Phase Ib/II Trial of Copanlisib in Combination With Trastuzumab and Pertuzumab After Induction Treatment of HER2 Positive (HER2+) Metastatic Breast Cancer (MBC) With PIK3CA Mutation or PTEN Mutation
Phase: PHASE1
Conditions: Anatomic Stage IV Breast Cancer AJCC v8, HER2-Positive Breast Carcinoma, Metastatic Breast Carcinoma
Sponsor: National Cancer Institute (NCI)

 
 
 
To: 
Cancer Therapeutic Evaluation Program 
 
From: 
Senthilkumar Damodaran, MD 
 
Date:         February 21, 2022 
 
Re: 
Response to Request for Amendment for Protocol #10296: “Phase Ib/II trial of 
copanlisib in combination with trastuzumab and pertuzumab after induction treatment 
of HER2 positive (HER2+ ) metastatic breast cancer (MBC) with PIK3CA mutation or 
PTEN mutation.” 
 
SUMMARY OF CHANGES – Protocol 
 
 
# 
Section 
Comments 
1. 
Title Page 
Added Keena Woods as a study coord. Removed Danielle Kwiatkowski.  
 
 
2. 
Section 4.1 
Revised the following excerpt as indicated. 
Food and Drug Administration (FDA) regulations and National Cancer Institute (NCI) policy require all 
individuals contributing to NCI-sponsored trials to register and to renew their registration annually. To 
register, all individuals must obtain a Cancer Therapy Evaluation Program (CTEP) Identity and Access 
Management (IAM) account at https://ctepcore.nci.nih.gov/iam. In addition, persons with a registration type of 
Investigator (IVR), Non-Physician Investigator (NPIVR), or Associate Plus (AP) (i.e., clinical site staff 
requiring write access to Oncology Patient Enrollment Network (OPEN), Rave, or acting as a primary site 
contact) must complete their annual registration using CTEP’s web-based Registration and Credential 
Repository (RCR) at https://ctepcore.nci.nih.gov/rcr. 
 
RCR utilizes five person registration types. 
• 
IVR: MD, DO, or international equivalent, 
• 
NPIVR: advanced practice providers (e.g., NP or PA) or graduate level researchers (e.g., PhD), 
• 
AP: clinical site staff (e.g., RN or CRA) with data entry access to CTSU applications such as the 
Roster Update Management System (RUMS), OPEN, Rave, acting as a primary site contact, or with 
consenting privileges, (e.g., Roster Update Management System [RUMS], OPEN, Rave,), 
• 
Associate (A): other clinical site staff involved in the conduct of NCI-sponsored trials, and 
• 
Associate Basic (AB): individuals (e.g., pharmaceutical company employees) with limited access to 
NCI-supported systems. 
In addition, all investigators act as the Site-Protocol PI (Investigator listed on the IRB approval), 
consenting/treating/drug shipment investigator in OPEN, or as the Clinical Investigator (CI) on the DTL must be 
rostered at the enrolling site with a participating organization., consenting/treating/drug shipment, or as the CI on the 
DTL must be rostered at the enrolling site with a participating organization (i.e., Alliance). 
 
 
3. 
 
Section 4.2.1 
 
Added highlighted sentence in the excerpt below. 
Download the site registration forms from the protocol-specific page located on the CTSU members’ website. 
Permission to view and download this protocol and its supporting documents is restricted based on person and site roster 
assignment. To participate, the institution and its associated investigators and staff must be associated with the LPO or a 
Participating Organization on the protocol. One way to search for a protocol is listed below. 
 
4. 
Section 4.2.2 
 
Added the following bullet point to this section, as it has been indicated that a Site Initiation Visit is required. 
• 
Site Initiation Visit 
 
5. 
Section 4.2.3 
 
Replaced the indicated sentence below as specified. 
To access the Regulatory Submission Portal, log on to the CTSU members’ website, go to the Regulatory section, and 

 
select Regulatory Submission. 
To access the Regulatory Submission Portal, log on to the CTSU members’ website → Regulatory → Regulatory 
Submission. 
 
6. 
Section 7.2 
 
Deleted the old table under section 7.2 and added the new table below. Updated paragraph as per PI request 
Dose may be suspended for up to 3 weeks due to toxicity. Patients requiring treatment to be held for >3 weeks can 
resume treatment after discussion and approval by the study PI.  
Dose may be suspended for up to 3 weeks due to toxicity. Patients requiring treatment to be held for >3 weeks will be 
taken off treatment. Dose re-escalation is not allowed after a dose reduction 
• 
Dose re-escalation maybe allowed when a patient has achieved controlled glucose levels per investigator 
judgement after discussion with study PI. 
• 
The need for additional glucose monitoring at home should be determined by the investigator based on post-
infusion glucose profile and clinical status of the patient. 
• 
Patient with non-fasting plasma glucose values can be treated at investigator discretion. 
 
 
 
CTCAE Grade 
Intervention 
Dose Adjustment 
Grade 1  
FPG > ULN-160 
mg/dL or > ULN-8.9 
mmol/L 
Initiation of an oral anti-hyperglycemic agent (eg., 
metformin) and additional glucose monitoring 
should be considered 
No change 
Grade 2  
FPG > 160-250 mg/dL 
or > 8.9-13.9 mmol/L  
 
Initiation or increased dose of an oral anti-
hyperglycemic agent (eg: metformin) and additional 
glucose monitoring should be considered 
Dosing with copanlisib may either be he
continued per investigator evaluation 
Grade 3, asymptomatic, 
> 250-500 mg/dL 
or > 13.9-27.8 
mmol/L  
Patient should be managed as per standard of care, 
including implementation of additional glucose 
monitoring and initiation and/or increase of anti-
hyperglycemic therapy (eg., metformin) 
Consideration should be given to suspen
dosing until the hyperglycemia resolved
Dosing with copanlisib may resume at t
or at one dose level lower than the curre
discussion with study PI 
Grade 3, symptomatic, 
> 250-500 mg/dL 
or > 13.9-27.8 
mmol/L 
Patient should be managed as per standard of care, 
including implementation of additional glucose 
monitoring and initiation and/or increase of anti-
hyperglycemic therapy 
Copanlisib dosing should be suspended 
hyperglycemia resolved to grade </=2. T
discontinued from the study if such ther
their hyperglycemia. Dosing with copan
otherwise resume at one dose level lowe
level. 
Grade 4  
> 500 mg/dL 
or ≥ 27.8 mmol/L 
Patient should be managed as per standard of care, 
including intensification of appropriate anti-diabetic 
treatment, intravenous hydration and intervention for 
electrolyte/ketoacidosis/hyperosmolar disturbances. 
Suspend copanlisib.  Re-check FPG wit
clinically indicated.  
If FPG decreases to ≤ 500 mg/dL or 27.
FPG value specific recommendations fo
If FPG is confirmed at > 500 mg/dL or 2
permanently discontinue alpelisib treatm
7. 
3.1.1 
Updated language of eligibility criteria 
Phase-1B: Any number of prior of lines of therapy in the metastatic setting is allowed, provided patients are considered 
candidates for trastuzumab and pertuzumab combination or on maintenance trastuzumab and pertuzumab (with or 
without prior chemotherapy) as long as DLT can be determined. 
 
For Phase-2: Patients should have only received first line of induction chemotherapy (taxane) with trastuzumab and 
pertuzumab in the metastatic setting. 
 
8. 
3.1.1.1 
Presence of actionable mutation in either PIK3CA gene or PTEN gene on molecular testing 
(Appendix E, F), in primary or metastatic tumor at based on tissue or ctDNA testing in a 
CLIA certified laboratory. Results of molecular testing will be reviewed to confirm 
eligibility by MD Anderson Precision Oncology Decision Support team and captured in 
patient’s record. 
 
Management of Hyperglycemia (based on fasting glucose) 

 
9. 
3.1.1.2 
For Phase-2 - Patients must be within 8 weeks of completion of first-line induction 
chemotherapy (i.e., 4-8 cycles of any taxane, trastuzumab and pertuzumab) without 
evidence of progression. Patients may receive up to 2 doses of HER2 targeted treatment 
between end of induction treatment and start of trial, while eligibility is being confirmed. In 
addition, for phase-1 portion, patients on any period of maintenance on trastuzumab and 
pertuzumab in the advanced setting are also eligible as long as DLT can be determined. 
10. 
3.1.1.7 
Removed Leukocytes as it is not required as per PI 
Patients must have adequate organ and bone marrow function as defined below: 
 
 
leukocytes 
≥3,000/mcL 
11. 
3.1.1.12 
Updated eligibility criteria 
Hormone receptor positive (ER+ and / PR+) breast cancer patients will be allowed to continue endocrine 
therapy as clinically indicated while participating in this clinical trial the study. 
 
12. 
4.4 
Deleted as per PI 
Patients should begin protocol treatment within 8 weeks of the last dose of induction 
chemotherapy. Sites are allowed 5 business days to order and receive the study agent after 
registration, and this should be taken into account when registering the patient. Issues that 
would cause treatment delays should be discussed with the Principal Investigator. If a 
patient does not receive protocol therapy following registration, the patient’s registration on 
the study may be canceled. The Study Coordinator should be notified of cancellations as 
soon as possible. 
13. 
5.1 
1If available archival tissue Page:41 must be collected within 6 12 months prior to registration and must consist of 
metastatic tumor tissue. For archival tissue, a copy of the corresponding anatomic pathology report must be sent with 
the tissue and uploaded to Rave. 
2For new biopsies, a copy of the radiology and operative reports from the tissue removal procedure must be sent 
with the tissue to the ETCTN Biorepository. When completed, upload the corresponding pathology reports to Rave. 
3Optional if archival tissue is present 
 
14. 
5.4.1.1 
As per PI: A maximum number of 5 cores (1 cm in length) will be obtained from the 
procedure is recommended. 
15. 
5.6 
Timeline of available archival tissue changed from 6 to 12 months as per PI request. 
A pre- treatment biopsy is optional if archival tumor tissue from metastatic site (collected within 612 months prior to 
registration) is available. 
Added ctDNA as specimen testing assay for PIK3CA mutations and PTEN mutations 
16. 
6.1 
For Phase-2, Patients enrolled in phase Ib/safety run-in phase will receive triplet combination therapy with copanlisib, 
trastuzumab and pertuzumab, , after completion of induction chemotherapy with 4-8 cycles of any taxane, trastuzumab 
and pertuzumab. Ppatients may receive up to 2 doses of  
trastuzumab / pertuzumab between end of induction treatment and start of the trial, while eligibility is being confirmed. 
Based on the company-sponsored studies with copanlisib in patients with oncologic malignancies, the RP2D of 
copanlisib monotherapy is 60 mg administered by the 1 hour IV infusion for 3 weeks (Days 1, 8, and 15) every 4 
weeks. A copanlisib dose reduction to 45 mg has been allowed for toxicities (Copanlisib Investigator’s Brochure, 
2017). For ease of scheduling, copanlisib will be administered intravenously on days 1 and 8 of 21 day cycle. To 
determine the recommended phase 2 dose of copanlisib in the triplet combination, a 3+3 dose de-escalation design will 
be employed in the phase Ib part of the study. The 3+3 dose de-escalation plan is described in further detail under 
Section 6.2. The starting dose of copanlisib for this combination trial is 60 mg. 
 
17. 
6.1.1 
Updated pre dose glucose level and post dose C1D1as per PI request 
Day 1 of 
cycle 1 
<160 mg/dL (fasting*) 
<200 mg/dl (non fasting **) 
 
 
On Day 1 of cycle 1, patients should be fasting for at least 8 h prior to the pre-dose glucose 
measurement. Glucose will be measured at pre-dose and post dose 1 hour and 2 hours after 
the end of copanlisib infusion (window of  10 min is allowed except for the pre-dose 
measurement). Additional measurements to can be performed at the clinic as clinically 
indicated. 
18. 
6.3 
Updated language as per PI request 
Once RP2D is reached, a protocol amendment will be submitted for CTEP’s review and approval prior to starting 
phase 2.  Phase II/ dose expansion phase will enroll an additional 96 patients with HER2+ metastatic breast cancer 
patients with PI3K-AKT pathway alterations (PIK3CA mutation or PTEN  mutationmutation), after completion of 
induction chemotherapy with 4-8 cycles of any taxane, trastuzumab and pertuzumab. Patients may receive upto 2 doses 
of trastuzumab / pertuzumab between end of induction treatment and start of the trial, while eligibility is being 
confirmed. Patients enrolled in phase II trial will undergo 1:1 randomization to receive maintenance with either dual 
anti-HER2 targeted therapy (trastuzumab + pertuzumab) or the triplet combination (copanlisib + trastuzumab + 

 
pertuzumab). Please see SCHEMA. An actionable molecular alteration in the PI3K-AKT pathway (PIK3CA mutation 
or PTEN mutation) is a pre-requisite for enrollment in the phase II clinical trial. The Precision Oncology Decision 
Support (PODS) team at MD Anderson will review each patient’s NGS test results to annotate PIK3CA and PTEN 
mutations for functional significance and actionability. This report will be captured in patient’s medical record. 
For the expansion cohort, patients will continue to be monitored for occurrence of DLT. If 2 of the first 5 
patients or if ≥2 of 6 patients experience DLT, the Principal Investigator will discuss with all study 
investigators and with CTEP whether further addition of patients is needed to re- assess the RP2D. 
Monitoring of all safety and toxicity data is done by the Principal Investigator and the Corresponding 
Organization on a real-time basis as data are entered into Medidata Rave using the Web Reporting Module. 
All participating sites are expected to notify the Principal Investigator when a DLT has occurred. 
 
 
19. 
7.1 
*Only one dose level reduction is allowed for copanlisib. Copanlisib is to be administered after trastuzumab and 
pertuzumab. Biosimilars/ interchangeable products of trastuzumab and pertuzumab as well as other subcutaneous 
forms of injections can be used as per FDA prescribing information guidelines 
#Starting dose 
20. 
7.2.1.1 
Updated glucose monitoring restricted to only prior dose of Copanlisib. Also updated table of management of 
Hyperglycemia as per PI request 
 From Cycle 1 Day 8 and onwards, gGlucose monitoring is required before each copanlisib infusion. The study drug 
will be administered only if pre-dose glucose level is < 160 mg/dL (fasting) or < 200 mg/dL (non- fasting). 
• 
Continuing/ persistent occurrence of post-infusion blood glucose >500 mg/dL, based 
on repeated laboratory analysis despite optimal glucose lowering therapy after 2 
infusions of copanlisib (at least 1 treatment cycle), will require dose reduction by one 
dose level. 
• 
Dose re-escalation may be allowed when a patient has achieved controlled glucose levels  after 
discussion with study PI.Persistent occurrence of post-infusion blood glucose >500 mg/dL based 
on laboratory analysis which occurred at the lowest dose level despite optimal glucose lowering 
therapy (after at least one cycle of treatment) with consultation of a diabetes specialist requires 
permanent discontinuation of the study drug. 
• 
The need for additional glucose monitoring at home should be determined by the 
investigator based on post-infusion glucose profile and clinical status of the patient. 
• 
Patient with non-fasting plasma glucose values can be treated at investigator discretion. 
 
 
21  
9.1 
Please refer to “SCHEMA” section for study design schema. 
 
22  
11 
Added ECHO/MUGA at pre study and deleted at baseline in study calendar. Updated tumor measurement repeated 
from every 9 weeks to 12 weeks as per PI request 
g: Normal LVEF (≥ 50%) is required prior to study treatment. EKG and ECHO or MUGA will be performed at 
baseline, and then ECHO/MUGA to be performed at baseline and every 12-16 weeks weeks as per treating physician’s 
discretion. After baseline, EKG will can be performed repeated if clinically indicated. 
 k: Optional tumor biopsies and blood samples should be strongly encouraged if clinically feasible. 
 
schema 
Deleted and updated language in schema (phase 2) 
 

NCI Protocol #: 10296  
Version Date:February 21, 2022 
1 
 
 
 
 
 
Protocol #: 10296 
 
Local Protocol #: 
MDACC# 2020-0260 
 
ClinicalTrials.gov Identifier: NCT04108858 
 
TITLE: Phase Ib/II trial of copanlisib in combination with trastuzumab and pertuzumab after 
induction treatment of HER2 positive (HER2+ ) metastatic breast cancer (MBC) with 
PIK3CA mutation or PTEN mutation. 
 
Corresponding Organization: LAO-TX035 / University of Texas MD Anderson Cancer 
Center LAO 
 
Principal Investigator: 
Senthilkumar Damodaran, MD. PhD 
Department of Breast Medical Oncology, CPB5.3494 
1515 Holcombe Blvd., Unit 1354 
Houston, TX 77030 
713-792-2817 (telephone) 
713-794-4385 (Fax) 
SDamodaran@mdanderson.org 
 
 
 
Participating Organizations 
Phase 1b/ Safety run-in: 
 
 
LAO-TX035 / University of Texas MD Anderson Cancer Center LAO 
LAO-MD017 / JHU Sidney Kimmel Comprehensive Cancer Center LAO 
LAO-OH007 / Ohio State University Comprehensive Cancer Center LAO 
LAO-11030 / University Health Network Princess Margaret Cancer 
Center LAO 
LAO-CA043 / City of Hope Comprehensive Cancer Center LAO 
LAO-CT018 / Yale University Cancer Center LAO 
LAO-MA036 / Dana-Farber – Harvard Cancer Center LAO 
LAO-MN026 / Mayo Clinic Cancer Center LAO 
LAO-PA015 / University of Pittsburgh Cancer Center LAO 
LAO-NCI / National Cancer Institute LAO 
 
Phase 2: 
LAO-11030 / University Health Network Princess Margaret Cancer Center LAO 
LAO-CA043 / City of Hope Comprehensive Cancer Center LAO 

NCI Protocol #: 10296  
Version Date:February 21, 2022 
2 
 
 
 
LAO-CT018 / Yale University Cancer Center LAO 
LAO-MA036 / Dana-Farber – Harvard Cancer Center LAO 
LAO-MD017 / JHU Sidney Kimmel Comprehensive Cancer Center LAO 
LAO-MN026 / Mayo Clinic Cancer Center LAO 
LAO-OH007 / Ohio State University Comprehensive Cancer Center LAO 
LAO-PA015 / University of Pittsburgh Cancer Center LAO 
LAO-TX035 / University of Texas MD Anderson Cancer Center LAO 
LAO-NCI / National Cancer Institute LAO 
 
LAO-PA015 / University of Pittsburgh Cancer Institute LAO 
LAO-TX035 / University of Texas MD Anderson Cancer Center LAO 
LAO-NCI / National Cancer Institute LAO 
EDDOP / Early Drug Development Opportunity Program 
CATCHUP / Creating Access to Targeted Cancer Therapy for Underserved Populations 
 
 
Statistician: 
Study Coordinator: 
Kim-Anh Do, Ph.D. 
 Keena Woods, CS 1515 
Holcombe Blvd., Unit 1411 
1515 Holcombe Blvd., Unit 1354 
Houston, TX 77030 
Houston, TX 77030 
(713)-794-4155 
(713) 792-6679 
(713)-563-4243 kimdo@mdanderson.org 
 Kmwoods@mdanderson.org  
 
Responsible Research Nurse: 
Responsible Data Manager: 
Jill Schwartz-Gomez, RN 
Peter Flores, DC 
1515 Holcombe Blvd. Unit 1354 
1515 Holcombe Blvd. Unit 1354 
Houston, TX 77030 
Houston, TX 77030 
(713)-792-2768 
(713) 745-0699 
JSchwartz@mdanderson.org 
prflores@mdanderson.org 
 
 
NCI-Supplied Agent: Copanlisib, (NSC 784727) 
Other Agents: Trastuzumab, (NSC 688097, Commercial) 
Pertuzumab, (NSC 740102, Commercial) 
 
 
IND #:  
IND Sponsor: DCTD, NCI 
 
Protocol Type / Version # / Version Date: 
Original / April 2, 2019 
Revision 1 / July 5, 2019 
Revision 2 / August 16, 2019 
Revision 3a / November 1, 2019 

NCI Protocol #: 10296  
Version Date:February 21, 2022 
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Revised 7/ October 30, 2020 
Revised 8/November 20,2020 
Revised 9/April 21, 2021 
Revised 10/January 3, 2022 
Revised 11/February 21, 2022  
 
Revision 4 / November 27, 2019 
Revised 5 / January 20, 2020 
Revision 6 / June 30, 2020 

NCI Protocol #: 10296  
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SCHEMA 
 
Phase 1b/ Safety Run-in Phase 
 
 
 
 
 
 
Phase 2 
 
 

NCI Protocol #: 10296  
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TABLE OF CONTENTS 
Protocol #: 
10296..................................................................................................................................... 1 
TITLE: Phase Ib/II trial of copanlisib in combination with trastuzumab and pertuzumab after induction 
treatment of HER2 positive (HER2+ ) metastatic breast cancer (MBC) with PIK3CA mutation or 
PTEN mutation. ................................................................................................................................ 1 
SCHEMA ...................................................................................................................................................... 4 
TABLE OF CONTENTS .............................................................................................................................. 5 
1. 
OBJECTIVES ................................................................................................................................... 8 
1.1 Primary Objectives ................................................................................................................... 8 
1.2 Secondary Objectives ................................................................................................................ 8 
1.3 Exploratory Objectives ............................................................................................................. 8 
2. 
BACKGROUND .............................................................................................................................. 9 
2.1 Invasive Breast Carcinoma ...................................................................................................... 9 
2.2 CTEP IND Agent .................................................................................................................... 10 
2.3 Commercial Agents ................................................................................................................. 23 
2.4 Rationale .................................................................................................................................. 25 
2.5 Correlative Studies Background............................................................................................ 27 
3. PATIENT SELECTION ......................................................................................................................... 30 
3.1 Eligibility Criteria ................................................................................................................... 30 
3.2 Exclusion Criteria ................................................................................................................... 32 
3.3 Inclusion of Women and Minorities ...................................................................................... 34 
4. REGISTRATION PROCEDURES......................................................................................................... 34 
4.1 Investigator and Research Associate Registration with CTEP ........................................... 34 
4.2 Site Registration ...................................................................................................................... 36 
Additional Requirements ................................................................................................................ 36 
4.3 Patient Registration ................................................................................................................ 38 
4.4 General Guidelines .................................................................................................................. 41 
5. BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES .............................................................. 42 
5.1 Summary Table for Specimen Collection ............................................................................. 42 
5.2 Specimen Procurement Kits and Scheduling ....................................................................... 43 
5.3 Specimen Tracking System Instructions ............................................................................... 43 
5.4 Specimen Collection ................................................................................................................ 47 
5.5 Shipping Specimens from Clinical Site to the ETCTN Biorepository ................................ 49 
5.6 Biomarker Plan ....................................................................................................................... 52 

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5.7 Integral Laboratory Studies ................................................................................................... 55 
5.8 Integrated Correlative Studies ............................................................................................... 55 
5.9 Exploratory/Ancillary Correlative Studies ........................................................................... 56 
6. 
TREATMENT PLAN ..................................................................................................................... 58 
6.1 Agent Administration ............................................................................................................. 58 
6.2 Definition of Dose-Limiting Toxicity ..................................................................................... 63 
6.3 Dose Expansion Cohorts: ....................................................................................................... 64 
6.4 General Concomitant Medication and Supportive Care Guidelines ................................. 64 
6.5 Duration of Therapy ............................................................................................................... 65 
6.6 Duration of Follow-Up ............................................................................................................ 66 
7. 
DOSING DELAYS/DOSE MODIFICATIONS ............................................................................. 66 
7.1 Dose de-escalation schema for the triplet combination of copanlisib, trastuzumab, and 
pertuzumab ........................................................................................................................ 67 
7.2 Management of copanlisib related toxicities ........................................................................ 67 
7.3 Management of overlapping toxicities .................................................................................. 70 
8. 
PHARMACEUTICAL INFORMATION ....................................................................................... 71 
8.1 CTEP IND Agent(s) ................................................................................................................ 72 
8.2 Commercial Agents ................................................................................................................. 75 
9. 
STATISTICAL CONSIDERATIONS ............................................................................................ 78 
9.1 Study Design/Endpoints ......................................................................................................... 78 
9.2 Sample Size/Accrual Rate ...................................................................................................... 80 
9.3 Stratification Factors .............................................................................................................. 81 
9.4 Analysis of Secondary Endpoints .......................................................................................... 81 
9.5 For Phase 2: Reporting and Exclusions ................................................................................ 82 
9.6 Data Safety Monitoring board (DSMB) Phase 2 .................................................................. 82 
10. 
ADVERSE EVENTS: LIST AND REPORTING REQUIREMENTS .......................................... 83 
10.1 Comprehensive Adverse Events and Potential Risks Lists (CAEPRs) ............................ 83 
10.2 Adverse Event Characteristics ............................................................................................. 94 
10.3 Expedited Adverse Event Reporting ................................................................................... 94 
10.4 Routine Adverse Event Reporting ....................................................................................... 97 
10.5 Pregnancy .............................................................................................................................. 98 
10.6 Secondary Malignancy ......................................................................................................... 98 
10.7 Second Malignancy ............................................................................................................... 98 
11. 
STUDY CALENDAR..................................................................................................................... 98 
12. 
MEASUREMENT OF EFFECT ................................................................................................... 103 
12.1 Antitumor Effect – Solid Tumors ...................................................................................... 103 
13. 
STUDY OVERSIGHT AND DATA REPORTING / REGULATORY REQUIREMENTS ....... 109 
13.1 Study Oversight ................................................................................................................... 110 
13.2 Data Reporting .................................................................................................................... 111 

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13.3 CTEP Multicenter Guidelines ........................................................................................... 114 
13.4 Collaborative Agreements Language ................................................................................ 114 
13.5 Genomic Data Sharing Plan ............................................................................................... 116 
13.6 Incidental/Secondary Findings Disclosure Procedure ..................................................... 116 
14. 
REFERENCES ............................................................................................................................. 118 
APPENDIX A PERFORMANCE STATUS CRITERIA ...................................................................... 123 
APPENDIX C LIST OF PROHIBITED MEDICATIONS WHILE ON COPANLISIB TREATMENT 
125 
APPENDIX D PATIENT CLINICAL TRIAL WALLET CARD ......................................................... 126 
 
APPENDIX F LIST OF INACTIVATING OR INFERRED INACTIVATING PTEN MUTATIONS 
PROVIDED BY MD ANDERSON PRECISION ONCOLOGY DECISION SUPPORT TEAM 
128 
 
APPENDIX G RPPA ASSAY INFORMATION .................................................................................. 124 

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1. OBJECTIVES 
 
1.1 Primary Objectives 
 
1.1.1 Phase 1b / safety run-in phase 
 
1.1.1.1 To determine the safety and recommended phase 2 dose (RP2D) of the combination of copanlisib, 
trastuzumab and pertuzumab in patients with metastatic epidermal growth factor receptor 2 (HER2)- positive 
breast cancer. 
 
1.1.2 Phase 2 trial 
 
1.1.2.1 To assess the benefit of adding copanlisib to trastuzumab and pertuzumab in HER2- positive 
metastatic breast cancer patients with PIK3CA mutations or PTEN mutation receiving maintenance therapy 
after induction treatment, as measured by progression free survival (PFS). 
 
1.2 Secondary Objectives 
 
1.2.1 Phase 2 trial  
 
1.2.1.1 To assess the benefit of adding copanlisib to trastuzumab and pertuzumab in HER2- positive 
metastatic breast cancer patients with PIK3CA mutations or PTEN mutation receiving maintenance therapy 
after induction treatment, as measured by OS. 
 
1.2.1.2 To evaluate the safety of copanlisib given at the RP2D in combination with trastuzumab and 
pertuzumab. 
 
 
1.3 Exploratory Objectives 
 
1.3.1 All trials 
 
1.3.1.1 To correlate PFS and OS of the patients who receive the triplet combination with: 
 
• the number of induction cycles 
 
• hormone receptor status (ER and PR) 
 
• PTEN Loss by IHC 
 
• PIK3CA mutations or PTEN mutations (Phase 1b) 
 

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1.3.1.2 To assess PTEN IHC, Ki-67 IHC and Cleaved Caspase-3 IHC and to perform molecular profiling 
assays on malignant and normal tissues, including, but not limited to, whole exome sequencing (WES) and 
messenger RNA sequencing (RNAseq), in order to: 
 
• identify potential predictive and prognostic biomarkers associated with treatment outcomes (PFS 
and OS) with the addition of copanlisib to dual HER2-targeted treatment, and 
 
• identify resistance mechanisms using genomic DNA- and RNA-based assessment platforms. 
 
1.3.1.3 To contribute genetic analysis data from de-identified biospecimens to Genomic Data Commons 
(GDC), a well annotated cancer molecular and clinical data repository, for current and future research; 
specimens will be annotated with key clinical data, including presentation, diagnosis, staging, summary 
treatment, and if possible, outcome. 
 
1.3.1.4 To bank formalin-fixed, paraffin-embedded (FFPE) tissue, blood (for cell-free DNA analysis), and 
nucleic acids obtained from patients at the ETCTN Biorepository at Nationwide Children's Hospital. 
 
2. 
BACKGROUND 
 
2.1 Invasive Breast Carcinoma 
 
2.1.1 PI3K pathway alterations in breast cancer 
 
The phosphatidylinositol-3 kinase (PI3K) pathway has been implicated in cancer proliferation 
and survival in many tumor types, including breast cancer (Miller et al., 2011). Class IA PI3Ks 
(α, β, and δ) are heterodimeric proteins with a regulatory subunit (p85) and one of several 
isoforms of a catalytic subunits (p110). The p110α isoform is encoded by the PIK3CA gene and 
are activated when growth factors bind to the upstream receptor tyrosine kinases. The PI3K 
pathway is pathologically activated through different genetic alterations in >70% of breast cancer 
patients, such as through amplification of receptor tyrosine kinases (e.g. HER2), activating 
mutations in PI3K p110α catalytic subunit (PIK3CA mutations), or loss of tumor suppressor 
phosphatase and tensin homolog (PTEN loss) (Miller et al., 2011; Yang et al., 2016; Hernandez- 
Aya and Gonzalez-Angulo, 2011). PIK3CA mutations are found in different subtypes of breast 
cancer (Zardavas et al., 2018; Arsenic et al., 2014). PIK3CA mutations have been reported to be 
most common in estrogen receptor positive (ER+) HER2 negative (HER2-) subset of breast 
cancer with a prevalence of 37%, and also co-exist with HER2 amplification in 22% of patients 
(Zardavas et al., 2018). Targeted inhibition of the PI3K pathway has anti-tumor activity in pre- 
clinical models of breast cancer, as well as in patients (Hernandez-Aya and Gonzalez-Angulo, 
2011; Bahrami et al., 2018; Patnaik et al., 2016). However, single agent PI3K inhibitors have 
limited activity in patients, and combination therapies are urgently needed. PIK3CA mutations 
are a predictive biomarker of response to α-selective PI3K inhibitors, and tumors with PTEN loss 
are more sensitive to β-selective PI3K inhibitors. 

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2.1.2 HER2 amplification in breast cancer: 
 
The HER2 and human epidermal growth factor receptor 3 (HER3) are receptor tyrosine kinases 
located in the cell membrane of the cancer cell. HER3 has weak intrinsic tyrosine kinase 
activity, and forms heterodimers with HER2 resulting in its activation and downstream signal 
transduction through the PI3K pathway (Patel et al., 2014). HER2 amplifications are seen in 20- 
30 % of breast cancers. Historically, HER2 positive breast cancers had the worst prognosis of all 
breast cancer subtypes, with median OS of less than two years (Larionov, 2018). With the 
development of HER2 targeted treatments, HER2 positive breast cancer now has the best 
prognosis of all subtypes with overall survival of >4 years in 2017. 
 
2.2 CTEP IND Agent 
 
2.2.1 Copanlisib (BAY 80-6946) 
 
Copanlisib (BAY 80-6946) is a novel small-molecule pan-class I PI3K inhibitor with exceptional 
inhibitory potency against δ and α PI3K isoforms (Copanlisib Investigator’s Brochure, 2017). 
Copanlisib is an active ingredient (free base) of copanlisib dihydrochloride (BAY 84-1236), 
which is intended for an intravenous (IV) administration in humans. The copanlisib 
hydrochloride product for clinical use is formulated as a lyophilized product for reconstitution in 
saline to be administered by IV. Copanlisib dihydrochloride product is supplied in three 
formulation strengths: 20 mg, 60 mg, or 80 mg (free base) in a 6 mL injection vial for 
reconstitution with 2 mL, 4.4 mL, or 4 mL of saline, respectively, to produce copanlisib solution 
for injection at concentration of 10 mg/mL, 15 mg/mL, or 20 mg/mL, respectively. 
 
On September 14, 2017, the FDA granted approval to copanlisib solution (IV) for the treatment 
of adult patients with relapsed follicular lymphoma who have received at least two prior systemic 
therapies (Food and Drug Administration, 2017). 
 
PI3K transmits signals from receptor tyrosine kinases (RTKs) to numerous cellular targets that 
are important for cell proliferation, survival, differentiation, and migration (Liu et al., 2013). 
PI3K/AKT signaling is commonly dysregulated in human cancers via various mechanisms, e.g., 
gene amplification, rearrangement, or activating and/or loss-of-function mutations of the 
pathway’s molecular components (Westin, 2014). Aberrant activation of class I PI3Ks has been 
associated with intrinsic and acquired resistance of tumors to targeted agents, chemotherapy, and 
radiotherapy (Liu et al., 2013). 
 
Four PI3K isoforms (PI3Kα, PI3Kβ, PI3Kγ, and PI3Kδ), all of which have a catalytic p110 
subunit (p110α/β/γ/δ), comprise the class I PI3K subfamily (Liu et al., 2013; Westin, 2014). 
PI3Kα signaling is frequently active in human malignancies, and tumors with activating 
mutations in PIK3CA or loss of PTEN have been found to be sensitive to PI3Kα inhibitors. 
PI3Kδ-specific inhibitors have shown remarkable therapeutic efficacy in some human leukemias 
and lymphomas (Yang et al., 2015). A major component of the mechanism of action of PI3Kδ 
inhibition in the B-cell malignancies is to attenuate the responsiveness of the tumor cells to 
supportive stimuli from the microenvironment (Okkenhaug and Burger, 2016). Inhibition of 
PI3Kδ has been shown to protect mice against a broad range of cancers, including non- 

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hematological solid tumors (Ali et al., 2014). Inactivation of PI3Kδ breaks Treg-mediated 
immune tolerance that unleashes a cytotoxic T-cell response and resulting in tumor regression. 
Copanlisib is a pan-class I PI3K small-molecule inhibitor exhibiting activity predominantly 
against the PI3Kα and PI3Kδ isoforms. Preclinical data suggest that copanlisib may be more 
efficient in inhibiting survival of leukemia cells than idelalisib (PI3Kδ inhibitor) or duvelisib 
[PI3Kα/γ] (Gockeritz et al., 2015). 
 
2.2.1.1 Nonclinical Studies 
 
A majority of nonclinical data were produced using the copanlisib free-base. 
 
