseline, then resume  90mg daily                        | Do NOT escalate dose                      |
| 4                                            | Hold until event is Grade ≤ 1 or has returned to baseline, then  resume at 60 mg daily.                                                                                                      | Do NOT escalate dose                      |
| 1Per NCI CTCAE v4.0                          |                                                                                                                                                                                              |                                           |  
4.4.1 Non-Hematologic Treatment-Related AEs during Brigatinib 90mg Daily 7day lead-in other than **Pneumonitis**  
4.4.2 **Hematologic Treatment-Related AEs during Brigatinib 90mg**  
Daily 7 day lead-in  
Grade1 Dose Modification **Criteria for Dose Escalation**  
| Grade1                              | Dose Modification                         | Criteria for Dose Escalation              |
|-------------------------------------|-------------------------------------------|-------------------------------------------|
| 1 or 2                              | Continue 90mg daily                       | Escalate to 180 mg daily D8 as  scheduled |
| 3 or 4                              | Hold until event is ≤ Grade 2 or returned | Do NOT escalate dose                      |
| to baseline, then resume 90mg daily |                                           |                                           |
| 1Per NCI CTCAE v4.0                 |                                           |                                           |  
4.4.3 Non-Hematologic Treatment-Related AEs during Brigatinib 180mg Daily other than Pneumonitis  
| Grade1   | Dose Modification     |
|----------|-----------------------|
| 1 or 2   | Continue current dose |  
| Drug Substance: brigatinib   | ATOMIC Protocol Number: ARI-AT-002                                                                                                                                                       |                                                                                                                                                                             |
|------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 3                            | -                                                                                                                                                                                        | When the current dose is 180 mg QD: Hold until event is grade ≤ 1,  or has returned to baseline. Resume at 180 mg QD or 120 mg QD at  the discretion of the investigator    |
| -                            | Upon recurrence at 180 mg QD: Hold until event is grade ≤ 1, or has returned to baseline and resume at 120 mg QD                                                                         |                                                                                                                                                                             |
| -                            | When the current dose is 120 mg QD: Hold until event is ≤Grade1, or has returned to baseline. Resume at 90 mg QD after recovery                                                          |                                                                                                                                                                             |
| -                            | When the current dose is 90 mg QD: Hold until event is ≤Grade 1,  or has returned to baseline. Resume at 60 mg QD after recovery, or  discontinue at the discretion of the Investigator. |                                                                                                                                                                             |
| -                            | When the current dose is 60 mg QD: Consider discontinuing  treatment at the discretion of investigator                                                                                   |                                                                                                                                                                             |
| 4                            | -                                                                                                                                                                                        | When the current dose is 180 mg QD: Hold until event is grade ≤1,  or has returned to baseline. Resume at 120 mg QD, or discontinue,  at the discretion of the investigator |
| -                            | When the current dose is 120 mg QD, hold until event is grade ≤ 2, or has returned to baseline. Resume at 90 mg QD after recovery                                                        |                                                                                                                                                                             |
| -                            | When the current dose is 90 mg QD: Hold until event is grade ≤ 1,  or has returned to baseline. Resume at 60 mg QD after recovery, or  discontinue at the discretion of the Investigator |                                                                                                                                                                             |
| -                            | When the current dose is 60 mg QD: Consider discontinuing  treatment at the discretion of investigator                                                                                   |                                                                                                                                                                             |
| 1 Per NCI CTCAE v4.0         |                                                                                                                                                                                          |                                                                                                                                                                             |
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4.4.4 hematologic treatment-related aes during