2.2.1.1.1 Mechanism of Action 
 
Copanlisib is a stronger inhibitor of PI3Kα (half-maximal inhibitory concentration [IC50] 0.5 
nmol/L) and PI3Kδ (IC50 0.7 nmol/L) than of PI3Kβ (IC50 3.7 nmol/L) or PI3Kγ [IC50 6.4 
nmol/L] (Liu et al., 2013). Compared to the PI3K isoforms, copanlisib was a much weaker 
inhibitor of mTOR (IC50=45 nmol/L). In a panel of ~220 kinases, copanlisib (1 mcmol/L) failed 
to achieve a 50% inhibition of any kinase other than PI3K isoforms and mechanistic target of 
rapamycin (mTOR). In tumor cell lines with hyperactive PI3K signaling, copanlisib antitumor 
activity was paralleled by a robust decrease in basal levels of phosphorylated protein kinase B 
(AKT), both at serine 473 (AKTpS473) and threonine 308 (AKTpT308), and by increases in 
caspase-9 levels, which is suggestive of induction of apoptosis. 
 
2.2.1.1.2 Nonclinical in vitro Antitumor Activity 
 
Copanlisib potently inhibited tumor cell proliferation (IC50 of 1-760 nmol/L) in human tumor 
cell lines of various histologies, including breast, ovary, endometrial, prostate, colon, lung, liver, 
brain, kidney, melanoma, pancreas, and hematological tumors (Figure 1); many of which exhibit 
constitutively activated PI3K signaling resulting from somatic mutations in PIK3CA and PTEN 
(Liu et al., 2013). 

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Figure 1: Antiproliferative activity against a panel of human tumor cell lines. 
Panel A: Cell lines of various tumor histologies. Panel B: Breast cancer cell lines. Panel C: Molecular and 
histological characterization of breast cancer cell lines shown in panel B. Subtype Legend: B: basal–like breast 
cancer cell lines; L: luminal-type breast cancer cell lines; H: human epidermal growth factor receptor 2 (HER 2)- 
positive breast cancer cell lines (Copanlisib Investigator’s Brochure, 2017). 
 
To further analyze a relationship between molecular features and copanlisib activity, copanlisib 
was tested against 24 breast cancer cell lines with known PI3KCA gene mutation, PTEN gene 
mutation or expression, and HER2 expression status (Liu et al., 2013). Antiproliferation IC50s of 
copanlisib were ~40-fold lower in cells with activating mutations in PIK3CA (IC50=19 nmol/L; 
n=9) or HER2-positive cells (IC50=17 nmol/L; n=7) than for cells with PIK3CA wild-type (WT) 
and HER2-negative status (average IC50=774 nmol/L; n=11). However, no clear correlation has 
been found between sensitivity of cells to copanlisib and the loss of PTEN. Of note, copanlisib 
efficiently inhibited cell proliferation of breast cancer cell lines that are resistant to HER2 
inhibitors (trastuzumab or lapatinib) such as T47D (mutant PIK3CA), ZR-75-1 (PTEN null), or 
MCF7 (mutant PIK3CA) with IC50s of 6, 24, and 27 nmol/L, respectively. 
 
Following a 24-hour incubation of the BT20 breast cancer cells (mutant PIK3CA and resistant to 
the HER2 inhibitor lapatinib) in the presence of copanlisib at a dose of 62 nmol/L induced 2- to 
3-fold increases in caspase-9 activities [Figure 2A] (Liu et al., 2013). After 24-hour and 48-hour 
incubations with copanlisib (200 nmol/L), several fold increases in phosphorylated p53 at serine 
15 [p53pS15] (Figure 2B) and cleaved poly adenosine diphosphate ribose polymerase [PARP] 

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(Figure 2C) were observed. These results were consistent with increased caspase-9 activity. In 
the lapatinib-sensitive breast cancer cell line BT474, copanlisib alone caused caspase-9 
activation at a half maximal effective concentration (EC50) of 340 nmol/L. In contrast, lapatinib, 
was not able to activate caspase-9, even at a concentration as high as 10 mcmol/L. When BT474 
cells were exposed to a combination of copanlisib and lapatinib, the same level of caspase-9 
activation was achieved at markedly lower concentrations of copanlisib (61 nmol/L) and 
lapatinib (184 nmol/L). 
 
Collectively, these data suggest that copanlisib could induce apoptosis in both HER2 inhibitor- 
resistant and sensitive breast cancer cell lines at clinically achievable concentrations. 
 
Figure 2: Induction of apoptosis by copanlisib (BAY 806946) in lapatinib-resistant breast cancer cell line 
BT20. Panel A: Activation of caspase-9 by copanlisib. Panel B: Induction of phosphorylation of p53 at serine 15 
by copanlisib. Panel C: Induction of cleaved PARP by copanlisib. 
 
Copanlisib was also tested against a panel of 32 human hematological cancer cell lines 
(Copanlisib Investigator’s Brochure, 2017). Copanlisib was a more potent inhibitor than 
idelalisib, the PI3Kδ-selective inhibitor; idelalisib IC50s were 1.4-fold to several thousand-fold 
higher than copanlisib IC50s against these cell lines. Copanlisib IC50s were <100 nmol/L for 14 
cell lines, including acute lymphoblastic leukemia (ALL), acute myelogenous leukemia (AML), 
NHL, and myeloma. Some of the strongest responses to copanlisib (IC50 <10 nmol/L) occurred 
in AML (Kasumi-1, IC50=1.1 nmol/L), the Burkitt's lymphoma subtype of NHL (NAMALWA, 
IC50=1.7 nmol/L), the diffuse large B-cell lymphoma (DLBCL) subtype of NHL (Pfeiffer, 
IC50=0.8 nmol/L), and myeloma (MM-1R, IC50=1.0 nmol/L; and NCI-H929, IC50=2.7 and 2.2 

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nmol/L in 2 different experiments). Copanlisib was also more potent inhibitor against an 
aggressive NHL type such as DLBCL than idelalisib or a Bruton’s tyrosine kinase (BTK) 
inhibitor ibrutinib (Figure 3). 
 
 
Figure 3 Antiproliferative effects of copanlisib (BAY 80-6946), idelalisib 
(CAL-101), and ibrutinib (PCI-32765) against DLBCL cell lines. Legend: IC50: a drug concentration causing 
50% inhibition of cell proliferation. 
 
Concurrent treatment with copanlisib and ibrutinib resulted in synergistic effects of the two 
inhibitors against ibrutinib-sensitive cell lines but antagonistic effects in ibrutinib-resistant cell 
lines. 
 
2.2.1.1.3 In vivo Antitumor Activity 
 
Copanlisib demonstrated antitumor activity in vivo in a variety of xenograft models of tumors 
exhibiting an activated PI3K pathway (Liu et al., 2013). The drug displayed robust antitumor 
activity in the nude rat xenograft model of the KPL4 breast tumor cell line, which is an estrogen- 
independent HER2-positive breast carcinoma that carries a somatic PIK3CA mutation. 
Copanlisib was administered on day 14 post-implant at doses ranging from 0.5-6 mg/kg IV every 
second day (Q2D) for a total of five doses. On day 25, 3 days after the last dose, tumor growth 

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inhibition (TGI) rates of 77%-100% were observed in the dose range (Figure 4A). The complete 
tumor regressions were observed in 100% of animals receiving dose of 3 or 6 mg/kg, and all rats 
remained tumor free at the termination of the study on day 73. Delays in tumor growth of >25 
days were observed in the 0.5 and 1 mg/kg groups. Copanlisib administered at 3 and 6 mg/kg IV 
Q2D x 5 in PIK3CA and mutant KRAS HCT 116 xenograft rat models resulted in the TGI of 75% 
and 88% (Figure 4B). Copanlisib was also effective in the nude mouse patient-tumor xenografts 
of Lu7860 (erlotinib-resistant non-small cell lung carcinoma [NSCLC]) and MAXF1398 
(luminal breast tumor).  Copanlisib administered at 14 mg/kg twice a day (BID), Q2D for 10 
days resulted in the 88% TGI in the NSCLC model (Figure 4C) and 71% TGI in the breast 
cancer model (Figure 4D). 
 
 
Figure 4: Activity of copanlisib (BAY 80-6946) in xenograft models using Q2D treatment schedule. Panel A: 
KPL4 breast cancer xenografts in nude rats (n=10/group). Panel B: HCT116 colon cancer xenografts in nude rats 
(n=10/group). Panel C: Lu7860 erlotinib-resistant, patient-derived NSCLC xenografts in nude mice (n=5/group). 
Panel D: MAXF1398 patient-derived luminal breast cancer xenografts in nude mice (n=6/group). Legend: Q2D: 
every 2 days; BID: twice a day; IV: intravenously; TGD: tumor growth delay; PR: partial response; CR: 
complete response 
 
Copanlisib was also evaluated on a weekly schedule. Two doses of 9 mg/kg on day 1/week 
caused 64% TGI in the HCT-116 xenograft model, which was equivalent to the effect of 
copanlisib given at 6 mg/kg Q2D for 10 doses (Figure 5A). 

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Figure 5: Activity of copanlisib (BAY 80-6946) in xenograft models using a twice a day (BID) 
once-weekly schedule. Copanlisib was formulated in 5% mannitol vehicle. Panel A: HCT-116 colon cancer 
xenografts in nude rats (8 rats/group). Panel B: Lu7343 patient-derived NSCLC xenografts in nude mice (10 
mice/group). Legend: BID: twice a day; Q2D: every 2 days 
 
In vivo antitumor activity of copanlisib was also tested in combination with cytotoxic agent 
paclitaxel in the mutant PIK3CA squamous cell NSCLC patient-derived Lu7343 xenograft 
mouse model (Liu et al., 2013). Paclitaxel was given weekly at 15 or 25 mg/kg on days 14, 21, 
and 28, followed 24 hours later by copanlisib at 10 mg/kg BID on weekly schedule (days 15, 22, 
and 29) in a group of 10 animals. In addition, both drugs were tested as single agents (n=10); the 
control group received a vehicle (no drug). The drug combination was more potent in inhibiting 
tumor growth than either drug alone (Figure 5B). Although single-agent paclitaxel dosed at the 
maximum-tolerated dose (MTD) of 25 mg/kg was highly efficacious for the duration of 
treatment (33 days), showing tumor regression in 70% of animals, discontinuation of the 
treatment dropped the response rate to 30% (day 55), with 60% of animals demonstrating tumor 
re-growth. In contrast, the copanlisib + paclitaxel combination produced long-lasting tumor 
regressions, with a CR observed in 6/10 animals and a PR observed in 4/10 animals 22 days after 
stopping treatment (day 55). 
 
Copanlisib was well tolerated at all doses and schedules tested in these studies without producing 
any lethality (Liu et al., 2013). The MTD in rats was 6 mg/kg Q2D. A maximum mean body 
weight loss of 6%-10% occurred during the first few days at this dose and then consistently 
returned to the normal range by the end of the dosing period. The MTD in mice was more than 
14 mg/kg Q2D. 
 
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copanlisib was tested in vivo alone and in the combination with ibrutinib in the TMD-8 severe 
combined immunodeficiency (SCID) mouse model (Copanlisib Investigator’s Brochure, 2017). 
The TMD-8 DLBCL cell line harbors activating mutations in CD79B and MYD88. Copanlisib 
hydrochloride was dosed at 14 mg/kg IV daily (QD) for 2 days on and 5 days off/week and 
ibrutinib was administered at 20 mg/kg orally (PO) QD. The combination demonstrated 
synergistic activity, with 100% response rate (5 CRs and 3 PRs in 8 animals) observed compared 
to 12.5% (1 PR in 8 animals) and no responses seen in the copanlisib alone treatment group. 
 
2.2.1.1.4 Nonclinical Pharmacokinetics and Pharmacodynamics 
 
Copanlisib plasma-free fraction across species was as follows: 35% in rats, 14% in mice, 33% in 
dogs, and 16% in humans (Liu et al., 2013). The pharmacokinetic (PK) profile of copanlisib was 
evaluated following single and multiple IV doses in nude rats. Single-dosed copanlisib exhibited 
a very large volume of distribution (Vd=32 L/kg), high plasma clearance (3.95 L/kg/h) and a long 
half-life [t1/2] (6.0 h). The copanlisib PK parameters at repeat dosing (Q2D x 5 doses), were 
similar those from single-dosing studies and suggested no drug accumulation in plasma. 
Copanlisib had a higher clearance (16 L/kg/h), shorter t1/2 (0.7 h) and smaller volume of 
distribution [Vd] (12.9 L/kg) in mice than rats. A single bolus IV dose of copanlisib (6 mg/kg) in 
the H460 NSCLC xenograft rat model produced 100 times higher concentration of the drug in 
tumor tissue than in plasma at 48 hours post-dosing; the drug clearance from the tumor was 
slower than from plasma. The pharmacodynamics analysis showed 90% inhibition of 
AKTpS473 at 24 hours post-dosing compared to the control animals, and the AKTpS473 level 
remained suppressed up to 72 hours. In addition, 65% and 75% reductions in Ki-67 and 
phospho-histone H3 levels, respectively, were observed at 24 hours in the copanlisib group 
compared to the control group, suggesting copanlisib-induced G0 cell-cycle arrest. Copanlisib 
also demonstrated sustained inhibition (over 24-48 hours) of 18F-deoxyglucose (FDG) uptake in 
tumor. These preclinical data suggested that high and prolonged copanlisib tumor exposures can 
be reached in vivo, and there was a correlation between copanlisib exposure and inhibition of the 
PI3K pathway in the tumor. 
 
In the rat tumor xenograft model studies, the efficacious exposure of copanlisib was estimated as 
the area under the concentration-time curve (AUC) for the unbound/free drug (AUCu) in plasma 
of 370 mcg•h/L based on weekly dosing (Copanlisib Investigator’s Brochure, 2017). 
 
2.2.1.1.5 Summary of Nonclinical Metabolism 
 
Copanlisib is primarily metabolized by the cytochrome P450 (CYP)3A4 with a minor 
contribution of CYP1A1 (Copanlisib Investigator’s Brochure, 2017). Copanlisib is a weak 
substrate of P-glycoprotein (P-gp) and of breast cancer resistance protein (BCRP). There is a 
low risk for clinically relevant PK drug-drug interactions (DDI) through inhibition or induction 
of CYP enzymes, inhibition of uridine diphosphate glucuronosyltransferase (UGT) enzymes and 
inhibition of dihydropyrimidine dehydrogenase (DPD) by copanlisib. Copanlisib also inhibited 
P-gp- and BCRP-mediated transport in vitro at concentrations much higher than those observed 
at the approved 60 mg clinical dose. Furthermore, copanlisib was a strong inhibitor of the drug 
transporter multidrug and toxin extrusion protein 2 (MATE2K). 

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2.2.1.1.6 Summary of Nonclinical Safety 
 
IV infusion of copanlisib caused vasoconstriction, enhanced insulin and glucose levels, impaired 
glucose tolerance, reduced gastrointestinal (GI) motility, increased renal volume and electrolyte 
excretion, and central nervous system (CNS) depressant effects in nonclinical species 
(Copanlisib Investigator’s Brochure, 2017). A majority of these effects could be explained by 
inhibition of PI3K-dependent signaling, and they occurred at or slightly above the plasma 
concentrations shown to be efficacious in tumor xenograft rat models (maximum concentration 
[Cmax]=30-80 mcg/L; Cmax of unbound fraction [Cmax,u] 11-28 mcg/L). The CNS depressant 
effects occurred at high plasma concentrations and are considered secondary to hyperglycemia. 
At pharmacodynamically relevant concentrations, copanlisib does not interfere with cardiac 
repolarization in vitro or in vivo. 
 
Based on the findings from repeat-dose toxicity studies in nonclinical species, copanlisib is 
expected to adversely affect male and female reproduction. Developmental and reproductive 
toxicity of PI3K inhibitors is known. Maternal toxicity of increasing severity, severe post- 
implantation loss, and developmental toxicity, including teratogenicity, were seen in rats starting 
at low doses. Copanlisib was not genotoxic in vitro or in vivo. There is no evidence that 
copanlisib has phototoxic potential. Significant toxicities were observed in animals at doses 
achieving plasma concentrations observed in humans. 
 
2.2.1.2 Effects in Humans 
 
2.2.1.2.1 The First-in-Human Copanlisib Study 
 
In the first-in human (FIH) phase 1 trial in patients with advanced and/or refractory 
malignancies, of 57 patients (51 non-diabetic) treated, 17 took part in the dose-escalation phase 
with copanlisib (0.1-1.2 mg/kg) administered IV weekly for 3 weeks of a 4-week cycle (Patnaik 
et al., 2016). The copanlisib MTD was 0.8 mg/kg IV (1 h) weekly for 3 weeks on a 28-day 
cycle. An additional 34 patients were treated in the MTD expansion cohorts: the solid tumor 
cohort (n=25), NHL cohort (n=9; 6 patients with follicular lymphoma [FL] and 3 patients with 
DLBCL). Finally, 6 patients with diabetes mellitus were treated with copanlisib at 0.4 mg/kg 
weekly x 3 weeks. 
 
2.2.1.2.2 Clinical Safety 
 
The most common (≥20%) copanlisib-related adverse events [AEs] (regardless of grade) 
included hyperglycemia (63%), nausea (37%), and hypertension (21%). The most common 
drug-related grade 3 AEs were hyperglycemia (30%), hypertension (14%), and rash (7%) 
(Patnaik et al., 2016). Grade 3+ diarrhea occurred in one patient. Two patients (4%) 
experienced three drug-related grade 4 AEs: a dose-limiting hyperglycemia and increased 
aspartate aminotransferase (AST) in one patient and elevated serum amylase in another patient. 
Overall, serious AEs (SAEs) with positive association to copanlisib were observed in six patients 
(11%): grade 3 left ventricular systolic dysfunction (LVSD) which was a dose-limiting toxicity 
(DLT), chest pain, hypertension, and hyperglycemia (in one patient each), and pneumonitis (in 
two patients). None of seven grade 5 AEs (12%) was considered drug related. Dose 

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modifications (delays, interruptions, and reductions) caused by drug-related AEs occurred in 14 
patients (25%). Four patients discontinued treatment due to toxicity. One drug-related AE 
(dose-limiting LVSD) led to permanent discontinuation of treatment. No patient discontinued 
the study because of hyperglycemia. 
 
Hyperglycemia was transient, with a glucose level peaking at 5–8 hours after copanlisib infusion 
on cycle 1 day 1 and declining to baseline by the time of the next infusion. Sixty-five percent of 
non-diabetic patients (33/51) received at least one dose of short-acting insulin to manage high 
blood glucose (>200 mg/dL). There was no trend for increased pre-dose glucose values over 
time, and no patients developed diabetic ketoacidosis during the study. Hemoglobin A1c 
(HbA1c) levels changed only modestly over the course of copanlisib treatment. Post-infusion 
increases in blood pressure (BP) peaked at 1–2 hours and resolved within 24 hours post-infusion. 
 
A similar transient pattern of elevated blood glucose post-infusion was seen for the cohort of six 
diabetic patients treated with 0.4 mg/kg copanlisib, all of whom received insulin following the 
first copanlisib infusion. The AE profile in the diabetic cohort of patients was similar to that in 
non-diabetic patients, with a total of four drug-related grade 3 AEs observed in three patients: 
hypertension in two patients, and hyperglycemia and rash/desquamation in one patient each. 
 
2.2.1.2.3 Pharmacokinetics/Pharmacodynamics 
 
Copanlisib plasma Cmax was typically reached between 0.5 and 1 hour (time to maximum 
concentration [tmax]) following the infusion (Patnaik et al., 2016). Copanlisib exposure, 
expressed either as Cmax or AUC between 0-25 hours (AUC0–25h), increased proportionally with 
dose between 0.1 and 1.2 mg/kg, and exhibited a moderate to high inter-patient variability. The 
terminal t1/2 was 38.2 hours and no accumulation was observed after once-weekly administration. 
The trough levels of copanlisib on cycle 1 day 8 were 4.92 mcg/L (range, 2.74–23.0 mcg/L). 
 
A pharmacodynamic effect event was defined as an increase in plasma glucose level of ≥50 
mg/dL from baseline within 2 hours after the completion of the copanlisib infusion, and / or an 
increase in plasma insulin level to greater than two times the baseline value (Copanlisib 
Investigator’s Brochure, 2017). At the MTD (0.8 mg/kg), 100% of patients showed the pre- 
defined increases in glucose and insulin. Overall, 53/57 (93%) patients experienced a predefined 
pharmacodynamics effect of an increased glucose plasma level following the first copanlisib 
infusion. Increases in glucose levels strongly correlated with copanlisib exposure (AUC0-25h) 
(Patnaik et al., 2016). A weak correlation between exposure and change in tumor FDG uptake 
(via 18FDG-positron emission tomography [PET]) from baseline to cycle 1 day 3 or day 4 was 
seen in 19/21 patients evaluated, with >25% reduction in the FDG uptake observed in the tumor 
of 7 patients (33%). 
 
2.2.1.2.4 Antitumor Activity/Response 
 
Among patients with solid tumors (n=48), clinical responses were observed only in patients 
treated at the copanlisib MTD (Patnaik et al., 2016). The responses were: 1 CR (2%) in a 
patient with endometrial cancer, 2 PRs (4%) in patients with breast cancer, 15 cases of stable 
disease patients (SD) (31%), and 15 cases of progressive disease (PD) (31%) according to the 

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Response Evaluation Criteria in Solid Tumors (RECIST) version 1.1. In comparison, by clinical 
assessment, 7 patients (15%) had PD, and 8 patients (17%) were not assessed. Overall clinical 
benefit rate (CBR) was 38%. 
 
The CR responder had endometrial cancer with PIK3CA and PTEN mutations and complete 
PTEN loss. Of the two breast cancer patients who had PR, both had tumors positive for estrogen 
receptor (ER) and progesterone receptor. One was negative and the other positive for HER2; 1 
had mutant and the other WT PIK3CA; and PTEN status was unavailable in both. No clear 
relationship was found between PI3KCA mutational status and disease control (P=1.0). 
 
All 9 patients with NHL were evaluable for response using the International Working Group 
criteria. There were 1 CR (FL), 6 PRs (5 FL and 1 DLBCL), and 2 PD (DLBCL). A post-hoc 
radiologic review determined that two patients with FL achieved a CR. In addition, two FL 
patients had long-term durable responses, one of whom was on treatment for approximately 4 
years before coming off study because of disease progression; the other patient was still on 
treatment as of 19 January 2016 (>3 years). All seven NHL responders had PI3KCA WT status; 
by immunohistochemistry (IHC), one patient had complete PTEN loss, two had low PTEN 
expression, two had positive PTEN expression, and two had unknown PTEN expression. Both 
patients with disease progression had low PTEN expression. 
 
2.2.1.2.5 The Copanlisib Phase 2 Study in Refractory Lymphoma 
 
In the phase 2 study of copanlisib in patients with various indolent and aggressive, relapsed or 
refractory NHL, copanlisib demonstrated antitumor activity (Copanlisib Investigator’s Brochure, 
2017). At the time of the data analysis, seven patients (8.3%) still were ongoing treatment, 
including four patients in the indolent NHL / chronic lymphocytic leukemia (CLL) cohort and 
three patients in the aggressive NHL cohort. 
 
Among 32 patients with indolent NHL (15 with FL, 3 with marginal-zone lymphoma [MZL], 
and 1 with small lymphocytic lymphoma [SLL]) and 13 patients with CLL, 14 patients achieved 
objective tumor responses (2 CR, 1 unconfirmed CR, and 11 PR) resulting in an ORR of 44%. 
In addition, 15 patients (47%) achieved SD; 1 patient had PD. Of 48 patients with aggressive 
lymphoma, 13 patients achieved objective tumor responses (2 CR, 2 unconfirmed CR, and 9 PR) 
resulting in 27% ORR. In addition, 11 patients achieved SD (23%); 16 had PD (33%).  The 
ORR was also analyzed by histological subtype; the data are summarized in the following table. 
 
Clinical Activity Stratified by Histology Subtype 
Histology 
N 
Total OR 
(ORR) 
CR 
CRu 
PR 
SD 
PD 
NE 
NA 
INDOLENT 
Indolent NHL 
19 
9 (47%) 
2 
1 
6 
9 
0 
0 
1 
FL 
15 
6 (40%) 
2 
2 
3 
8 
0 
0 
1 
MZL 
3 
2 (67%) 
0 
0 
2 
1 
0 
0 
1 
SLL 
1 
1 (100%) 
0 
0 
1 
0 
0 
0 
0 
CLL 
13 
5 (38%) 
0 
0 
5 
6 
1 
0 
1 
AGGRESSIVE 
DLBCL 
15 
1 (6.7%) 
0 
0 
1 
0 
4 
1 
3 
MCL 
11 
7 (64%) 
0 
2 
5 
0 
3 
0 
1 

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Histology 
N 
Total OR 
(ORR) 
CR 
CRu 
PR 
SD 
PD 
NE 
NA 
Transformed 
indolent NHL 
6 
2 (33%) 
0 
0 
2 
0 
3 
0 
1 
Peripheral T- 
cell lymphoma 
14 
3 (21%) 
2 
0 
0 
1 
5 
0 
1 
Mediastinal large 
B-cell lymphoma 
1 
FL grade3b 
1 
N: total number of patients; NE: non-evaluable; NA: not available; OR: objective response: ORR: OR rate; CR: 
complete response; CRu: unconfirmed complete response; PR: partial response; SD: stable disease; PD: 
progressive disease; NHL: non-Hodgkin’s lymphoma; FL: follicular lymphoma; CLL: chronic lymphocytic 
leukemi; MZL: marginal-zone lymphoma; SLL: small lymphocytic lymphoma; DLBCL: diffuse large B-cell 
lymphoma; MCL: mantle cell lymphoma. Copanlisib Investigator’s Brochure, 2017. 
 
2.2.1.2.6 Safety 
 
Hyperglycemia and hypertension are on-target AEs for PI3K inhibitors. The most common 
copanlisib-related AEs (all grades), by the medical dictionary for regulatory activities preferred 
term (MedDRA PT), that occurred in ≥20% of the patients in this study were hyperglycemia 
(54.8%), hypertension (51.2%), diarrhea (32.1%), neutropenia (23.8%) [by Common 
Terminology Criteria for Adverse Events (CTCAE) terms: neutrophil count decreased (28.6%)], 
and fatigue [20.2%] (Copanlisib Investigator’s Brochure, 2017). 
 
2.2.1.2.7 Copanlisib Clinical Pharmacology Summary 
 
Copanlisib plasma exposure (Cmax and AUC) increased in a dose-proportional manner over an 
absolute dose range of 5 to 93 mg (0.08 to 1.55 times the approved recommended dose of 60 
mg). There is no time-dependency and no accumulation in the PK of copanlisib administered 
weekly. The geometric mean terminal elimination half-life (CV%) of copanlisib was 39.1 h 
(40.8%) based on the pooled analysis of 3 phase 1 studies (12871, 15205 and 16270). The 
geometric mean clearance (CV%) was 17.9 L/hr (45.6%). Copanlisib is eliminated 
predominantly via feces (64% of the administrative radioactive dose mean recovery with 30% 
unchanged copanlisib) compared to urine (22% mean recovery with 15% unchanged copanlisib) 
(Copanlisib Investigator’s Brochure, 2017). 
 
Population PK analyses suggest that body weight, age (20 to 90 years), gender, race (White, 
Asian, Hispanic and Black), smoking status, body weight (41 to 130 kg), mild hepatic 
impairment and mild to moderate renal impairment had no clinically significant effect on the 
pharmacokinetics of copanlisib (Copanlisib Investigator’s Brochure, 2017). No dose adjustment 
is necessary based on these specific populations. Preliminary analysis of central tendency and 
exposure-response analyses suggest that copanlisib does not prolong QT/QTc interval. 
Further details can be found in the latest available version of the investigator's brochure (2017), 
which contains comprehensive information on the study drug and also the US prescription drug 
label. 
 
2.2.1.3 Copanlisib Reference Safety Information 

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2.2.1.3.1 The recommended dose and administration of copanlisib 
 
Based on the FIH company-sponsored study, the MTD of copanlisib in non-diabetic patients 
with solid malignancies was 0.8 mg/kg (equivalent to 60mg approved dose) administered IV 
over 1 hour once weekly for 3 weeks (days 1, 8, and 15) on a 28-day cycle (Copansilib 
Investigator’s Brochure, 2017). 
 
A preliminary population PK analysis revealed no impact of either body weight, body surface 
area (BSA), or other body size-related factors on the clearance of copanlisib and thus a flat-dose 
regimen of copanlisib has been recommended (Copansilib Investigator’s Brochure, 2017). 
 
Based on these data, the RP2D and approved dose for copanlisib monotherapy is 60 mg given 
over a 1-hour IV infusion once a week for 3 weeks (days 1, 8, and 15) every 4 weeks. A dose 
reduction to 45 mg for toxicities have been allowed. 
 
2.2.1.3.2 Drug-drug interactions 
 
Copanlisib metabolism is predominantly mediated by CYP3A4 (> 90%) and to a minor extent by 
CYP1A1 (< 10%) (Copanlisib Investigator’s Brochure, 2017). Itraconazole, a strong CYP3A4 
inhibitor and a P-gp and BCRP transporter inhibitor, increased copanlisib (60 mg) AUC by 1.53- 
fold with no effect on Cmax (1.03–fold). If concomitant use with strong CYP3A inhibitors cannot 
be avoided, a dosage reduction to 45mg is recommended. Rifampin, a strong CYP3A4 inhibitor 
and a P-gp transporter inhibitor, decreased the AUC of copanlisib (60 mg) by 63% with minimal 
effect on Cmax (15%) and strong inducers should be avoided (Copanlisib Investigator’s Brochure, 
2017). 
 
2.2.1.3.3 Pregnancy and lactation 
 
Due to a mechanism of action as a PI3K inhibitor, adverse effects on development and 
reproduction are expected for copanlisib (Copanlisib Investigator’s Brochure, 2017). 
Nonclinical repeat-dose toxicity studies demonstrated adverse effects of copanlisib on male and 
female reproduction. Maternal toxicity of increasing severity, severe post-implantation loss, and 
developmental toxicity, including teratogenicity were seen in a rat pilot developmental toxicity 
study beginning at a low dose. In the rat study with 14C-labeled copanlisib, radioactivity was 
secreted into the milk of lactating animals although at a low extent (1.7% of dose). No data are 
available on the distribution of copanlisib to human milk. Therefore, unless potential benefits to 
patients outweigh unknown risks, women who are pregnant or nursing and children should be 
excluded from the clinical studies of copanlisib. In addition, women of child-bearing potential or 
female partners of male patients will be required to use an adequately effective barrier method of 
birth control. 
 
2.2.1.3.4 Special safety warnings and precautions 
 
Nonclinical studies suggest and clinical studies confirm, blood glucose increases persisting for 
approximately 1-3 days after study copanlisib administration (Copansilib Investigator’s 

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Brochure, 2017). Blood or serum glucose, serum and urine ketones, and electrolytes should be 
monitored while on copanlisib treatment. 
 
Standard cardiovascular parameters, including pulse and BP should be monitored because of 
hypertension (during the first 3 h after start of infusion) that has been observed. 
 
Respiratory infections (including pneumonia, Pneumocystis jirovecii pneumonia, cryptococcosis 
and bronchopulmonary aspergillosis) have been observed in studies with monotherapy and 
combination therapies. Some of these infections may have life-threatening or fatal outcome. 
Cases of pneumonitis observed in studies with monotherapy and in combination therapies were 
generally ≤grade 3 in severity and responded well to corticosteroid treatment; occasional events 
with life-threatening or fatal outcome have been observed. Since the early symptoms of 
pneumonitis overlap with those of a respiratory infection, monitoring of patients for typical 
clinical symptoms like cough, dyspnea or fever and further evaluation for respiratory infections 
is recommended. Patients suspected of having a respiratory infection or noninfectious 
pneumonitis should be promptly treated with appropriate antimicrobial agents and/or 
corticosteroids as indicated. 
 
2.3 Commercial Agents 
 
2.3.1 Trastuzumab 
 
2.3.1.1 Description 
 
Trastuzumab is a humanized IgG1 kappa monoclonal antibody that selectively binds with high 
affinity to the extracellular domain of the human epidermal growth factor receptor 2 protein, 
HER2 (Herceptin Package Insert, 2018). Trastuzumab is produced by recombinant DNA 
technology in a mammalian cell (Chinese Hamster Ovary) culture containing the antibiotic 
gentamicin. Gentamicin is not detectable in the final product. 
 
2.3.1.2 Mechanism of Action 
 
The HER2 (or c-erbB2) proto-oncogene encodes a transmembrane receptor protein of 185 kDa, 
which is structurally related to the epidermal growth factor receptor (Herceptin Package Insert, 
2018). Trastuzumab has been shown, in both in vitro assays and in animals, to inhibit the 
proliferation of human tumor cells that overexpress HER2. 
 
Trastuzumab is a mediator of antibody-dependent cellular cytotoxicity (ADCC). In vitro, 
trastuzumab-mediated ADCC has been shown to be preferentially exerted on HER2 
overexpressing cancer cells compared with cancer cells that do not overexpress HER2. 
 
2.3.1.3 Pharmacokinetics 
 
The pharmacokinetics of trastuzumab was evaluated in a pooled population pharmacokinetic 
(PK) model analysis of 1,582 subjects with primarily breast cancer and metastatic gastric cancer 

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(MGC) receiving intravenous Herceptin (Herceptin Package Insert, 2018). Total trastuzumab 
clearance increases with decreasing concentrations due to parallel linear and non-linear 
elimination pathways. 
 
Although the average trastuzumab exposure was higher following the first cycle in breast cancer 
patients receiving the three-weekly schedule compared to the weekly schedule of Herceptin, the 
average steady-state exposure was essentially the same at both dosages. The average 
trastuzumab exposure following the first cycle and at steady state as well as the time to steady 
state was higher in breast cancer patients compared to MGC patients at the same dosage; 
however, the reason for this exposure difference is unknown. 
 
2.3.1.4 Clinical Safety 
 
The most common adverse reactions in patients receiving Herceptin in the adjuvant and 
metastatic breast cancer setting are fever, nausea, vomiting, infusion reactions, diarrhea, 
infections, increased cough, headache, fatigue, dyspnea, rash, neutropenia, anemia, and myalgia 
(Herceptin Package Insert, 2018). Adverse reactions requiring interruption or discontinuation of 
Herceptin treatment include CHF, significant decline in left ventricular cardiac function, severe 
infusion reactions, and pulmonary toxicity 
 
2.3.2 Pertuzumab 
 
2.3.2.1 Description 
 
Pertuzumab is a recombinant humanized monoclonal antibody that targets the extracellular 
dimerization domain (Subdomain II) of the human epidermal growth factor receptor 2 protein 
(HER2) (Perjeta Package Insert, 2018). Pertuzumab is produced by recombinant DNA 
technology in a mammalian cell (Chinese Hamster Ovary) culture. 
 
2.3.2.2 Mechanism of Action 
 
Pertuzumab blocks ligand-dependent heterodimerization of HER2 with other HER family 
members, including EGFR, HER3, and HER4 (Perjeta Package Insert, 2018). As a result, 
pertuzumab inhibits ligand-initiated intracellular signaling through two major signal pathways, 
mitogen-activated protein (MAP) kinase, and phosphoinositide 3-kinase (PI3K). Inhibition of 
these signaling pathways can result in cell growth arrest and apoptosis, respectively. In addition, 
pertuzumab mediates antibody-dependent cell-mediated cytotoxicity (ADCC). 
 
2.3.2.3 Pharmacokinetics 
 
Pertuzumab demonstrated linear pharmacokinetics at a dose range of 2 – 25 mg/kg (Perjeta 
Package Insert, 2018). Based on a population PK analysis that included 481 patients, the median 
clearance (CL) of pertuzumab was 0.24 L/day and the median half-life was 18 days. With an 
initial dose of 840 mg followed by a maintenance dose of 420 mg every three weeks thereafter, 
the steady-state concentration of pertuzumab was reached after the first maintenance dose. 
 

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The population PK analysis suggested no PK differences based on age, gender, ethnicity (Japanese vs. 
non-Japanese), or disease status (neoadjuvant or adjuvant vs. metastatic setting) (Perjeta Package Insert, 
2018). Baseline serum albumin level and lean body weight as covariates only exerted a minor influence on 
PK parameters. Therefore, no dose adjustments based on body weight or baseline albumin level are 
needed. 
 
No dedicated renal impairment trial for pertuzumab has been conducted (Perjeta Package Insert, 
2018). Based on the results of the population pharmacokinetic analysis, pertuzumab exposure in 
patients with mild (CLcr 60 to 90 mL/min, n=200) and moderate renal impairment (CLcr 30 to 
60 mL/min, n=71) were similar to those in patients with normal renal function (CLcr greater than 
90 mL/min, n=200). No relationship between CLcr and pertuzumab exposure was observed over 
the range of observed CLcr (27 to 244 mL/min). 
 
2.3.2.4 Clinical Safety 
 
The most common adverse reactions (> 30%) seen with PERJETA in combination with 
trastuzumab and docetaxel were diarrhea, alopecia, neutropenia, nausea, fatigue, rash, and 
peripheral neuropathy (Perjeta Package Insert, 2018). The most common NCI - CTCAE v5.0 
Grade 3 – 4 adverse reactions (> 2%) were neutropenia, febrile neutropenia, leukopenia, 
diarrhea, peripheral neuropathy, anemia, asthenia, and fatigue. 
 
2.4 Rationale 
 
2.4.1 Dual HER2 targeted therapy in breast cancer 
 
Trastuzumab containing combination regimens have revolutionized the treatment and prognosis 
of HER2 positive breast cancers. HER2 positive breast cancer now has the best prognosis of all 
subtypes with overall survival of >4 years in 2017 (Larionov, 2018). However, the duration of 
response to trastuzumab is finite and all cancers eventually progress reflecting the development 
of selective evolutionary or adaptive resistance. One proposed mechanism of resistance to 
trastuzumab is incomplete blockade of heterodimeric signaling or over-expression of HER3, 
which can be overcome by combined HER2 and HER3 inhibition (Patel et al., 2014). 
Pertuzumab is a humanized monoclonal antibody that binds to extracellular domain II of the 
HER2 receptor and blocks its dimerization with other HER receptors, in particular HER2-HER3 
complexes. Indeed, a phase 3 clinical trial showed improvement in progression free survival as 
well as unprecedented improvement in overall survival with the addition of pertuzumab to 
trastuzumab and docetaxel, compared with the addition of placebo to trastuzumab + docetaxel 
doublet in metastatic HER2 amplified breast cancer (Swain et al., 2018). The successful results 
of this clinical trial have led to the current standard of dual HER2 inhibition with trastuzumab 
and pertuzumab along with docetaxel or paclitaxel as the first line treatment of HER2 amplified/ 
overexpressed metastatic breast cancer (Smyth et al., 2016; NCCN Guidelines: Breast Cancer, 
Version 1, 2018). The additive benefit of pertuzumab to trastuzumab containing regimens has 
also been reported in the adjuvant and neoadjuvant settings (Gianni et al., 2012; Schneeweiss et 
al., 2013). Pertuzumab increased disease free survival compared to placebo when added to 
adjuvant trastuzumab and chemotherapy (von Minckwitz et al., 2017). 

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2.4.2 Rationale for combining PI3K inhibition with dual HER2 inhibition in breast cancer 
 
Genetic alterations in PI3K pathway (e.g., PTEN loss and PIK3CA mutations) have been 
associated with intrinsic resistance to trastuzumab and shorter time to progression in metastatic 
breast cancer patients (Razis et al., 2011; Berns et al., 2007). For example, metastatic breast 
cancer patients with PTEN loss have significantly worse response to trastuzumab and taxane 
combination therapy than patients with PTEN-positive tumors (Nagata et al., 2004). In the 
BOLERO 1 and BOLERO 3 trials (randomized breast cancer trials of oral everolimus), PIK3CA 
activating mutations and PTEN loss were reported in 30% and 16% of BOLERO1 samples and 
32% and 12% of BOLERO 3 samples, respectively (Andre et al., 2016). Further, in exploratory 
analyses, there was suggestion that patients with PI3KCA activating mutations or a hyperactive 
PI3K pathway could derive PFS benefit from the addition of everolimus to trastuzumab and 
chemotherapy. In the phase 3 CLEOPATRA trial of dual HER2 vs single antibody blockade and 
docetaxel, patients with PIK3CA mutations (22% PIK3CA mutation rate) had significantly 
shorter PFS (hazard rate 0.63) than PIK3CA wild-type patients in both arms (Baselga et al., 
2014). 
 
Data from BELLE-2 and BELLE-3 trials (randomized phase 3 trials of fulvestrant with or 
without pan-PI3K inhibitor buparlisib in advanced breast cancer) suggest that PI3K pathway 
alterations are a predictive biomarkers of PI3K inhibitor activity (Baselga et al., 2017; Di Leo et 
al., 2018). Prespecified exploratory analyses in BELLE-2 showed that patients with PIK3CA 
mutations in circulating tumor DNA (ctDNA) at study entry had meaningful clinical benefit from 
the combination regimen (Baselga et al., 2017). Similarly, in BELLE-3 trial, patients with 
PIK3CA mutations in tumor tissue derived a greater benefit from the combination regimen as 
compared to those with wild-type PIK3CA. With the fulvestrant and buparlisib combination, 
median PFS of patients with PIK3CA mutations detected in tumor tissue was 4.7 months, and the 
median PFS of patients with wild-type PIK3CA was 2.8 months (Di Leo et al., 2018). 
 
Acquired trastuzumab resistance through increased HER2/HER3 hetero-dimerization results in 
increased downstream activation of the PI3K-AKT pathway (Patel et al., 2014). Combined 
HER2 and PI3K inhibition has synergistic anti-tumor activity in mouse models of breast cancer 
(Choi et al., 2018). Based on pre-clinical evidence of synergism, a phase 1b/2 clinical trial is 
ongoing in metastatic HER2 positive breast cancer patients with at least one prior anti-HER2 
treatment, to determine the safety and efficacy of pan-PI3K inhibitor (copanlisib) in combination 
with trastuzumab (Keegan et al., 2018).  The interim results of this clinical trial were presented 
at the 2018 American Society of Clinical Oncology (ASCO) annual meeting.  The combination 
is safe with no dose limiting toxicities seen. Nine out of 12 patients had stable disease (Keegan 
et al., 2018). It was recently found in a breast cancer mouse model that the ability of HER2 to 
fully engage and activate PI3K depends on its ability to dimerize with and phosphorylate HER3, 
which then directly binds PI3K. HER3 deletion decreased AKT phosphorylation in this study 
(Cook et al., 2011). Therefore, combined inhibition of HER3, HER2 and PI3K pathway has the 
potential to be more effective than HER2 and PI3K inhibition in breast cancer patients with 
PI3K-activating genetic alterations. Further rationale for this combination is apparent through 
studies showing that adaptive resistance to PI3K-AKT inhibition is mediated through increased 
phosphorylation of HERs and increased expression of HER3 in HER2 overexpressing breast 
cancer cell lines (Serra et al., 2011). HER3 inhibitors also enhance the response to PI3K-AKT 

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pathway inhibitors in triple negative breast cancer (Tao et al., 2014). The interaction between 
receptor tyrosine kinases such as HER and HER3, and PI3K signaling pathway is depicted in 
Figure 6. 
 
Figure 6: Interaction between HERs and PI3K signaling pathway. Dimerization and phosphorylation of HER2 and 
HER3 activates the PI3K signaling pathway, with subsequent feedback suppression of phosphorylation as well as 
transcription of HERs. Monotherapy with PI3K pathway inhibitors disrupts this feedback suppression of HERs 
which mediates resistance. 
 
2.5 Correlative Studies Background 
 
2.5.1 Integral Studies 
To be eligible for this study, patients must have HER2-positive advanced breast cancer, with one 
of the following actionable alterations: activating mutations in the PIK3CA gene, inactivating 
mutations in the PTEN gene by NGS (next generation sequencing). 
 
2.5.1.1 HER2 Amplifications 
 
HER2 expression status will be determined on breast cancer metastases using 
immunohistochemistry and / FISH. A positive result will be defined per ASCO CAP guidelines 
as detailed in inclusion criteria (Section 3.1). If a HER2 positive status has been established on 
metastasis for a given patient, it will be not be repeated prior to enrollment in the study. HER2 
amplifications are a known driver of breast cancer owing to the constitutive activation of PI3K- 
Akt signaling pathway. HER2 positive breast cancer is sensitive to treatment with anti-HER2 
monoclonal antibodies, such as trastuzumab. 

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2.5.1.2 PIK3CA mutations 
 
PIK3CA mutational status will be determined prior to study initiation based on next generation 
sequencing (NGS) or equivalent clinical laboratory improvements amendment (CLIA)-certified 
assay in tissue or ctDNA. A list of activating PIK3CA alterations is given in Appendix E. 
Mutations other than these will be annotated by the MD Anderson Precision Oncology Decision 
Support team for functional significance to determine eligibility. PIK3CA mutations result in 
aberrant activation of the PI3K/Akt cell signaling pathway, causing proliferative and cell 
survival advantages to tumor cells. By specifically targeting PIK3CA mutations, we hope to 
induce significant anti-tumor responses in patients with cancers harboring these mutations. 
PIK3CA mutations have shown to be a predictive biomarker of response to PI3K pathway 
inhibitors in clinical trials (Baselga et al., 2017; Di Leo et al., 2018). 
 
2.5.1.3 PTEN mutations 
 
PTEN mutational status will be determined prior to study entry based on NGS or equivalent 
CLIA-certified assay in tissue or ctDNA. A list of inactivating PTEN alterations is given in 
Appendix F. Mutations other than these will be annotated by the MD Anderson Precision 
Oncology Decision Support team for functional significance to determine eligibility. PTEN is an 
important cellular phosphatase that regulates PI3K/Akt signaling. As a tumor suppressor, PTEN 
functions to limit the PI3K/Akt pathway and prevent uncontrolled cell growth. Therefore, tumor 
cells with defects in PTEN exhibit constitutive activation of the PI3K/Akt pathway, and 
proliferative and survival advantages. 
 
2.5.2 Integrated Studies 
 
2.5.2.1 RPPA 
 
RPPA assay will be used to assess treatment induced changes in PI3K pathway signaling (e.g. 
phosphorylated Akt (pAkt), phosphorylated ribosomal protein S6 (pS6), phosphorylated 4E 
binding protein 1 (p4EBP1), and to correlate said changes with treatment outcomes (PFS and 
OS); and to evaluate changes in signaling pathways that may be reflective of treatment 
resistance. 
 
2.5.2.2 Whole Exome Sequencing (WES) 
 
The molecular landscape of cancer is just beginning to be defined. However, we do not know 
enough about the genomic and molecular landscape of tumors from patients who enter early 
phase clinical trials. With this study, we will attempt to learn more about specific molecular 
features of cancers from this patient subgroup. It is particularly important to learn, as early as 
possible, if there are molecular features within a particular malignant histology or across 
malignant histologies that can inform about potential response or resistance to treatments in early 
phase clinical trials. Such knowledge will be used to design more efficient later stage clinical 
trials for more efficient and more effective drug development. 

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WES of tumor tissue will be used to correlate single nucleotide variation (SNV) and copy 
number variation (CNV) profiles with treatment outcomes (PFS and OS). The objective of this 
assay is to help identify predictive and prognostic biomarkers associated with the addition of 
copanlisib to dual HER2 therapy in the maintenance setting. The WES profile of tumor will be 
compared with WES results of peripheral blood mononuclear cells to distinguish somatic 
alterations from germline ones. 
 
2.5.3 Exploratory Assays 
 
2.5.3.1 PTEN expression 
 
In tumors with PTEN loss, the activated PI3K/AKT/mTOR pathway constitutes an attractive 
target of therapy. PTEN may be silenced at protein level due to epigenetic modifications in 
absence of inactivating PTEN alterations. Hence, loss of PTEN expression detected by 
immunohistochemistry (IHC) is regarded as the most accurate reflection of the loss of PTEN 
function. PTEN loss of expression by IHC has been associated with poor disease free survival (Li 
et al, 2017). At the end of the trial, we will evaluate the PTEN IHC status of all patients in the 
trial on research biopsies or archival tissue, to correlate PTEN status with PFS and OS on the 
trial. 
 
2.5.3.2 RNA Sequencing (RNASeq) 
 
RNASeq uses next generation sequencing (NGS) technology to sequence cDNA that has been 
derived from an RNA sample. Analysis of transcriptomic data helps to identify differentially 
expressed genes between groups of interest. RNASeq analysis will be used to correlate gene 
expression profiles with treatment outcomes (PFS and OS). 
 
2.5.3.3 Circulating Tumor DNA (ctDNA) Sequencing 
 
ctDNA accumulates in plasma of cancer patients through apoptosis and necrosis of cancer cells 
as well as through secretion by the tumor. The molecular profile of ctDNA has a high 
concordance with that of tumor tissue. ctDNA is analysis is an emerging modality to evaluate for 
the changes in molecular profile of the tumor during treatment, and to detect the emergence of 
genetic alterations after exposure to the trial combination that may be associated with acquired 
resistance. Significant decreases in ctDNA levels and aggregate VAF of mutated DNA correlate 
with CT responses. 
 
2.5.3.4 Ki-67 Expression 
 
Uncontrolled cell proliferation is a hallmark of cancer. Ki-67 protein (also known as MKI67) is a 
nuclear antigen that is present in all but the G0 phase of the cell cycle, and therefore, its 
expression is strictly associated with cell proliferation. To assess the proliferation of the tumor 
tissue, we will perform Ki-67 immunohistochemical staining. The proportion of tumor cells 
staining positive for Ki-67 has prognostic significance for metastatic breast cancer patients. Ki- 
67 levels >20% have been found to be associated with shorter survival after relapse in metastatic 

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breast cancer patients (Falato et al., 2011). In this study, we will correlate baseline Ki-67 levels, 
and changes in Ki-67 levels after treatment, with outcomes (PFS and OS). 
 
2.5.3.5 Cleaved caspase-3 expression 
 
Caspase-3 is cleaved and activated by both the extrinsic and intrinsic apoptosis (programmed cell 
death) pathways. Studies have shown that apoptotic tumor cells compensatory increase the 
proliferation of neighboring surviving cells by cleaved caspase-3 regulation. Elevated tumor 
cleaved (and thus activated) caspase-3 expression levels predict worse treatment outcomes in 
cancer patients (Hu et. al., 2014). We will determine cleaved caspase-3 expression level by 
immunohistochemical staining, and estimate the percentage of positive tumor cells. Cleaved 
caspase-3 level at baseline and change after treatment will be correlated with treatment 
outcomes. 
 
3. PATIENT SELECTION 
 
3.1 Eligibility Criteria 
 
 
3.1.1 Phase-1B: Any number of prior of lines of therapy in the metastatic setting is allowed, provided patients 
are considered candidates for trastuzumab and pertuzumab combination or on maintenance trastuzumab 
and pertuzumab (with or without prior chemotherapy) as long as DLT can be determined. For Phase-2: 
Patients should have only received first line of induction chemotherapy (taxane) with trastuzumab and 
pertuzumab in the metastatic setting. 
  
 
3.1.1.1 Presence of actionable mutation in either PIK3CA or PTEN on molecular testing (Appendix E, F),  
 
3.1.1.2 For Phase 2-Patients must be within 8 weeks of completion of first-line induction chemotherapy (i.e., 4-8 
cycles of any taxane, trastuzumab and pertuzumab) without evidence of progression. Patients may receive up to 2 
doses of HER2 targeted treatment between end of induction treatment and start of trial, while eligibility is being 
confirmed.  
 
3.1.1.3 Clinical Stage IV as assessed by American Joint Committee on Cancer (AJCC) (8th edition, anatomic 
staging) guidelines with known metastatic disease (Edge and Compton, 2010; Amin et al., 2017). 
 
3.1.1.4 HER2+ breast cancer patients with any ER/PR status as assessed by the ASCO- College of American 
Pathologists (ASCO-CAP) guidelines (Wolff et al., 2013; Wolff 

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et al., 2018). HER2 testing of metastasis will be required. 
 
3.1.1.5 Age ≥18 years (both male and female). Because no dosing or adverse event data are currently available on 
the use of copanlisib in combination with trastuzumab and pertuzumab in patients <18 years of age, children are 
excluded from this study, but will be eligible for future pediatric trials. 
 
3.1.1.6 Eastern Cooperative Oncology Group (ECOG) performance status ≤2 (Karnofsky ≥50%, see 
Appendix A). 
 
3.1.1.7 Patients must have adequate organ and bone marrow function as defined below: 
 
− 
absolute neutrophil count (ANC) 
≥1,500/mcL 
− 
platelets 
≥100,000/mcL 
− 
hemoglobin 
≥9 g/dL 
− 
left ventricular ejection fraction (LVEF) ≥ 50% by echocardiogram or Multigated 
Acquisition Scan (MUGA) 
− 
total bilirubin 
≤1.5 × institutional upper limit of normal 
(ULN) 
OR 
Direct bilirubin ≤ULN for subjects with total 
bilirubin levels >1.5 × ULN 
− 
AST(SGOT)/ALT(SGPT) 
≤2.5 × institutional ULN OR ≤5 × ULN for 
subjects with liver metastases 
 
− 
creatinine 
≤1.5 × institutional ULN 
OR 
Measured or calculated creatinine clearance 
≥60 mL/min for subject with creatinine 
levels >1.5 × institutional ULN (glomerular 
filtration rate [GFR] can also be used in 
place of creatinine or CrCl). Creatinine 
clearance should be calculated per 
institutional standard (see Appendix B) 
− 
International Normalized Ratio (INR) 
≤1.5 × ULN unless patient is receiving 
OR Prothrombin Time (PT) 
anticoagulation as long as PT or partial 
thromboplastin time (PTT) is within 
therapeutic range of intended use of 
anticoagulants 
− 
Activated Partial Thromboplastin 
≤1.5 × ULN unless patient is receiving 
Time (aPTT) 
anticoagulation as long as PT or PTT is 
within therapeutic range of intended use of 
anticoagulants 
 
3.1.1.8 Patients with treated brain metastases are eligible if follow-up brain imaging 30 days after central 
nervous system (CNS)-directed therapy shows no evidence of progression. 
 

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3.1.1.9 Patients who are therapeutically treated with anticoagulation including warfarin will be allowed to participate 
provided that their medication dose and INR/PTT is stable. Due to interaction of copanlisib with warfarin, patients 
who are on warfarin should be monitored closely while on this trial. 
 
3.1.1.10 Women of child-bearing potential MUST have a negative serum or urine human chorionic gonadotropin 
(HCG) test unless prior tubal ligation (>/= 1 year before screening), total hysterectomy or menopause (defined as 12 
consecutive months of amenorrhea). Patients should not become pregnant or breastfeed while on this study. 
 
3.1.1.11 Patients and their partners, if sexually active and of childbearing potential, must agree to the use of two 
highly effective forms of contraception in combination throughout the period of taking study treatment and for 7 
months after last dose of study drug(s) to prevent pregnancy in the study patient or partner. 
 
3.1.1.12 Hormone receptor positive (ER+ and / PR+) breast cancer patients will be allowed to continue endocrine 
therapy as clinically indicated while participating inthe study. 
 
3.1.1.13 Ability to understand and the willingness to sign a written informed consent document. 
 
3.2 Exclusion Criteria 
 
3.2.1 Known active Hepatitis B or Hepatitis C infection. All patients must be screened for HBV and HCV up 
to 28 days prior to study drug start using the routine hepatitis virus lab panel. For patients with evidence of 
chronic hepatitis B virus (HBV) infection, the HBV viral load must be undetectable on non-CYP3A4- 
interactive suppressive therapy, if indicated. Patients with a history of hepatitis C virus (HCV) infection must 
have been treated and cured. Patients positive for anti-HCV antibody will be eligible if they are negative for 
HCV RNA. 
 
3.2.2 Human immunodeficiency virus (HIV)-positive patients, unless they have CD4 counts >500 cells/mm3 
in the past 6 months and do not require CYP3A4-interactive antiretroviral therapy. 
 
3.2.3 Active infection requiring IV antibiotics or other uncontrolled intercurrent illness requiring 
hospitalization. 
 
3.2.4 Inability to comply with the study and follow-up procedures. 
 
3.2.5 History of cerebrovascular accident (CVA), myocardial infarction, symptomatic congestive heart 
failure, cardiac arrhythmia, or unstable angina within the previous 6 months before starting therapy. 
 
3.2.6 Patients who have not recovered from adverse events due to prior anti-cancer therapy (i.e., have 
residual toxicities > Grade 1) with the following exceptions: alopecia (any grade is acceptable); neuropathy 
must have resolved to ≤ Grade 2. CHF due to prior anti- cancer therapy must have been ≤ Grade 1 in severity 
at the time of occurrence, and must have resolved completely. 
 
3.2.7 Current uncontrolled hypertension (≥150/90). 
 

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3.2.8 Has a known additional malignancy that is progressing or requires active treatment. Exceptions include 
basal cell carcinoma of the skin, squamous cell carcinoma of the skin that has undergone potentially curative 
therapy or in situ cervical cancer. 
 
3.2.9 Has a known psychiatric or substance abuse disorders that would interfere with cooperation with the 
requirements of the trial. 
 
3.2.10 Patients with uncontrolled Type I or II diabetes mellitus (DM); uncontrolled DM is defined as HbA1c 
>8.5% and a fasting blood glucose of >120 mg/dL within 14 days prior to trial entry. 
 
3.2.11 Immunosuppressive therapy is not allowed while on study. 
 
3.2.12 Patients who are receiving any other investigational agents. 
 
3.2.13 Patients with leptomeningeal disease or active untreated brain metastases 
 
3.2.14 Prior exposure to any PI3K, AKT or mTOR inhibitors. History of allergic reactions attributed to 
compounds of similar chemical or biologic composition to copanlisib, PI3K inhibitors, or HER2 inhibitors. 
 
3.2.15 Copanlisib is primarily metabolized by CYP3A4. Therefore, the concomitant use of strong inhibitors 
of CYP3A4 (e.g., ketoconazole, itraconazole, clarithromycin, ritonavir, indinavir, nelfinavir and saquinavir), 
and strong inducers of CYP3A4 (e.g. rifampin, phenytoin, carbamazepine, phenobarbital, St. John’s Wort) 
are not permitted from 14 days prior to enrollment until the end of the study. 
 
Other medications that are prohibited while on copanlisib treatment: 
• Herbal medications/preparations (except for vitamins) 
• Anti-arrhythmic therapy other than beta blockers or digoxin 
For the list of specific medications prohibited while on copanlisib treatment refer to the 
APPENDIX C). Because the lists of these agents are constantly changing, it is important 
to regularly consult a frequently updated medical reference for a list of drugs to avoid or 
minimize use of. APPENDIX D (Patient Clinical Trial Wallet Card) should be provided 
to patients. As part of the enrollment/informed consent procedures, the patient will be 

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counseled on the risk of interactions with other agents, and what to do if new medications 
need to be prescribed or if the patient is considering a new over-the-counter medicine or 
herbal product. 
 
3.2.16 Systemic corticosteroid therapy at a daily dose higher than 15 mg prednisone or equivalent is not 
permitted while on study. Previous corticosteroid therapy must be stopped or reduced to the allowed dose at 
least 7 days prior to the CT/MRI screening. If a patient is on chronic corticosteroid therapy, corticosteroids 
should be de-escalated to the maximum allowed dose before the screening. Patients may be using topical or 
inhaled corticosteroids. 
 
3.2.17 Patients with non-healing wound, ulcer, or bone fracture. 
 
3.2.18 Pregnant women are excluded from this study because copanlisib is a PI3K inhibitor agent with the 
potential for teratogenic or abortifacient effects. Because there is an unknown but potential risk for adverse 
events in nursing infants secondary to treatment of the mother with copanlisib, breastfeeding should be 
discontinued if the mother is treated with copanlisib. These potential risks may also apply to other agents 
used in this study. 
 
3.2.19 Patients are eligible to receive standard of care therapy that would confer clinical benefit to the 
patient. 
 
3.3 Inclusion of Women and Minorities 
 
NIH policy requires that women and members of minority groups and their subpopulations be 
included in all NIH-supported biomedical and behavioral research projects involving NIH- 
defined clinical research unless a clear and compelling rationale and justification establishes to 
the satisfaction of the funding Institute & Center (IC) Director that inclusion is inappropriate 
with respect to the health of the subjects or the purpose of the research. Exclusion under other 
circumstances must be designated by the Director, NIH, upon the recommendation of an IC 
Director based on a compelling rationale and justification. Cost is not an acceptable reason for 
exclusion except when the study would duplicate data from other sources. Women of 
childbearing potential should not be routinely excluded from participation in clinical research. 
Please see http://grants.nih.gov/grants/funding/phs398/phs398.pdf. 
 
This study will be open to all individuals regardless of gender, ethnicity, or race provided that the 
aforementioned inclusion and exclusion criteria are met. 
 
4. REGISTRATION PROCEDURES 
 
4.1 Investigator and Research Associate Registration with CTEP 
 
Food and Drug Administration (FDA) regulations and National Cancer Institute (NCI) policy 
require all individuals contributing to NCI-sponsored trials to register and to renew their 
registration annually. To register, all individuals must obtain a Cancer Therapy Evaluation 
Program (CTEP) Identity and Access Management (IAM) account at 
https://ctepcore.nci.nih.gov/iam. In addition, persons with a registration type of Investigator 

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(IVR), Non-Physician Investigator (NPIVR), or Associate Plus (AP) must complete their 
annual registration using CTEP’s web-based Registration and Credential Repository (RCR) 
at https://ctepcore.nci.nih.gov/rcr. 
 
RCR utilizes five-person registration types. 
• IVR: MD, DO, or international equivalent, 
• NPIVR: advanced practice providers (e.g., NP or PA) or graduate level researchers (e.g., 
PhD), 
• AP: clinical site staff (e.g., RN or CRA) with data entry access to CTSU applications such 
as the Roster Update Management System (RUMS), OPEN, Rave, acting as a primary site contact, or 
with consenting privileges,  
• Associate (A): other clinical site staff involved in the conduct of NCI-sponsored trials, and 
• Associate Basic (AB): individuals (e.g., pharmaceutical company employees) with limited 
access to NCI-supported systems. 
 
RCR requires the following registration documents: 
 
Documentation Required 
IVR 
NPIVR 
AP 
A 
FDA Form 1572 


Financial Disclosure Form 



NCI Biosketch (education, training, employment, 
license, and certification) 



HSP/GCP training 



Agent Shipment Form (if applicable) 

CV (optional) 



 
An active CTEP-IAM user account and appropriate RCR registration is required to access all 
CTEP and Cancer Trials Support Unit (CTSU) websites and applications. In addition, IVRs 
and NPIVRs must list all clinical practice sites and Institutional Review Boards (IRBs) 
covering their practice sites on the FDA Form 1572 in RCR to allow the following: 
 
• Addition to a site roster, 
• Assign the treating, credit, consenting, or drug shipment (IVR only) tasks in OPEN, 
• Act as the site-protocol Principal Investigator (PI) on the IRB approval, and 
• Assign the Clinical Investigator (CI) role on the Delegation of Tasks Log (DTL). 
 
In addition, all investigators act as the Site-Protocol PI, (Investigator listed on the IRB 
approval), consenting/treating/drug shipment investigator in OPEN, or as the Clinical 
Investigator (CI) on the DTL must be rostered at the enrolling site with a participating 

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organization   
 
Additional information is located on the CTEP website at 
https://ctep.cancer.gov/investigatorResources/default.htm. For questions, please contact the 
RCR Help Desk by email at RCRHelpDesk@nih.gov. 
. 
 
4.2 Site Registration 
 
This study is supported by the NCI Cancer Trials Support Unit (CTSU). 
 
Sites participating with the NCI Central Institutional Review Board (NCI CIRB) must submit 
the Study Specific Worksheet for Local Context (SSW) to the CIRB using IRBManager to 
indicate their intent to open the study locally. The NCI CIRB’s approval of the SSW is 
automatically communicated to the CTSU Regulatory Office, but sites are required to contact 
the CTSU Regulatory Office at CTSURegPref@ctsu.coccg.org to establish site preferences 
for applying NCI CIRB approvals across their Signatory Network. Site preferences can be 
set at the network or protocol level. Questions about establishing site preferences can be 
addressed to the CTSU Regulatory Office by emailing the email address above or calling 1- 
888-651-CTSU (2878). 
 
Sites using their local IRB or REB must submit their approval to the CTSU Regulatory 
Office using the Regulatory Submission Portal located in the Regulatory section of the 
CTSU website. Acceptable documentation of local IRB/REB approval includes: 
• Local IRB documentation, 
• IRB-signed CTSU IRB Certification Form, and/or 
• Protocol of Human Subjects Assurance Identification/IRB Certification/Declaration of 
Exemption Form. 
 
In addition, the Site-Protocol PI (i.e., the investigator on the IRB/REB approval) must meet 
the following five criteria to complete processing of the IRB/REB approval record: 
• Holds an Active CTEP status, 
• Rostered at the site on the IRB/REB approval (applies to US and Canadian sites only) and 
on at least one participating roster, 
• If using NCI CIRB, rostered on the NCI CIRB Signatory record, 
• Includes the IRB number of the IRB providing approval in the Form FDA 1572 in the RCR 
profile, and 
• Holds the appropriate CTEP registration type for the protocol. 
 
Additional requirements to obtain an approved site registration status include: 
• An active Federalwide Assurance (FWA) number, 

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• An active roster affiliation with the Lead Protocol Organization (LPO) or a Participating 
Organization, and 
• Compliance with all protocol-specific requirements (PSRs). 
 
4.2.1 Downloading Regulatory Documents 
 
Download the site registration forms from the protocol-specific page located on the CTSU members’ 
website. Permission to view and download this protocol and its supporting documents is restricted based on 
person and site roster assignment. To participate, the institution and its associated investigators and staff 
must be associated with the LPO or a Participating Organization on the protocol. One way to search for a 
protocol is listed below. 
 
• Log on to the CTSU members’ website (https://www.ctsu.org) using your CTEP-IAM 
username and password, 
• Click on Protocols in the upper left of your screen 
o Enter the protocol number in the search field at the top of the protocol tree, or 
o Click on the By Lead Organization folder to expand, then select LAO-TX035, and 
protocol number 10296, 
• Click on Documents, select Site Registration, and download and complete the forms 
provided. (Note: For sites under the CIRB initiative, IRB data will load automatically to 
the CTSU as described above.) 
 
4.2.2 Requirements For 10296 Site Registration 
• 
Site Initiation visit 
• 
ETCTN Specimen Tracking Training with Theradex 
• All data entry users (Clinical Research Associate role) at each participating 
site will need to complete the Theradex-led training. 
• Theradex will provide a certificate of completion, which will need to be 
submitted to the CTSU through the Regulatory Submission Portal. 
• The training is a one-time only requirement per individual. If an individual 
has previously completed the training for another ETCTN study, the training 
does not need to be completed again nor does the certificate of completion 
need to be resubmitted to the CTSU. However, new versions of the Specimen 
Tracking system may require new training. 
• This training will need to be completed before the first patient enrollment at 
a given site. 
• Please contact STS Support at Theradex for the training 
(STS.Support@theradex.com, Theradex phone: 609-799-7580). 
 
4.2.3 Submitting Regulatory Documents 
 
Submit required forms and documents to the CTSU Regulatory Office via the Regulatory 
Submission Portal on the CTSU website. 
 

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To access the Regulatory Submission Portal, log on to the CTSU members’ website go to the 
Regulatory section, and select Regulatory Submission  
Institutions with patients waiting that are unable to use the Portal should alert the CTSU 
Regulatory Office immediately at 1-866-651-2878 in order to receive further instruction 
and support. 
 
4.2.4 Checking Site Registration Status 
 
Site’s registration status may be verified on the CTSU website.  
• 
Click on Regulatory at the top of the screen, 
• 
Click on Site Registration, and  
• 
Enter the site’s 5-character CTEP Institution Code and click on Go. 
o 
Additional filters are available to sort by Protocol, Registration Status,   Protocol 
Status, and/or IRB Type. 
Note:  The status shown only reflects institutional compliance with site registration requirements as 
outlined within the protocol.  It does not reflect compliance with protocol requirements for individuals 
participating on the protocol or the enrolling investigator’s status with NCI or their affiliated networks. 
 
4.3 Patient Registration 
 
4.3.1 OPEN/IWRS 
 
The Oncology Patient Enrollment Network (OPEN) is a web-based registration system 
available on a 24/7 basis. OPEN is integrated with CTSU regulatory and roster data and 
with the LPOs registration/randomization systems or the Theradex Interactive Web 
Response System (IWRS) for retrieval of patient registration/randomization assignment. 
OPEN or IWRS will populate the patient enrollment data in NCI’s clinical data 
management system, Medidata Rave. 
 
Requirements for OPEN access: 
 
• 
A valid CTEP-IAM account. 
• 
To perform enrollments or request slot reservations: Must be on an LPO roster, 
ETCTN corresponding roster, or PO roster with the role of Registrar. Registrars must 
hold a minimum of an Associate Plus (AP) registration type. 
• 
If a DTL is required for the study, the registrar must hold the OPEN Registrar task 
on the DTL for the site. 
• 
Have an approved site registration for the protocol prior to patient enrollment. 
 
To assign an Investigator (IVR) or Non-Physician Investigator (NPIVR) as the treating, 
crediting, consenting, drug shipment (IVR only), or receiving investigator for a patient 
transfer in OPEN, the IVR or NPIVR must list the IRB number used on the site’s IRB 
approval on their Form FDA 1572 in RCR. If a DTL is required for the study, the IVR 
or NPIVR must be assigned the appropriate OPEN-related tasks on the DTL. 

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Prior to accessing OPEN, site staff should verify the following: 
 
• 
Patient has met all eligibility criteria within the protocol stated timeframes, and 
• 
All patients have signed an appropriate consent form and HIPAA authorization 
form (if applicable). 
 
Note: The OPEN system will provide the site with a printable confirmation of 
registration and treatment information. IWRS system also sends an email confirmation 
of the registration. You may print this confirmation for your records. 
 
Access OPEN at https://open.ctsu.org or from the OPEN link on the CTSU members’ 
website. Further instructional information is in the OPEN section of the CTSU website 
at https://www.ctsu.org or https://open.ctsu.org. For any additional questions, contact 
the CTSU Help Desk at 1-888-823-5923 or ctsucontact@westat.com. 
 
Patient enrollment for this study will be facilitated using the Slot Reservation System in conjunction with the 
registration system in OPEN. Prior to discussing protocol entry with the patient, all site staff must use the CTSU 
OPEN Slot Reservation System or the IWRS Slot Reservation System to ensure that a slot on the protocol is 
available to the patient. Once a slot reservation confirmation is obtained, site staff may then proceed to enroll the 
patient to this study. 
 
4.3.2 Special Instructions for Patient Enrollment 
 
This Study will use the ETCTN Specimen Tracking System (STS). 
 