| Drug Substance: brigatinib   | ATOMIC Protocol Number: ARI-AT-002                                                                                                                                                      |                                                                                                                                                                       |
|------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| 3                            | -                                                                                                                                                                                       | When the current dose is 180 mg QD: hold until event is grade ≤  2, or has returned to baseline. Resume at 180 mg or 120 mg QD at  the discretion of the investigator |
| -                            | Upon recurrence at 180 mg QD: Hold until event is grade ≤ 2, or has returned to baseline. Resume at 120 mg QD                                                                           |                                                                                                                                                                       |
| -                            | When the current dose is 120 mg QD: Hold until event is grade≤ 2, or has returned to baseline. Resume at 90 mg QD                                                                       |                                                                                                                                                                       |
| -                            | When the current dose is 90 mg QD: Hold until event is grade ≤1,  or has returned to baseline. Resume at 60 mg QD after recovery,  or discontinue at the discretion of the investigator |                                                                                                                                                                       |
| -                            | When the current dose is 60 mg QD: Consider discontinuing  treatment                                                                                                                    |                                                                                                                                                                       |
| 4                            | -                                                                                                                                                                                       | When the current dose is 180 mg QD: Hold until event is grade≤  2, or has returned to baseline. Resume at 120 mg QD after  recovery                                   |
| -                            | When the current dose is 120 mg QD, hold until event is grade ≤ 2, or has returned to baseline. Resume at 90 mg QD after recovery                                                       |                                                                                                                                                                       |
| -                            | When the current dose is 90 mg QD: Hold until event is ≤Grade1,  or has returned to baseline. Resume at 60 mg QD after recovery,  or discontinue at the discretion of the Investigator  |                                                                                                                                                                       |
| -                            | When the current dose is 60 mg QD Consider discontinuing  treatment                                                                                                                     |                                                                                                                                                                       |
| 1 Per NCI CTCAE v4.0         |                                                                                                                                                                                         |                                                                                                                                                                       |
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4.4.5 treatment-related pneumonitis during brigatinib

| Grade1               | Recommended Action                                                    |                                                                                                               |
|----------------------|-----------------------------------------------------------------------|---------------------------------------------------------------------------------------------------------------|
| 1                    | -                                                                     | Withhold the dose until pneumonitis returns to grade 0 (baseline), then  resume at 90 mg and do not escalate. |
| -                    | If pneumonitis recurs, permanently discontinue treatment.             |                                                                                                               |
| -                    | Withhold dose until pneumonitis returns to grade 0, then resume at 60 |                                                                                                               |
| 2                    | mg and do not escalate.                                               |                                                                                                               |
| -                    | If pneumonitis recurs, permanently discontinue treatment.             |                                                                                                               |
| 3 or 4               | Permanently discontinue treatment                                     |                                                                                                               |
| 1 Per NCI CTCAE v4.0 |                                                                       |                                                                                                               |  
| Grade1               | Recommended Action                                                |                                                                                               |
|----------------------|-------------------------------------------------------------------|-----------------------------------------------------------------------------------------------|
| 1                    | -                                                                 | Withhold the dose until pneumonitis returns to grade 0 (baseline), then  resume at same dose. |
| -                    | If pneumonitis recurs, permanently discontinue treatment.         |                                                                                               |
| -                    | Withhold dose until pneumonitis returns to grade 0, then resumeat |                                                                                               |
| 2                    | 120 mg QD.                                                        |                                                                                               |
| -                    | If pneumonitis recurs, permanently discontinue treatment.         |                                                                                               |
| 3 or 4               | Permanently discontinue treatment                                 |                                                                                               |
| 1 Per NCI CTCAE v4.0 |                                                                   |                                                                                               |
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4.5 toxicities and dose modifications

Patients on cohort C will have tolerated brigatinib 180 mg daily and experienced disease progression. Patients will receive 240 mg daily. Since the purpose of this cohort is to investigate doses of brigatinib at dose greater than 180 mg daily and patients have experienced disease progression on that dose, dose reduction to 180 mg daily will not be permitted. One cycle is 28 days.  
| Dose level   | Brigatinib dose   | Schedule   |
|--------------|-------------------|------------|
| 1            | 240 mg            | Daily      |
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brigatinib dose modification recommendations for