• All biospecimens collected for this trial must be submitted using the ETCTN Specimen 
Tracking System (STS) unless otherwise noted. 
• The system is accessed through special Rave user roles: “CRA Specimen Tracking” for 
data entry at the treating institutions and “Biorepository” for users receiving the 
specimens for processing and storage at reference labs and the Biorepository. 
• Please refer to the Medidata Account Activation and Study Invitation Acceptance link on 
the CTSU website under the Rave/DQP tab. 
• Important: Failure to complete required fields in STS may result in a delay in 
sample processing. Any case reimbursements associated with sample submissions will 
not be credited if samples requiring STS submission are not logged into STS. 
 
Detailed instructions can be found in Section 5.3. 
 
4.3.3 OPEN/IWRS Questions? 
 
Further instructional information on OPEN is provided on the OPEN tab of the CTSU 
website at https://www.ctsu.org or at https://open.ctsu.org. For any additional questions 
contact the CTSU Help Desk at 1-888-823-5923 or ctsucontact@westat.com. 
 
Theradex has developed a Slot Reservations and Cohort Management User Guide, which is 
available on the Theradex website: http://www.theradex.com/clinicalTechnologies/?National-

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Cancer-Institute-NCI-11. This link to the Theradex website is also on the CTSU website OPEN 
tab. For questions about the use of IWRS for slot reservations, contact the Theradex Helpdesk at 
609-619-7862 or Theradex main number 609-799-7580; CTMSSupport@theradex.com. 
 
5. 4.4 BIOMARKER, CORRELATIVE, AND SPECIAL STUDIES 
 
5.1 Summary Table for Specimen Collection 
 
 
Specimen and Quantity 
Send Specimens To: 
Baseline 
• Archival FFPE tumor block1 (mandatory) 
OR 
• 3 tissue cores in formalin (mandatory)2 
ETCTN Biorepository 
2 cores snap frozen (optional)3 
1x 10 mL blood in Streck tube (mandatory) 
1 x 10 mL blood in Streck tube (optional) 
Cycle 1 Day 15 (C1D15) 
3 tissue cores in formalin (optional)2 
ETCTN Biorepository 
2 cores snap frozen (optional) 
ETCTN Biorepository 
Cycle 2 Day 1 (C2D1) 
1 x 10 mL blood in cfDNA Streck tube (optional) 
ETCTN Biorepository 
Cycle 3 Day 1 (C3D1) 
1 x 10 mL blood in cfDNA Streck tube (optional) 
ETCTN Biorepository 
Each Restaging 
1 x 10 mL blood in cfDNA Streck tube (optional) 
ETCTN Biorepository 
At Disease Progression 
3 tissue cores in formalin (optional) 
ETCTN Biorepository 
2 tissue cores snap frozen (optional) 
ETCTN Biorepository 

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1 x 10 mL blood in cfDNA Streck tube (optional) 
ETCTN Biorepository 
 
 
 
5.2 Specimen Procurement Kits and Scheduling 
 
5.2.1 Specimen Shipping Kits 
 
Kits for the collection and shipment of specimens to the ETCTN Biorepository can be 
ordered online via the Kit Management system: 
(https://ricapps.nationwidechildrens.org/KitManagement). 
 
Users at the clinical sites will need to set up an account in the Kit Management system 
and select a specific clinical trial protocol to request a kit. Please note that protocol may 
include more than one type of kit. Each user may order two kit types per protocol per 
day (daily max = 6 kits).  Kits are shipped ground, so please allow 5-7 days for receipt. 
A complete list of kit contents for each kit type is located on the Kit Management system 
website. 
 
Note: Kits or supplies are only provided for specimens shipped to the Biorepository. 
Institutional supplies must be used for all other specimen collection and processing. 
 
5.2.2 Scheduling of Specimen Collections ETCTN Biorepository 
 
Please adhere to the following guidelines when scheduling procedures to collect tissue: 
 
• 
Tumor tissue specimens collected during biopsy procedures and fixed in formalin 
must be shipped on the same day of collection. 
• 
Tissue in formalin can be collected Monday through Wednesday and shipped 
overnight for arrival on Tuesday through Thursday at the ETCTN Biorepository 
at Nationwide Children’s Hospital. 
• 
Specimens submitted frozen may be shipped in a provided dry shipper or on dry 
ice on the same day of collection. Tissue can be collected Monday through 
Thursday (FedEx Priority Overnight). 
• 
Fresh blood specimens may be collected and shipped Monday through Friday. 
 
5.3 Specimen Tracking System Instructions 
 
1If available archival tissue  
must be collected within 12 months prior to registration and must consist of metastatic tumor 
tissue. For archival tissue, a copy of the corresponding anatomic pathology report must be sent 
with the tissue and uploaded to Rave. 
2For new biopsies, a copy of the radiology and operative reports from the tissue removal 
procedure must be sent with the tissue to the ETCTN Biorepository. When completed, upload 
the corresponding pathology reports to Rave. 

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For the ETCTN STS, the following information will be requested: 
• Protocol Number 
• Investigator Identification 
o Institution and affiliate name 
o Investigator’s name 
• Eligibility Verification: Patients must meet all the eligibility requirements listed in 
Section 3. 
• Additional Requirements: 
o Patients must provide a signed and dated, written informed consent form. 
Upon enrolling a patient, IWRS will communicate with OPEN, assigning two separate and 
unique identification numbers to the patient, a Universal patient ID (UPID) and a Treatment 
patient ID. The UPID is associated with the patient and used each and every time the patient 
engages with the portion of this protocol that uses the ETCTN Specimen Tracking System. The 
UPID contains no information or link to the treatment protocol. IWRS will maintain an 
association between the UPID for ETCTN biobanking and molecular characterization and any 
treatment protocols the patient participates in, thereby allowing analysis of the molecular 
characterization results with the clinical data. 
 
Immediately following enrollment, the institutional anatomical pathology report for the diagnosis 
under which the patient is being enrolled must be uploaded into Rave. The report must include 
the surgical pathology ID (SPID), collection date, block number, and the IWRS-assigned UPID 
and patient study ID for this trial. For newly acquired biopsies, the radiology and operative 
report(s) must also be uploaded into Rave. Important: Remove any personally identifying 
information, including, but not limited to, the patient’s name, initials, medical record 
number, and patient contact information from the institutional pathology report prior to 
submission. 
 
Additionally, please note that the STS software creates pop-up windows when reports are 
generated, so you will need to enable pop-ups within your web browser while using the software. 
 
For questions regarding the Specimen Tracking System, please contact the Theradex Help Desk 
at CTMSSupport@theradex.com. 
 
A shipping manifest must be included with all sample submissions. 
 
5.3.1 Specimen Labeling 
 
5.3.1.1 Blood Specimen Labels 
 
Include the following on blood specimens (including whole blood and frozen, processed blood 
products – like serum and plasma): 
• Patient Study ID 
• Universal Patient ID (UPID) 
• Specimen ID (automatically generated by Rave) 
• Time point 

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• Specimen type (e.g., blood, serum) 

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• Collection date (to be added by hand) 
 
5.3.1.2 Tissue Specimen Labels 
 
Include the following on all tissue specimens or containers (e.g., formalin jar): 
• Patient Study ID 
• Universal Patient ID (UPID) 
• Specimen ID (automatically generated by Rave) 
• Time point 
• Specimen type (e.g., FFPE Block, Formalin Fixed Tissue, Fresh Tissue in Media, 
etc.) 
• Tissue type (P for primary, M for metastatic or N for normal) 
• Surgical pathology ID (SPID) number 
• Block number from the corresponding pathology report (archival only) 
• Collection date (to be added by hand) 
• Core number (formalin-fixed and snap frozen tissue cores only) (to be added by hand) 
 
5.3.1.3 Example of Specimen Label 
 
The following image is an example of a tissue specimen label printed on a standard Avery label 
that is 1” high and 2.625” wide. 
 
 
The QR code in the above example is for the Specimen ID shown on the second line. 
NOTE: The QR code label is currently under development at Theradex as of 31-Aug-2018; 
therefore, labels generated by the STS for this study may not include a QR code. 
 
The second line item from the end includes four data points joined together: 
1. Tissue only: Primary (P), Metastatic (M), Normal (N) tissue indicated at the 
beginning of the specimen ID; this field is blank if not relevant (e.g., for blood) 
2. Block ID or blank if not relevant 
3. SPID (Surgical Pathology ID) or blank if none 
4. The last alpha-numeric code is protocol specific and is only included if the protocol 
requires an additional special code classification 
 
The last line on the example label is for the handwritten date and optional time. 

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5.3.2 Overview of Process at Treating Site 
 
5.3.2.1 OPEN Registration 
 
All registrations will be performed using the Oncology Patient Enrollment Network (OPEN) 
system. OPEN communicates automatically with the Interactive Web Response System (IWRS) 
which handles identifier assignments, any study randomization and any prescribed slot 
assignments. If specimen analysis is required to determine eligibility, the protocol will be setup 
with multi-step registration. 
 
Registration without eligibility specimen analysis: 
1. Site enters registration data into OPEN during one or more steps. 
2. IWRS receives data from OPEN, generates the Patient Study ID and the Universal 
Patient ID, both of which are sent back to OPEN. 
3. IWRS sends all applicable registration data directly to Rave at the end of the final 
registration step. 
 
Any data entry errors made during enrollment should be corrected in Rave. 
 
5.3.2.2 Rave Specimen Tracking Process Steps 
 
Step 1: Complete the Histology and Disease form (but do not upload reports until a 
specimen label can be applied to them) and the Baseline forms regarding Prior 
Therapies. Enter the initial clinical specimen data: 
• Specimen Tracking Enrollment CRF: Enter Time Point, Specimen Category, 
Specimen Type, Block number, Tissue type, Surgical Path ID, number of labels 
needed (include extra labels to apply to reports to be uploaded). CRF generates 
unique Specimen ID. 
 
Step 2: Print labels using report in EDC and collect specimen. 
• Label specimen containers and write collection date on each label. 
• After collection, store labeled specimens as described in Section 5.3.1. 
• Apply an extra specimen label to each report before scanning. Return to the 
Histology and Disease form to upload any initial Pathology, Radiology, 
Molecular Reports (up to 4), Surgical (or Operative) reports and Pathology 
Verification form (when applicable). Return to Specimen Tracking Enrollment 
CRF to upload any molecular report (one per specimen) and/or specimen specific 
pathology or related report (one per specimen). Uploaded reports should have 
protected health information (PHI) data, like name, mailing address, medical 
record number or social security number (SSN), redacted. Do not redact SPID, 
block number or relevant dates, and include the UPID and patient study ID on 
each document. 
 
Step 3: Complete specimen data entry. 
• Specimen Transmittal Form: Enter Collection date and time and other required 
specimen details. 

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Step 4: When ready to ship, enter shipment information. 
• Shipping Status CRF: Enter tracking number, your contact information, 
recipient, number of containers and ship date once for the 1st specimen in a 
shipment. 
• Copy Shipping CRF: Select additional specimens to add to an existing shipment 
referenced by the tracking number. 
 
Step 5: Print shipping list report and prepare to ship. 
• Print two copies of the shipping list, one to provide in the box, the other for your 
own records. 
• Print pathology or other required reports to include in the box. Be sure the printed 
copy includes the specimen label. 
 
Step 6: Send email notification. 
• For only one of the specimens in the shipment, click “Send Email Alert” 
checkbox on the Shipping Status CRF to email recipient. 
 
Step 7: Ship the specimen(s). 
 
5.4 Specimen Collection 
 
5.4.1 Biopsy Collection Procedure ETCTN Biorepository 
 
5.4.1.1 Core needle biopsy 
 
A maximum number of 5 cores (1 cm in length) is recommended. The number of specimens 
obtained will be affected by the patient’s clinical condition at the time of biopsy and 
determined by the specialist performing the procedure. Core biopsy should be performed using 
a 16-18-gauge needle, condition permitting. 
• At least 2 cores (1 cm in length) should be obtained for nucleic acid analysis. At least 1 
core (1 cm in length) should be obtained for analysis at the MD Anderson RPPA Core 
Laboratory. At least 1 core should be obtained for IHC of PTEN, Ki-67 and cleaved 
caspase 3 (CC-3). 
• Alternating passes: First obtain a core for formalin-fixed processing (core 1 is for IHC of 
PTEN, Ki-67 IHC, and CC-3 IHC), followed by a core for flash freezing (core 2 is for 
RPPA), followed by 2 cores for formalin fixed processing (cores 3 and 4 for WES and 
RNASeq), followed by a core for flash freezing (core 5 is also for RPPA). 
 
5.4.1.2 Flash Freezing of Core Needle Biopsy 
 
1. Arrive at the biopsy collection site early enough to allow sufficient time to set up 
laboratory supplies, collect relevant clinical information, and ensure rapid transport of 
specimens to the laboratory for placement at -80ºC (or lower) after collection. 
2. Bring all necessary lab supplies including disposable tweezers, a minimum of two 1.5- 

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mL Sarstedt tubes or any other screw-top vial that can be used to freeze in liquid nitrogen 
vapor (one for each whole biopsy core) pre-cooled on liquid nitrogen or dry ice/ethanol in an 
insulated bucket, and one pre-printed specimen label (see Section 5.3.1.3) to give to the research 
nurse for the patient record. 
Note: Pre-chill additional 1.5-mL Sarstedt tubes or any other screw-top vial that can be 
used to freeze in liquid nitrogen vapor for specimen collection in case the interventional 
radiologist collects additional passes, or one of the other tubes is compromised prior to 
collection. 
3. The total time elapsed between biopsy collection and placement into the pre-chilled tube 
is of key importance to biomarker analysis; biopsies should be frozen within 2 min of 
collection. The interventional radiologist will eject the biopsy onto a sterile slide (for 
optimal analyte recovery the slide should be pre-chilled). Start a stop watch (or note the 
time) at this point (Appendix G, Section 1) and immediately walk the slide to the sample 
preparation table. 
Note: The preferred method of collection, when whole biopsies are collected, is for the 
interventional radiologist to eject the biopsy directly into the pre-chilled tube (next step). 
This minimizes the time between collection and fixation of analytes. 
4. Indicate if a full or halved biopsy is prepared in the Batch Record (Appendix G, Section 
1). 
a. For whole biopsies: Uncap an empty, prechilled 1.5-mL Sarstedt tube and using 
disposable tweezers, pick up the freshly collected needle biopsy with the tweezers 
at one end, and touch the opposite end of the biopsy to the inner surface of the 
prechilled 1.5-mL Sarstedt tube. This should attach the tissue to the tube, 
allowing it to be dropped into the tube while releasing the tissue from the 
tweezers without sticking. Dispose of the tweezers in the appropriate 
biohazardous waste container(s). 
b. For halved biopsies: Use 1-2 disposable tweezers and cut/shear the biopsy in half 
cross-wise while it is on the slide (do not pull or stretch the biopsy 
longitudinally). Use the tweezers to transfer the halved biopsies to sterile pre- 
chilled tubes as indicated above. 
5. Immediately snap freeze the biopsy by placing the tube in liquid nitrogen or a dry 
ice/ethanol bath. 
6. Calculate the total time elapsed from biopsy collection to biopsy freezing and record the 
total number of minutes and seconds elapsed in the Batch Record (Appendix G, Section 
1). 
7. If biopsy procedure details can be obtained from the interventional radiologist or research 
nurse, record them in the Batch Record (Appendix G, Section 2.). Some information may 
not be available until a later time from the clinical staff. 
8. Return to the sample processing laboratory and transfer the frozen biopsy specimen(s) to 
-80ºC (or lower) for storage until shipment to the pharmacodynamic processing 
laboratory. Record the date and time specimens are placed at -80ºC (or lower; Appendix 
G, Section 3). 
9. Review and finalize the Batch Record and document ANY and ALL deviations from this 
SOP in the Batch Record (Appendix G, Section 5). 
10. The Laboratory Director/Supervisor should review the Batch Record and sign to affirm 
the data contained within are correct (Appendix G, Section 6). 

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5.4.1.3 Archival or Formalin-Fixed Paraffin-Embedded (FFPE) Tumor Specimen 
 
If previously collected FFPE tissue will be submitted, then the following criteria must be 
met: 
 
• Tissue must have been collected within 6 months prior to registration 
• Tissue must be from a metastatic site. 
• Formalin-fixed paraffin-embedded tumor tissue block(s) must be submitted. The 
optimal block is at least 70% tumor. Specimen size requirement is as follows: 
o Surface area: 25 mm2 is optimal. Minimum is 5 mm2. 
o Volume: 1 mm3 optimal. Minimum volume is 0.2 mm3, however the success of 
DNA extraction decreases at suboptimal tissue volume. 
 
5.4.2 Formalin-Fixed Tumor Biopsies 
 
1. Label formalin-filled containers according to instructions in section 5.3.1. 
2. Obtain 2-3 16-gauge or 18-gauge core needle biopsy specimens, and place one core in 
each cassette. 
3. Snap the cassette lids closed and place cassettes into a formalin-filled pre-labeled 
container as soon as possible after collection to prevent air drying. Up to two 
cassettes may be placed in one formalin jar. 
4. Secure the container lids and package containers into the shipping kit according to 
instructions in 5.5. Keep tissue in formalin jars at room temperature until shipment to 
the ETCTN Biorepository. 
 
5.4.3 Blood Collection 
 
5.4.3.1 Collection of Blood in cfDNA Streck Tube 
 
1. Label one 10 mL cfDNA Streck tube according to the instructions in section 5.3.1. 
2. Collect 10 mL of blood into the pre-labeled tube and gently invert to mix. Note: 
blood must be thoroughly mixed to ensure preservation of specimen. 
3. After collection, do not process. Blood in cfDNA Streck tubes should never be 
refrigerated, as this will compromise the specimen. Blood collected in cfDNA 
Streck tubes is stable at room temperature. 
 
5.5 Shipping Specimens from Clinical Site to the ETCTN Biorepository 
 
Core biopsies that are fixed in formalin and fresh blood should be shipped as one 
shipment at ambient temperature, whenever possible. The same box sent with kit 
contents should be used to ship specimens to the ETCTN Biorepository. In winter 
months, please include extra insulation, such as bubble wrap, inside the shipping 
container. 
 
For formalin-fixed biopsies, if the corresponding anatomical pathology report is not 
available at the time of shipment, then the surgical and/or radiology report, and the most 

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recent anatomic pathology report, must be uploaded to the ETCTN specimen tracking 
system and included in the package, or the specimen will not be processed. 
 
For all archival tissue, the corresponding anatomical clinical pathology report is required 
both in the package and uploaded in the ETCTN specimen tracking system. If this is not 
available at the time of shipment, then it must be uploaded to the ETCTN specimen 
tracking system, or the specimen will not be processed. The pathology report must state 
the disease diagnosis made by the reviewing pathologist. 
 
5.5.1 Specimen Shipping Instructions 
 
Tissue in formalin must be shipped on the day of collection. Collect and ship on Monday 
through Wednesday. 
 
Frozen specimens and archival (FFPE) tissue may be shipped on Monday through 
Thursday. 
 
Fresh blood may be shipped on Monday through Friday. Please select “Saturday 
Delivery” when shipping fresh blood on a Friday. 
 
5.5.1.1 Shipping Blood in an Ambient Shipper 
 
1. Before packaging specimens, verify that each specimen is labeled according to the 
instructions above and that the lids of all primary receptacles containing liquid are 
tightly sealed. 
2. Prepare the SAF-T-TEMP Gel Pak for shipment. Note: If contents of the Pak are 
crunchy, place Pak in a warm water bath until gel is smooth. Do not refrigerate, 
freeze, or microwave. 
3. Place the SAF-T-TEMP Pak in bottom of insulated chest. Note: The insulated chest 
must be shipped inside the provided cardboard box(es). 
4. Place the blood collection tubes in zip-lock bags. 
5. Next, place blood into a biohazard envelope with absorbent material. Expel as much 
air as possible and seal the envelope securely. 
6. Place the biohazard envelope into a Tyvek envelope. Expel as much air as possible 
and seal securely. 
7. Place packaged blood collection tube(s) and a copy of the shipping manifest from the 
Sample Tracking System on top of SAF-T-TEMP Pak. 
8. Place the lid on the insulated chest. 
9. Close the outer flaps of the shipping box and tape shut. 
10. Attach a shipping label to the top of the shipping container. 
11. Attach an Exempt Human Specimen sticker to the side of the box. 
12. Ship specimens via overnight courier to the address below. FedEx Priority Overnight 
is strongly recommended to prevent delays in package receipt. 

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5.5.1.2 Shipping Frozen and Ambient Specimens in a Dual-Chamber Kit 
 
The Dual-Chambered Specimen Procurement Kit is constructed to allow the shipment of 
frozen (on dry ice) and ambient (room temperature) specimens in the same container. Dry 
ice may be placed in either compartment of the kit but should not be put in both. The 
dual chambered kit is only used for shipments that contain both frozen and ambient 
specimens. If formalin-fixed tissue is shipped separately (not in the same shipment as 
frozen specimens), then it must be shipped using institutional shipping supplies. 
 
• Frozen specimens may be shipped on Monday through Thursday. Ensure that 
sufficient dry ice is included to completely encase the specimens to maintain 
specimen integrity during shipment. 
• Formalin-fixed tissue may only be shipped on Monday through Wednesday. 
 
13. Before packaging specimens, verify that each specimen is labeled according to the 
instructions above and that lids of all primary receptacles containing liquid are 
tightly sealed. 
14. Pre-fill one of the kit chambers about 1/3 with dry ice. 
15. Prepare the frozen specimens for shipment: 
a. Place the specimens into zip-lock bags. 
b. Place the zip-lock bags into a biohazard envelope containing absorbent material. 
Expel as much air as possible before sealing thebiohazard envelope. 
c. Put each biohazard envelope into a Tyvek envelope. Expel as much air as possible 
and then seal the Tyvek envelope 
16. Quickly place the Tyvek envelope containing frozen specimens in the kit compartment 
that is pre-filled with dry ice. Place the Tyvek envelope on top of the dry ice. Cover the 
specimens with additional dry ice until the compartment is almost completely full. 
17. Place the Styrofoam lid on top to secure specimens during shipment. Do not tape the 
inner chamber shut. 
18. Prepare the ambient specimens for shipment: 
a. Seal the lids of the formalin jars with parafilm. Place absorbent material around 
the primary container of each liquid specimen. Place the specimens into zip-lock 
bags. 
b. Place specimens inside the secondary pressure vessel with bubble wrap. 
c. Secure the lid on the secondary pressure vessel and set it inside the kit chamber. 
19. Insert a copy of the required forms in the kit chamber with the ambient specimens. 
20. Place the Styrofoam lid on top of the kit compartment to secure specimens during 
shipment. Do not tape the inner chamber shut. 
21. Close the outer lid of the Specimen Procurement Kit and tape it shut with durable sealing 
tape. Do not completely seal the container. 
22. Complete a FedEx air bill and attach to top of shipping container. 
23. Complete a dry ice label. 

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24. Attach the dry ice label and an Exempt Human Specimen sticker to the side of the 
shipping container. 
25. Ship specimens via overnight courier to the address below. FedEx Priority Overnight is 
strongly recommended to prevent delays in packagereceipt. 
 
 
5.5.2 Shipping Address 
 
Ship to the address below. Ship formalin-fixed and fresh blood specimens the same day of 
specimen collection. Do not ship specimens the day before a holiday. 
 
ETCTN Biorepository 
The Research Institute at Nationwide Children's Hospital 
700 Children's Drive, WA1340 
Columbus, Ohio 43205 
PH: (614) 722-2865 
FAX: (614) 722-2897 
Email: BPCBank@nationwidechildrens.org 
 
FedEx Priority Overnight service is very strongly preferred. 
 
NOTE: The ETCTN Biorepository FedEx Account will not be provided to submitting 
institutions. 
 
5.5.3 Contact Information for Assistance 
 
For all queries, please use the contact information below: 
 
ETCTN Biorepository 
Toll-free Phone: (800) 347-2486 
E-mail: BPCBank@nationwidechildrens.org 
 
5.6 Biomarker Plan 
 
At baseline, pre-treatment biopsy or archival tissue from metastatic tumor is mandatory. A pre- 
treatment biopsy is optional if archival tumor tissue from metastatic site (collected within 12 
months prior to registration) is available. For patients who undergo a pre-treatment biopsy, on- 
treatment biopsies on C1D15 and on disease progression are optional but strongly encouraged. 
In the event of limited tumor materials being available for biomarker testing, available tumor 
materials will be prioritized for the following analyses as follows: 1. PTEN IHC, 2. RPPA, 3. 
Whole exome sequencing, 4. RNA sequencing, 5. IHC for Ki-67, 6. IHC for cleaved caspase-3. 
 
In addition, blood for WES will be obtained at baseline. Blood for ctDNA testing will be 
obtained at baseline, C2D1, C3D1, and every restaging and at progression. ctDNA testing will be 
optional at all time points. 

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List of Biomarker Assays in Order of Priority 
Prior 
ity 
Biomark 
er Name 
Assay 
(CLIA: 
Y/N) 
Use in the 
Trial and 
Purpose 
Specim 
ens 
Tested 
Collection Time 
Points 
Mandat 
ory or 
Optiona 
l 
Assay Laboratory 
and Lab PI 
 
N/A 
Her2Neu 
Amplifica 
tion 
IHC or 
FISH 
(any 
local 
CLIA 
certified 
assay 
will be 
accepte 
d) 
Integral 
To qualify 
for 
enrollment 
in this 
clinical 
trial. 
Tissue 
(Archiv 
al# or 
Fresh) 
Baseline 
M 
Local CLIA-certified 
Laboratory 
CLIA: 
Y 
N/A 
PIK3CA 
mutations 
NGS or 
equival 
ent (any 
local 
CLIA 
certified 
assay 
will be 
accepte 
d) 
CLIA: 
Y 
Integral  
To qualify 
for 
enrollment 
in this 
clinical 
trial. 
Tissue 
(Archiv 
al# or 
Fresh) 
Or 
ctDNA 
Baseline 
M 
Local CLIA-certified 
Laboratory 
N/A 
PTEN 
mutations 
NGS or 
equival 
ent (any 
local 
CLIA 
certified 
assay 
will be 
accepte 
d) 
CLIA: 
Y 
Integral  
To qualify 
for 
enrollment 
in this 
clinical 
trial. 
Tissue 
(Archiv 
al# or 
Fresh) 
Or 
ctDNA 
Baseline 
M 
Local CLIA-certified 
Laboratory 

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Prior 
ity 
Biomark 
er Name 
Assay 
(CLIA: 
Y/N) 
Use in the 
Trial and 
Purpose 
Specim 
ens 
Tested 
Collection Time 
Points 
Mandat 
ory or 
Optiona 
l 
Assay Laboratory 
and Lab PI 
Tissue-based Biomarkers 
1 
PTEN 
expressio 
n 
IHC 
CLIA: 
N 
Explorator 
y 
To 
correlate 
presence 
or absence 
of PTEN 
expression 
by IHC 
with PFS 
and OS. 
Tissue 
(Archiv 
al# or 
Fresh) 
Baseline 
M 
Clinical IHC 
laboratory 
Wei-Lien Wang, MD 
/ MD Anderson 
wlwang@mdanderson 
.org 
2 
RPPA 
RPPA 
Integrated 
Frozen 
tissue 
• 
Baseline 
• 
C1D15 
• 
At disease 
progression 
O 
RPPA Core Facility 
CLIA: 
N 
To assess 
treatment 
induced 
changes in 
PI3K 
pathway 
signaling 
(e.g., 
pAKT, 
pS6, 
p4EBP1); 
and to 
correlate 
change in 
PI3K 
signaling 
with 
treatment 
outcomes 
(PFS and 
OS). 
Yiling Lu, MD / MD 
Anderson 
yilinglu@mdanderson 
.org 
3 
Whole 
exome 
sequencin 
g 
(WES) 
NGS 
CLIA: 
N 
Integrated 
To 
correlate 
SNV and 
CNV 
profiles 
with 
treatment 
outcomes 
(PFS, OS) 
Tissue 
(Archiv 
al# or 
Fresh) 
• 
Baseline 
(mandatory) 
• 
At disease 
progression 
(optional) 
M/O 
NCLN Genomics 
Laboratory 
Dr. P. Mickey 
Williams 
Mickey.williams@nih 
.gov 

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Prior 
ity 
Biomark 
er Name 
Assay 
(CLIA: 
Y/N) 
Use in the 
Trial and 
Purpose 
Specim 
ens 
Tested 
Collection Time 
Points 
Mandat 
ory or 
Optiona 
l 
Assay Laboratory 
and Lab PI 
Tissue-based Biomarkers 
4 
RNA 
sequencin 
g 
(RNAseq) 
RNA 
sequenc 
ing 
CLIA: 
N 
Explorator 
y 
To 
correlate 
gene 
expression 
profiles 
with 
treatment 
outcomes 
(PFS and 
OS) 
Tissue 
(Archiv 
al# or 
Fresh) 
• 
Baseline 
(mandatory) 
• 
C1D15 
(optional) 
• 
At disease 
progression 
(optional) 
M/O 
NCLN Genomics 
Laboratory 
Dr. P. Mickey 
Williams. 
Mickey.williams@nih 
.gov 
5 
IHC for 
Ki-67 
IHC 
CLIA: 
N 
Explorator 
y 
To 
correlate 
baseline 
Ki-67 IHC 
status and 
change in 
Ki-67 
after 
treatment 
with PFS 
and OS 
Tissue 
(Archiv 
al# or 
Fresh) 
• 
Baseline 
(mandatory) 
• 
C1D15 
(optional) 
• 
At disease 
progression(o 
ptional) 
M/O 
Clinical IHC 
laboratory 
Wei-Lien Wang, MD 
/ MD Anderson 
wlwang@mdanderson 
.org 
6 
IHC for 
cleaved 
caspase-3 
IHC 
CLIA: 
N 
Explorator 
y 
To 
correlate 
induction 
of cleaved 
caspase-3 
expression 
by IHC 
with PFS 
and OS 
Tissue 
(Archiv 
al# or 
Fresh) 
• 
Baseline 
(mandatory) 
• 
C1D15(option 
al) 
• 
At disease 
progression(o 
ptional) 
M/O 
Clinical IHC 
laboratory 
Wei-Lien Wang, MD 
/ MD Anderson 
wlwang@mdanderson 
.org 
Blood-based Biomarkers 
1 
Whole- 
exome 
sequencin 
g 
WES 
CLIA: 
N 
Integrated 
Blood 
• 
Baseline 
M 
NCLN Genomics 
Laboratory 
Dr. P. Mickey 
Williams 
Mickey.williams@nih 
.gov 

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Prior 
ity 
Biomark 
er Name 
Assay 
(CLIA: 
Y/N) 
Use in the 
Trial and 
Purpose 
Specim 
ens 
Tested 
Collection Time 
Points 
Mandat 
ory or 
Optiona 
l 
Assay Laboratory 
and Lab PI 
Tissue-based Biomarkers 
2 
ctDNA 
sequencin 
g 
Hybrid- 
capture 
based 
NGS or 
Guarda 
nt 360 
CLIA: 
N 
Explorator 
y 
To 
correlate 
baseline 
ctDNA 
mutation 
profiles 
and early 
changes in 
maximum 
variant 
allele 
frequencie 
s with 
treatment 
outcomes, 
and assess 
acquired 
resistance 
mechanis 
ms. 
Blood 
(Plasma 
) 
• 
Baseline 
• 
C2D1 
• 
C3D1 
• 
Every 
restaging 
• 
At disease 
progression 
(optional) 
O 
Karina Eterovic, PhD 
/ MD Anderson 
AKEterovic@mdande 
rson.org 
#Archival tissue must be collected within 6 months prior to registration and must consist of metastatic tumor, not an 
earlier diagnostic specimen. 

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5.7 Integral Laboratory Studies 
 
5.7.1 Her2Neu amplification 
 
5.7.1.1 Sites Performing Correlative Study 
 
A local CLIA-certified laboratory will analyze samples. 
 
5.7.2 PIK3CA mutations (Phase 2) 
 
5.7.2.1 Sites Performing Correlative Study 
 
A local CLIA-certified laboratory will analyze samples. 
 
5.7.3 PTEN mutations (Phase 2) 
 
5.7.3.1 Sites Performing Correlative Study 
 
A local CLIA-certified laboratory will analyze samples. 
 
5.8 Integrated Correlative Studies 
 
5.8.1 RPPA 
 
5.8.1.1 Specimens Receipt and Processing at the ETCTN Biorepository 
 
Upon receipt at the Biorepository, the snap-frozen tissue will be accessioned, barcoded and 
banked in a liquid nitrogen vapor phase freezer until distribution for testing. 
 
Snap frozen tissue will be shipped from ETCTN biorepository to the RPPA core lab at MD 
Anderson. 
 
Functional proteomics RPPA core facility 
MD Anderson Cancer Center 
6565 MD Anderson Blvd. 
Room Z4.2040 
Houston, TX 77030 
Phone: 713-792-5743 
Email: ccsgrppa@mdanderson.org 
 
 
 
5.8.1.2 Sites Performing Correlative Study 
RPPA will be performed on tissue specimens at RPPA Core laboratory at MD Anderson (Dr 
Yiling Lu). 

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The RPPA uses 302 unique antibodies to stain the slides, which are then analyzed on Array-Pro 
then by SuperCurve Rx64 3.1.1. QC tests are performed for each antibody staining (slide) and 
the QC Score (Probability) values are generated. A QC score above 0.8 indicates good antibody 
staining. Tumor or cell lysates will be serially diluted two-fold for 5 dilutions (from undiluted to 
1:16 dilution) and arrayed on nitrocellulose-coated slides in an 11x11 format. Saples will be 
probed with antibodies by tyramide-based signal amplification approach and visualized by DAB 
colorimetric reaction. Slides will be scanned on a flatbed scanner to produce 16-bit tiff image. 
Spots from tiff images will be identified and the density was quantified by Array-Pro Analyzer. 
Relative protein levels for each sample will be determined by interpolation of each dilution 
curves from the "standard curve" (supercurve) of the slide (antibody). Supercurve will be 
constructed by a script in R, written by Bioinformatics, and values generated will be defined as 
Supercurve Log2 (Raw) values. All the data points will be normalized for protein loading and 
transformed to linear value, designated as "Normalized Linear". Protein loading correction will 
be calculated among the sample set (CF 1) and for each sample in the entire RPPA set (CF 2). A 
CF of < 0.25 or >2.5 would indicated a much lower or higher protein concentration than other 
samples (outliers). "Normalized Linear" values will be transformed to Log2 values, and then 
median-centered for hierarchical clustering analysis. Median-centered values will be formatted 
for heatmap generation. Heatmaps will be generated using supervised and unsupervised 
hierarchal clustering in Cluster 3.0, using Pearson Correlation and a center metric. 
 
5.8.2 Whole-exome sequencing 
 
5.8.2.1 Specimen(s) Receipt and Processing at the ETCTN Biorepository 
 
Tumor tissue received in formalin will be paraffin-embedded. All FFPE blocks will be sectioned 
to generate an initial hematoxylin and eosin (H&E)-stained slide, and for nucleic acid extractions 
additional RNase-free slides. 
 
Whole blood collected in Streck tubes will be centrifuged to separate buffy coat and plasma and, 
after appropriate processing, will be stored in a -80°C freezer. 
DNA and RNA will be co-extracted from tumor tissue and also DNA will be extracted from 
residual cells from cfDNA Streck tubes.. The nucleic acids will be analyzed to determine 
concentration and quality. Aliquots of DNA will be shipped to the central sequencing 
laboratory for analysis. 
 
5.9 Exploratory/Ancillary Correlative Studies 
 
5.9.1 PTEN expression 
 
5.9.1.1 Specimens Receipt and Processing at the ETCTN Biorepository 
 
The Biorepository will ship one FFPE block or fresh cut slides to the Wang Laboratory for 
testing for PTEN IHC, Ki-67 IHC and Cleaved Caspase-3 IHC. Any blocks with tumor tissue 
remaining after testing will be returned to the ETCTN biorepository. 

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5.9.1.2 Sites Performing Correlative Study 
 
PTEN immunohistochemistry will be performed at clinical IHC lab at MD Anderson (Dr. Wei- 
Lien Wang). The IHC lab at MD Anderson has a robust quality control and quality improvement 
program. All elements of the program fully apply to the anti-PTEN IHC assay. A positive and 
negative control is added to every IHC run (batch control) and is reviewed by a member of the 
IHC medical directorship team. Records of batch control results are documented daily in internal 
laboratory records. PTEN loss is defined as complete loss of cytoplasmic and nuclear PTEN 
staining on immunohistochemistry as determined by the PTEN IHC assay performed at MD 
Anderson (Khoury et al., 2018). 
 
The final protocol is validated for use on 4 um FFPE tissue sections. In brief, following 
deparaffinization and rehydration of the tissues sections, antigen retrieval is performed at 100 °C 
for 20 minutes with Tris-EDTA buffer, pH 6.0. Endogenous peroxidase is blocked with 3% 
peroxide for 5 minutes. Primary PTEN antibody (Dako, clone 6H2.1) is applied at 1:100 dilution. 
Primary antibody detection is carried out using a commercial polymer system (Bond Polymer 
Refine Detection, Leica), and staining development is achieved by incubation with DAB and 
DAB Enhancer (Leica). 
 
5.9.2 PIK3CA mutations (Phase 1b) 
 
5.9.2.1 Sites Performing Correlative Study 
 
A local CLIA-certified laboratory will analyze samples. 
 
5.9.3 PTEN mutations (Phase 1b) 
 
5.9.3.1 Sites Performing Correlative Study 
 
A local CLIA-certified laboratory will analyze samples. 
 
5.9.4 RNA sequencing 
 
5.9.4.1 Specimen(s) Receipt and Processing at the ETCTN 
 
Tumor tissue received in formalin will be paraffin-embedded. All FFPE blocks will be sectioned 
to generate an initial hematoxylin and eosin (H&E)-stained slide, and for nucleic acid 
extractions, additional RNase-free slides. 
 
DNA and RNA will be co-extracted from tumor tissue. DNA will be extracted from the residual 
blood cells from the Streck cfDNA tube at baseline. The nucleic acids will be analyzed to 
determine concentration and quality. Aliquots of DNA and RNA will be shipped to the central 
sequencing laboratory for analysis. 
 
5.9.5 ctDNA sequencing 

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5.9.5.1 Specimen(s) Receipt and Processing at the ETCTN Biorepository 
 
Whole blood collected in Streck tubes will be centrifuged to separate buffy coat and plasma and 
will be stored in a -80°C freezer. 
 
5.9.6 IHC for Ki-67 
 
5.9.6.1 Specimen(s) Receipt and Processing at the ETCTN Biorepository 
 
Tumor tissue received in formalin will be paraffin embedded. The formalin fixed paraffin 
embedded (FFPE) blocks will be stored at room temperature until distribution for testing. 
 
The Biorepository will ship one FFPE block to the Wang Laboratory for testing for PTEN IHC, 
Ki-67 IHC and Cleaved Caspase-3 IHC. Any blocks with tumor tissue remaining after testing 
will be returned to the ETCTN biorepository 
 
5.9.7 IHC for cleaved caspase-3 
 
5.9.7.1 Specimen(s) Receipt and Processing at the ETCTN Biorepository 
 
Tumor tissue received in formalin will be paraffin embedded. The formalin fixed paraffin 
embedded (FFPE) blocks will be stored at room temperature until distribution for testing. 
 
The Biorepository will ship one FFPE block to the Wang Laboratory for testing for PTEN IHC, 
Ki-67 IHC and Cleaved Caspase-3 IHC. Any blocks with tumor tissue remaining after testing 
will be returned to the ETCTN biorepository 
 
 
6. TREATMENT PLAN 
 
6.1 Agent Administration 
 
Treatment will be administered on an outpatient basis. Reported adverse events and potential 
risks are described in Section 10. Dose de-escalation schema and appropriate dose modifications 
are described in Section 7. No investigational or commercial agents or therapies other than those 
described below may be administered with the intent to treat the patient's malignancy. 
 
Biosimilars/ interchangeable products of trastuzumab and pertuzumab as well as other 
subcutaneous forms of injections (e.g. phesgo (pertuzumab, trastuzumab, and hyaluronidase- 
zzxf) can be substituted for intravenous Herceptin and Perjeta where applicable following 
administration guidelines as laid out in FDA’s prescribing information. 
 
For Phase-2patients may receive up to 2 doses of 

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trastuzumab / pertuzumab between end of induction treatment and start of the trial, while 
eligibility is being confirmed. Based on the company-sponsored studies with copanlisib in 
patients with oncologic malignancies, the RP2D of copanlisib monotherapy is 60 mg 
administered by the 1-hour IV infusion for 3 weeks (Days 1, 8, and 15) every 4 weeks. A 
copanlisib dose reduction to 45 mg has been allowed for toxicities (Copanlisib Investigator’s 
Brochure, 2017). For ease of scheduling, copanlisib will be administered intravenously on days 
1 and 8 of 21-day cycle. To determine the recommended phase 2 dose of copanlisib in the triplet 
combination, a 3+3 dose de-escalation design will be employed in the phase Ib part of the study. 
The 3+3 dose de-escalation plan is described in further detail under Section 6.2. The starting 
dose of copanlisib for this combination trial is 60 mg. 
 
Trastuzumab will be administered intravenously as 8mg/kg loading, then 6 mg/kg every 3 weeks. 
Pertuzumab is given intravenously as 840 mg IV loading, then 420 mg every 3 weeks. Loading 
doses will not be required if patients have received Trastuzumab and Pertuzumab within 6 weeks 
of starting the study. 
 
Regimen description is tabulated in the table below: 
 
Dose de-escalation schema for the triplet combination of copanlisib, trastuzumab, and pertuzumab 
Dose Level 
Copanlisib 
Trastuzumab 
Pertuzumab 
1# 
60 mg IV on days 1 
and 8 of 21-day cycle 
8 mg/kg IV loading*, 
then 6 mg/kg every 3 
weeks.** 
840 mg IV loading*, 
then 420 mg every 3 
weeks 
-1 
45 mg IV on days 1 
and 8 of 21-day cycle 
#Starting dose 
*Loading doses will not be required if patients have received trastuzumab and pertuzumab within 6 weeks of 
starting the study. 
** Dose rounding as per institutional guidelines is allowed. Biosimilars/ interchangeable products of 
trastuzumab and pertuzumab as well as other subcutaneous forms of injections can be used as per FDA 
prescribing information guidelines 
 
Regimen Description# 
Agent 
Premedications; 
Precautions 
Dose 
Route 
Schedule Cycle 
Length 
No IV glucose 
As 
Copanlisib 
preparations 
should be 
administered on 
the days of 
appropriate 
for assigned 
dose level in 
50-200 mL 
IV over 60 minutes (+/- 
10 minutes) 
D1 and 8 
of every 
cycle 
21 days 
(3 
infusion* 
NSS 
weeks) 
Trastuzumab 
8 mg/kg 
loading**, 
then 6 mg/kg 
every 3 weeks 
IV (initial loading dose 
should be administered 
as a 90 minute IV 
infusion (+/- 10 
D1 of 
every 
cycle 

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minutes). Subsequent 
doses should be 
administered by IV 
infusion over 30 to 90 
minutes.) 
Pertuzumab 
840 mg/kg 
loading*, then 
420 mg/kg 
every 3 weeks 
IV (initial loading dose 
should be administered 
as a 60 minute IV 
infusion (+/- 10 
minutes). Subsequent 
doses should be 
administered by IV 
infusion over 30 to 60 
minutes.) 
D1 of 
every 
cycle 
#Patients with ER+ disease may continue their endocrine therapy 
*Copanlisib is to be administered after trastuzumab and pertuzumab 
**Loading doses will not be required if patients have received trastuzumab and pertuzumab within 6 weeks of 
starting the study. 
 
A regimen description table for the phase 2 portion will be added once the RP2D is determined. 
Once RP2D is reached, a protocol amendment will be submitted for CTEP’s review and approval 
prior to starting phase 2. 
 
6.1.1. Copanlisib 
 
The use of corticosteroids as antiemetics prior to copanlisib administration is not allowed. 
Administer copanlisib as an IV infusion over one hour. After administration, flush the line with 
0.9 % sodium chloride to ensure complete dose is given. No IV glucose preparations should be 
administered on the days of infusion. 
 
Blood pressure monitoring on copanlisib infusion days 
 
BP will be measured every 5-10 min prior to each copanlisib dose (no more than 4 
measurements) until there are two consecutive results <150/90 mmHg. If blood pressure is ≥ 
150/90 mmHg, the investigator can consider a medical intervention or delaying the infusion of 
study drug. The patient should rest for 5-10 min before blood pressure is recorded. 
On infusion days, blood pressure will be measured at 0 hour (pre-dose), 30 min (mid-infusion), 
60 min (end of infusion). If BP is elevated at 60 min, it will be rechecked at 1 hour after the end 
of infusion; if still elevated, BP should be checked at 2 hour after the end of infusion after 
appropriate measures have been taken to decrease blood pressure. 
NOTE: A window of ±10 min is allowed for all BP measurements, except for pre-dose (0 hour) 
measurement. 
 
Recommendations on meal timing on copanlisib infusion days 

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Because of an inhibitory effect on PI3Kα-isoform, which is implicated in insulin metabolism, 
copanlisib infusions could be associated with temporarily increase in blood glucose. Consuming 
meal in close proximity to copanlisib infusion may exacerbate a glucose level increase. It is 
recommended that timing and content of caloric intake on infusion days is monitored by the 
investigators. Consultation with diabetologist or endocrinologist is advised. 
 
The investigator may manage the timing of post-infusion meals based on the glucose profile 
during prior infusion days to minimize glucose increases. This is in addition to glucose lowering 
medication, if indicated. On infusion days a low carbohydrate diet is recommended, the timing 
and content of meal intake and additional glucose testing (if clinically indicated) is managed and 
monitored by the investigators based on glucose response patterns during prior treatment days. 
However, caloric restriction is not intended for the population under study. 
 
NOTE: The glucose test should be taken prior to meal intake. 
 
NOTE: Caloric intake and timing recommendations for diabetic patients who require insulin 
treatment prior to the infusion at any cycle visit should be managed by the investigator based on 
consultation with treating physician or diabetes/endocrinologist physician. 
 
Pre-dose glucose levels 
 
Period 
Pre-dose glucose levels 
(first glucose measurement) 
Day 1 of 
cycle 1 
<160 mg/dL (fasting*) 
 
Subsequent 
infusions after 
Cycle 1 Day 1 
<160 mg/dL (fasting*) 
< 200 mg/dL (non-fasting**) 
*Fasting refers to a ≥ 8 h fast. 
**Non-fasting status includes any caloric intake such as meals and also 
juice, snacks, and other caloric intake not consistently called a meal. 
 
. 
 
On Day 1 of cycle 1, patients should be fasting for at least 8 h prior to the pre-dose glucose 
measurement. Additional measurements can be performed at the clinic as clinically indicated. 
 
NOTE: When fasting is not feasible due to age or medical condition, and for patients who have 
their infusions scheduled at a later hour: a small, light low glycemic index meal may be taken at 
least 4 hours before the start of the copanlisib infusion. If patient needs to take a meal, then 
glucose test should be taken prior to meal intake. 
On subsequent visits after Cycle 1 Day1 visit, fasting is not required prior to pre-dose glucose 

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measurement. Additional measurements to be performed at the clinic as clinically indicated. 
Note: If patient needs to take a meal, then glucose test should be taken prior to meal intake. 
From Cycle 1 Day 8 onwards, glucose measurements at the site may be done either by laboratory 
analysis or in capillary blood (finger stick). 
 
Additional measurements are to be performed at the clinic as clinically indicated at the 
investigator’s discretion. Review blood glucose measurements/meal timing/insulin 
administration/oral glucose lowering medication, if applicable. 
 
All glucose measurements done at the site, oral glucose lowering medication and/or insulin 
administration, if applicable, fasting/non-fasting status and meal intake timing on infusion days 
will be collected as part of the clinical source documentation. 
 
6.1.2 Trastuzumab 
 
For IV infusion only. Do not administer as an IV push or bolus. Do not substitute Herceptin 
(trastuzumab) for or with ado-trastuzumab emtansine. Do not use dextrose (5%) solution. The 
initial loading dose should be administered as a 90-minute IV infusion. Subsequent doses should 
be administered by IV infusion over 30 to 90 minutes. Monitoring should be conducted per 
institutional guidelines. 
 
For missed doses: A dose delay >1 week would require ~6 weeks to return to steady state range; 
if a maintenance dose is missed by >1 week, a reloading dose is required. If a dose is missed by 1 
week or less, the usual maintenance dose (6 mg/kg every 3 week schedule) should be 
administered as soon as possible (do not wait until the next planned cycle) and subsequent 
maintenance doses should be administered 21 days later; if a dose is missed by more than 1 
week, then a re-loading dose (8 mg/kg) should be administered (over 90 minutes) as soon as 
possible, followed by the usual maintenance dose administered 21 days later. 
 
6.1.3 Pertuzumab 
 
Administer as an IV infusion only. Do not administer as an IV push or bolus. Do not mix 
pertuzumab with other drugs. Do not use dextrose (5%) solution. The initial dose should be 
administered as a 60-minute IV infusion. Subsequent doses should be administered as a 30 to 
60-minute IV infusion. Monitoring should be conducted per institutional guidelines. 
 
For missed doses: If <6 weeks has elapsed from the last dose of pertuzumab, administer the 420 
mg maintenance dose; do not wait until the next planned dose. If ≥6 weeks has elapsed, 
readminister the 840 mg initial dose (over 60 minutes), and then three weeks later, follow with a 
maintenance dose of 420 mg (over 30 to 60 minutes), and continue maintenance dose every 3 
weeks. 

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6.2 Definition of Dose-Limiting Toxicity 
 
Patients will be considered “DLT-evaluable” if they receive at least one dose of study therapy 
(antibodies and copanlisib). Patients who (a) fail to receive the second dose of copanlisib for 
reasons unrelated to toxicities or treatment side effects and (b) who have not experienced a DLT, 
will be included in the dose escalation decisions for the phase1b portion. (NOTE – They need to 
have been followed for the full requisite DLT period) 
Severity of adverse events (AEs) will be graded according to CTCAE v5.0. Any of the 
following AEs occurring during the DLT observation period (Cycle 1; a cycle will be 21 days in 
duration), which are attributable to at least one of the investigational products will be classified 
as DLTs: 
 
Hematological: 
• Grade 4 neutropenia (ANC <0.5 × 109/L) lasting >7 days 
• Febrile neutropenia, defined as ANC <1000/mm3 with a single temperature of >38.3°C 
(>101°F) or a sustained temperature of ≥38°C (100.4°F) for more than 1 hour 
• Neutropenic infection (ANC <1,000/mm3 or <1.0 × 109/L, and Grade >3 infection) 
• Grade 3 thrombocytopenia (platelet count <50 × 109/L) with bleeding 
• Grade 4 thrombocytopenia (platelet count <25 × 109/L) 
• Grade 4 anemia (life-threatening consequences; urgent intervention indicated) 
 
Non-hematological: 
• Non-hematological toxicities: 
o Grade ≥3 toxicities 
o Confirmation of QTc prolongation (>500 msec) or QTc increase >60 msec from 
baseline 
o ≥ Grade 3 hyperglycemia based on fasting blood glucose levels for more than 1 
week, despite optimal intervention which is not attributable to another co- 
morbidity 
o Grade 4 hyperglycemia 
o Grade 3 skin rash despite optimal medical intervention 
o Grade 3 diarrhea despite maximal medical intervention 
• Any other toxicity that is greater than that at baseline, is clinically significant and/or 
unacceptable, does not respond to supportive care and results in a disruption of dosing 
schedule of more than 14 days 
• Any event, including significant dose reductions or omissions, judged to be a DLT by the 
Safety Review Committee 
• Any other toxicity in any course of treatment that in the opinion of the investigators and 
medical monitors is dose-limiting 
 
The following toxicities will not be considered DLTs: 
• Isolated laboratory changes of any grade without clinical sequelae or clinical 
significance. 

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Dose de-escalation will proceed within each cohort according to the following scheme. Dose- 
limiting toxicity (DLT) is defined above. 
 
Number of Patients with DLT at a 
Given Dose Level 
De-escalation Decision Rule 
≤1 out of 3 
Enter another 3 patients at this dose level. 
≥2 out of 3, or >2 out of 6 
This dose level will be declared the maximally 
administered dose (highest dose administered). Three 
(3) additional patients will be entered at dose level -1. 
≤1 out of 6 at dose level 1 (or -1 if 
dose reduction was needed). 
This is generally the recommended phase 2 dose. At 
least 6 patients must be entered at the recommended 
phase 2 dose. 
 
6.3 Dose Expansion Cohorts: 
 
Once RP2D is reached, a protocol amendment will be submitted for CTEP’s review and approval 
prior to starting phase 2.  Phase II/ dose expansion phase will enroll an additional 96 patients 
with HER2+ metastatic breast cancer patients with (PIK3CA or PTEN mutation), after 
completion of induction chemotherapy with 4-8 cycles of any taxane, trastuzumab and 
pertuzumab. Patients may receive upto 2 doses of trastuzumab / pertuzumab between end of 
induction treatment and start of the trial, while eligibility is being confirmed. Patients enrolled in 
phase II trial will undergo 1:1 randomization to receive maintenance with either dual anti-HER2 
targeted therapy (trastuzumab + pertuzumab) or the triplet combination (copanlisib + 
trastuzumab + pertuzumab).  
 
 
6.4 General Concomitant Medication and Supportive Care Guidelines 
 
Because there is a potential for interaction of copanlisib with other concomitantly administered 
drugs, the case report form must capture the concurrent use of all other drugs, over-the-counter 
medications, or alternative therapies. The Principal Investigator should be alerted if the patient is 

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taking any agent known to affect or with the potential for drug interactions. The known potential 
targets for drug interaction are CYP3A4 inducers or inhibitors, as well as drugs modulating 
glucuronidation, P-gp, BCRP, and MATE2K function. Concomitant use of medications listed in 
APPENDIX C is prohibited while on copanlisib. APPENDIX D (Patient Clinical Trial Wallet 
Card) should be provided to patients if available. 
 
6.4.1 Substrates of P-gp and/or BCRP with narrow therapeutic index should be used with caution and 
patients monitored for any sign of toxicity. Furthermore, sensitive substrates of the renal drug transporter 
MATE2K (e.g. metformin) need to be used with caution. Metformin should be interrupted for 48 hours after 
receiving iodinated contrast media. Please see prescribing information for further information. 
 
6.4.2 Patients taking medications with narrow therapeutic index should be proactively monitored if these 
medications cannot be avoided. These medications may include quinidine, cyclosporine, and digoxin. 
 
6.4.3 Prophylactic antiemetics may be administered according to standard practice. The routine use of 
standard antiemetics, including 5-HT3 blockers, such as granisetron, ondansetron, or an equivalent agent, is 
allowed as needed. 
 
6.4.4 Systemic corticosteroid therapy at a daily dose higher than 15 mg prednisone or equivalent is not 
permitted while on study. Patients may be using topical or inhaled corticosteroids. Short-term (up to 7 days) 
systemic corticosteroids above 15 mg prednisolone or equivalent will be allowed for the management of 
acute conditions (e.g., treatment non-infectious pneumonitis). The use of corticosteroids as antiemetics prior 
to copanlisib administration will not be allowed. 
 
6.4.5 Patients should stop using herbal medications at least 7 days prior to the first dose of copanlisib. Herbal 
medications include, but are not limited to: St. John’s Wort, Kava, ephedra, gingko biloba, 
dehydroepiandrosterone (DHEA), yohimbe, saw palmetto, black cohosh and ginseng. Ingredients for such 
medicines have not been fully studied, and their use may result in unanticipated drug-drug interactions that 
may cause or confound assessment of toxicity. 
 
6.4.6 Concomitant therapy with agents that are strong inhibitors or inducers of cytochrome P450 3A4 
(CYP3A4) is prohibited, as copanlisib is primarily metabolized by CYP3A4 (Appendix C). 
 
 
6.5 Duration of Therapy 
 
Patients may continue treatment on the clinical trial as long as they are getting clinical benefit 
and have no evidence of disease progression. Treatment should be discontinued for one of the 
following conditions: 
 
• 
Disease progression 

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• 
Intercurrent illness that prevents further administration of treatment 
 
• 
Unacceptable adverse event(s) 
 
• 
Patient decides to withdraw from the study 
 
• 
General or specific changes in the patient's condition render the patient unacceptable 
for further treatment in the judgment of the investigator 
 
• 
Clinical progression 
 
• 
Patient non-compliance 
 
• 
Pregnancy 
 
o All women of childbearing potential should be instructed to contact the 
investigator immediately if they suspect they might be pregnant (e.g., missed 
or late menstrual period) at any time during study participation. 
 
o The investigator must immediately notify CTEP in the event of a confirmed 
pregnancy in a patient participating in the study. 
 
• 
Termination of the study by sponsor 
 
• 
The drug manufacturer can no longer provide the study agent 
 
The reason(s) for protocol therapy discontinuation, the reason(s) for study removal, and the 
corresponding dates must be documented in the Case Report Form (CRF). 
 
6.6 Duration of Follow-Up 
 
Patients will undergo final end of study evaluation by the treating physician within 30 ± 7 days 
after administration of the last dose. Patients who discontinue the study prematurely for any 
reason will also be instructed to return to the clinic within 30 days of last dose and all procedures 
to be performed at the final end of study visit should be performed at this time. Patients who 
discontinue the study prematurely due to an adverse event will be followed by the investigator 
until the patient is medically stable or the adverse event is resolved. After the End-of-Study 
visit, patients will have 3 months post-accrual follow-up via telephone. 
 
 
7. DOSING DELAYS/DOSE MODIFICATIONS 
 
Dose modification tables apply to signs and symptoms that arise or worsen after starting the 
clinical trial and are attributed to the trial per the clinical judgement of the investigator. 

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7.1 Dose de-escalation schema for the triplet combination of copanlisib, trastuzumab, and pertuzumab 
 
Dose Level 
Copanlisib* 
Trastuzumab 
Pertuzumab 
1# 
60 mg IV on days 1 
and 8 of 21-day cycle 
8 mg /kg IV leading, 
then 6 mg/kg every 3 
weeks. 
840 mg IV loading, 
then 420 mg every 3 
weeks 
-1 
45 mg IV on days 1 
and 8 of 21-day cycle 
*Only one dose level reduction is allowed for copanlisib. Copanlisib is to be administered after trastuzumab and 
pertuzumab, Biosimilars/ interchangeable products of trastuzumab and pertuzumab as well as other subcutaneous 
forms of injections can be used as per FDA prescribing information guidelines  
#Starting dose 
 
7.2 Management of copanlisib related toxicities 
 
7.2.1 Hyperglycemia 
 
7.2.1.1 Dose Modification Guidelines for Hyperglycemia 
Guidelines for the management of transient glucose increases are given in the tables below 
 
 
• Continuing/ persistent occurrence of post-infusion blood glucose >500 mg/dL, based on 
repeated laboratory analysis despite optimal glucose lowering therapy after 2 infusions of 
copanlisib (at least 1 treatment cycle), will require dose reduction by one dose level. 
• Dose re-escalation may be allowed when a patient has achieved controlled glucose levels  
after discussion with study PI. 
• Persistent occurrence of post-infusion blood glucose >500 mg/dL based on laboratory 
analysis which occurred at the lowest dose level despite optimal glucose lowering therapy 
(after at least one cycle of treatment) with consultation of a diabetes specialist requires 
permanent discontinuation of the study drug. 
• The need for additional glucose monitoring at home should be determined by the 
investigator based on post-infusion glucose profile and clinical status of the patient. 
• Patient with non-fasting plasma glucose values can be treated at investigator discretion. 

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Management of Hyperglycemia (based on fasting glucose) 
 
Fasting Plasma 
Glucose Value 
Intervention 
Dose Adjustment 
> ULN-160 mg/dL 
or > ULN-8.9 
mmol/L 
Initiation of an oral anti-hyperglycemic 
agent (eg., metformin) and additional 
glucose monitoring should be considered 
No change 
> 160-250 mg/dL 
or > 8.9-13.9 
mmol/L 
 
Initiation or increased dose of an oral anti-
hyperglycemic agent (eg: metformin) and 
additional close glucose monitoring should 
be considered.  
Dosing with copanlisib may either be held or 
continued per investigator evaluation 
asymptomatic, 
> 250-500 mg/dL 
or > 13.9-27.8 
mmol/L 
Patient should be managed as per standard 
of care, including implementation of 
additional glucose monitoring and initiation 
and/or increase of anti-hyperglycemic 
therapy (eg., metformin) 
Consideration should be given to suspend 
copanlisib dosing until the hyperglycemia 
improves to </= 250 mg/dL or </= 13.9 mmol/L. 
Dosing with copanlisib may resume at the same 
dose level or at one dose level lower than the 
current and after discussion with study PI 
symptomatic, 
> 250-500 mg/dL 
or > 13.9-27.8 
mmol/L 
Patient should be managed as per standard 
of care, including implementation of 
additional glucose monitoring and initiation 
and/or increase of anti-hyperglycemic 
therapy (eg., metformin) 
Copanlisib dosing should be suspended until the 
hyperglycemia improves to </= 250 mg/dL or 
</=13.9 mmol/L. The patient will be 
discontinued from the study if such therapy fails 
to control their hyperglycemia. Dosing with 
copanlisib may otherwise resume at one dose 
level lower than current dose level. 
> 500 mg/dL 
or >27.8 mmol/L 
Patient should be managed as per standard 
of care, including intensification of 
appropriate anti-diabetic treatment, 
intravenous hydration and intervention for 
electrolyte/ketoacidosis/hyperosmolar 
disturbances. 
Suspend copanlisib.  Re-check FPG within 24 
hours and as clinically indicated.  If FPG 
decreases to ≤ 500 mg/dL or 27.8 mmol/L, follow 
FPG value specific recommendations for 
symptomatic glucose value > 250-500 mg/dL 
or > 13.9-27.8 mmol/L .  If FPG is confirmed at 
> 500 mg/dL or > 27.8 mmol/L, permanently 
discontinue copanlisib treatment. 

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1FPG/Blood Glucose/Grade levels reflect hyperglycemia grading according to CTCAE 
Version 4.03 (CTCAE=Common Terminology Criteria for Adverse Events) 
. 
 
7.2.1.2 Monitoring of diabetic patients 
 
If the patient already monitors his/her blood glucose as part of routine anti-diabetic care, the 
routine measurements should not be replaced by the study specific measurements. 
 
7.2.2 Treatment of Blood Pressure Increases Associated with Copanlisib 
 
It is important that patients with pre-existing arterial hypertension adhere to their regular 
medication schedule and take their usual doses on the days of study drug infusion. 
The management of acute blood pressure (BP) increases following copanlisib will need to be 
individualized for each patient, but experience from a Bayer-sponsored phase 1 study with 
copanlisib has suggested the benefit of dihydropyridine calcium channel blockers (i.e., 
amlodipine, felodipine). Topical nitrates should also be considered. Verapamil and diltiazem 
(non-dihydropyridine calcium channel blockers and moderate inhibitors of CYP3A4) should be 
used with caution due to a potential CYP3A4 interaction. In general, it is advisable for sites to 
be prepared, so that anti-hypertensive medication is readily available in case of need. 
In the event of the occurrence of arterial hypertension ≥150/90 mmHg during infusion of 
copanlisib at any cycle, antihypertensive treatment is suggested as indicated in the Dose 
Modification of Copanlisib for Arterial Hypertension Table below. In the event of the 
occurrence of grade 3 arterial hypertension (≥160/100 mmHg) during infusion of copanlisib, the 
infusion should be interrupted, and anti-hypertensive treatment as suggested above is 
administered. Infusion can be resumed when BP has returned to <150/90 mmHg. 
 
Dose Modification of Copanlisib for Arterial Hypertension Table below 
 
Toxicity (CTCAE 
5.0) 
Study drug action 
Recommendation 
Pre-dose 
measurements 
BP ≥150/90 mmHg 
No dose should be 
given until recovery 
to <150/90 mmHg 
• Consider BP lowering medication. Dosing 
can proceed on the scheduled day if after at 
least 2 consecutive measurements BP 
returns to <150/90 mmHg. 
• If BP doesn’t return to <150/90 mmHg, 
delay dosing until next visit. 
During infusion: 
CTCAE 
hypertension of 
grade 3 
or ≥160/100 mmHg 
Infusion can be 
interrupted or 
slowed down and 
administration of BP 
lowering therapy 
should be initiated. 
• Infusion may be resumed when BP has 
returned to <150/90 mmHg at the 
investigator’s discretion or skipped. 
• Subsequent study drug administrations 
may be reduced by 1 dose level at the 
investigator’s discretion.a 

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Post-dose: 
– 
• Administration of BP lowering therapy 
should be initiated according to local 
standard of care. Additional measurements 
to be performed as clinically indicated 
until recovery to <150/90 mmHg. 
• Subsequent study drug administrations 
may be reduced by 1 dose level at the 
investigator’s discretion.a 
Drug-related 
CTCAE 
hypertension of 
grade 3 
or ≥160/100 mmHg 
a 
CTCAE 
hypertension of 
grade 4 
Permanent 
discontinuation 
– 
a: Not manageable despite optimal antihypertensive treatment. 
CTCAE = Common Terminology Criteria for Adverse Events; BP = blood pressure, 
 
7.2.3 Non-Infectious Pneumonitis 
 
The investigator is requested to differentiate between non-infectious pneumonitis, and infectious 
pneumonitis (viral, bacterial, or fungal), aspiration pneumonitis, or other pneumonitis clearly not 
due to a potential hypersensitivity reaction to the copanlisib infusion; and provide the basis for 
his/her assessment that it is infectious or other, as appropriate. The investigator is requested to 
report with the most specific clinical terms to describe the condition, not simple “pneumonitis”. 
In the event of suspected non-infectious pneumonitis, modify copanlisib treatment as per table 
below. 
 
Dose adjustment for non-infectious pneumonitis 
Suspected or confirmed NIP per 
CTCAE 
Action Taken 
Re-treatment dose after recovery 
Grade 1 
No Change 
NA 
Grade 2 
Dose Interruption Until recovery to 
≤grade 1 
Decrease dose to the next lowest 
dose level a 
Grade 2 second re-occurrence 
Permanent Discontinuation 
NA 
Grade 3 
Permanent Discontinuation 
NA 
Grade 4 
Permanent Discontinuation 
NA 
NA = Not applicable; NIP = Non-infectious pneumonitis; CTCAE = Common Terminology Criteria for Adverse Events. 
a: Not applicable for 45 mg dose level. No re-escalation is allowed after the dose reduction. 
The lowest dose level is 45 mg; if a patient is already on the 45 mg dose level and cannot tolerate treatment study treatment will 
be discontinued permanently. 
 
7.2.4 Monitoring guidelines for opportunistic infections 
 
The investigator is requested to keep a high suspicion for opportunistic infections (e.g. 
Pneumocystis jirovecii, Cryptococcosis, Bronchopulmonary Aspergillosis, Cytomegalovirus and 
Herpes virus) and initiate the appropriate diagnostic workup and management quickly as 
medically indicated. Copanlisib should be withheld for Grade 3 and higher infections until 
resolution. 

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Before initiating treatment with Copanlisib, PJP prophylaxis should be considered for 
populations at risk. Copanlisib should be withheld in patients with suspected PJP infection of any 
grade. If confirmed, infection should be treated until resolution, then Copanlisib may be resumed 
at previous dose with concomitant PJP prophylaxis. 
 
Opportunistic Infections 
Management/Next Dose for Copanlisib 
≤ Grade 1 
For infections other than PJP*, Copanlisib may be continued 
along with appropriate treatment for infection. 
Grade 2 
For infections other than PJP*, Copanlisib may be continued 
along with appropriate treatment for infection. 
Grade 3 
Hold until infection resolves, then resume at same dose level. 
Consider prophylaxis for opportunistic infection. 
Grade 4 
Hold until infection resolves, then resume at same dose level. 
Consider prophylaxis for opportunistic infection. 
*PJP = Pneumocystis jiroveci pneumonia. Copanlisib should be withheld in patients with 
suspected PJP infection of any grade. If confirmed, infection should be treated until resolution, 
then Copanlisib may be resumed at previous dose with concomitant PJP prophylaxis. Before 
initiating treatment with Copanlisib, PJP prophylaxis should be considered for populations at 
risk. 
 
 
7.3 Management of overlapping toxicities 
 
Adverse event 
Severity 
Management/ Dose Modification 
Diarrhea 
Grade 2 
Hold until ≤ Grade 1 
Grade 3 
Hold until ≤ Grade 1. Resume at one dose level 
lower, if indicated 
Grade 4 
Permanently discontinue 
Nausea 
Grade 2 
Hold until ≤ Grade 1. Intensify anti-emetic regimen 
Grade 3 
Hold until ≤ Grade 1. Intensify anti-emetic regimen. 
Resume at one dose level lower. Patients requiring a 
delay of >2 weeks despite symptomatic treatment 
should go off protocol therapy. 
Grade 4 
Permanently discontinue 
Neutropenia 
Grade 2 
Maintain dose and monitor ANC weekly 
Grade 3 
Maintain dose and monitor ANC weekly 
Grade 4 
Hold dose and monitor ANC weekly till 
≥500 cells/mm3, then resume at same dose. For second 
recurrence of grade 4, reduce dose by one level. 
Discontinue if recovery does not occur in 21 days. 
Thrombocytopenia 
Grade 2 
No change in dose. Monitor weekly 
Grade 3 
No change in dose. Monitor weekly 
Grade 4 
Hold dose. Resume when 
≤ Grade 1 at one dose level lower if recovery within 
21 days. Discontinue if recovery does not occur in 21 

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days. 
Pulmonary toxicity 
Grade 2 
Hold until ≤ Grade 1. Resume at lower dose level. 
Grade 2 second re-occurrence: Off protocol treatment. 
Grade ≥3 
Off protocol treatment 
All other events* 
Grade 2 
No change 
Grade 3 
Hold until ≤ Grade 1, then resume at one dose level 
lower 
Grade 4 
Off protocol treatment 
*Recommended management: As clinically indicated 
 
 
7.4 Management of anti-HER2 therapy related toxicities 
 
Adverse event 
Severity 
Management/ Dose 
Modification 
Infusion Reaction 
Grade 3 
Decrease the rate of infusion 
Grade 3 
Hold and monitor patient till 
symptoms resolve 
completely. Resume the 
infusion at a lower rate* after 
pre-medication* with close 
monitoring. Discontinue 
completely for second 
recurrence. 
Grade 4 
Off protocol therapy 
Cardiomyopathy 
LVEF ≤40% or 40-45% with 
an absolute decrease of ≥10% 
from pre-treatment values. 
Hold for at least 3 weeks.** 
Resume at same dose if 
LVEF recovers to >45%, or 
40-45% with a fall of <10% 
from pre-treatment values. 
Persistent decrease in LVEF 
(>8 weeks) 
Permanently discontinue, off 
protocol 
Dose interruption on > 3 
occasions 
Permanently discontinue, off 
protocol 
*Rate of infusion and pre-medication for management of infusion-related reactions are per institutional 
policy. 
**Please Section 6.1.2 and 6.1.3 for guidelines on delayed doses and need for re-load dose. 
Note: Patients who have to discontinue trastuzumab and pertuzumab due to cardiotoxicity or any 
other toxicity will be taken off protocol 
 
8. PHARMACEUTICAL INFORMATION 
 
A list of the adverse events and potential risks associated with the investigational or commercial 
agents administered in this study can be found in Section 10.1. 