| Toxicity  Grade per  CTCAE v4.0                                                     | Recommended Action                                                                                                                                              |
|-------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Grade 1                                                                             | Withhold the dose until pneumonitis returns to grade 0 (baseline), then  resume at the same dose. If pneumonitis recurs, permanently discontinue treatment.     |
| Grade 2                                                                             | Withhold the dose until pneumonitis returns to Grade 0. Resume at 240  mg daily If pneumonitis recurs or remains grade ≥ 1, permanently discontinue  treatment. |
| Grade 3                                                                             | Permanently discontinue treatment.                                                                                                                              |
| Grade 4                                                                             | Permanently discontinue treatment.                                                                                                                              |
| Abbreviations: CTCAE=Common Terminology Criteria for Adverse Events; QD=once  daily |                                                                                                                                                                 |  
Brigatinib Dose Modification Recommendations for TRAEs (Excluding Pneumonitis)  
for **cohort C**  
| for cohort C       |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             |
|--------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Toxicity Grade     | Recommended Action*                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| per CTCAE v4.0     | Hematologic Toxicity                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        |
| Grade 1 or Grade 2 | Continue at current dose                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
| Grade 3            | First grade AE: Hold until event is ≤ grade 1, or has returned to  baseline If grade 3 AE for < 7 days then resume therapy at 240 mg daily. If  second grade 3 hematologic toxicity occurs then discontinue  brigatinib If grade 3 AE for ≥ 7 days then discontinue study therapy                                                                                                                                                                                                                                           |
| Grade 4            | Discontinue study therapy Nonhematologic Toxicity                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| Grade 1 or Grade 2 | Manage the toxicity with supportive care while continuing at the  same dose                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| Grade 3            | First grade AE: Hold until event is ≤ grade 1, or has returned to baseline If grade 3 AE for < 7 days then resume therapy at 240 mg daily. If  second grade 3 non-hematologic toxicity occurs then discontinue  brigatinib If grade 3 AE for ≥ 7 days then discontinue study therapy                                                                                                                                                                                                                                        |
| Grade 4            | Discontinue study therapy Bradycardia (heart rate less than 60 bpm)                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| Grade 1            | Continue at current dose                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
| Grade 2 or Grade 3 | Withhold until recovery to ≤ grade 1 or to heart rate 60 bpm or above  Evaluate concomitant medications known to cause bradycardia, as  well as antihypertensive medications If contributing concomitant medication is identified and  discontinued, or its dose is adjusted, resume at previous dose upon  recover to ≤ grade 1 or to heart rate 60 bpm or above If no contributing concomitant medication is identified, or if  contributing concomitant medications are not discontinued then  discontinue study therapy |
| Grade 4            | Discontinue treatment if no contributing concomitant medication is  identified                                                                                                                                                                                                                                                                                                                                                                                                                                              |  
  
  
* Apply these recommendations after either dose escalation was accomplished, or after dose reduction for grade 3 or grade 4 toxicity was implemented resulting in no dose escalation.  
Abbreviations: bpm=beats/minute; CTCAE=Common Terminology Criteria for Adverse Events; QD=once daily
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4.6 concomitant medications/juices/herbal supplements

Patients may receive standard supportive care at the discretion of investigator (i.e. anti-emetics, bisphosphonates, narcotics for pain control, etc.).  
In vitro studies suggest that brigatinib, at the doses being evaluated clinically, is unlikely to inhibit CYPs 1A2, 2B6, 2C8, 2C9, 2C19, 2D6, and 3A4/5. Thus, drug interactions (DDIs) due to inhibition of CYPs by brigatinib are highly unlikely. However, other medications that inhibit CYPs may cause DDIs because of their impact on brigatinib's metabolism as outlined in section 1.3.9 and management is outlined in section 4.6.3.
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4.7 prohibited palliative radiotherapy

Patients who require palliative radiotherapy for symptomatic or asymptomatic metastases will be considered as experiencing disease progression as per Section 4.5 and will be followed up per protocol. Patients on cohort A or B who receive local ablative therapies such as radiation to sites of oligo-and/or isolated CNS progression should be considered for cohort C.
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4.8 prohibited systemic therapy

Patients cannot receive systemic therapy (i.e. chemotherapy or targeted therapy) while on protocol therapy.
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4.9 prohibited medications/juices/herbal supplements

See section 1.3.9 for rationale of why use of concomitant medications that fall into the following categories are prohibited: medications/juices/herbal supplements that are strong or moderate inducers or strong inhibitors of CYP3A4. Please refer to Appendix C (see as auxiliary patient document).
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4.10 duration of therapy

Patients should continue on protocol therapy until one of the following events:
- Disease progression - Inter-current illness that prevents further administration of treatment - Unacceptable adverse event(s)
- Pregnancy
- Patient decides to withdraw from study treatment, OR
- General or specific changes in the patient's condition render the patient unacceptable for further treatment in the judgment of the investigator.  
4.11 **Duration of Follow Up**
Long-term follow up will occur every 3 months from the last administration of protocol-directed therapy for up to 2 years or until death, whichever occurs first. Subsequent therapy and survival status will be documented. NOTE: follow-up may occur via review of medical records, on-site visits are not required.
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4.12 removal of patients from

Patients will be removed from protocol therapy and the PI notified when any of the criteria listed in section 4.5 apply. The reason for discontinuation of protocol therapy will be documented on the eCRF. In case a patient decides to prematurely discontinue protocol therapy ("refuses Treatment or withdraws consent") the patient should be asked if she or he may still be contacted for further scheduled study assessments. The outcome of that discussion should be documented in both the medical records and in the eCRF. Excessive patient withdrawals from protocol therapy or from the study can render the study un-interpretable; therefore, unnecessary withdrawal of patients should be avoided.  
4.13 **Study Withdrawal**
If a patient decides to withdraw from the study (and not just from protocol therapy) all efforts should be made to complete and report study assessments as thoroughly as possible. The investigator should contact the patient or a responsible relative by telephone or through a personal visit to establish as completely as possible the reason for the study withdrawal. A complete final evaluation at the time of the patient's study withdrawal should be made with an explanation of why the patient is withdrawing from the study. If the reason for removal of a patient from the study is an adverse event, the principal specific event will be recorded on the eCRF.
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5.0 drug information 5.1 investigational

Brigatinib is a novel, orally active, small molecule tyrosine kinase inhibitor (TKI). Brigatinib drug substance is isolated in crystalline form as a free base. Brigatinib has a melting point of 214°C (determined by differential scanning calorimetry [DSC]). The aqueous solubility of brigatinib is pH-dependent (e.g., at a pH of approximately 2.4, aqueous solubility is > 300 mg/mL, and at a pH of approximately 7.2, aqueous solubility is 11 mg/mL). Brigatinib does not contain any chiral centers.
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5.1.2 formulation

Brigatinib drug product is supplied as film-coated tablets, which contain brigatinib active pharmaceutical ingredient (please refer to pharmacy manual).  
All strengths are dose-weight proportional and manufactured with a commonblend including typical pharmaceutical excipients (lactose monohydrate, microcrystalline cellulose, sodium starch glycolate, hydrophobic colloidal silica, magnesium stearate); tablet film-coating is comprised of typical pharmaceutical grade coating components (talc, polyethylene glycol, polyvinyl alcohol, titanium dioxide).  
The drug product is manufactured under Current Good Manufacturing Practice (cGMP) in accordance with approved procedures.
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5.1.3 supplier storage and stability

Brigatinib will be provided at no cost to the study patient by Takeda Pharmaceuticals Inc., the manufacturer of the drug. Takeda will ship the drug to the main study center. Brigatinib will be supplied in white high density polyethylene (HDPE) bottles with induction sealed caps. Bottle labels will bear the appropriate label text as required by governing regulatory agencies. At a minimum, such text will include product name, product strength, number of tablets, lot number, and use by dating. The recommended storage condition for brigatinib is under 30°C. It should not be refrigerated or frozen.
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5.1.4 handling and disposal