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8.1 CTEP IND Agent(s) 
 
8.1.1 Copanlisib (NSC 784727) 
 
Chemical Name or Amino Acid Sequence: 2-amino-N-[7-methoxy-8-(3-morpholin-4- 
ylpropoxy)-2,3-dihydroimidazo[1,2-c]quinazolin-5-yl]pyrimidine-5-carboxamide 
dihydrochloride 
 
Other Names: BAY 80-6946 (free base); BAY 84-1236 (dihydrochloride salt) 
 
Classification: Pan class I PI3K inhibitor 
 
Molecular Formula: C23H28N8O4 2HCl 
M.W.: 553.45 g/mol 
 
Approximate Solubility: Freely soluble in water and 0.1 M hydrochloric acid (HCl) 
 
Mode of Action: Copanlisib is a pan class I PI3K inhibitor with potent activity against the delta and 
alpha isoforms. Class I PI3K is downstream of most cancer associated tyrosine kinase growth 
factor receptors or mesenchymal epithelial transition factor. PI3K delta has a critical role in 
regulating downstream events of the B-cell receptor. 
 
Description: The powder is white to yellow solid substance. 
 
How Supplied: Copanlisib is supplied by Bayer HealthCare AG and distributed by the 
Pharmaceutical Management Branch (PMB), CTEP, Division of Cancer Treatment and Diagnosis 
(DCTD), NCI. The agent is available as a lyophilized product containing 60 mg of copanlisib in a 6 
mL injection vial. The excipients are mannitol, sodium hydroxide, citric acid, and water for 
injection. 
 
Preparation: Using appropriate aseptic technique, reconstitute the 60 mg vial of copanlisib with 
4.4 mL of 0.9% sodium chloride resulting in a concentration of 15 mg/ml. Gently shake for 30 
seconds and allow the vial to stand for 1 minute to let bubbles rise to the surface. Repeat if 
undissolved substance is still present. The reconstituted solution may be slightly yellow and should 
be clear prior to being withdrawn from the vial. Withdraw the appropriate volume of the 
reconstituted solution and further dilute by adding to a 50-200 mL 0.9% sterile sodium chloride bag. 
Mix well by inverting. 
 
Storage: Store intact vials between 2°C and 8°C. 
 
If a storage temperature excursion is identified, promptly return copanlisib to between 2°C and 
8°C and quarantine the supplies. Provide a detailed report of the excursion (including 
documentation of temperature monitoring and duration of the excursion) to 
PMBAfterHours@mail.nih.gov for determination of suitability. 
 
Stability: Stability studies of the vials are ongoing. The diluted solution should be used 
immediately (stored up to 4 hours at room temperature including preparation and administration). If 

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the diluted solution for infusion is not used immediately, it is stable for up to 24 hours refrigerated 
between 2°C and 8°C. It takes approximately 60 minutes for the diluted solution to return to room 
temperature after refrigeration. The infusion should be completed within 24 hours of preparation. 
 
Route of Administration: IV infusion 
 
Method of Administration: The diluted solution for infusion is administered IV over 1 hour. 
After administration, flush the line to ensure complete dose is given. No IV glucose preparations 
should be administered on the days of infusion. 
 
Potential Drug Interactions: In vitro, copanlisib is metabolized primarily via CYP3A4 and to a 
minor extent by CYP1A1. It is also a substrate of P-gp and BCRP, but not a substrate of MATEs, 
OCTs, OATs, or organic anion transporting polypeptides (OATPs). Concomitant administration 
with strong inhibitors or inducers of CYP3A4 should be avoided. Use caution when administered 
with strong inhibitors and inducers of CYP1A1, P-gp, and BCRP. 
 
In vitro, copanlisib is a strong inhibitor of MATE2K. Copanlisib and its metabolite M-1 have alow 
risk for inhibition or induction of CYP isoforms, inhibition of UGT isoforms, and inhibition of 
dihydropyrimidine dehydrogenase. Copanlisib does not inhibit P-gp, BCRP, OATP1B1, 
OATP1B3, OAT1, OAT3, OCT1, OCT2, bile salt export pump (BSEP), multidrug resistant protein 
2 (MRP-2), or MATE1 at therapeutic 60 mg dose plasma concentrations. Use caution when 
administered with sensitive drug substrates of MATE2K. 
 
Copanlisib is not an inducer of CYP1A2, 2B6, and 3A. 
 
Special Handling: Copanlisib is not genotoxic in vitro or in vivo. Copanlisib is expected to 
adversely affect male and female reproduction. 
 
Patient Care Implications: Females of child-bearing potential and male patients must use 
adequate contraception while receiving copanlisib and for 1 month after last dose of copanlisib. Do 
not breastfeed during treatment with copanlisib and for at least 1 month after the last dose of 
copanlisib. 
 
Hypertension is frequently observed within the first 3 hours after start of infusion and 
hyperglycemia is frequently observed persisting for approximately 1-3 days after study drug 
administration. Refer to protocol document for treatment and monitoring guidelines. 
 
Availability 
 
Copanlisib is an investigational agent supplied to investigators by the DCTD, NCI. 
Copanlisib is provided to the NCI under a Collaborative Agreement between the 
CAUTION: The single-use lyophilized dosage form contains no antibacterial 
preservatives. Therefore, it is advised that the reconstituted product be 
discarded 4 hours after initial entry. 

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Pharmaceutical Collaborator and the DCTD, NCI (see Section 13.4). 
 
8.1.2 Agent Ordering and Agent Accountability 
 
8.1.2.1 NCI-supplied agents may be requested by eligible participating Investigators (or their authorized 
designee) at each participating institution. The CTEP-assigned protocol number must be used for ordering all 
CTEP-supplied investigational agents. The eligible participating investigators at each participating institution 
must be registered with CTEP, DCTD through an annual submission of FDA Form 1572 (Statement of 
Investigator), NCI Biosketch, Agent Shipment Form, and Financial Disclosure Form (FDF). If there are 
several participating investigators at one institution, CTEP- supplied investigational agents for the study 
should be ordered under the name of one lead participating investigator at that institution. 
 
Please submit agent order requests to PMB after patient enrollment onto the study. 
 
Submit agent requests through the PMB Online Agent Order Processing (OAOP) 
application. Access to OAOP requires the establishment of a CTEP Identity and 
Access Management (IAM) account and the maintenance of an “active” account 
status, a “current” password, and active person registration status. For questions 
about drug orders, transfers, returns, or accountability, call or email PMB any time. 
Refer to the PMB’s website for specific policies and guidelines related to agent 
management. 
 
8.1.2.2 Agent Inventory Records – The investigator, or a responsible party designated by the investigator, 
must maintain a careful record of the receipt, dispensing and final disposition of all agents received from the 
PMB using the appropriate NCI Investigational Agent (Drug) Accountability Record (DARF) available on 
the CTEP forms page. Store and maintain separate NCI Investigational Agent Accountability Records for 
each agent, strength, formulation and ordering investigator on this protocol. 
 
8.1.3 Investigator Brochure Availability 
The current versions of the IBs for the agents will be accessible to site investigators and 
research staff through the PMB OAOP application. Access to OAOP requires the 
establishment of a CTEP IAM account and the maintenance of an “active” account status, 
a “current” password and active person registration status. Questions about IB access 
may be directed to the PMB IB Coordinator via email. 
 
8.1.4 Useful Links and Contacts 
CTEP Forms, Templates, Documents: http://ctep.cancer.gov/forms/ 
NCI CTEP Investigator Registration: RCRHelpDesk@nih.gov 
PMB policies and guidelines: 
http://ctep.cancer.gov/branches/pmb/agent_management.htm 
PMB Online Agent Order Processing (OAOP) application: 
https://ctepcore.nci.nih.gov/OAOP 

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CTEP Identity and Access Management (IAM) account: 
https://ctepcore.nci.nih.gov/iam/ 
CTEP IAM account help: ctepreghelp@ctep.nci.nih.gov 
IB Coordinator: IBCoordinator@mail.nih.gov 
PMB email: PMBAfterHours@mail.nih.gov 
PMB phone and hours of service: (240) 276-6575 Monday through Friday 
between 8:30 am and 4:30 pm (ET) 
 
8.2 Commercial Agents 
 
8.2.1 Trastuzumab (NSC 688097) 
 
Other Names: HERCEPTIN®; rhuMAb HER-2/NEU; MoAb HER2/NEU 
 
Classification: Monoclonal antibody 
 
Mode of Action: The HER2 (or c-erbB2) proto-oncogene encodes a transmembrane 
receptor protein of 185 kDa, which is structurally related to the epidermal growth factor 
receptor. Trastuzumab has been shown, in both in vitro assays and in animals, to inhibit 
the proliferation of human tumor cells that overexpress HER2. 
-Trastuzumab is a mediator of antibody-dependent cellular cytotoxicity (ADCC). In vitro, 
trastuzumab-mediated ADCC has been shown to be preferentially exerted on HER2 
overexpressing cancer cells compared with cancer cells that do not overexpress HER2. 
 
Description: Trastuzumab is a humanized IgG1 kappa monoclonal antibody 
that selectively binds with high affinity to the extracellular domain of the human 
epidermal growth factor receptor 2 protein, HER2. Trastuzumab is produced by 
recombinant DNA technology in a mammalian cell (Chinese Hamster Ovary) culture 
containing the antibiotic gentamicin. Gentamicin is not detectable in the final product. 
 
How Supplied: Trastuzumab is commercially suppled for this protocol. Please refer to the FDA 
approved package insert for additional information. 
 
The commercially-labeled 150 mg vials are formulated in histidine/histidine-HCl monohydrate, 
α,α-trehalose dihydrate, and polysorbate 20. NOTE: The 150 mg vials are not multi-use vials. 
Preparation: 
Reconstitute each 150 mg vial of trastuzumab with 7.4 mL of Sterile Water for Injection 
(SWFI), USP to yield a solution containing approximately 21 mg/mL trastuzumab at a 
pH of approximately 6.0. Use of other reconstitution solvents should be avoided. A 
volume overfill ensures that the labeled dose of 150 mg can be withdrawn from each vial. 
 
Reconstitution 
Use appropriate aseptic technique when performing the following reconstitution 
steps: 

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• 150 mg vials 
• Using a sterile syringe, slowly inject the 7.4 mL of Sterile Water 
for Injection (SWFI), USP into the vial containing the lyophilized 
cake of trastuzumab. The stream of diluent should be directed into 
the lyophilized cake. 
• Swirl the vial gently to aid reconstitution. DO NOT SHAKE. 
• Slight foaming of the product may be present upon reconstitution. 
Allow the vial to stand undisturbed for approximately 5 minutes. 
• Parenteral drug products should be inspected visually for 
particulate matter and discoloration prior to administration, 
whenever solution and container permit. Inspect visually for 
particulates and discoloration. The solution should be free of 
visible particulates, clear to slightly opalescent and colorless to 
pale yellow. 
• Single-use vial should be used immediately after reconstitution. 
 
Dilution 
• Determine the dose (mg) of trastuzumab. Calculate the volume of the 21 mg/mL 
reconstituted trastuzumab solution needed, withdraw this amount from the vial 
and add it to an infusion bag containing 250 mL of 0.9% Sodium Chloride 
Injection, USP. DO NOT USE DEXTROSE (5%) SOLUTION. 
• Gently invert the bag to mix the solution. 
 
Storage: store intact vials at 2−8°C (36−46°F) prior to reconstitution. 
 
Stability: Do not use beyond the expiration date stamped on the product labelA vial of 
trastuzumab reconstituted with unpreserved SWFI (not supplied) should be used immediately 
and any unused portion discarded. Do Not Freeze trastuzumab following reconstitution or 
dilution. 
 
The solution of trastuzumab for infusion diluted in polyvinylchloride or polyethylene 
bags containing 0.9% Sodium Chloride Injection, USP, should be stored at 
2−8°C (36−46°F) for no more than 24 hours prior to use. 
 
Route(s) of Administration: intravenous infusion 
 
Method of Administration: Trastuzumab is given by slow intravenous infusion only. 
The loading dose is infused over 90 minutes. If this is well tolerated, subsequent 
infusions may be given over 30 or 90 minutes depending on how the initial dose was 
tolerated. 
 
Drug-Drug Interactions: Formal drug-drug interaction studies have not been performed, but 
clinical treatment with other chemotherapy agents (anthracyclines, cyclophosphamide, taxanes, 
fluoropyrimidines, cisplatin, gemcitabine, capecitabine, anastrozole) did not appear to influence 
trastuzumab kinetics. 

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8.2.2 Pertuzumab (NSC 740102) 
 
Other Names: Perjeta®, RO4368451 
 
Classification:  HER2/neu receptor antagonist 
M.W.: 148 kDa 
 
Mode of Action: 
Pertuzumab blocks ligand-dependent heterodimerization of HER2 with other HER family 
members, including EGFR, HER3, and HER4. As a result, pertuzumab inhibits ligand- 
initiated intracellular signaling through two major signal pathways, mitogen-activated 
protein (MAP) kinase, and phosphoinositide 3-kinase (PI3K). Inhibition of these signaling 
pathways can result in cell growth arrest and apoptosis, respectively. In addition, 
pertuzumab mediates antibody-dependent cell-mediated cytotoxicity (ADCC). 
 
Description: 
Pertuzumab is a recombinant humanized monoclonal antibody that targets the 
extracellular dimerization domain (Subdomain II) of the human epidermal growth factor 
receptor 2 protein (HER2). Pertuzumab is produced by recombinant DNA technology in 
a mammalian cell (Chinese Hamster Ovary) culture. 
 
How Supplied: 
Pertuzumab is commercially supplied for this protocol. Please refer to the FDA approved 
package insert for additional information. 
 
Pertuzumab is a sterile, clear to slightly opalescent, colorless to pale brown liquid for 
intravenous infusion. Each single use vial contains 420 mg of pertuzumab at a 
concentration of 30 mg/mL (14mL) in 20 mM L-histidine acetate (pH 6.0), 120 mM 
sucrose and 0.02% polysorbate 20. 
 
Preparation: 
Administer as an intravenous infusion only. Do not administer as an intravenous push or 
bolus. Do not mix pertuzumab with other drugs. 
Prepare the solution for infusion, using aseptic technique, as follows: 
• Parenteral drug products should be inspected visually for particulates and 
discoloration prior to administration. 
• Withdraw the appropriate volume of pertuzumab solution from the vial(s). 
• Dilute into a 250 mL 0.9% sodium chloride PVC or non-PVC polyolefin infusion 
bag. 
• Mix diluted solution by gentle inversion. Do not shake. 
• Administer immediately once prepared. 
Storage: 
Store vials in a refrigerator at 2°C to 8°C (36°F to 46°F) until time of use. 

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Keep vial in the outer carton in order to protect from light. DO NOT FREEZE. DO NOT 
SHAKE. 
 
Stability: 
If the diluted infusion solution is not used immediately, it can be stored at 2ºC to 8ºC for 
up to 24 hours. Dilute with 0.9% Sodium Chloride injection only. 
Diluted pertuzumab has been shown to be stable for up to 24 hours at a temperature up to 
30°C. However, since diluted pertuzumab contains no preservative, the diluted solution 
should be stored refrigerated (2°C–8°C). 
Route(s) of Administration: intravenous 
 
Method of Administration: 
 
The 840 mg dose is administered as a 60-minute intravenous infusion. 420 mg doses are 
administered by intravenous infusion over 30 or 60 minutes, depending on how the initial 
dose was tolerated 
 
Incompatibilities: Do not use dextrose (5%) solution. 
 
 
9. STATISTICAL CONSIDERATIONS 
 
9.1 Study Design/Endpoints 
 
Please refer to “SCHEMA” section for study design schema. 
 
9.1.1 Phase 1b/ Safety run-in: 
 
Primary Endpoint: Incidence of adverse events and serious adverse events to determine safety; 
incidence of DLTs to determine RP2D. 
 
Secondary Endpoint: PFS and OS 
 
The primary objective of the phase 1b (safety run-in) portion of this trial will be to determine the 
RP2D for combination of copanlisib, trastuzumab, and pertuzumab. The phase 1 portion of the 
trial will use a 3+3 dose de-escalation design and patients will begin therapy at dose level 1 (60 
mg IV weekly), which is the RP2D established by the phase 1b combination study of copanlisib 
with trastuzumab (Panther). If at least 2 of 3 patients treated within this dosing cohort develop 
DLT, it can be concluded with 90% confidence that the true probability of DLT at that dose is 
greater than 20% and further patients will be accrued to dose level -1 (45 mg IV weekly). If 
none of the 3 patients demonstrates DLT, it can be concluded with 90% confidence that the true 

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probability of DLT is less than 55%. These criteria are considered a standard for dose selection 
using the proposed phase 1 clinical trial design. 
 
If ≤1 of 3 patients develops DLT, the cohort will be expanded to 6 patients to further assess 
toxicity. If >2 of 6 develop DLT, further patients will be accrued at dose level -1 (45 mg IV 
weekly) using the same strategy as cohort 1 to define RP2D. The proposed plan provides 91% 
probability that dose escalation will not be stopped at doses associated with DLT probability of 
<10% and gives a 92% probability that escalation will not proceed beyond doses associated with 
DLT probability in excess of 60%. The plan also protects against defining an RP2D associated 
with excessive toxicity. For a wide variety of dose-toxicity curves, the probability is 
approximately 85-90% that the defined RP2D will be associated with DLT probability of 
approximately 10-45%. 
 
RP2D is defined in Section 6.2. We will tabulate the toxicity data by grade, severity and dose 
level. No hypothesis testing will be done for this objective. 
 
9.2.1 Phase 2  
Primary endpoint: PFS 
Secondary endpoint: 
1) OS 
2) Incidence of adverse events and serious adverse events to determine the safety of copanlisib 
given at the RP2D in combination with trastuzumab and pertuzumab. 
 
Correlative endpoint: 
(1) Correlation of PFS and OS with number of induction cycles 
(2) Correlation of PFS and OS with hormone receptor status (ER and PR) 
(3) Correlation of PFS and OS with molecular alterations identified through whole exome 
sequencing (WES) and RNA sequencing in tumor tissue, as well as circulating tumor DNA 
analysis. 
(4) Correlation of PFS and OS with change in expression of pharmacodynamics markers 
downstream of PI3K inhibition and change in expression of genes involved in alternate signaling 
pathways identified through reverse phase protein array (RPPA). 
 
Once RP2D is reached, a protocol amendment will be submitted for CTEP’s review and approval 
prior to starting phase 2. The primary objective of the phase 2 portion of the trial is to determine 
a difference in PFS with the addition of copanlisib (pan-PI3K inhibitor) to dual anti-HER2 
targeted therapy for maintenance after induction chemotherapy in metastatic breast cancer. The 
analysis population for PFS is all eligible patients who are randomized (i.e. an intention-to-treat 
analysis). 
Projected median PFS in control group is 8 months and 16 months in the experimental arm 
(copanlisib + dual anti-Her2neu therapy). This PFS estimate is derived from the CLEOPATRA 
study with adjustment for “induction time” (subtracting 4-5 months). In the Cleopatra trial, 
PIK3CA mutant patients who received dual HER2 targeted therapy and docetaxel had a median 

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PFS of 12.5 months. Subtracting 4.5 months for induction chemotherapy, the projected median 
PFS of the control arm on maintenance therapy is 8 months. We aim to detect a HR of 0.50 with 
power of 0.90 with 1-sided alpha of 0.1 (assume trastuzumab and pertuzumab plus copanlisib 
beats trastuzumab and pertuzumab). With a sample size (N) of 82, 12 months post-accrual 
follow-up and patient accrual rate of 5 patients per month, the study is expected to last for 30 
months. To get 82 evaluable patients with a 15% drop-out rate, we would need to enroll 96 
patients. 
 
The statistical test for the primary analysis will be the partial likelihood ratio test of a stratified 
Cox PH model with treatment group as a covariate. 
 
A Wieand rule futility interim analysis will be conducted when half of the total of 54 required 
PFS events are observed. The study will be stopped for futility if the stratified PFS hazard ratio 
comparing trastuzumab and pertuzumab plus copanlisib to trastuzumab and pertuzumab > 1.0. 
 
To ensure the safety of the experimental treatment arm in phase II part of the trial, pertuzumab 
plus copanlisib to trastuzumab and pertuzumab (HP+C), we will apply a safety monitoring rule 
as follows. If prob (tox (DLT) >.30)>0.875, stop enrollment for this arm. The stopping 
boundaries and their operating characteristics are provided in the following two tables. For 
example, after the first 10 patients are treated and their toxicities are evaluated in the HP+C arm, 
the trial is suggested to be terminated if 5 or more DLTs are observed. 
 
Stopping Boundaries 
# Patient treated (inclusive) 
# DLT (inclusive) 
10 
5-10 
20 
9-20 
30 
13-30 
 
Operating characteristics of toxicity monitoring 
True Toxicity Rate 
Prob (stop the trial early) 
0.20 
0.038 
0.30 
0.216 
0.40 
0.576 
0.50 
0.883 
 
 
 
At the time of the interim analysis, we will cease consenting for optional biopsy collection if we 
do not have at least 5 patients per arm who have consented to the additional optional biopsies. 
 
9.2 Sample Size/Accrual Rate 
 
Estimated Monthly Accrual: 
Safety run-in: 3-4/month 
Dose expansion: 4-5/ month 
Proposed Sample Size: 
Maximum: 12 + 96 patients 

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Earliest date the study can begin: 
May, 2019 
Projected Accrual Dates: 
May, 2019 to Feb, 2021 
 
The study is expected to last 30 months. 
 
PLANNED ENROLLMENT REPORT 
 
Racial Categories 
Ethnic Categories 
Total 
Not Hispanic or Latino 
Hispanic or Latino 
Female 
Male 
Female 
Male 
American Indian/ Alaska 
Native 
1 
0 
1 
0 
2 
Asian 
3 
0 
1 
0 
4 
Native Hawaiian or 
Other Pacific Islander 
1 
0 
0 
0 
1 
Black or African 
American 
23 
0 
1 
0 
24 
White 
55 
1 
10 
0 
66 
More Than One Race 
4 
0 
1 
0 
5 
Total 
87 
1 
14 
0 
102 
PHS 398 / PHS 2590 (Rev. 08/12 Approved Through 8/31/2015) 
OMB No. 0925-0001/0002 
 
 
9.3 Stratification Factors 
 
Stratification factors for the phase 2 portion of the study will include HR status and the number 
of cycles of induction chemotherapy received. We will use Cox proportional hazards regression 
to assess the associations between PFS/OS and HR status and number of induction cycles. 
Patients that receive up to 2 doses of HER2 targeted agents post induction will be noted and 
randomized 
 
9.4 Analysis of Secondary Endpoints 
 
The secondary objective of this study is to assess OS. We will use the Kaplan-Meier method to 
estimate OS. 
 
Analysis of the exploratory correlative studies will include: (1) assessing the extent to which 

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treatment effects (measured as hazard ratio for time to progression and odds ratio for response) 
depend on HR status or number of induction cycles (using product terms in logistic and Cox PH 
regression models); (2) assessing the extent to which select biomarkers change with treatment 
(using either paired t-test or Wilcoxon signed rank test depending on whether data are Normally 
distributed; (3) assess the extent to which select biomarkers correlate with response to treatment 
(using ROC curve analysis and/or logistic regression analysis); (4) assess the extent to which 
select biomarkers correlate with time to progression (using time-dependent ROC curve analysis 
and/or Cox PH regression analysis); (5) assess the extent to which ctDNA levels correlate with 
NGS results (using ROC curve analysis and/or logistic regression analysis). 
 
9.5 For Phase 2: Reporting and Exclusions 
 
9.5.1 Evaluation of Toxicity 
 
All patients will be evaluable for toxicity from the time of their first treatment with 
copanlisib. 
 
9.5.2 Evaluation of Response 
 
All patients included in the study must be assessed for response to treatment, even if there 
are major protocol treatment deviations or if they are ineligible. Each patient will be 
assigned one of the following categories: 1) complete response, 2) partial response, 3) 
stable disease, 4) progressive disease, 5) early death from malignant disease, 6) early 
death from toxicity, 7) early death because of other cause, or 9) unknown (not assessable, 
insufficient data). [Note: By arbitrary convention, category 9 usually designates the 
“unknown” status of any type of data in a clinical database.] 
 
All of the patients who met the eligibility criteria (with the possible exception of those 
who received no study medication) should be included in the main analysis of the 
response rate. Patients in response categories 4-9 should be considered to have a 
treatment failure (disease progression). Thus, an incorrect treatment schedule or drug 
administration does not result in exclusion from the analysis of the response rate. Precise 
definitions for categories 4-9 will be protocol specific. 
 
All conclusions should be based on all eligible patients. Subanalyses may then be 
performed on the basis of a subset of patients, excluding those for whom major protocol 
deviations have been identified (e.g., early death due to other reasons, early 
discontinuation of treatment, major protocol violations, etc.). However, these 
subanalyses may not serve as the basis for drawing conclusions concerning treatment 
efficacy, and the reasons for excluding patients from the analysis should be clearly 
reported. The 95% confidence intervals should also be provided. 
 
9.6 Data Safety Monitoring board (DSMB) Phase 2 
 
The conduct of this study will be overseen by the ETCTN DSMB. The DSMB will be 
responsible for recommendations to the Principal Investigator and NCI regarding possible 

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trial closure and/or early reporting of the study. The study team (with the exception of the 
study statistician) will not have access to the summary outcome data until released by the 
DSMB. 
 
10. ADVERSE EVENTS: LIST AND REPORTING REQUIREMENTS 
 
Adverse event (AE) monitoring and reporting is a routine part of every clinical trial. The 
following list of AEs (Section 10.1) and the characteristics of an observed AE (Sections 10.2 and 
10.3) will determine whether the event requires expedited reporting via the CTEP Adverse Event 
Reporting System (CTEP-AERS) in addition to routine reporting. 
 
10.1 Comprehensive Adverse Events and Potential Risks Lists (CAEPRs) 
 
The Comprehensive Adverse Events and Potential Risks list (CAEPR) provides a single list of 
reported and/or potential adverse events (AE) associated with an agent using a uniform 
presentation of events by body system. In addition to the comprehensive list, a subset, the 
Specific Protocol Exceptions to Expedited Reporting (SPEER), appears in a separate column and 
is identified with bold and italicized text. This subset of AEs (SPEER) is a list of events that are 
protocol specific exceptions to expedited reporting to NCI (except as noted below). Refer to the 
'CTEP, NCI Guidelines: Adverse Event Reporting Requirements' 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/aeguidelines.pdf for 
further clarification. 
NOTE: Report AEs on the SPEER ONLY IF they exceed the grade noted in parentheses next to 
the AE in the SPEER. If this CAEPR is part of a combination protocol using multiple 
investigational agents and has an AE listed on different SPEERs, use the lower of the grades to 
determine if expedited reporting is required. 
 
10.1.1 CAEPRs for CTEP IND Agent 
 
10.1.1.1 CAEPR for Copanlisib 
 
Comprehensive Adverse Events and Potential Risks list (CAEPR) for Copanlisib dihydrochloride  
(BAY 80-6946 dihydrochloride, NSC 784727) 
 
 
Version 2.2, June 18, 20191 
Adverse Events with Possible Relationship to 
Copanlisib dihydrochloride (BAY 80-6946 dihydrochloride) 
(CTCAE 5.0 Term) 
[n= 702] 
Specific Protocol Exceptions 
to Expedited Reporting 
(SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
BLOOD AND LYMPHATIC SYSTEM DISORDERS 
Anemia 
Anemia (Gr 2) 
Febrile neutropenia 
GASTROINTESTINAL DISORDERS 

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Adverse Events with Possible Relationship to 
Copanlisib dihydrochloride (BAY 80-6946 dihydrochloride) 
(CTCAE 5.0 Term) 
[n= 702] 
Specific Protocol Exceptions 
to Expedited Reporting 
(SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
Diarrhea 
Diarrhea (Gr 2) 
Mucositis oral 
Nausea 
Nausea (Gr 2) 
Pancreatitis 
Vomiting 
Vomiting (Gr 2) 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 
Fatigue 
Fatigue (Gr 2) 
INFECTIONS AND INFESTATIONS 
Infection2 
Infection2 (Gr 2) 
INVESTIGATIONS 
Neutrophil count decreased 
Neutrophil count decreased (Gr 2) 
Platelet count decreased 
Platelet count decreased (Gr 2) 
White blood cell decreased 
METABOLISM AND NUTRITION DISORDERS 
Anorexia 
Anorexia (Gr 2) 
Hyperglycemia 
Hyperglycemia (Gr 2) 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS 
Muscle cramp 
Muscle cramp (Gr 2) 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS 
Pneumonitis3 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS 
Erythroderma 
Pruritus 
Rash maculo-papular 
Rash maculo-papular (Gr 2) 
VASCULAR DISORDERS 
Hypertension 
Hypertension (Gr 2) 
 
1This table will be updated as the toxicity profile of the agent is revised. Updates will be distributed to all 
Principal Investigators at the time of revision. The current version can be obtained by 
contactingPIO@CTEP.NCI.NIH.GOV. Your name, the name of the investigator, the protocol and the 
agent should be included in the e-mail. 
 
2Infection includes all 75 sites of infection under the INFECTIONS AND INFESTATIONS SOC. 
 
3Pneumonitis is a group term that includes interstitial lung disease, dyspnea, dyspnea at rest, and 
dyspnea exertional. 
 
 
Adverse events reported on Copanlisib dihydrochloride (BAY 80-6946 dihydrochloride) trials, but 
for which there is insufficient evidence to suggest that there was a reasonable possibility that 
Copanlisib dihydrochloride (BAY 80-6946 dihydrochloride) caused the adverse event: 
 
BLOOD AND LYMPHATIC SYSTEM DISORDERS - Eosinophilia 
CARDIAC DISORDERS - Atrial fibrillation; Cardiac arrest; Left ventricular systolic dysfunction; Myocardial 
infarction; Sinus tachycardia 
GASTROINTESTINAL DISORDERS - Abdominal pain; Colitis; Constipation; Dry mouth; Dyspepsia; 
Esophagitis; Flatulence; Gastritis; Gastroesophageal reflux disease; Oral dysesthesia; Oral pain; Upper 

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gastrointestinal hemorrhage 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS - Chills; Death NOS; Fever; 
General disorders and administration site conditions - Other (failure to thrive); Non-cardiac chest pain 
IMMUNE SYSTEM DISORDERS - Allergic reaction; Autoimmune disorder 
INJURY, POISONING AND PROCEDURAL COMPLICATIONS - Fracture; Infusion related reaction; 
Injury, poisoning and procedural complications - Other (drug eruption) 
INVESTIGATIONS - Activated partial thromboplastin time prolonged; Alanine aminotransferase 
increased; Alkaline phosphatase increased; Aspartate aminotransferase increased; Blood bilirubin 
increased; CPK increased; Ejection fraction decreased; Electrocardiogram QT corrected interval 
prolonged; Electrocardiogram T wave abnormal; Investigations - Other (electrocardiogram U wave 
abnormal); Lipase increased; Lymphocyte count decreased; Serum amylase increased 
METABOLISM AND NUTRITION DISORDERS - Dehydration; Hypertriglyceridemia; Hyperuricemia; 
Hypocalcemia; Hypokalemia; Hypomagnesemia; Hyponatremia; Hypophosphatemia; Metabolism and 
nutrition disorders - Other (blood insulin increased) 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS - Arthralgia; Generalized muscle 
weakness; Musculoskeletal and connective tissue disorder - Other (psoriatic arthropathy); Myalgia 
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS AND POLYPS) - Tumor 
hemorrhage 
NERVOUS SYSTEM DISORDERS - Amnesia; Dizziness; Dysesthesia; Dysgeusia; Headache; 
Paresthesia; Peripheral sensory neuropathy; Presyncope; Reversible posterior leukoencephalopathy 
syndrome 
PSYCHIATRIC DISORDERS - Confusion 
RENAL AND URINARY DISORDERS - Acute kidney injury; Renal and urinary disorders - Other (renal 
insufficiency) 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS - Cough; Dyspnea3; Hypoxia; Pleural 
effusion; Pulmonary hypertension; Respiratory failure; Respiratory, thoracic and mediastinal disorders - 
Other (pulmonary congestion) 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS - Alopecia; Dry skin; Purpura; Rash acneiform; 
Stevens-Johnson syndrome 
VASCULAR DISORDERS - Hypotension; Thromboembolic event; Vascular disorders - Other (circulatory 
collapse) 
 
 
Note: Copanlisib dihydrochloride (BAY 80-6946 dihydrochloride) in combination with other agents could 
cause an exacerbation of any adverse event currently known to be caused by the other agent, or the 
combination may result in events never previously associated with either agent. 
 
10.1.2 CAEPRs for Commercial Agents 
 
10.1.2.1 CAEPR for Trastuzumab and Herceptin HylectaTM 
 
Comprehensive Adverse Events and Potential Risks list (CAEPR) for 
Trastuzumab (Herceptin, NSC 688097) and Herceptin HylectaTM (SQ trastuzumab, NSC 827797) 
The Comprehensive Adverse Events and Potential Risks list (CAEPR) provides a single list of reported 
and/or potential adverse events (AE) associated with an agent using a uniform presentation of events by 
body system. In addition to the comprehensive list, a subset, the Specific Protocol Exceptions to 
Expedited Reporting (SPEER), appears in a separate column and is identified with bold and italicized 
text. This subset of AEs (SPEER) is a list of events that are protocol specific exceptions to expedited 
reporting to NCI (except as noted below). Refer to the 'CTEP, NCI Guidelines: Adverse Event Reporting 
Requirements' http://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/aeguidelines.pdf 
for further clarification. Frequency is provided based on 4407 patients. Below is the CAEPR for 
Trastuzumab (Herceptin) and Herceptin HylectaTM (SQ trastuzumab). 