Brigatinib should be handled using standard precautions for the safe handling of antineoplastic agents. Latex gloves are recommended. It must be dispensed only from official study sites by authorized personnel according to local regulations, and stored in a secure area according to local regulations. It is the responsibility of the investigator to ensure that study drug is only dispensed to eligible study patients. The study pharmacist or designee at the site will be responsible for handling and dispensing study drug, and completing associated documentary paperwork. The site must use an appropriate dispensing log/accountability form.
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5.1.5 return and retention of

All used bottles or blister packs of study drug must be returned to Takeda or destroyed in an appropriate manner according to the standard practice at each study center. Destruction of such supplies will be documented. During the study and at termination, patients must return all unused study drug supplies to their study site and the return of these unused study drug supplies must be recorded. Returned supplies must not be re-dispensed.
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5.1.6 management of adverse events

See section 6.1.2.1 of the Investigator's Brochure for additional information on the safety of brigatinib. The study sponsor will be responsible for distributing the IB to all sites when a new version is released from Takeda.
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pulmonary symptoms

Pulmonary events occurring within the first week of brigatinib treatment, including, but not limited to, dyspnea, hypoxia, dry cough, chest tightness, and presumptive lung infection (pneumonia) that may be accompanied by chest x-ray or CT findings of linear or ground-glass opacities should be monitored and reported. In some patients, the symptoms resolved without drug interruption, dose modification, or specific intervention. This suggests that the pathogenesis and natural history of this condition may differ from later-onset pneumonitis, rarely observed with brigatinib, but described with other TKIs. Pulmonary events have been observed after a single dose of brigatinib in patients. It is possible that patients with pre-existing pulmonary interstitial disease, including lymphangitic involvement by tumor, may be at increased risk. Nonetheless, investigators must be aware that these pneumonitis-like symptoms may present within 24 hours of initial dosing. The management of these pulmonary events should include drug interruption, monitoring of oxygen saturation, and radiographic evaluation, and treatment with high-dose corticosteroids, supplemental oxygen therapy, and empiric antibiotics, as indicated. The diagnosis of pneumonitis and determination of causal relationship to the drug is often confounded by the underlying disease (especially lymphangitic carcinomatosis) and other factors such as lung infection and radiation effect due to non-specific signs and symptoms as well as similar radiological appearance. Pneumonitis should be suspected when such signs and symptoms develop or in asymptomatic patients when a new ground glass opacity or interstitial infiltration is noted in imaging studies. If a patient is considered to have the potential diagnosis of drug-related pneumonitis, physical examination, assessment of O2 saturation, and evaluation for infectious etiologies, and thoracentesis, bronchoscopy, or open lung biopsy should be considered to reach a diagnosis After dose interruption and symptom work-up, dose modification should be accomplished according to the recommendations in section 4.3.4 and 4.3.5 (treatment-related pneumonitis). If the symptoms include documented hypoxia and/or radiologic evidence of interstitial or ground glass changes, or result in an SAE, the early onset condition should be treated according to section 4.3.4 and 4.3.5 (treatment-related pneumonitis)
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hypertension

Brigatinib may result in elevations in BP (blood pressure, systolic or diastolic). During brigatinib treatment, BP should be regularly monitored and hypertension should be clinically managed. Brigatinib treatment might need to be temporarily interrupted if hypertension is not medically controlled.
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bradycardia

Treatment with brigatinib may result in bradycardia. An analysis of intensive ECG
and PK data indicates a decrease in heart rate is associated with the timing of brigatinib maximum plasma concentrations (Cmax). During brigatinib treatment, heart rate should be monitored at each physician visit; especially in patients who have a medical history of bradycardia.
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6.0 evaluations and assessments

| 6.1                               | Time and Events Table                                                                                |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
|-----------------------------------|------------------------------------------------------------------------------------------------------|-------------------|--------------------------------------------------------------------------------------------|-------|------------------|------------------|----|-----|-----|-----|----|----|----|----|----|
| Assessment                        | Screening                                                                                            | C1                |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| 1                                 | EOT3                                                                                                 | FU4               |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| D11,2                             |                                                                                                      |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| C2                                |                                                                                                      |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| D8 2 C1                           | C3                                                                                                   | C4                | C5                                                                                         | C6    | C7               | C8               | C9 | C10 | C11 | C12 |    |    |    |    |    |
| D11,2                             | D11,2                                                                                                | D11,2,  14 D1 1,2 | D11,2                                                                                      | D11,2 | D11,2,  14 D11,2 | D11,2,  14 D11,2 |    |     |     |     |    |    |    |    |    |
| D11,2,  14                        |                                                                                                      |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Informed consent12                | X                                                                                                    |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Medical History5                  | X                                                                                                    | X                 |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Prior cancer                      | X                                                                                                    |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| therapy13 Physical exam &         | X                                                                                                    | X                 | X                                                                                          | X     | X                | X                | X  | X   | X   | X   | X  | X  | X  | X  |    |
| vital signs5, 14 ECOG Performance | X                                                                                                    | X                 | X                                                                                          | X     | X                | X                | X  | X   | X   | X   | X  | X  | X  | X  |    |
| Status CBC with                   | X                                                                                                    | X                 | X                                                                                          | X     | X                | X                | X  | X   | X   | X   | X  | X  | X  | X  | X  |
| differential6 Serum Chemistries7  | X                                                                                                    | X                 | X                                                                                          | X     | X                | X                | X  | X   | X   | X   | X  | X  | X  | X  | X  |
| Testosterone (males)              | X                                                                                                    | X                 | X                                                                                          | X     | X                | X                |    |     |     |     |    |    |    |    |    |
| ECG                               | X                                                                                                    |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Serum pregnancy                   | X                                                                                                    |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Test8 CT scan                     | X                                                                                                    | X2                | X2                                                                                         | X2    | X2               | X2               |    |     |     |     |    |    |    |    |    |
| chest/abdomen2 Brain MRI2         | X                                                                                                    | X2                | X2                                                                                         | X2    | X2               |                  |    |     |     |     |    |    |    |    |    |
| Peripheral blood  sample9         | X9                                                                                                   | X9                | X9                                                                                         | X9    | X9               | X9               | X9 |     |     |     |    |    |    |    |    |
| Tumor sample                      | X10                                                                                                  | X10               |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Adverse event                     | X                                                                                                    | X                 | X                                                                                          | X     | X                | X                | X  | X   | X   | X   | X  | X  | X  | X  |    |
| 5, 14                             |                                                                                                      |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| assessment Patient Diary          | Provide11 Review Review Review Review Review Review Review Review Review Review Review Review Review |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Concomitant Meds                  | Review                                                                                               | Review            | Review Review Review Review Review Review Review Review Review Review Review Review Review |       |                  |                  |    |     |     |     |    |    |    |    |    |
| Subsequent Therapy                | X                                                                                                    |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
| and Survival Status Brigatinib    | See section 4.2 for brigatinib schedule and dose                                                     |                   |                                                                                            |       |                  |                  |    |     |     |     |    |    |    |    |    |
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key to footnotes