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NOTE: Report AEs on the SPEER ONLY IF they exceed the grade noted in parentheses next to the AE 
in the SPEER. If this CAEPR is part of a combination protocol using multiple investigational agents and 
has an AE listed on different SPEERs, use the lower of the grades to determine if expedited reporting is 
required. 
Frequency is provided based on 4407 patients. 
Version 2.6, December 14, 20211 

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Adverse Events with Possible 
Relationship to Trastuzumab (Herceptin) 
(CTCAE 5.0 Term) 
[n= 4621] 
Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
BLOOD AND LYMPHATIC SYSTEM DISORDERS 
Anemia 
Anemia (Gr3) 
Febrile neutropenia2 
CARDIAC DISORDERS 
Heart failure 
Left ventricular systolic 
dysfunction 
Left ventricular systolic dysfunction 
(Gr 3) 
Pericardial effusion 
Pericarditis 
Palpitations 
Restrictive cardiomyopathy 
Sinus tachycardia3 
Sinus tachycardia (Gr 2) 
Supraventricular tachycardia3 
EYE DISORDERS 
Watering eyes 
GASTROINTESTINAL DISORDERS 
Abdominal pain 
Abdominal pain (Gr 2) 
Diarrhea 
Diarrhea (Gr 3) 
Mucositis oral 
Mucositis oral (Gr 2) 
Nausea 
Nausea (Gr 3) 
Pancreatitis 
Vomiting 
Vomiting (Gr 3) 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 
Chills3 
Chills3 (Gr 2) 
Edema limbs 
Fatigue 
Fatigue (Gr 3) 
Fever3 
Fever3 (Gr 2) 
Flu like symptoms 
Flu like symptoms (Gr 2) 
Injection site reaction4 
Injection site reaction4 Gr 2) 
Non-cardiac chest pain 
Non-cardiac chest pain (Gr 2) 
Pain 
Pain (Gr 2) 
IMMUNE SYSTEM DISORDERS 
Allergic reaction5 
Anaphylaxis 
INFECTIONS AND INFESTATIONS 
Infection6 
Infection6 (Gr 3) 
INJURY, POISONING AND PROCEDURAL COMPLICATIONS 
Infusion related reaction7 
Infusion related reaction7 (Gr 2) 
INVESTIGATIONS 
Alkaline phosphatase increased 
Alkaline phosphatase increased (Gr 2) 
Aspartate aminotransferase 
increased 
Aspartate aminotransferase increased 
(Gr 2) 
Cardiac troponin I increased 

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Adverse Events with Possible 
Relationship to Trastuzumab (Herceptin) 
(CTCAE 5.0 Term) 
[n= 4621] 
Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
Ejection fraction decreased 
Ejection fraction decreased (Gr 3) 
GGT increased 
GGT increased (Gr 2) 
Neutrophil count decreased2 
Neutrophil count decreased2 (Gr 4) 
Weight loss 
METABOLISM AND NUTRITION DISORDERS 
Anorexia 
Anorexia (Gr 2) 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS 
Arthralgia 
Arthralgia (Gr 2) 
Back pain 
Back pain (Gr 2) 
Bone pain 
Bone pain (Gr 2) 
Muscle cramp 
Myalgia 
Myalgia (Gr 2) 
Pain in extremity 
NEOPLASMS BENIGN, MALIGNANT AND UNSPECIFIED (INCL CYSTS 
AND POLYPS) 
Tumor pain 
Tumor pain (Gr 2) 
NERVOUS SYSTEM DISORDERS 
Dysgeusia 
Dizziness 
Headache 
Headache (Gr 2) 
Peripheral sensory neuropathy 
PSYCHIATRIC DISORDERS 
Depression 
Insomnia 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS 
Adult respiratory distress 
syndrome3,5 
Allergic rhinitis 
Allergic rhinitis (Gr 2) 
Bronchospasm3,4 
Cough 
Cough (Gr 2) 
Dyspnea3,5 
Dyspnea3,5(Gr 3) 
Hypoxia5 
Hypoxia5 (Gr 2) 
Pneumonitis5 
Pulmonary edema5 
Pulmonary fibrosis 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS 
Alopecia 
Nail changes 
Nail loss 
Rash acneiform 
Rash acneiform (Gr 2) 
Rash maculo-papular 
Rash maculo-papular (Gr 2) 
Urticaria3 
Urticaria3 (Gr 2) 
VASCULAR DISORDERS 
Hot flashes 

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Adverse Events with Possible 
Relationship to Trastuzumab (Herceptin) 
(CTCAE 5.0 Term) 
[n= 4621] 
Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
Hypertension3 
Hypotension3 
Lymphedema 
Vascular disorders - Other 
(vasodilation) 
 
1This table will be updated as the toxicity profile of the agent is revised. Updates will be distributed to all 
Principal Investigators at the time of revision. The current version can be obtained by contacting 
PIO@CTEP.NCI.NIH.GOV. Your name, the name of the investigator, the protocol and the agent should 
be included in the e-mail. 
 
2Fatal event when given in combination with Xeloda® (capecitabine) and Taxotere® (docetaxel). 
 
3Associated with infusion-related reactions or administration-related reactions (ARRs). 
 
4Injection site reaction was observed primarily in subjectes treated with Herceptin HylectaTM SC 
formuation. 
 
5Severe hypersensitivity reactions including angioedema and pulmonary adverse events (e.g., hypoxia, 
dyspnea, pulmonary infiltrates, pleural effusion, intersitial lung disease, wheezing, and acute respiratory 
distress syndrome) have been reported. 
 
6Infection may include any of the 75 sites of infection under the INFECTIONS AND INFESTATIONS 
SOC. 
 
7Infusion related reaction was obseved primarily subjects treated with the trastuzumab IV formulation. 
 
 
 
Adverse events reported on trastuzumab (Herceptin) and/or Herceptin HylectaTM (SQ trastuzumab) 
trials, but for which there is insufficient evidence to suggest that there was a reasonable 
possibility that trastuzumab (Herceptin) and/or Herceptin HylectaTM (SQ trastuzumab) caused the 
adverse event: 
 
CARDIAC DISORDERS - Asystole; Atrial fibrillation; Atrial flutter; Chest pain - cardiac; Myocardial 
infarction; Myocarditis; Sinus bradycardia; Ventricular arrhythmia; Ventricular tachycardia 
EAR AND LABYRINTH DISORDERS - Hearing impaired; Vertigo 
EYE DISORDERS - Dry eye; Extraocular muscle paresis 
GASTROINTESTINAL DISORDERS - Ascites; Colitis; Constipation; Duodenal ulcer; Dyspepsia; 
Enterocolitis; Esophagitis; Gastric hemorrhage; Gastritis; Gastrointestinal pain; Small intestinal 
perforation; Typhlitis 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS - Generalized edema; Sudden 
death NOS 
HEPATOBILIARY DISORDERs - Cholecystitis 
INJURY, POISONING AND PROCEDURAL COMPLICATIONS - 
Dermatitis radiation; Fracture; Injury, poisoning and procedural complications - Other (incision site pain); Injury, 
poisoning and procedural complications - Other (procedural pain) 
INVESTIGATIONS - Alanine aminotransferase increased; Creatinine increased; Weight gain; White blood 
cell decreased 

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METABOLISM AND NUTRITION DISORDERS - Dehydration; Hyperkalemia; Hypoalbuminemia; 
Hypokalemia; Hypophosphatemia 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS - Arthritis; Chest wall pain; Flank pain; 
Generalized muscle weakness; Neck pain 
NERVOUS SYSTEM DISORDERS - Amnesia; Depressed level of consciousness; Encephalopathy; 
Leukoencephalopathy; Muscle weakness left-sided; Paresthesia; Seizure; Syncope PSYCHIATRIC 
DISORDERS - Anxiety; Confusion 
RENAL AND URINARY DISORDERS - Acute kidney injury; Proteinuria 
REPRODUCTIVE SYSTEM AND BREAST DISORDERS - Amenorrhea 

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RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS - Epistaxis; Nasal congestion; 
Oropharyngeal pain; Pharyngolaryngeal pain; Pleural effusion4; Pulmonary hypertension; Respiratory 
failure; Wheezing4 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS - Eczema; Erythema multiforme; Hyperhidrosis; 
Palmar-plantar erythrodysesthesia syndrome; Pruritus; Skin hyperpigmentation; Stevens-Johnson 
syndrome 
VASCULAR DISORDERS - Hematoma; Thromboembolic event 
 
 
Note: Trastuzumab (Herceptin) in combination with other agents could cause an exacerbation of any 
adverse event currently known to be caused by the other agent, or the combination may result in events 
never previously associated with either agent. 
 
 
10.1.1.1 CAEPR for Pertuzumab 
 
Comprehensive Adverse Events and Potential Risks list (CAEPR) for Pertuzumab (NSC 740102) 
 
Frequency is provided based on 9575 patients. 
NOTE: Report AEs on the SPEER ONLY IF they exceed the grade noted in parentheses next to the 
AE in the SPEER. If this CAEPR is part of a combination protocol using multiple investigational 
agents and has an AE listed on different SPEERs, use the lower of the grades to determine if 
expedited reporting is required. 
NOTE: Frequencies of AEs on this CAEPR are based on pooled clinical data from treatment arms, 
pivotal clinical trials using pertuzumab in combination with trastuzumab and docetaxel in patients with 
MBC (metastatic breast cancer), and pertuzumab in combination with trastuzumab and chemotherapy 
in patients with EBC (early stage breast cancer). 
Version 2.4, July 6, 20191 
Adverse Events with Possible 
Relationship to Pertuzumab 
(CTCAE 5.0 Term) 
[n= 9575] 
Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
BLOOD AND LYMPHATIC SYSTEM DISORDERS 
Anemia 
Anemia (Gr 3) 
Febrile neutropenia 
Febrile neutropenia (Gr 2) 
CARDIAC DISORDERS 
Heart failure 
EYE DISORDERS 
Watering eyes 
GASTROINTESTINAL DISORDERS 
Abdominal pain 
Constipation 
Constipation (Gr 2) 
Diarrhea 
Diarrhea (Gr 3) 
Dyspepsia 
Mucositis oral 
Mucositis oral (Gr 2) 
Nausea 
Nausea (Gr 3) 
Vomiting 
Vomiting (Gr 3) 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS 

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Adverse Events with Possible 
Relationship to Pertuzumab 
(CTCAE 5.0 Term) 
[n= 9575] 
Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
Edema limbs 
Edema limbs (Gr 2) 
Fatigue 
Fatigue (Gr 2) 
Fever 
Fever (Gr 2) 
General disorders and 
administration site conditions - 
Other (mucosal inflammation) 
IMMUNE SYSTEM DISORDERS 
Allergic reaction2 
Allergic reaction2 (Gr 2) 
Anaphylaxis2 
INFECTIONS AND INFESTATIONS 
Infection3 
Infection3 (Gr 3) 
INJURY, POISONING AND PROCEDURAL COMPLICATIONS 
Dermatitis radiation 
Infusion related reaction4 
Infusion related reaction4 (Gr 2) 
INVESTIGATIONS 
Alanine aminotransferase 
increased 
Aspartate aminotransferase 
increased 
Ejection fraction decreased 
Neutrophil count decreased 
Neutrophil count decreased 
(Gr 2) 
White blood cell decreased 
White blood cell decreased (Gr 
2) 
METABOLISM AND NUTRITION DISORDERS 
Anorexia 
Anorexia (Gr 2) 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS 
Arthralgia 
Arthralgia (Gr 2) 
Back pain 
Myalgia 
Myalgia (Gr 2) 
Pain in extremity 
NERVOUS SYSTEM DISORDERS 
Dizziness 
Dizziness (Gr 2) 
Dysgeusia 
Dysgeusia (Gr 2) 
Headache 
Headache (Gr 2) 
Paresthesia 
Peripheral motor neuropathy 
Peripheral sensory neuropathy 
PSYCHIATRIC DISORDERS 
Insomnia 
Insomnia (Gr 2) 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS 
Cough 
Dyspnea 
Dyspnea (Gr 2) 
Epistaxis 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS 
Alopecia 
Alopecia (Gr 2) 
Dry skin 

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Adverse Events with Possible 
Relationship to Pertuzumab 
(CTCAE 5.0 Term) 
[n= 9575] 
Specific Protocol 
Exceptions to Expedited 
Reporting (SPEER) 
Likely (>20%) 
Less Likely (<=20%) 
Rare but Serious (<3%) 
Nail changes 
Nail changes (Gr 2) 
Palmar-plantar erythrodysesthesia 
syndrome 
Pruritus 
Pruritus (Gr 2) 
Rash5 
Rash5 (Gr 2) 
VASCULAR DISORDERS 
Hot flashes 
 
1This table will be updated as the toxicity profile of the agent is revised. Updates will be distributed to all 
Principal Investigators at the time of revision. The current version can be obtained by contacting 
PIO@CTEP.NCI.NIH.GOV. Your name, the name of the investigator, the protocol and the agent should 
be included in the e-mail. 
 
2Symptoms of allergic reaction and anaphylaxis may include bronchospasm. 
 
3Infection may include any of the 75 infection sites under the INFECTIONS AND INFESTATIONS SOC 
and may be due to concomitant chemotherapy. 
 
 
4In pivotal studies adverse events that occurred during or within 24 hours after study drug administration 
and were judged to be related to the infusion of study drug were captured as associated signs and 
symptoms, not as a diagnosis (e.g., “infusion-related reaction”). 
 
5Rash includes the terms rash, exfoliative rash, rash papular, rash maculo-papular. 
 
 
Adverse events reported on pertuzumab trials, but for which there is insufficient evidence to 
suggest that there was a reasonable possibility that pertuzumab caused the adverse event: 
 
BLOOD AND LYMPHATIC SYSTEM DISORDERS - Bone marrow hypocellular; Leukocytosis 
CARDIAC DISORDERS - Atrial fibrillation; Chest pain - cardiac; Left ventricular systolic dysfunction; 
Pericardial effusion 
EYE DISORDERS - Blurred vision; Dry eye; Eye disorders - Other (diplopia) 
GASTROINTESTINAL DISORDERS - Abdominal distension; Ascites; Dry mouth; Esophagitis; 
Gastroesophageal reflux disease; Hemorrhoids 
GENERAL DISORDERS AND ADMINISTRATION SITE CONDITIONS - Chills; Death NOS; Flu like 
symptoms; Generalized edema; Non-cardiac chest pain; Pain 
HEPATOBILIARY DISORDERS - Cholecystitis; Hepatobiliary disorders - Other (hepatitis fulminant); 
Hepatobiliary disorders - Other (hepatocellular injury) 
INJURY, POISONING AND PROCEDURAL COMPLICATIONS - Fracture; Injury, poisoning and 
procedural complications - Other (post-procedural inflammation); Injury, poisoning and procedural 
complications - Other (procedural pain); Injury, poisoning and procedural complications - Other (skin 
toxicity); Wound complication; Wound dehiscence 
INVESTIGATIONS - Alkaline phosphatase increased; Blood bilirubin increased; Creatinine increased; 
GGT increased; Investigations - Other (granulocytopenia); Lymphocyte count decreased; Platelet count 
decreased; Weight gain; Weight loss 
METABOLISM AND NUTRITION DISORDERS - Dehydration; Hyperglycemia; Hypoglycemia; 
Hypokalemia; Hypomagnesemia 
MUSCULOSKELETAL AND CONNECTIVE TISSUE DISORDERS - Bone pain; Muscle cramp; 

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Musculoskeletal and connective tissue disorder - Other (dermatomyositis syndrome); Musculoskeletal and 
connective tissue disorder - Other (spinal pain) 
NERVOUS SYSTEM DISORDERS - Amnesia; Dysarthria; Lethargy; Nervous system disorders - Other 
(osmotic demyelination syndrome); Somnolence; Syncope 
PSYCHIATRIC DISORDERS - Anxiety; Depression 
RENAL AND URINARY DISORDERS - Acute kidney injury; Dysuria; Urinary frequency 
REPRODUCTIVE SYSTEM AND BREAST DISORDERS - Amenorrhea; Breast pain; Irregular 
menstruation; Reproductive system and breast disorders - Other (metrorrhagia); Vaginal dryness 
RESPIRATORY, THORACIC AND MEDIASTINAL DISORDERS - Bronchospasm4; Nasal congestion; 
Oropharyngeal pain; Pleural effusion; Pneumonitis; Postnasal drip; Respiratory failure; Respiratory, 
thoracic and mediastinal disorders - Other (painful respiration); Rhinorrhea 
SKIN AND SUBCUTANEOUS TISSUE DISORDERS - Erythema multiforme; Erythroderma; 
Hyperhidrosis; Nail discoloration; Pain of skin; Rash acneiform; Skin and subcutaneous tissue disorders - 
Other (onycholysis); Skin and subcutaneous tissue disorders - Other (onychomadesis); Skin 
hyperpigmentation; Urticaria 
VASCULAR DISORDERS - Flushing; Hypertension; Hypotension; Lymphedema; Thromboembolic event; 
Vascular disorders - Other (hyperemia) 
 
 
Note: Pertuzumab in combination with other agents could cause an exacerbation of any adverse 
event currently known to be caused by the other agent, or the combination may result in events 
never previously associated with either agent. 
10.2 Adverse Event Characteristics 
 
• CTCAE term (AE description) and grade: The descriptions and grading scales found 
in the revised NCI Common Terminology Criteria for Adverse Events (CTCAE) version 
5.0 will be utilized for AE reporting. All appropriate treatment areas should have access 
to a copy of the CTCAE version 5.0. A copy of the CTCAE version 5.0 can be 
downloaded from the CTEP website 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/ctc.htm. 
 
For expedited reporting purposes only: 
- AEs for the agent that are bold and italicized in the CAEPR (i.e., those listed in the 
SPEER column, Section 10.1) should be reported through CTEP-AERS only if the 
grade is above the grade provided in the SPEER. 
 
• Attribution of the AE: 
- 
Definite – The AE is clearly related to the study treatment. 
- 
Probable – The AE is likely related to the study treatment. 
- 
Possible – The AE may be related to the study treatment. 
- 
Unlikely – The AE is doubtfully related to the study treatment. 
- 
Unrelated – The AE is clearly NOT related to the study treatment. 
 
10.3 Expedited Adverse Event Reporting 
 
10.3.1 RAVE-CTEP-AERS 
 
The Rave Cancer Therapy Evaluation Program Adverse Event Reporting System (CTEP- 
AERS) integration enables evaluation of post-baseline AEs entered in Rave to determine 
whether they require expedited reporting, and facilitates entry in CTEP-AERS for those 
AEs requiring expedited reporting. 

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All AEs that occur after baseline are collected in Medidata Rave using the Adverse Event 
form, which is available for entry at each treatment or reporting period, and used to 
collect AEs that start during the period or persist from the previous reporting period. 
CRA will enter AEs that occur prior to the start of treatment on a baseline form that is not 
included in the Rave-CTEP-AERS integration. AEs that occur prior to enrollment must 
begin and end on the baseline Adverse Event form and should not be included on the 
standard Adverse Events form that is available at treatment unless there has been an 
increase in grade. 
Prior to sending AEs through the rules evaluation process, site staff should verify the 
following on the Adverse Event form in Rave: 
 
• 
The reporting period (course/cycle) is correct, and 
• 
AEs are recorded and complete (no missing fields) and the form is query-free. 
 
The CRA reports AEs in Rave at the time the Investigator learns of the event. If the CRA 
modifies an AE, it must be re-submitted for rules evaluation. 
 
Upon completion of AE entry in Medidata Rave, the CRA submits the AE for rules 
evaluation by completing the Expedited Reporting Evaluation form. Both NCI and 
protocol-specific reporting rules evaluate the AEs submitted for expedited reporting. A 
report is initiated in CTEP-AERS using information entered in Medidata Rave for AEs 
that meet reporting requirements. The CRA completes the report by accessing CTEP- 
AERS via a direct link on the Medidata Rave Expedited Reporting Evaluation form. 
 
In the rare occurrence that Internet connectivity is lost, a 24-hour notification is to be 
made to CTEP by telephone at 301-897-7497. Once internet connectivity is restored, the 
24-hour notification that was phoned in must be entered immediately into CTEP-AERS 
using the direct link from Medidata Rave. 
 
Additional information about the CTEP-AERS integration is available on the CTSU 
website: 
 
• 
Study specific documents: Protocols > Documents > Education and Promotion, 
and 
• 
Expedited Safety Reporting Rules Evaluation user guide: Resources > CTSU 
Operations Information > User Guides & Help Topics. 
 
NCI requirements for SAE reporting are available on the CTEP website: 
 
• 
NCI Guidelines for Investigators: Adverse Event Reporting Requirements is 
available at 
https://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/aeguidelines.p 
df 
 
10.3.2 Distribution of Adverse Event Reports 
 
CTEP-AERS is programmed for automatic electronic distribution of reports to the 

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following individuals: Principal Investigator and Adverse Event Coordinator(s) (if 
applicable) of the Corresponding Organization or Lead Organization, the local treating 
physician, and the Reporter and Submitter. CTEP-AERS provides a copy feature for 
other e-mail recipients. 
 
10.3.3 Expedited Reporting Guidelines 
 
Use the NCI protocol number and the protocol-specific patient ID assigned during trial 
registration on all reports. 
 
Note: A death on study requires both routine and expedited reporting, regardless of causality. 
Attribution to treatment or other cause must be provided. 
 
Death due to progressive disease should be reported as Grade 5 “Disease progression” 
in the system organ class (SOC) “General disorders and administration site conditions.” 
Evidence that the death was a manifestation of underlying disease (e.g., radiological 
changes suggesting tumor growth or progression: clinical deterioration associated with a 
disease process) should be submitted. 
 
Phase 1 and Early Phase 2 Studies: Expedited Reporting Requirements for Adverse Events that Occur 
on Studies under an IND/IDE within 30 Days of the Last Administration of the Investigational 
Agent/Intervention 1, 2 
 
FDA REPORTING REQUIREMENTS FOR SERIOUS ADVERSE EVENTS (21 CFR Part 312) 
NOTE: Investigators MUST immediately report to the sponsor (NCI) ANY Serious Adverse Events, whether or not 
they are considered related to the investigational agent(s)/intervention (21 CFR 312.64) 
An adverse event is considered serious if it results in ANY of the following outcomes: 
1) 
Death 
2) 
A life-threatening adverse event 
3) 
An adverse event that results in inpatient hospitalization or prolongation of existing hospitalization for ≥ 24 
hours 
4) 
A persistent or significant incapacity or substantial disruption of the ability to conduct normal life functions 
5) 
A congenital anomaly/birth defect. 
6) 
Important Medical Events (IME) that may not result in death, be life threatening, or require hospitalization 
may be considered serious when, based upon medical judgment, they may jeopardize the patient or 

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subject and may require medical or surgical intervention to prevent one of the outcomes listed in this 
definition. (FDA, 21 CFR 312.32; ICH E2A and ICH E6). 
ALL SERIOUS adverse events that meet the above criteria MUST be immediately reported to the NCI via electronic 
submission within the timeframes detailed in the table below. 
Hospitalization 
Grade 1 and Grade 2 Timeframes 
Grade 3-5 
Timeframes 
Resulting in 
Hospitalization 
≥ 24 hrs 
10 Calendar Days 
24-Hour 5 Calendar 
Days 
Not resulting in 
Hospitalization 
≥ 24 hrs 
Not required 
NOTE: Protocol specific exceptions to expedited reporting of serious adverse events are found in the Specific 
Protocol Exceptions to Expedited Reporting (SPEER) portion of the CAEPR. 
Expedited AE reporting timelines are defined as: 
o 
“24-Hour; 5 Calendar Days” - The AE must initially be submitted electronically within 24 hours of learning 
of the AE, followed by a complete expedited report within 5 calendar days of the initial 24-hour report. 
o 
“10 Calendar Days” - A complete expedited report on the AE must be submitted electronically within 10 
calendar days of learning of the AE. 
1Serious adverse events that occur more than 30 days after the last administration of investigational 
agent/intervention and have an attribution of possible, probable, or definite require reporting as follows: 
Expedited 24-hour notification followed by complete report within 5 calendar days for: 
• 
All Grade 3, 4, and Grade 5 AEs 
Expedited 10 calendar day reports for: 
• 
Grade 2 AEs resulting in hospitalization or prolongation of hospitalization 
2For studies using PET or SPECT IND agents, the AE reporting period is limited to 10 radioactive half-lives, 
rounded UP to the nearest whole day, after the agent/intervention was last administered. Footnote “1” above 
applies after this reporting period. 
Effective Date: May 5, 2011 
 
10.3.4 Adverse Events of Special Safety Interest 
 
• 
Non-infectious pneumonitis 
 
Non-infectious pneumonitis has been observed in studies with copanlisib. As soon as 
there is a reasonable suspicion of a patient experiencing non-infectious pneumonitis, 
the investigator should report it within 24 hours via CTEP-AERS regardless of 
whether the event is assessed as causally related/not related to the study therapy, or as 
serious/non-serious by an investigator. 
 
10.4 Routine Adverse Event Reporting 
 
All Adverse Events must be reported in routine study data submissions. AEs reported 
expeditiously through CTEP-AERS must also be reported in routine study data 
submissions. 
 
Adverse event data collection and reporting, which are required as part of every clinical trial, are 
done to ensure the safety of patients enrolled in the studies as well as those who will enroll in 

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future studies using similar agents. AEs are reported in a routine manner at scheduled times 
during the trial using Medidata Rave. For this trial the Adverse Event CRF is used for routine 
AE reporting in Rave. 
 
10.5 Pregnancy 
 
Although not an adverse event in and of itself, pregnancy as well as its outcome must be 
documented via CTEP-AERS. In addition, the Pregnancy Information Form included within 
the NCI Guidelines for Adverse Event Reporting Requirements must be completed and 
submitted to CTEP. Any pregnancy occurring in a patient or patient’s partner from the time of 
consent to 90 days after the last dose of study drug must be reported and then followed for 
outcome.  Newborn infants should be followed until 30 days old.  Please see the “NCI 
Guidelines for Investigators: Adverse Event Reporting Requirements for DCTD (CTEP and CIP) 
and DCP INDs and IDEs” (at http://ctep.cancer.gov/protocolDevelopment/adverse_effects.htm) 
for more details on how to report pregnancy and its outcome to CTEP. 
 
10.6 Secondary Malignancy 
 
A secondary malignancy is a cancer caused by treatment for a previous malignancy (e.g., 
treatment with investigational agent/intervention, radiation or chemotherapy). A secondary 
malignancy is not considered a metastasis of the initial neoplasm. 
 
CTEP requires all secondary malignancies that occur following treatment with an agent under an 
NCI IND/IDE be reported expeditiously via CTEP-AERS. Three options are available to 
describe the event: 
 
• Leukemia secondary to oncology chemotherapy (e.g., acute myelocytic leukemia 
[AML]) 
• Myelodysplastic syndrome (MDS) 
• Treatment-related secondary malignancy 
 
Any malignancy possibly related to cancer treatment (including AML/MDS) should also be 
reported via the routine reporting mechanisms outlined in each protocol. 
 
10.7 Second Malignancy 
 
A second malignancy is one unrelated to the treatment of a prior malignancy (and is NOT a 
metastasis from the initial malignancy). Second malignancies require ONLY routine AE 
reporting unless otherwise specified. 
 
11. STUDY CALENDAR 
 
Baseline evaluations are to be conducted within 1 week prior to start of protocol therapy. Scans 
and x-rays must be done <4 weeks prior to the start of protocol therapy. In the event that the 
patient’s condition is deteriorating, laboratory evaluations should be repeated within 48 hours 
prior to initiation of the next cycle of therapy. All assessments are to be performed within +/- 7 

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days to accommodate for holidays, inclement weather, etc. 

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Pre- 
Study Baseline 
Cycle 1 
Cycle 2 
Cycle 3 
Cycle 4+ 
Restaging 
Progression / Off 
Studyd 
D1 
D8 
D15 
D1 
D8 
D15 
D1 
D8 
D15 
D1 
D8 
D5 
Copanlisiba 
X 
X 
X 
X 
X 
X 
X 
X 
Trastuzumabb 
X 
X 
X 
X 
Pertuzumabc 
X 
X 
X 
X 
Informed 
consent 
X 
Demographics 
X 
Medical 
history 
X 
Concurrent 
meds 
X 
X ------------------------------------------------------------------------- X 
Physical exam 
X 
X 
X 
X 
X 
X 
X 
Vital signs 
X 
X 
X 
X 
X 
X 
X 
X 
X 
X 
Height 
X 
Weight 
X 
X 
X 
X 
X 
X 
Performance 
statuse 
X 
X 
X 
X 
X 
X 
CBC w/diff, 
plts 
X 
X 
X 
X 
X 
X 
Serum 
chemistryf 
X 
X 
X 
X 
XL 
X 
XL 
X 
XL 
X 
EKGg 
X 
ECHO/MUG 
Ag 
X 
 
X 

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HbA1ch 
X 
X 
X 
Adverse event 
evaluation 
X 
X ------------------------------------------------------------------------- X 
Tumor 
measurements 
X 
Tumor measurements are repeated every 12 weeks. Documentation (radiologic) must be provided for patients 
removed from study for progressive disease 
Pregnancy 
testi 
X 
Archived 
tumor 
collection 
X 
Tumor Biopsy 
(PTEN 
Expression) 
Xj 
Tumor Biopsy 
(WES) 
Xj 
Xk 
Tumor Biopsy 
(RNA Seq) 
Xj 
Xk 
Xk 
Tumor Biopsy 
(Ki-67 and 
caspase 3) 
Xj 
Xk 
Xk 
Frozen tumor 
biopsy (RPPA 
assay) 
X 
Xk 
Xk 
Blood 
collection 
(ctDNA) 
Xk 
Xk 
Xk 
Xk 
Xk 
Blood 
collection 
(WES) 
X 
a: Copanlisib: Dose as assigned; Days 1 and 8 of each 21 day cycle. Copanlisib is administered after Trastuzumab and Pertuzumab. 

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b: Trastuzumab: Dose as assigned; Day 1 of each 21 day cycle. 
c: Pertuzumab: Dose as assigned; Day 1 of each 21 day cycle.  
d: Off-study evaluation. 
e: Note: Performance status evaluations are based on a 3 week cycle. At minimum, performance status should be evaluated at the beginning of every 
cycle. 
f: Albumin, alkaline phosphatase, total bilirubin, bicarbonate, BUN, calcium, chloride, creatinine, fasting glucose, LDH, phosphorus, potassium, total 
protein, SGOT [AST], SGPT [ALT], sodium. 
g: ECHO/MUGA to be performed at baseline and every 12-16 weeks as per treating physician’s discretion. After baseline, EKG can be repeated if clinically 
indicated. 
h: HbA1c will be performed at baseline, day 1 of every 3rd cycle (4, 7, 10, etc.), and at end of treatment (if last test was >4 weeks ago). 
i: Pregnancy test for women of childbearing potential. 
j: Fresh tumor sample can be collected in lieu of archival tissue 
k: Optional tumor biopsies should be strongly encouraged if clinically feasible. L: Serum fasting 
glucose only prior to infusion with copanlisib 

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12. MEASUREMENT OF EFFECT 
 
Although the clinical benefit of this drug combination has not yet been established, the intent of 
offering this treatment is to provide a possible therapeutic benefit, and thus the patient will be 
carefully monitored for tumor response and symptom relief in addition to safety and tolerability. 
Patients with measurable disease will be assessed by standard criteria. 
 
12.1 Antitumor Effect – Solid Tumors 
 
For the purposes of this study, patients should be re-evaluated for response every 9 weeks (every 
3 cycles). Restaging scans may be performed less frequently (every 12 weeks or every 4 cycles) 
for patients on study for more than 1 year. 
 
Response and progression will be evaluated in this study using the new international criteria 
proposed by the revised Response Evaluation Criteria in Solid Tumors (RECIST) guideline 
(version 1.1) [Eur J Ca 45:228-247, 2009]. Changes in the largest diameter (unidimensional 
measurement) of the tumor lesions and the shortest diameter in the case of malignant lymph 
nodes are used in the RECIST criteria. 
 
12.1.1 Definitions 
 
Evaluable for toxicity. All patients will be evaluable for toxicity from the time of their 
first treatment with copanlisib, trastuzumab, and pertuzumab. 
 
Evaluable for objective response. Only those patients who have measurable disease 
present at baseline, have received at least one cycle of therapy, and have had their disease 
re-evaluated will be considered evaluable for response. These patients will have their 
response classified according to the definitions stated below. (Note: Patients who exhibit 
objective disease progression prior to the end of cycle 1 will also be considered 
evaluable.) 
 
Evaluable Non-Target Disease Response. Patients who have lesions present at baseline 
that are evaluable but do not meet the definitions of measurable disease, have received at 
least one cycle of therapy, and have had their disease re-evaluated will be considered 
evaluable for non-target disease. The response assessment is based on the presence, 
absence, or unequivocal progression of the lesions. 
 
12.1.2 Disease Parameters 
 
Measurable disease. Measurable lesions are defined as those that can be accurately 
measured in at least one dimension (longest diameter to be recorded) as ≥20 mm (≥2 cm) 
by chest x-ray or as ≥10 mm (≥1 cm) with CT scan, MRI, or calipers by clinical exam. 
All tumor measurements must be recorded in millimeters (or decimal fractions of 
centimeters). 
 
Note: Tumor lesions that are situated in a previously irradiated area might or might not 

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be considered measurable. A previously irradiated lesion maybe considered measurable if 
subsequent growth is seen on imaging indicating cancer recurrence in the previously 
irradiated location. 
 
Malignant lymph nodes. To be considered pathologically enlarged and measurable, a 
lymph node must be ≥15 mm (≥1.5 cm) in short axis when assessed by CT scan (CT scan 
slice thickness recommended to be no greater than 5 mm [0.5 cm]). At baseline and in 
follow-up, only the short axis will be measured and followed. 
 
Non-measurable disease. All other lesions (or sites of disease), including small lesions 
(longest diameter <10 mm [<1 cm] or pathological lymph nodes with ≥10 to <15 mm [≥1 
to <1.5 cm] short axis), are considered non-measurable disease. Bone lesions, 
leptomeningeal disease, ascites, pleural/pericardial effusions, lymphangitis 
cutis/pulmonitis, inflammatory breast disease, and abdominal masses (not followed by 
CT or MRI), are considered as non-measurable. 
 
Note: Cystic lesions that meet the criteria for radiographically defined simple cysts 
should not be considered as malignant lesions (neither measurable nor non-measurable) 
since they are, by definition, simple cysts. 
 
‘Cystic lesions’ thought to represent cystic metastases can be considered as measurable 
lesions, if they meet the definition of measurability described above. However, if non- 
cystic lesions are present in the same patient, these are preferred for selection as target 
lesions. 
 
Target lesions. All measurable lesions up to a maximum of 2 lesions per organ and 5 
lesions in total, representative of all involved organs, should be identified as target 
lesions and recorded and measured at baseline. Target lesions should be selected on the 
basis of their size (lesions with the longest diameter), be representative of all involved 
organs, but in addition should be those that lend themselves to reproducible repeated 
measurements. It may be the case that, on occasion, the largest lesion does not lend itself 
to reproducible measurement in which circumstance the next largest lesion which can be 
measured reproducibly should be selected. A sum of the diameters (longest for non- 
nodal lesions, short axis for nodal lesions) for all target lesions will be calculated and 
reported as the baseline sum diameters. If lymph nodes are to be included in the sum, 
then only the short axis is added into the sum. The baseline sum diameters will be used 
as reference to further characterize any objective tumor regression in the measurable 
dimension of the disease. 
 
Non-target lesions. All other lesions (or sites of disease) including any measurable 
lesions over and above the 5 target lesions should be identified as non-target lesions and 
should also be recorded at baseline. Measurements of these lesions are not required, but 
the presence, absence, or in rare cases unequivocal progression of each should be noted 
throughout follow-up. 

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12.1.3 Methods for Evaluation of Measurable Disease 
 
All measurements should be taken and recorded in metric notation using a ruler or 
calipers. All baseline evaluations should be performed as closely as possible to the 
beginning of treatment and never more than 4 weeks before the beginning of the 
treatment. 
 
The same method of assessment and the same technique should be used to characterize 
each identified and reported lesion at baseline and during follow-up. Imaging-based 
evaluation is preferred to evaluation by clinical examination unless the lesion(s) being 
followed cannot be imaged but are assessable by clinical exam. 
 
Clinical lesions Clinical lesions will only be considered measurable when they are 
superficial (e.g., skin nodules and palpable lymph nodes) and ≥10 mm (≥1 cm) diameter 
as assessed using calipers (e.g., skin nodules). In the case of skin lesions, documentation 
by color photography, including a ruler to estimate the size of the lesion, is 
recommended. 
 