1 Within 28 days prior to Day 1 of brigatinib unless otherwise noted. If screening (baseline)
hematology and serum chemistries were performed within 7 days of D1 of cycle 1, these do not need to be repeated.  
2 Unless otherwise noted, a window of 2 days will be applied to all study visits; for every other cycle tumor imaging starting with D1 of cycle 3, imaging may take place within 7 days prior to the study visit to accommodate holiday, weekends, and transportation issues. CT scan should be of the chest and abdomen. The pelvis should only be performed if there is evidence on metastatic disease in the pelvis. Brain imaging MRI of the brain should be performed at baseline. In patients with known brain metastases MRI is performed every 3 cycles to assess for intracranial disease progression. Patients without brain metastases on screening MRI will undergo repeat brain imaging as clinically indicated or institutional standard (i.e. a specific interval is not mandated by the protocol). If patient cannot tolerate or has contraindication to brain MRI, a CT scan with and without contrast can be used.  
3 This visit should occur 30 days (+/- 3 days) after brigatinib treatment stops for whatever reason (adverse event, progression, or at discretion of the investigator). Patients who have an ongoing grade 4 AE or SAE at the time of discontinuation from treatment will be contacted every 2 weeks until the event is resolved, determined to be irreversible by the investigator, or until the patient begins an alternate form of treatment. For patients participating on cohorts A or B who are enrolled in cohort C this visit is omitted.  
4 Long-term follow up will occur every 3 months from the last administration of protocoldirected therapy for up to 2 years or until death, whichever occurs first. Subsequent therapy and survival status will be documented. NOTE: follow-up may occur via review of medical records, on-site visits are not required.  
5 Complete history at baseline only, thereafter focused history on symptoms/adverse event. Blood pressure and heart rate should be checked at each physician visit 6 This includes CBC with differential and platelet count 7 Serum chemistries include blood urea nitrogen (BUN), creatinine, bilirubin, ALT (SGPT),
AST (SGOT), alkaline phosphatase, amylase, creatinine phosphokinase (CPK). Additional can be ordered if clinically indicated or at the discretion of the investigator but are not required by the protocol 8 Within 7 days of D1 of treatment with brigatinib in women of child-bearing potential 9 This blood sample will be used to explore whether resistance mutations can be detected in ctDNA; see laboratory manual for additional details. Sample is to be drawn on C1D1 and Day 1 of every odd cycle (3, 5, etc.) while patient is receiving treatment with brigatinib.  
10 Biopsy after progression on previous ALK inhibitor and within 60 days prior to D1 of treatment is mandatory (i.e., if tissue available from pre-study biopsy, this
54 of 82 tissue will be accessed for correlative studies, otherwise, patients must consent to tumor biopsy to meet eligibility criteria). All subjects must consent to provide tumor blocks or slides. Patients treated on cohorts A or B and enrolling in cohort C are required to undergo biopsy.  
Biopsy specimens and peripheral blood samples will be destroyed as per standard institutional procedures at the time study termination or may be stored for future research. Patients will be provided both options on the informed consent document.  
11 On C1D1 provide the patient diary for use. D1 of all subsequent cycles patient diary is to be collected from previous cycle, reviewed with the patient, and a new diary provided.  
12 Patients in cohort A and B are brigatinib treatment naïve and receiving brigatinib at a standard dose. Patients in cohort C will have progressed on brigatinib and will be receiving a higher than the standard dose brigatinib. Depending on the institutional practice and policies this may require patients on cohort C to sign a "post-progression" treatment informed consent document.  
13 Prior systemic therapy will be collected including number of prior ALK TKI's and names, prior chemotherapy treatment. The sites of disease progression (CNS, extra-CNS or both) and if the patient received local therapy (e.g. radiation therapy, SBRT, etc.) to site of disease progression between disease progression and enrollment in study (i.e. disease progression in brain and lungs, brain metastases treated with SBRT and lungs metastases or primary not)
14 Even day cycle visits not including Brain MRI imaging and are conducted (at treating physician's discretion) as telemedicine visits will not include standard clinic assessments (i.e., symptoms/adverse event, blood pressure and heart rate). To maintain data integrity, these missed assessments are to be noted in the EDC as deviations (planned) and indicate that visit was conducted remotely.  
6.2 Pre-Study **Assessments**
The assessments required as part of screening can be completed in one or more visits, as long as the assessments are completed within the time frames listed in the Key to the Time and Events table. Clinical evaluation: complete history, comprehensive physical examination (to include height and weight), vital signs, ECOG performance status
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laboratory studies

- **Pregnancy Test**: Serum pregnancy test is required for all women of childbearing potential within 7 days prior to D1
- **Hematology**: CBC with differential - **Serum Chemistries**: blood urea nitrogen (BUN), creatinine, bilirubin, ALT (SGPT), AST (SGOT), alkaline phosphatase, amylase, creatinine phosphokinase (CPK)
- **Serum Testosterone**: Limited to male patients
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cardiac studies ecg

Tumor measurement: Tumor imaging should remain consistent throughout study, and should always include CT scans of chest and abdomen. CT scan of the pelvis should only be done if there is known metastatic disease to the pelvis. Brain MRI should be done, and if the patient cannot tolerate or has contraindication to MRI a CT scan with and without contrast should be done. Concomitant medications: Documentation of all concomitant medications, and in particular any drugs that moderately or strongly inhibit or induce CYP3A4 and/or CYP2C8. **NOTE**: Patients will be instructed to bring their list of medications (all, including over the counter medications) to each study visit for review by their study team and for all visits to healthcare professionals (e.g., primary care physicians, consultants) while on study. Patient diary: Patients will be provided a diary at baseline and instructed to document all doses of study medication (referenced herein as Appendix B, see as independent IRB/REB approved (patient) document). Tissue acquisition: Tumor biopsy after progression on previous ALK inhibitor and within 60 days prior to study entry is mandatory i.e., if tissue available from pre-study biopsy, this tissue will be accessed for correlative studies, otherwise, patients must consent to tumor biopsy to meet eligibility criteria; see section 6.6 and laboratory manual for additional details. If patients have undergone NGS testing, as part of standard of care, on tumor sample after experiencing disease progression on prior therapy and prior to starting study therapy we will collect redacted report. If not performed/unavailable, sites will note not performed/not available in the database. Prior cancer therapy: Prior systemic therapy will be collected including number of prior ALK TKI's and names, prior chemotherapy treatment. The sites of disease progression (CNS, extra-CNS or both) and if the patient received local therapy (e.g. radiation therapy, SBRT, etc.) to site of disease progression between disease progression and enrollment in study (i.e. disease progression in brain and lungs, brain metastases treated with SBRT and lungs metastases or primary not)
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6.3 treatment assessments 6.3.1 d1

Tests and procedures in this Section 6.3.1 are to be conducted during each Day 1 cycle visit. Sections 6.3.3 and 6.3.4 include additional assessments to be conducted during each Day 1 at specific numbered cycle visit (e.g., odd cycles, each third cycle visit).  
Clinical evaluation: focused medical history on symptoms/adverse events, comprehensive physical examination (to include weight), vital signs, ECOG performance status Laboratory studies:
- **Hematology**: CBC with differential - **Serum Chemistries**: blood urea nitrogen (BUN), creatinine, bilirubin, ALT (SGPT), AST (SGOT), alkaline phosphatase, amylase, creatinine phosphokinase (CPK).  
- **Blood sample:** A blood sample for ctDNA will be requested (mandatory);
see section 6.6 and the laboratory study for additional details. (Cycle 1 Day 1 & Day 1 of every odd cycle- 3, 5, etc.).  
Patient diary: Collect, review with patient, and provide patient with new diary. (C1D1- provide patient with initial diary)
Concomitant medications: Review any additions or deletions. AE: Adverse events will be assessed according to the NCI CTCAE v. 4.0.  
6.3.2 **D8 Cycle 1**
Clinical evaluation: focused medical history on symptoms/adverse events, Laboratory studies:
- **Hematology**: CBC with differential - **Serum Chemistries**: blood urea nitrogen (BUN), creatinine, bilirubin, ALT (SGPT), AST (SGOT), alkaline phosphatase, amylase, creatinine phosphokinase (CPK)
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patient diary review

Concomitant medications: Review any additions or deletions. AE: Adverse events will be assessed according to the NCI CTCAE v. 4.0.
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6.3.3 d1 cycle 3 and

Tumor measurement: Tumor imaging should remain consistent throughout study, and should include CT scans of chest and abdomen. Pelvis should only be done if there is known metastatic disease in the pelvis.
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laboratory studies - serum testosterone

Blood sample: A blood sample for ctDNA will be requested (mandatory); see section 6.6 and the laboratory study for additional details.
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6.3.4 d1 cycle 3 and

Brain metastases: Brain MRI or CT scan with or without contrast should be done every 3 cycles (3 months) for patients with known brain metastases to evaluated for CNS disease progression.