Chest x-ray Lesions on chest x-ray are acceptable as measurable lesions when they are 
clearly defined and surrounded by aerated lung. However, CT is preferable. 
 
Conventional CT and MRI This guideline has defined measurability of lesions on CT 
scan based on the assumption that CT slice thickness is 5 mm (0.5 cm) or less. If CT 
scans have slice thickness greater than 5 mm (0.5 cm), the minimum size for a 
measurable lesion should be twice the slice thickness. MRI is also acceptable in certain 
situations (e.g. for body scans). 
 
Use of MRI remains a complex issue. MRI has excellent contrast, spatial, and temporal 
resolution; however, there are many image acquisition variables involved in MRI, which 
greatly impact image quality, lesion conspicuity, and measurement. Furthermore, the 
availability of MRI is variable globally. As with CT, if an MRI is performed, the 
technical specifications of the scanning sequences used should be optimized for the 
evaluation of the type and site of disease. Furthermore, as with CT, the modality used at 
follow-up should be the same as was used at baseline and the lesions should be 
measured/assessed on the same pulse sequence. It is beyond the scope of the RECIST 
guidelines to prescribe specific MRI pulse sequence parameters for all scanners, body 
parts, and diseases. Ideally, the same type of scanner should be used and the image 
acquisition protocol should be followed as closely as possible to prior scans. Body scans 
should be performed with breath-hold scanning techniques, if possible. 
 
PET-CT At present, the low dose or attenuation correction CT portion of a combined 
PET-CT is not always of optimal diagnostic CT quality for use with RECIST 
measurements. However, if the site can document that the CT performed as part of a 
PET-CT is of identical diagnostic quality to a diagnostic CT (with IV and oral contrast), 
then the CT portion of the PET-CT can be used for RECIST measurements and can be 
used interchangeably with conventional CT in accurately measuring cancer lesions over 

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time. Note, however, that the PET portion of the CT introduces additional data which 
may bias an investigator if it is not routinely or serially performed. 
 
Ultrasound Ultrasound is not useful in assessment of lesion size and should not be used 
as a method of measurement. Ultrasound examinations cannot be reproduced in their 
entirety for independent review at a later date and, because they are operator dependent, it 
cannot be guaranteed that the same technique and measurements will be taken from one 
assessment to the next. If new lesions are identified by ultrasound in the course of the 
study, confirmation by CT or MRI is advised.  If there is concern about radiation 
exposure at CT, MRI may be used instead of CT in selected instances. 
 
Endoscopy, Laparoscopy The utilization of these techniques for objective tumor 
evaluation is not advised. However, such techniques may be useful to confirm complete 
pathological response when biopsies are obtained or to determine relapse in trials where 
recurrence following complete response (CR) or surgical resection is an endpoint. 
 
Tumor markers Tumor markers alone cannot be used to assess response. If markers are 
initially above the upper normal limit, they must normalize for a patient to be considered 
in complete clinical response. Specific guidelines for both CA-125 response (in recurrent 
ovarian cancer) and PSA response (in recurrent prostate cancer) have been published 
[JNCI 96:487-488, 2004; J Clin Oncol 17, 3461-3467, 1999; J Clin Oncol 26:1148-1159, 
2008]. In addition, the Gynecologic Cancer Intergroup has developed CA-125 
progression criteria which are to be integrated with objective tumor assessment for use in 
first-line trials in ovarian cancer [JNCI 92:1534-1535, 2000]. 
 
Cytology, Histology These techniques can be used to differentiate between partial 
responses (PR) and complete responses (CR) in rare cases (e.g., residual lesions in tumor 
types, such as germ cell tumors, where known residual benign tumors can remain). 
 
The cytological confirmation of the neoplastic origin of any effusion that appears or 
worsens during treatment when the measurable tumor has met criteria for response or 
stable disease is mandatory to differentiate between response or stable disease (an 
effusion may be a side effect of the treatment) and progressive disease. 
 
FDG-PET While FDG-PET response assessments need additional study, it is sometimes 
reasonable to incorporate the use of FDG-PET scanning to complement CT scanning in 
assessment of progression (particularly possible 'new' disease). New lesions on the basis 
of FDG-PET imaging can be identified according to the following algorithm: 
a. Negative FDG-PET at baseline, with a positive FDG-PET at follow-up is a sign of 
PD based on a new lesion. 
b. No FDG-PET at baseline and a positive FDG-PET at follow-up: If the positive FDG- 
PET at follow-up corresponds to a new site of disease confirmed by CT, this is PD. If 
the positive FDG-PET at follow-up is not confirmed as a new site of disease on CT, 
additional follow-up CT scans are needed to determine if there is truly progression 
occurring at that site (if so, the date of PD will be the date of the initial abnormal 
FDG-PET scan). If the positive FDG-PET at follow-up corresponds to a pre-existing 

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site of disease on CT that is not progressing on the basis of the anatomic images, this 
is not PD. 
c. FDG-PET may be used to upgrade a response to a CR in a manner similar to a biopsy 
in cases where a residual radiographic abnormality is thought to represent fibrosis or 
scarring. The use of FDG-PET in this circumstance should be prospectively 
described in the protocol and supported by disease-specific medical literature for the 
indication. However, it must be acknowledged that both approaches may lead to false 
positive CR due to limitations of FDG-PET and biopsy resolution/sensitivity. 
 
Note: A ‘positive’ FDG-PET scan lesion means one which is FDG avid with an uptake 
greater than twice that of the surrounding tissue on the attenuation corrected image. 
 
12.1.4 Response Criteria 
 
12.1.4.1 Evaluation of Target Lesions 
 
Complete Response (CR): Disappearance of all target lesions. Any pathological 
lymph nodes (whether target or non-target) must have reduction in short axis to <10 
mm (<1 cm). 
 
Partial Response (PR): At least a 30% decrease in the sum of the diameters of target 
lesions, taking as reference the baseline sum diameters. 
 
Progressive Disease (PD): At least a 20% increase in the sum of the diameters of 
target lesions, taking as reference the smallest sum on study (this includes the 
baseline sum if that is the smallest on study). In addition to the relative increase of 
20%, the sum must also demonstrate an absolute increase of at least 5 mm (0.5 cm). 
(Note: the appearance of one or more new lesions is also considered progressions). 
 
Stable Disease (SD): Neither sufficient shrinkage to qualify for PR nor sufficient 
increase to qualify for PD, taking as reference the smallest sum diameters while on 
study. 
 
12.1.4.2 Evaluation of Non-Target Lesions 
 
Complete Response (CR): Disappearance of all non-target lesions and normalization 
of tumor marker level. All lymph nodes must be non-pathological in size (<10 mm 
[<1 cm] short axis). 
 
Note: If tumor markers are initially above the upper normal limit, they must 
normalize for a patient to be considered in complete clinical response. 
 
Non-CR/Non-PD: Persistence of one or more non-target lesion(s) and/or 
maintenance of tumor marker level above the normal limits. 
 
Progressive Disease (PD): Appearance of one or more new lesions and/or 

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unequivocal progression of existing non-target lesions. Unequivocal progression 
should not normally trump target lesion status. It must be representative of overall 
disease status change, not a single lesion increase. 
 
Although a clear progression of “non-target” lesions only is exceptional, the opinion 
of the treating physician should prevail in such circumstances, and the progression 
status should be confirmed at a later time by the review panel (or Principal 
Investigator). 
 
12.1.4.3 Evaluation of Best Overall Response 
 
The best overall response is the best response recorded from the start of the treatment 
until disease progression/recurrence (taking as reference for progressive disease the 
smallest measurements recorded since the treatment started). The patient's best 
response assignment will depend on the achievement of both measurement and 
confirmation criteria. 
 
For Patients with Measurable Disease (i.e., Target Disease) 
 
Target 
Lesions 
Non-Target 
Lesions 
New 
Lesions* 
Overall 
Response 
CR 
CR 
No 
CR** 
CR 
Non-CR/Non- 
PD 
No 
PR 
CR 
Not evaluated 
No 
PR 
PR 
Non-CR/Non- 
PD/not 
evaluated 
No 
PR 
SD 
Non-CR/Non- 
PD/not 
evaluated 
No 
SD 
PD 
Any 
Yes or No 
PD 
Any 
PD*** 
Yes or No 
PD 
Any 
Any 
Yes 
PD 
 
See RECIST 1.1 manuscript for further details on what is evidence of a new lesion. 
** In some circumstances, it may be difficult to distinguish residual disease from normal 
tissue. When the evaluation of CR depends on this determination, it is recommended that 
the residual lesion be investigated (fine-needle aspiration/biopsy) before confirming the 
CR status. 
*** In exceptional circumstances, unequivocal progression in non-target lesions may be 
accepted as disease progression. 
Note: Patients with a global deterioration of health status requiring discontinuation of 
treatment without objective evidence of disease progression at that time should be 
reported as “symptomatic deterioration.” Every effort should be made to document the 
objective progression even after discontinuation of treatment. 

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For Patients with Non-Measurable Disease (i.e., Non-Target Disease) 
 
Non-Target Lesions 
New Lesions 
Overall Response 
CR 
No 
CR 
Non-CR/non-PD 
No 
Non-CR/non-PD* 
Not all evaluated 
No 
not evaluated 
Unequivocal PD 
Yes or No 
PD 
Any 
Yes 
PD 
 
‘Non-CR/non-PD’ is preferred over ‘stable disease’ for non-target disease since SD is 
increasingly used as an endpoint for assessment of efficacy in some trials so to assign this 
category when no lesions can be measured is not advised 
 
12.1.5 Duration of Response 
 
Duration of overall response: The duration of overall response is measured from the time 
measurement criteria are met for CR or PR (whichever is first recorded) until the first 
date that recurrent or progressive disease is objectively documented (taking as reference 
for progressive disease the smallest measurements recorded since the treatment started). 
 
The duration of overall CR is measured from the time measurement criteria are first met 
for CR until the first date that progressive disease is objectively documented. 
 
Duration of stable disease: Stable disease is measured from the start of the treatment 
until the criteria for progression are met, taking as reference the smallest measurements 
recorded since the treatment started, including the baseline measurements. 
 
12.1.6 Progression-Free Survival 
 
For Phase 1b patients, PFS is defined as the duration of time from start of treatment to 
time of progression or death, whichever occurs first. For Phase 2 patients, PFS is defined 
as the duration of time from randomization to time of progression or death, whichever 
occurs first. 
 
 
13. STUDY OVERSIGHT AND DATA REPORTING / REGULATORY 
REQUIREMENTS 
 
Adverse event lists, guidelines, and instructions for AE reporting can be found in Section 10 
(Adverse Events: List and Reporting Requirements). 
 
Data Quality Portal 
 
The Data Quality Portal (DQP) provides a central location for site staff to manage unanswered 
queries and form delinquencies, monitor data quality and timeliness, generate reports, and review 
metrics. 

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The DQP is located on the CTSU members’ website under Data Management. The Rave Home 
section displays a table providing summary counts of Total Delinquencies and Total Queries. DQP 
Queries, DQP Delinquent Forms, and the DQP Reports modules are available to access details and 
reports of unanswered queries, delinquent forms, and timeliness reports. Review the DQP modules 
on a regular basis to manage specified queries and delinquent forms. 
 
The DQP is accessible by site staff that are rostered to a site and have access to the CTSU website. 
Staff that have Rave study access can access the Rave study data using a direct link on the DQP. 
 
To learn more about DQP use and access, click on the Help icon displayed on the Rave Home, DQP 
Queries, and DQP Delinquent Forms modules. 
 
Note: Some Rave protocols may not have delinquent form details or reports specified on the DQP. 
A protocol must have the Calendar functionality implemented in Rave by the Lead Protocol 
Organization (LPO) for delinquent form details and reports to be available on the DQP. Site staff 
should contact the LPO Data Manager for their protocol regarding questions about Rave 
Calendaring functionality. 
 
 
13.1 Study Oversight 
 
This protocol is monitored at several levels, as described in this section. The Protocol Principal 
Investigator is responsible for monitoring the conduct and progress of the clinical trial, including 

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the ongoing review of accrual, patient-specific clinical and laboratory data, and routine and 
serious adverse events; reporting of expedited adverse events; and accumulation of reported 
adverse events from other trials testing the same drug(s). The Protocol Principal Investigator and 
statistician have access to the data at all times through the CTMS web-based reporting portal. 
 
For the Phase 1 portion of this study, all decisions regarding dose escalation/expansion/de- 
escalation require sign-off by the Protocol Principal Investigator through the CTMS/IWRS. In 
addition, for the Phase 1 portion, the Protocol Principal Investigator will have at least monthly, 
or more frequently, conference calls with the Study Investigators and the CTEP Medical 
Officer(s) to review accrual, progress, and adverse events and unanticipated problems. 
 
Enrollment to the Phase 2 portion of the trial will not begin until a protocol amendment has been 
submitted which summarizes the Phase 1 results, the recommended Phase 2 dose, and the 
rationale for selecting it. The amendment must be reviewed and approved by CTEP before 
enrollment to the Phase 2 portion can begin. 
 
During the Phase 2 portion of the study, the Protocol Principal Investigator will have, at a 
minimum, quarterly conference calls with the Study Investigators and the CTEP Medical 
Officer(s) to review accrual, progress, and pharmacovigilance. Decisions to proceed to the 
second stage of a Phase 2 trial will require sign-off by the Protocol Principal Investigator and the 
Protocol Statistician. 
 
All Study Investigators at participating sites who register/enroll patients on a given protocol are 
responsible for timely submission of data via Medidata Rave and timely reporting of adverse 
events for that particular study. This includes timely review of data collected on the electronic 
CRFs submitted via Medidata Rave. 
 
All studies are also reviewed in accordance with the enrolling institution’s data safety monitoring 
plan. 
 
13.2 Data Reporting 
 
Medidata Rave is a clinical data management system being used for data collection for this 
trial/study. Access to the trial in Rave is controlled through the CTEP-IAM system and role 
assignments. 
Requirements to access Rave via iMedidata: 
 
• A valid account, and 
• Assigned a Rave role on the LPO or PO roster at the enrolling site of: Rave CRA, Rave Read 
Only, Rave CRA (LabAdmin), Rave SLA, or Rave Investigator. 
Rave role requirements: 
 
o Rave CRA or Rave CRA (Lab Admin) role, must have a minimum of an Associate 
Plus (AP) registration type, 
o Rave Investigator role, must be registered as an Non-Physician Investigator (NPIVR) 
or Investigator (IVR), and 
o Rave Read Only role, site staff must have at a minimum an Associates (A) registration 
type. 

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• Refer to https://ctep.cancer.gov/investigatorResources/default.htm for registration types and 
documentation required. 
 
Upon initial site registration approval for the study in Regulatory Support System (RSS), all 
persons with Rave roles assigned on the appropriate roster will be sent a study invitation e-mail 
from iMedidata. To accept the invitation, site staff must log in to the Select Login 
(https://login.imedidata.com/selectlogin) using their CTEP-IAM username and password and 
click on the accept link in the upper right-corner of the iMedidata page. Site staff will not be 
able to access the study in Rave until all required Medidata and study specific trainings are 
completed. Trainings will be in the form of electronic learnings (eLearnings) and can be 
accessed by clicking on the link in the upper right pane of the iMedidata screen.  If an 
eLearning is required and has not yet been taken, the link to the eLearning will appear under the 
study name in iMedidata instead of the Rave EDC link; once the successful completion of the 
eLearning has been recorded, access to the study in Rave will be granted, and a Rave EDC link 
will display under the study name. 
 
Site staff that have not previously activated their iMedidata/Rave account at the time of initial 
site registration approval for the study in RSS will receive a separate invitation from iMedidata 
to activate their account. Account activation instructions are located on the CTSU website in 
the Data Management section under the Rave resource materials (Medidata Account Activation 
and Study Invitation Acceptance). Additional information on iMedidata/Rave is available on 
the CTSU members’ website in the Data Management > Rave section at www.ctsu.org/RAVE/ 
or by contacting the CTSU Help Desk at 1-888-823-5923 or by e-mail at 
ctsucontact@westat.com. 
 
13.2.1 Method 
 
This study will be monitored by the Clinical Trials Monitoring Service (CTMS). Data 
will be submitted to CTMS at least once every two weeks via Medidata Rave (or other 
modality if approved by CTEP). Information on CTMS reporting is available at 
http://www.theradex.com/clinicalTechnologies/?National-Cancer-Institute-NCI-11. On- 
site audits will be conducted three times annually (one annual site visit and two data 
audits). For CTMS monitored studies, after users have activated their accounts, please 
contact the Theradex Help Desk at (609) 619-7862 or by email at 
CTMSSupport@theradex.com for additional support with Rave and completion of CRFs. 
 
13.2.2 Responsibility for Data Submission 
 
For ETCTN trials, it is the responsibility of the PI(s) at the site to ensure that all 
investigators at the ETCTN Sites understand the procedures for data submission for each 
ETCTN protocol and that protocol specified data are submitted accurately and in a timely 
manner to the CTMS via the electronic data capture system, Medidata Rave. 
 
Data are to be submitted via Medidata Rave to CTMS on a real-time basis, but no less 
than once every 2 weeks. The timeliness of data submissions and timeliness in resolving 
data queries will be tracked by CTMS. Metrics for timeliness will be followed and 
assessed on a quarterly basis. For the purpose of Institutional Performance Monitoring, 
data will be considered delinquent if it is greater than 4 weeks past due. 

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114 
 
 
Data from Medidata Rave and CTEP-AERS is reviewed by the CTMS on an ongoing 
basis as data is received. Queries will be issued by CTMS directly within Rave. The 
queries will appear on the Task Summary Tab within Rave for the CRA at the ETCTN to 
resolve. Monthly web-based reports are posted for review by the Drug Monitors in the 
IDB, CTEP. Onsite audits will be conducted by the CTMS to ensure compliance with 
regulatory requirements, GCP, and NCI policies and procedures with the overarching 
goal of ensuring the integrity of data generated from NCI-sponsored clinical trials, as 
described in the ETCTN Program Guidelines, which may be found on the CTEP 
(http://ctep.cancer.gov/protocolDevelopment/electronic_applications/adverse_events.htm 
and CTSU websites. 
 
CTMS will utilize a core set of eCRFs that are Cancer Data Standards Registry and 
Repository (caDSR) compliant (http://cbiit.nci.nih.gov/ncip/biomedical-informatics- 
resources/interoperability-and-semantics/metadata-and-models). Customized eCRFs will 
be included when appropriate to meet unique study requirements. The PI is encouraged 
to review the eCRFs, working closely with CTMS to ensure prospectively that all 
required items are appropriately captured in the eCRFs prior to study activation. CTMS 
will prepare the eCRFs with built-in edit checks to the extent possible to promote data 
integrity. 
 
CDUS data submissions for ETCTN trials activated after March 1, 2014, will be carried 
out by the CTMS contractor, Theradex. CDUS submissions are performed by Theradex 
on a monthly basis. The trial’s lead institution is responsible for timely submission to 
CTMS via Rave, as above. 
 
Further information on data submission procedures can be found in the ETCTN Program 
Guidelines. 
http://ctep.cancer.gov/protocolDevelopment/electronic_applications/adverse_events.htm 
 
 
13.3 CTEP Multicenter Guidelines 
 
N/A 
 
13.4 Collaborative Agreements Language 
 
The agent(s) supplied by CTEP, DCTD, NCI used in this protocol is/are provided to the NCI 
under a Collaborative Agreement (CRADA, CTA, CSA) between the Pharmaceutical 
Company(ies) (hereinafter referred to as “Collaborator(s)”) and the NCI Division of Cancer 
Treatment and Diagnosis. Therefore, the following obligations/guidelines, in addition to the 
provisions in the “Intellectual Property Option to Collaborator” 
(http://ctep.cancer.gov/industryCollaborations2/intellectual_property.htm) contained within the 
terms of award, apply to the use of the Agent(s) in this study: 
 
1. Agent(s) may not be used for any purpose outside the scope of this protocol, nor can 
Agent(s) be transferred or licensed to any party not participating in the clinical study. 
Collaborator(s) data for Agent(s) are confidential and proprietary to Collaborator(s) and shall 
be maintained as such by the investigators. The protocol documents for studies utilizing 

NCI Protocol #: 10296 Version 
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115 
 
 
Agents contain confidential information and should not be shared or distributed without the 
permission of the NCI. If a copy of this protocol is requested by a patient or patient’s family 
member participating on the study, the individual should sign a confidentiality agreement. A 
suitable model agreement can be downloaded from: http://ctep.cancer.gov. 
 
2. For a clinical protocol where there is an investigational Agent used in combination with 
(an)other Agent(s), each the subject of different Collaborative Agreements, the access to and 
use of data by each Collaborator shall be as follows (data pertaining to such combination use 
shall hereinafter be referred to as "Multi-Party Data”): 
 
a. NCI will provide all Collaborators with prior written notice regarding the existence and 
nature of any agreements governing their collaboration with NCI, the design of the 
proposed combination protocol, and the existence of any obligations that would tend to 
restrict NCI's participation in the proposed combination protocol. 
 
b. Each Collaborator shall agree to permit use of the Multi-Party Data from the clinical trial 
by any other Collaborator solely to the extent necessary to allow said other Collaborator 
to develop, obtain regulatory approval or commercialize its own Agent. 
 
c. Any Collaborator having the right to use the Multi-Party Data from these trials must 
agree in writing prior to the commencement of the trials that it will use the Multi-Party 
Data solely for development, regulatory approval, and commercialization of its own 
Agent. 
 
3. Clinical Trial Data and Results and Raw Data developed under a Collaborative Agreement 
will be made available to Collaborator(s), the NCI, and the FDA, as appropriate and unless 
additional disclosure is required by law or court order as described in the IP Option to 
Collaborator (http://ctep.cancer.gov/industryCollaborations2/intellectual_property.htm). 
Additionally, all Clinical Data and Results and Raw Data will be collected, used and 
disclosed consistent with all applicable federal statutes and regulations for the protection of 
human subjects, including, if applicable, the Standards for Privacy of Individually 
Identifiable Health Information set forth in 45 C.F.R. Part 164. 
 
4. When a Collaborator wishes to initiate a data request, the request should first be sent to the 
NCI, who will then notify the appropriate investigators (Group Chair for Cooperative Group 
studies, or PI for other studies) of Collaborator's wish to contact them. 
 
5. Any data provided to Collaborator(s) for Phase 3 studies must be in accordance with the 
guidelines and policies of the responsible Data Monitoring Committee (DMC), if there is a 
DMC for this clinical trial. 
 
6. Any manuscripts reporting the results of this clinical trial must be provided to CTEP by the 
Group office for Cooperative Group studies or by the principal investigator for non- 
Cooperative Group studies for immediate delivery to Collaborator(s) for advisory review and 
comment prior to submission for publication. Collaborator(s) will have 30 days from the 
date of receipt for review. Collaborator shall have the right to request that publication be 
delayed for up to an additional 30 days in order to ensure that Collaborator’s confidential and 
proprietary data, in addition to Collaborator(s)’s intellectual property rights, are protected. 
Copies of abstracts must be provided to CTEP for forwarding to Collaborator(s) for courtesy 

NCI Protocol #: 10296 Version 
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116 
 
 
review as soon as possible and preferably at least three (3) days prior to submission, but in 
any case, prior to presentation at the meeting or publication in the proceedings. Press releases and 
other media presentations must also be forwarded to CTEP prior to release. Copies of any 
manuscript, abstract and/or press release/ media presentation should be sent to: 
 
Email: ncicteppubs@mail.nih.gov 
 
The Regulatory Affairs Branch will then distribute them to Collaborator(s). No publication, 
manuscript or other form of public disclosure shall contain any of Collaborator’s confidential/ 
proprietary information. 
 
13.5 Genomic Data Sharing Plan 
 
The investigators and statistician and/or bioinformaticians for a study will have access to all data 
on mutations and variants stored in the Theradex Data Base and the GDC. This information will 
be sequestered from access throughout the study until it is analyzed for purposes of reporting and 
publishing of the study results. As specified in the CRADA for the agents used in the clinical 
study, the pharmaceutical collaborator will have at least 6 months, longer if needed for a 
regulatory filing, to review the data and or receive copies of the data once the study is completed 
and analyzed, or sooner, if specified for purposes of generating Intellectual Property. Once these 
timeframes have been exceeded, the data will be available through a Data Access Committee 
(DAC) in the GDC following NCI and Collaborator review of the proposals. 
 
13.6 Incidental/Secondary Findings Disclosure Procedure 
 
Given the potential clinical implications conferred by detecting a germline and/or somatic 
mutation in one of the proven cancer susceptibility genes, this protocol will use the following 
disclosure procedure, consistent with the recommendations of the American College of Medical 
and Genomics (ACMG) (Green et al., 2013 and Kalia et al., 2016): 
 
When whole exome sequencing analysis is completed, each pathogenic or likely pathogenic 
germline variant detected in the WES of blood, will be reviewed by the MD Anderson Precision 
Oncology Decision Support (PODS) Program. The study PI with the support of the PODS team 
will contact Theradex to obtain the name of investigator treating the patient, and the Principal 
Investigator at the site. The treating physician will be contacted by phone and in writing, and the 
treating physician will ask the patient whether he or she is interested in learning more about the 
finding. 
 
If the patient wants to know more, the physician should contact the Program Director for more 
information about the mutation/variant. The treating physician and a medical genetics counselor 
should meet with the patient to discuss the importance and meaning of the finding, but not the 
finding itself, and notify the patient that this research finding must be confirmed by a germline 
sequencing assay (by Sanger Sequencing or a next generation platform) in a Clinical Laboratory 
Improvement Amendments (CLIA)-approved laboratory at the patient’s/patient insurer’s 
expense. The treating physician and genetic counselor should inform the patient of the 
confirmed result and its meaning and significance to the patient. If desired, the patient may elect 
to undergo genetic counseling and confirmatory CLIA-approved clinical testing on his or her 

NCI Protocol #: 10296 Version 
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117 
 
 
 
own. Neither the research laboratory nor the National Cancer Institute will be responsible for the 
costs incurred for any confirmatory genetic testing or counseling. 
 
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Choi JH, Kim KH, Roh KH, et al. (2018). A PI3K p110alpha-selective inhibitor enhances 
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Gianni L, Pienkowski T, Im YH, et al. (2010). Efficacy and safety of neoadjuvant 
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Journal of Clinical Oncology. 36:981-990. 

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APPENDIX A 
PERFORMANCE STATUS CRITERIA 
 
ECOG Performance Status Scale 
Karnofsky Performance Scale 
Grade 
Descriptions 
Percent 
Description 
0 
Normal activity. Fully active, able 
to carry on all pre-disease 
performance without restriction. 
100 
Normal, no complaints, no evidence 
of disease. 
90 
Able to carry on normal activity; 
minor signs or symptoms of disease. 
1 
Symptoms, but ambulatory. 
Restricted in physically strenuous 
activity, but ambulatory and able 
to carry out work of a light or 
sedentary nature (e.g., light 
housework, office work). 
80 
Normal activity with effort; some 
signs or symptoms of disease. 
70 
Cares for self, unable to carry on 
normal activity or to do active work. 
2 
In bed <50% of the time. 
Ambulatory and capable of all 
self-care, but unable to carry out 
any work activities. Up and about 
more than 50% of waking hours. 
60 
Requires occasional assistance, but 
is able to care for most of his/her 
needs. 
50 
Requires considerable assistance and 
frequent medical care. 
3 
In bed >50% of the time. Capable 
of only limited self-care, confined 
to bed or chair more than 50% of 
waking hours. 
40 
Disabled, requires special care and 
assistance. 
30 
Severely disabled, hospitalization 
indicated. Death not imminent. 
4 
100% bedridden. Completely 
disabled. Cannot carry on any 
self-care. Totally confined to bed 
or chair. 
20 
Very sick, hospitalization indicated. 
Death not imminent. 
10 
Moribund, fatal processes 
progressing rapidly. 
5 
Dead. 
0 
Dead. 

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APPENDIX B FORMULA TO ESTIMATE RENAL FUNCTION USING SERUM 
CREATININE 
Formulas to estimate renal function using serum creatinine provided by the NCI’s Investigational 
Drug Steering Committee (IDSC) Pharmacological Task Force in table below. 
 
1. Estimated glomerular filtration rate (eGFR) using the Chronic Kidney Disease Epidemiology 
Collaboration (CKD-EPI) (Levey et al., 2009). 
Formulae: 
Race and 
Serum Creatinine (SCr), 
Equation 
Sex 
µmol/L (mg/dL) 
Black 
Female 
≤62 (≤0.7) 
GFR = 166 × (SCr/0.7)−0.329 ×(0.993)Age 
>62 (>0.7) 
GFR = 166 × (SCr/0.7)−1.209 ×(0.993)Age 
Male 
≤80 (≤0.9) 
GFR = 163 × (SCr/0.9)−0.411 ×(0.993)Age 
>80 (>0.9) 
GFR = 163 × (SCr/0.9)−1.209 ×(0.993)Age 
White or 
other 
Female 
≤62 (≤0.7) 
GFR = 144 × (SCr/0.7)−0.329 ×(0.993)Age 
>62 (>0.7) 
GFR = 144 × (SCr/0.7)−1.209 ×(0.993)Age 
Male 
≤80 (≤0.9) 
GFR = 141 × (SCr/0.9)−0.411 ×(0.993)Age 
>80 (>0.9) 
GFR = 141 × (SCr/0.9)−1.209 ×(0.993)Age 
SCr in mg/dL; Output is in mL/min/1.73 m2 and needs no further conversions. 
2. eGFR using the Modification of Diet in Renal Disease (MDRD) Study (Levey et al., 2006). 
175 x SCr–1.154 × age–0.203 × 0.742 (if female) × 1.212 (if black) 
Output is in mL/min/1.73 m2 and needs no further conversions. 
3. Estimated creatinine clearance (ClCr) by the Cockcroft-Gault (C-G) equation (Cockcroft and 
Gault, 1976). 
 
Followed by conversion to a value normalized to 1.73 m2 with the patient’s body surface area 
(BSA). 
 
References 
1. Levey, A.S., L.A. Stevens, C.H. Schmid, et al. (2009). A new equation to estimate 
glomerular filtration rate. Ann Inter Med. 150:604-612. 
2. Levey, A.S., J. Coresh, T. Greene, et al. (2006). Using standardized serum creatinine 
values in the modification of diet in renal disease study equation for estimating 
glomerular filtration rate. Ann Intern Med. 145:247-254. 
3. Cockcroft, D.W. and M.H. Gault. (1976). Prediction of creatinine clearance from serum 
creatinine. Nephron. 16:31-41. 

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APPENDIX C 
LIST OF PROHIBITED MEDICATIONS WHILE ON COPANLISIB 
TREATMENT 
 
This list is not comprehensive. Because the lists of these agents are constantly changing, it is 
important to regularly consult a frequently-updated medical reference for a list of drugs to avoid 
or minimize use of. 
 
Category 
Drug name 
Strong CYP3A Inhibitors 
Voriconazole, Boceprevir, clarithromycin, 
cobicistat, conivaptan, danoprevir/ritonavir, 
eltegravir/ritonavir, grapefruit juice, 
indinavir/ritonavir, itraconazole, ketoconazole, 
lopinavir/ritonavir, mibefradil, nefazodone, 
nelfinavir, posaconazole, ritonavir, saquinavir, 
saquinavir/ritonavir, telaprevir, telithromycin, 
tipranavir/ritonavir, troleandomycin, 
Strong CYP3A Inducers 
Avasimibe, carbamazepine, mitotane, 
phenobarbital, phenytoin, rifabutin, rifampin 
(rifampicin), St. John's wort (hypericum 
perforatum) 
Herbal Preparations/ 
Medications 
Herbal preparations/medications are prohibited 
throughout the study. These herbal medications 
include, but are not limited to: St. John’s Wort, 
Kava, ephedra (ma huang), gingko biloba, 
dehydroepiandrosterone (DHEA), yohimbe, saw 
palmetto, and ginseng. Patients should stop using 
these herbal medications 7 days prior to first 
dose of study drug 

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APPENDIX D 
PATIENT CLINICAL TRIAL WALLET CARD 
 
 
CLINICAL TRIAL WALLET CARD 
Show this card to all of 
your healthcare 
providers and keep it 
with you in case you go 
to the emergency room. 
Patient Name: 
Diagnosis: 
Study Doctor: 
Study Doctor Phone #: 
NCI Trial #: 
10296 
Study Drug(S): 
For more information: 1-800-4-CANCER 
cancer.gov | clinicaltrials.gov 

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APPENDIX E 
LIST OF ACTIVATING OR INFERRED ACTIVATING PIK3CA MUTATIONS 
PROVIDED BY MD ANDERSON PRECISION ONCOLOGY DECISION SUPPORT TEAM 
 
The 14 most common PIK3CA missense mutations are eligible for this trial: 
 
PIK3CA_C420R 
PIK3CA_E542K 
PIK3CA_E545A 
PIK3CA_E545G 
PIK3CA_E545G 
PIK3CA_E545K 
PIK3CA_H1047L 
PIK3CA_H1047R 
PIK3CA_H1047Y 
PIK3CA_M1043I 
PIK3CA_N345K 
PIK3CA_Q546K 
PIK3CA_Q546R 
PIK3CA_R88Q 

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APPENDIX F 
LIST OF INACTIVATING OR INFERRED INACTIVATING PTEN 
MUTATIONS PROVIDED BY MD ANDERSON PRECISION 
ONCOLOGY DECISION SUPPORT TEAM 
 
Truncations or frameshifts upstream of amino acid 350 will be eligible for this trial. 
 
The 18 most common inactivating PTEN missense mutations are also eligible for this trial: 
 
PTEN_A126T 
PTEN_C124S 
PTEN_C136R 
PTEN_D92E 
PTEN_G129R 
PTEN_G132D 
PTEN_G165R 
PTEN_G36R 
PTEN_H123Y 
PTEN_H61R 
PTEN_H93R 
PTEN_R130G 
PTEN_R130L 
PTEN_R130Q 
PTEN_R173C 
PTEN_R173H 
PTEN_Y155C 
PTEN_Y68H 

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Version Date: February 21, 
2022 
 
APPENDIX G 
RPPA ASSAY INFORMATION 
 
Reverse Phase Protein Array (RPPA) will be performed at the University of Texas MD Anderson Cancer 
Center (MD Anderson) on snap-frozen tissue provided by the Biorepository. 
 
Reverse Phase Protein Array (RPPA) 
 
Frozen tumors will be lysed and protein extracted. Lysates will be manually serial-diluted in 5 two-fold 
dilutions with lysis buffer and printed on nitrocellulose-coated slides using an Aushon Biosystems 2470 
arrayer. Slides will be probed with approximately 300 validated primary antibodies followed by detection 
with appropriate Biotinylated secondary antibodies (Goat anti-Rabbit IgG, Goat anti-Mouse IgG, or Rabbit 
anti-Goat IgG). The signal obtained will be amplified using a Cytomation–catalyzed system of Avidin- 
Biotinylated Peroxidase (Vectastain Elite ABC kit from Vector Lab) binding to the secondary antibody 
and catalyzing Tyramide-Biotin conjugation to form insoluble biotinylated phenols. Signals will be 
visualized by a secondary streptavidin-conjugated HRP and DAB colorimetric reaction. The slides will be 
scanned, analyzed, and quantified using Array-Pro Analyzer software (MediaCybernetics) to generate spot 
intensity (Level 1 data). 
 
Please refer to the MD Anderson RPPA Core Facility website for additional details including workflow 
and data processing: 
https://www.mdanderson.org/research/research-resources/core-facilities/functional-proteomics-rppa- 
core/rppa-process.html